Starting phenix.real_space_refine on Fri Mar 6 09:09:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6wdo_21643/03_2026/6wdo_21643.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wdo_21643/03_2026/6wdo_21643.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6wdo_21643/03_2026/6wdo_21643.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wdo_21643/03_2026/6wdo_21643.map" model { file = "/net/cci-nas-00/data/ceres_data/6wdo_21643/03_2026/6wdo_21643.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wdo_21643/03_2026/6wdo_21643.cif" } resolution = 3.6 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= 0.044 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: 5 Type Number sf(0) Gaussians Ca 2 9.91 5 S 124 5.16 5 C 19265 2.51 5 N 5081 2.21 5 O 5395 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 177 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29867 Number of models: 1 Model: "" Number of chains: 22 Chain: "G" Number of atoms: 2102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 2102 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 9, 'TRANS': 245} Chain breaks: 1 Chain: "H" Number of atoms: 400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 400 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 3, 'TRANS': 47} Chain: "C" Number of atoms: 2211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2211 Classifications: {'peptide': 268} Link IDs: {'PTRANS': 10, 'TRANS': 257} Chain: "D" Number of atoms: 400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 400 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 3, 'TRANS': 47} Chain: "A" Number of atoms: 2254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2254 Classifications: {'peptide': 273} Link IDs: {'PTRANS': 11, 'TRANS': 261} Chain: "B" Number of atoms: 414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 414 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 4, 'TRANS': 48} Chain: "E" Number of atoms: 2226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2226 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 11, 'TRANS': 258} Chain: "F" Number of atoms: 389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 389 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 3, 'TRANS': 46} Chain: "I" Number of atoms: 2254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2254 Classifications: {'peptide': 273} Link IDs: {'PTRANS': 11, 'TRANS': 261} Chain: "J" Number of atoms: 414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 414 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 4, 'TRANS': 48} Chain: "K" Number of atoms: 2211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2211 Classifications: {'peptide': 268} Link IDs: {'PTRANS': 10, 'TRANS': 257} Chain: "L" Number of atoms: 400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 400 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 3, 'TRANS': 47} Chain: "O" Number of atoms: 2102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 2102 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 9, 'TRANS': 245} Chain breaks: 1 Chain: "P" Number of atoms: 400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 400 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 3, 'TRANS': 47} Chain: "M" Number of atoms: 2226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2226 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 11, 'TRANS': 258} Chain: "N" Number of atoms: 400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 400 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 3, 'TRANS': 47} Chain: "Q" Number of atoms: 2136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2136 Classifications: {'peptide': 264} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 259} Chain breaks: 3 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 15 Chain: "R" Number of atoms: 2395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2395 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 3, 'TRANS': 283} Chain breaks: 1 Chain: "S" Number of atoms: 2136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2136 Classifications: {'peptide': 264} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 259} Chain breaks: 3 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 15 Chain: "T" Number of atoms: 2395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2395 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 3, 'TRANS': 283} Chain breaks: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.67, per 1000 atoms: 0.22 Number of scatterers: 29867 At special positions: 0 Unit cell: (201.3, 108.9, 182.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 2 19.99 S 124 16.00 O 5395 8.00 N 5081 7.00 C 19265 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.37 Conformation dependent library (CDL) restraints added in 1.1 seconds 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6958 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 23 sheets defined 66.5% alpha, 4.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.87 Creating SS restraints... Processing helix chain 'G' and resid 107 through 117 Processing helix chain 'G' and resid 140 through 146 Processing helix chain 'G' and resid 175 through 248 removed outlier: 3.797A pdb=" N THR G 181 " --> pdb=" O ASN G 177 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N GLU G 193 " --> pdb=" O THR G 189 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N GLN G 194 " --> pdb=" O LEU G 190 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN G 196 " --> pdb=" O ILE G 192 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N LEU G 197 " --> pdb=" O GLU G 193 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ARG G 201 " --> pdb=" O LEU G 197 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N GLU G 205 " --> pdb=" O ARG G 201 " (cutoff:3.500A) Proline residue: G 216 - end of helix removed outlier: 3.673A pdb=" N GLU G 223 " --> pdb=" O LYS G 219 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ARG G 231 " --> pdb=" O LYS G 227 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N TRP G 237 " --> pdb=" O THR G 233 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N TYR G 242 " --> pdb=" O GLY G 238 " (cutoff:3.500A) Processing helix chain 'G' and resid 263 through 286 removed outlier: 3.806A pdb=" N THR G 271 " --> pdb=" O THR G 267 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N TYR G 279 " --> pdb=" O ALA G 275 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE G 282 " --> pdb=" O MET G 278 " (cutoff:3.500A) Processing helix chain 'G' and resid 290 through 309 removed outlier: 3.855A pdb=" N GLN G 298 " --> pdb=" O ALA G 294 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LEU G 301 " --> pdb=" O ARG G 297 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLY G 306 " --> pdb=" O PHE G 302 " (cutoff:3.500A) Processing helix chain 'G' and resid 313 through 334 removed outlier: 3.653A pdb=" N ASP G 330 " --> pdb=" O GLN G 326 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU G 331 " --> pdb=" O ALA G 327 " (cutoff:3.500A) Processing helix chain 'H' and resid 65 through 94 removed outlier: 4.174A pdb=" N ILE H 73 " --> pdb=" O ARG H 69 " (cutoff:3.500A) Proline residue: H 76 - end of helix removed outlier: 3.568A pdb=" N THR H 82 " --> pdb=" O LEU H 78 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N SER H 85 " --> pdb=" O GLY H 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 95 Processing helix chain 'C' and resid 107 through 117 removed outlier: 4.376A pdb=" N ARG C 113 " --> pdb=" O GLY C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 146 removed outlier: 3.543A pdb=" N LEU C 146 " --> pdb=" O ASP C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 190 Processing helix chain 'C' and resid 191 through 257 Proline residue: C 216 - end of helix removed outlier: 3.800A pdb=" N LYS C 219 " --> pdb=" O ALA C 215 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N VAL C 220 " --> pdb=" O PRO C 216 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ARG C 221 " --> pdb=" O LEU C 217 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR C 232 " --> pdb=" O ALA C 228 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL C 235 " --> pdb=" O ARG C 231 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TRP C 237 " --> pdb=" O THR C 233 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N PHE C 247 " --> pdb=" O MET C 243 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY C 248 " --> pdb=" O ALA C 244 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG C 252 " --> pdb=" O GLY C 248 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TRP C 256 " --> pdb=" O ARG C 252 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLU C 257 " --> pdb=" O LEU C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 286 Proline residue: C 265 - end of helix removed outlier: 4.016A pdb=" N PHE C 269 " --> pdb=" O PRO C 265 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N THR C 271 " --> pdb=" O THR C 267 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N TYR C 279 " --> pdb=" O ALA C 275 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N PHE C 282 " --> pdb=" O MET C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 311 removed outlier: 4.089A pdb=" N SER C 310 " --> pdb=" O GLY C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 313 through 335 removed outlier: 3.633A pdb=" N GLN C 319 " --> pdb=" O GLU C 315 " (cutoff:3.500A) Processing helix chain 'D' and resid 65 through 72 Processing helix chain 'D' and resid 73 through 97 removed outlier: 3.554A pdb=" N SER D 85 " --> pdb=" O GLY D 81 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N GLU D 94 " --> pdb=" O ALA D 90 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N HIS D 95 " --> pdb=" O LEU D 91 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE D 97 " --> pdb=" O GLU D 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 119 removed outlier: 3.754A pdb=" N ARG A 113 " --> pdb=" O GLY A 109 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASP A 119 " --> pdb=" O LEU A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 146 Processing helix chain 'A' and resid 171 through 191 removed outlier: 3.553A pdb=" N ASP A 178 " --> pdb=" O ALA A 174 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N VAL A 179 " --> pdb=" O THR A 175 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N THR A 181 " --> pdb=" O ASN A 177 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN A 185 " --> pdb=" O THR A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 249 removed outlier: 3.727A pdb=" N LEU A 197 " --> pdb=" O GLU A 193 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLU A 205 " --> pdb=" O ARG A 201 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLU A 208 " --> pdb=" O ILE A 204 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA A 215 " --> pdb=" O LYS A 211 " (cutoff:3.500A) Proline residue: A 216 - end of helix removed outlier: 3.801A pdb=" N LYS A 219 " --> pdb=" O ALA A 215 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N VAL A 220 " --> pdb=" O PRO A 216 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ILE A 224 " --> pdb=" O VAL A 220 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N VAL A 235 " --> pdb=" O ARG A 231 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N TRP A 237 " --> pdb=" O THR A 233 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LEU A 240 " --> pdb=" O LEU A 236 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N PHE A 247 " --> pdb=" O MET A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 255 removed outlier: 3.584A pdb=" N TRP A 255 " --> pdb=" O ARG A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 285 removed outlier: 4.185A pdb=" N PHE A 269 " --> pdb=" O PRO A 265 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N THR A 271 " --> pdb=" O THR A 267 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N MET A 276 " --> pdb=" O TYR A 272 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA A 277 " --> pdb=" O GLY A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 311 removed outlier: 4.067A pdb=" N ASP A 296 " --> pdb=" O PRO A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 334 Processing helix chain 'A' and resid 334 through 340 Processing helix chain 'B' and resid 65 through 94 removed outlier: 3.723A pdb=" N ILE B 75 " --> pdb=" O PHE B 71 " (cutoff:3.500A) Proline residue: B 76 - end of helix removed outlier: 3.620A pdb=" N VAL B 80 " --> pdb=" O PRO B 76 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLY B 81 " --> pdb=" O PHE B 77 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE B 88 " --> pdb=" O ILE B 84 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU B 94 " --> pdb=" O ALA B 90 " (cutoff:3.500A) Processing helix chain 'E' and resid 107 through 119 removed outlier: 4.087A pdb=" N ARG E 113 " --> pdb=" O GLY E 109 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASP E 119 " --> pdb=" O LEU E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 140 through 146 Processing helix chain 'E' and resid 169 through 190 removed outlier: 3.564A pdb=" N THR E 181 " --> pdb=" O ASN E 177 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU E 186 " --> pdb=" O LEU E 182 " (cutoff:3.500A) Processing helix chain 'E' and resid 191 through 253 removed outlier: 3.588A pdb=" N LEU E 197 " --> pdb=" O GLU E 193 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLU E 205 " --> pdb=" O ARG E 201 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLU E 212 " --> pdb=" O GLU E 208 " (cutoff:3.500A) Proline residue: E 216 - end of helix removed outlier: 3.661A pdb=" N VAL E 220 " --> pdb=" O PRO E 216 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU E 234 " --> pdb=" O LYS E 230 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU E 240 " --> pdb=" O LEU E 236 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N PHE E 247 " --> pdb=" O MET E 243 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N LEU E 250 " --> pdb=" O GLN E 246 " (cutoff:3.500A) Processing helix chain 'E' and resid 263 through 285 removed outlier: 3.583A pdb=" N PHE E 269 " --> pdb=" O PRO E 265 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLY E 273 " --> pdb=" O PHE E 269 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N MET E 276 " --> pdb=" O TYR E 272 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N TYR E 279 " --> pdb=" O ALA E 275 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N PHE E 282 " --> pdb=" O MET E 278 " (cutoff:3.500A) Processing helix chain 'E' and resid 290 through 310 removed outlier: 3.875A pdb=" N LEU E 301 " --> pdb=" O ARG E 297 " (cutoff:3.500A) Processing helix chain 'E' and resid 313 through 335 removed outlier: 3.534A pdb=" N ASP E 322 " --> pdb=" O ASN E 318 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ALA E 323 " --> pdb=" O GLN E 319 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE E 324 " --> pdb=" O LEU E 320 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N MET E 329 " --> pdb=" O ALA E 325 " (cutoff:3.500A) Processing helix chain 'F' and resid 65 through 93 removed outlier: 3.965A pdb=" N PHE F 71 " --> pdb=" O LEU F 67 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N SER F 72 " --> pdb=" O LEU F 68 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ILE F 73 " --> pdb=" O ARG F 69 " (cutoff:3.500A) Proline residue: F 76 - end of helix removed outlier: 4.078A pdb=" N VAL F 80 " --> pdb=" O PRO F 76 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE F 84 " --> pdb=" O VAL F 80 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N SER F 85 " --> pdb=" O GLY F 81 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N PHE F 88 " --> pdb=" O ILE F 84 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LEU F 91 " --> pdb=" O ASN F 87 " (cutoff:3.500A) Processing helix chain 'I' and resid 107 through 118 removed outlier: 3.906A pdb=" N ARG I 113 " --> pdb=" O GLY I 109 " (cutoff:3.500A) Processing helix chain 'I' and resid 140 through 146 Processing helix chain 'I' and resid 171 through 249 removed outlier: 3.520A pdb=" N THR I 181 " --> pdb=" O ASN I 177 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU I 190 " --> pdb=" O LEU I 186 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N GLU I 193 " --> pdb=" O THR I 189 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N GLN I 194 " --> pdb=" O LEU I 190 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU I 197 " --> pdb=" O GLU I 193 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N GLU I 205 " --> pdb=" O ARG I 201 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLU I 208 " --> pdb=" O ILE I 204 " (cutoff:3.500A) Proline residue: I 216 - end of helix removed outlier: 3.908A pdb=" N LYS I 219 " --> pdb=" O ALA I 215 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N VAL I 220 " --> pdb=" O PRO I 216 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ILE I 224 " --> pdb=" O VAL I 220 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LYS I 230 " --> pdb=" O ARG I 226 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N VAL I 235 " --> pdb=" O ARG I 231 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N TRP I 237 " --> pdb=" O THR I 233 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N LEU I 240 " --> pdb=" O LEU I 236 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N PHE I 247 " --> pdb=" O MET I 243 " (cutoff:3.500A) Processing helix chain 'I' and resid 259 through 262 Processing helix chain 'I' and resid 263 through 285 removed outlier: 4.083A pdb=" N PHE I 269 " --> pdb=" O PRO I 265 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR I 271 " --> pdb=" O THR I 267 " (cutoff:3.500A) Processing helix chain 'I' and resid 290 through 311 removed outlier: 4.149A pdb=" N ASP I 296 " --> pdb=" O PRO I 292 " (cutoff:3.500A) Processing helix chain 'I' and resid 314 through 340 removed outlier: 3.745A pdb=" N GLN I 319 " --> pdb=" O GLU I 315 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N ASP I 336 " --> pdb=" O LYS I 332 " (cutoff:3.500A) Proline residue: I 337 - end of helix Processing helix chain 'J' and resid 66 through 80 removed outlier: 4.666A pdb=" N SER J 72 " --> pdb=" O LEU J 68 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ILE J 75 " --> pdb=" O PHE J 71 " (cutoff:3.500A) Proline residue: J 76 - end of helix Processing helix chain 'J' and resid 80 through 92 removed outlier: 4.167A pdb=" N LYS J 86 " --> pdb=" O THR J 82 " (cutoff:3.500A) Processing helix chain 'K' and resid 91 through 95 removed outlier: 3.685A pdb=" N GLU K 95 " --> pdb=" O SER K 92 " (cutoff:3.500A) Processing helix chain 'K' and resid 107 through 119 removed outlier: 3.940A pdb=" N ARG K 113 " --> pdb=" O GLY K 109 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASP K 119 " --> pdb=" O LEU K 115 " (cutoff:3.500A) Processing helix chain 'K' and resid 140 through 146 Processing helix chain 'K' and resid 171 through 190 Processing helix chain 'K' and resid 191 through 257 Proline residue: K 216 - end of helix removed outlier: 3.699A pdb=" N LYS K 219 " --> pdb=" O ALA K 215 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N VAL K 220 " --> pdb=" O PRO K 216 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ARG K 221 " --> pdb=" O LEU K 217 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N THR K 232 " --> pdb=" O ALA K 228 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL K 235 " --> pdb=" O ARG K 231 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TRP K 237 " --> pdb=" O THR K 233 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N PHE K 247 " --> pdb=" O MET K 243 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLY K 248 " --> pdb=" O ALA K 244 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ARG K 252 " --> pdb=" O GLY K 248 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU K 257 " --> pdb=" O LEU K 253 " (cutoff:3.500A) Processing helix chain 'K' and resid 259 through 286 Proline residue: K 265 - end of helix removed outlier: 4.131A pdb=" N PHE K 269 " --> pdb=" O PRO K 265 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N THR K 271 " --> pdb=" O THR K 267 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N TYR K 279 " --> pdb=" O ALA K 275 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N PHE K 282 " --> pdb=" O MET K 278 " (cutoff:3.500A) Processing helix chain 'K' and resid 290 through 309 removed outlier: 3.514A pdb=" N LYS K 309 " --> pdb=" O LYS K 305 " (cutoff:3.500A) Processing helix chain 'K' and resid 313 through 335 removed outlier: 3.729A pdb=" N TYR K 317 " --> pdb=" O ASP K 313 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLN K 319 " --> pdb=" O GLU K 315 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU K 331 " --> pdb=" O ALA K 327 " (cutoff:3.500A) Processing helix chain 'L' and resid 65 through 71 Processing helix chain 'L' and resid 75 through 94 removed outlier: 3.586A pdb=" N LYS L 86 " --> pdb=" O THR L 82 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LEU L 91 " --> pdb=" O ASN L 87 " (cutoff:3.500A) Processing helix chain 'O' and resid 107 through 118 removed outlier: 4.293A pdb=" N GLU O 118 " --> pdb=" O GLN O 114 " (cutoff:3.500A) Processing helix chain 'O' and resid 140 through 146 Processing helix chain 'O' and resid 175 through 248 removed outlier: 3.670A pdb=" N THR O 181 " --> pdb=" O ASN O 177 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU O 182 " --> pdb=" O ASP O 178 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N GLU O 193 " --> pdb=" O THR O 189 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N GLN O 194 " --> pdb=" O LEU O 190 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLN O 196 " --> pdb=" O ILE O 192 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N LEU O 197 " --> pdb=" O GLU O 193 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N GLU O 205 " --> pdb=" O ARG O 201 " (cutoff:3.500A) Proline residue: O 216 - end of helix removed outlier: 3.537A pdb=" N ARG O 231 " --> pdb=" O LYS O 227 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N VAL O 235 " --> pdb=" O ARG O 231 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N TRP O 237 " --> pdb=" O THR O 233 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLY O 238 " --> pdb=" O LEU O 234 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N TYR O 242 " --> pdb=" O GLY O 238 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N MET O 243 " --> pdb=" O GLY O 239 " (cutoff:3.500A) Processing helix chain 'O' and resid 248 through 253 removed outlier: 4.056A pdb=" N ARG O 252 " --> pdb=" O GLY O 248 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU O 253 " --> pdb=" O ILE O 249 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 248 through 253' Processing helix chain 'O' and resid 265 through 286 removed outlier: 3.512A pdb=" N ILE O 270 " --> pdb=" O VAL O 266 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N THR O 271 " --> pdb=" O THR O 267 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N TYR O 279 " --> pdb=" O ALA O 275 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N PHE O 282 " --> pdb=" O MET O 278 " (cutoff:3.500A) Processing helix chain 'O' and resid 290 through 310 removed outlier: 3.790A pdb=" N GLN O 298 " --> pdb=" O ALA O 294 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LEU O 301 " --> pdb=" O ARG O 297 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N SER O 310 " --> pdb=" O GLY O 306 " (cutoff:3.500A) Processing helix chain 'O' and resid 314 through 334 removed outlier: 3.896A pdb=" N GLU O 328 " --> pdb=" O ILE O 324 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU O 331 " --> pdb=" O ALA O 327 " (cutoff:3.500A) Processing helix chain 'P' and resid 65 through 96 removed outlier: 3.650A pdb=" N ILE P 73 " --> pdb=" O ARG P 69 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE P 75 " --> pdb=" O PHE P 71 " (cutoff:3.500A) Proline residue: P 76 - end of helix removed outlier: 3.519A pdb=" N THR P 82 " --> pdb=" O LEU P 78 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N GLU P 93 " --> pdb=" O ALA P 89 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU P 94 " --> pdb=" O ALA P 90 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N HIS P 95 " --> pdb=" O LEU P 91 " (cutoff:3.500A) Processing helix chain 'M' and resid 107 through 119 removed outlier: 3.913A pdb=" N ARG M 113 " --> pdb=" O GLY M 109 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU M 117 " --> pdb=" O ARG M 113 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASP M 119 " --> pdb=" O LEU M 115 " (cutoff:3.500A) Processing helix chain 'M' and resid 140 through 146 removed outlier: 3.614A pdb=" N LEU M 146 " --> pdb=" O ASP M 142 " (cutoff:3.500A) Processing helix chain 'M' and resid 169 through 190 removed outlier: 3.648A pdb=" N VAL M 179 " --> pdb=" O THR M 175 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LEU M 190 " --> pdb=" O LEU M 186 " (cutoff:3.500A) Processing helix chain 'M' and resid 191 through 256 removed outlier: 3.716A pdb=" N GLU M 212 " --> pdb=" O GLU M 208 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA M 215 " --> pdb=" O LYS M 211 " (cutoff:3.500A) Proline residue: M 216 - end of helix removed outlier: 3.554A pdb=" N VAL M 220 " --> pdb=" O PRO M 216 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N GLU M 229 " --> pdb=" O SER M 225 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR M 232 " --> pdb=" O ALA M 228 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU M 234 " --> pdb=" O LYS M 230 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU M 240 " --> pdb=" O LEU M 236 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N PHE M 247 " --> pdb=" O MET M 243 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU M 250 " --> pdb=" O GLN M 246 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU M 253 " --> pdb=" O ILE M 249 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TRP M 255 " --> pdb=" O ALA M 251 " (cutoff:3.500A) Processing helix chain 'M' and resid 264 through 268 Processing helix chain 'M' and resid 270 through 285 removed outlier: 4.172A pdb=" N MET M 276 " --> pdb=" O TYR M 272 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N TYR M 279 " --> pdb=" O ALA M 275 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N PHE M 282 " --> pdb=" O MET M 278 " (cutoff:3.500A) Processing helix chain 'M' and resid 290 through 310 removed outlier: 3.893A pdb=" N ASP M 296 " --> pdb=" O PRO M 292 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU M 301 " --> pdb=" O ARG M 297 " (cutoff:3.500A) Processing helix chain 'M' and resid 313 through 335 removed outlier: 3.645A pdb=" N TYR M 317 " --> pdb=" O ASP M 313 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N MET M 329 " --> pdb=" O ALA M 325 " (cutoff:3.500A) Processing helix chain 'N' and resid 65 through 79 removed outlier: 4.599A pdb=" N ILE N 73 " --> pdb=" O ARG N 69 " (cutoff:3.500A) Proline residue: N 76 - end of helix Processing helix chain 'N' and resid 79 through 93 removed outlier: 4.231A pdb=" N SER N 85 " --> pdb=" O GLY N 81 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N PHE N 88 " --> pdb=" O ILE N 84 " (cutoff:3.500A) Processing helix chain 'Q' and resid 110 through 121 removed outlier: 3.566A pdb=" N ASN Q 116 " --> pdb=" O MET Q 112 " (cutoff:3.500A) Processing helix chain 'Q' and resid 123 through 130 removed outlier: 3.903A pdb=" N ILE Q 127 " --> pdb=" O THR Q 123 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR Q 130 " --> pdb=" O LYS Q 126 " (cutoff:3.500A) Processing helix chain 'Q' and resid 150 through 156 Processing helix chain 'Q' and resid 193 through 198 Processing helix chain 'Q' and resid 206 through 218 Processing helix chain 'Q' and resid 219 through 231 removed outlier: 4.134A pdb=" N GLU Q 224 " --> pdb=" O GLN Q 220 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ILE Q 225 " --> pdb=" O ARG Q 221 " (cutoff:3.500A) Processing helix chain 'Q' and resid 239 through 249 removed outlier: 3.507A pdb=" N GLN Q 245 " --> pdb=" O GLU Q 241 " (cutoff:3.500A) Processing helix chain 'Q' and resid 277 through 283 Processing helix chain 'Q' and resid 292 through 294 No H-bonds generated for 'chain 'Q' and resid 292 through 294' Processing helix chain 'Q' and resid 295 through 315 Processing helix chain 'Q' and resid 317 through 319 No H-bonds generated for 'chain 'Q' and resid 317 through 319' Processing helix chain 'Q' and resid 323 through 336 removed outlier: 3.743A pdb=" N LEU Q 331 " --> pdb=" O PHE Q 327 " (cutoff:3.500A) Processing helix chain 'Q' and resid 339 through 353 removed outlier: 5.132A pdb=" N LYS Q 350 " --> pdb=" O GLN Q 346 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N LYS Q 351 " --> pdb=" O ARG Q 347 " (cutoff:3.500A) Processing helix chain 'Q' and resid 361 through 373 removed outlier: 4.318A pdb=" N PHE Q 367 " --> pdb=" O GLU Q 363 " (cutoff:3.500A) Processing helix chain 'Q' and resid 373 through 381 removed outlier: 3.566A pdb=" N VAL Q 377 " --> pdb=" O ASN Q 373 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N THR Q 379 " --> pdb=" O ASN Q 375 " (cutoff:3.500A) Processing helix chain 'Q' and resid 381 through 386 Processing helix chain 'Q' and resid 394 through 405 Processing helix chain 'Q' and resid 410 through 420 removed outlier: 3.987A pdb=" N VAL Q 416 " --> pdb=" O VAL Q 412 " (cutoff:3.500A) Processing helix chain 'Q' and resid 433 through 441 removed outlier: 3.875A pdb=" N LEU Q 441 " --> pdb=" O MET Q 437 " (cutoff:3.500A) Processing helix chain 'R' and resid 86 through 94 Processing helix chain 'R' and resid 105 through 115 Processing helix chain 'R' and resid 124 through 129 removed outlier: 3.540A pdb=" N LEU R 127 " --> pdb=" O VAL R 124 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR R 128 " --> pdb=" O LYS R 125 " (cutoff:3.500A) Processing helix chain 'R' and resid 130 through 140 removed outlier: 4.901A pdb=" N LEU R 136 " --> pdb=" O ILE R 132 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLN R 140 " --> pdb=" O LEU R 136 " (cutoff:3.500A) Processing helix chain 'R' and resid 160 through 171 removed outlier: 3.761A pdb=" N THR R 171 " --> pdb=" O LEU R 167 " (cutoff:3.500A) Processing helix chain 'R' and resid 173 through 184 removed outlier: 4.121A pdb=" N HIS R 178 " --> pdb=" O HIS R 174 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N VAL R 179 " --> pdb=" O SER R 175 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU R 184 " --> pdb=" O ALA R 180 " (cutoff:3.500A) Processing helix chain 'R' and resid 188 through 207 removed outlier: 5.310A pdb=" N LYS R 194 " --> pdb=" O GLU R 190 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ARG R 195 " --> pdb=" O MET R 191 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU R 196 " --> pdb=" O ILE R 192 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N PHE R 197 " --> pdb=" O GLU R 193 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ILE R 203 " --> pdb=" O LYS R 199 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE R 204 " --> pdb=" O LEU R 200 " (cutoff:3.500A) Processing helix chain 'R' and resid 232 through 240 Processing helix chain 'R' and resid 248 through 273 removed outlier: 3.519A pdb=" N LEU R 259 " --> pdb=" O PHE R 255 " (cutoff:3.500A) Processing helix chain 'R' and resid 281 through 292 removed outlier: 3.960A pdb=" N GLU R 285 " --> pdb=" O GLU R 281 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N TRP R 286 " --> pdb=" O ASP R 282 " (cutoff:3.500A) Processing helix chain 'R' and resid 296 through 307 removed outlier: 3.962A pdb=" N TRP R 300 " --> pdb=" O LYS R 296 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLU R 305 " --> pdb=" O LYS R 301 " (cutoff:3.500A) Processing helix chain 'R' and resid 314 through 327 Processing helix chain 'R' and resid 327 through 335 Processing helix chain 'R' and resid 335 through 342 Processing helix chain 'R' and resid 346 through 359 Processing helix chain 'R' and resid 363 through 375 removed outlier: 4.195A pdb=" N THR R 369 " --> pdb=" O ASN R 365 " (cutoff:3.500A) Processing helix chain 'R' and resid 383 through 392 removed outlier: 3.907A pdb=" N VAL R 390 " --> pdb=" O GLU R 386 " (cutoff:3.500A) Processing helix chain 'S' and resid 110 through 121 removed outlier: 3.566A pdb=" N ASN S 116 " --> pdb=" O MET S 112 " (cutoff:3.500A) Processing helix chain 'S' and resid 123 through 130 removed outlier: 3.903A pdb=" N ILE S 127 " --> pdb=" O THR S 123 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR S 130 " --> pdb=" O LYS S 126 " (cutoff:3.500A) Processing helix chain 'S' and resid 150 through 156 Processing helix chain 'S' and resid 193 through 198 Processing helix chain 'S' and resid 206 through 218 Processing helix chain 'S' and resid 219 through 231 removed outlier: 4.134A pdb=" N GLU S 224 " --> pdb=" O GLN S 220 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ILE S 225 " --> pdb=" O ARG S 221 " (cutoff:3.500A) Processing helix chain 'S' and resid 239 through 249 removed outlier: 3.506A pdb=" N GLN S 245 " --> pdb=" O GLU S 241 " (cutoff:3.500A) Processing helix chain 'S' and resid 277 through 283 Processing helix chain 'S' and resid 292 through 294 No H-bonds generated for 'chain 'S' and resid 292 through 294' Processing helix chain 'S' and resid 295 through 315 Processing helix chain 'S' and resid 317 through 319 No H-bonds generated for 'chain 'S' and resid 317 through 319' Processing helix chain 'S' and resid 323 through 336 removed outlier: 3.744A pdb=" N LEU S 331 " --> pdb=" O PHE S 327 " (cutoff:3.500A) Processing helix chain 'S' and resid 339 through 353 removed outlier: 5.131A pdb=" N LYS S 350 " --> pdb=" O GLN S 346 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N LYS S 351 " --> pdb=" O ARG S 347 " (cutoff:3.500A) Processing helix chain 'S' and resid 361 through 373 removed outlier: 4.319A pdb=" N PHE S 367 " --> pdb=" O GLU S 363 " (cutoff:3.500A) Processing helix chain 'S' and resid 373 through 381 removed outlier: 3.565A pdb=" N VAL S 377 " --> pdb=" O ASN S 373 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N THR S 379 " --> pdb=" O ASN S 375 " (cutoff:3.500A) Processing helix chain 'S' and resid 381 through 386 Processing helix chain 'S' and resid 394 through 405 Processing helix chain 'S' and resid 410 through 420 removed outlier: 3.987A pdb=" N VAL S 416 " --> pdb=" O VAL S 412 " (cutoff:3.500A) Processing helix chain 'S' and resid 433 through 441 removed outlier: 3.875A pdb=" N LEU S 441 " --> pdb=" O MET S 437 " (cutoff:3.500A) Processing helix chain 'T' and resid 86 through 94 Processing helix chain 'T' and resid 105 through 115 Processing helix chain 'T' and resid 124 through 129 removed outlier: 3.540A pdb=" N LEU T 127 " --> pdb=" O VAL T 124 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR T 128 " --> pdb=" O LYS T 125 " (cutoff:3.500A) Processing helix chain 'T' and resid 130 through 140 removed outlier: 4.902A pdb=" N LEU T 136 " --> pdb=" O ILE T 132 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLN T 140 " --> pdb=" O LEU T 136 " (cutoff:3.500A) Processing helix chain 'T' and resid 160 through 171 removed outlier: 3.761A pdb=" N THR T 171 " --> pdb=" O LEU T 167 " (cutoff:3.500A) Processing helix chain 'T' and resid 173 through 184 removed outlier: 4.120A pdb=" N HIS T 178 " --> pdb=" O HIS T 174 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N VAL T 179 " --> pdb=" O SER T 175 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU T 184 " --> pdb=" O ALA T 180 " (cutoff:3.500A) Processing helix chain 'T' and resid 188 through 207 removed outlier: 5.309A pdb=" N LYS T 194 " --> pdb=" O GLU T 190 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ARG T 195 " --> pdb=" O MET T 191 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLU T 196 " --> pdb=" O ILE T 192 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N PHE T 197 " --> pdb=" O GLU T 193 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ILE T 203 " --> pdb=" O LYS T 199 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE T 204 " --> pdb=" O LEU T 200 " (cutoff:3.500A) Processing helix chain 'T' and resid 232 through 240 Processing helix chain 'T' and resid 248 through 273 removed outlier: 3.519A pdb=" N LEU T 259 " --> pdb=" O PHE T 255 " (cutoff:3.500A) Processing helix chain 'T' and resid 281 through 292 removed outlier: 3.960A pdb=" N GLU T 285 " --> pdb=" O GLU T 281 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N TRP T 286 " --> pdb=" O ASP T 282 " (cutoff:3.500A) Processing helix chain 'T' and resid 296 through 307 removed outlier: 3.962A pdb=" N TRP T 300 " --> pdb=" O LYS T 296 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLU T 305 " --> pdb=" O LYS T 301 " (cutoff:3.500A) Processing helix chain 'T' and resid 314 through 327 Processing helix chain 'T' and resid 327 through 335 Processing helix chain 'T' and resid 335 through 342 Processing helix chain 'T' and resid 346 through 359 Processing helix chain 'T' and resid 363 through 375 removed outlier: 4.194A pdb=" N THR T 369 " --> pdb=" O ASN T 365 " (cutoff:3.500A) Processing helix chain 'T' and resid 383 through 392 removed outlier: 3.909A pdb=" N VAL T 390 " --> pdb=" O GLU T 386 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 88 through 89 Processing sheet with id=AA2, first strand: chain 'G' and resid 126 through 128 removed outlier: 3.698A pdb=" N ALA G 126 " --> pdb=" O VAL G 152 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE G 149 " --> pdb=" O VAL G 160 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU G 151 " --> pdb=" O TYR G 158 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 134 through 135 removed outlier: 6.941A pdb=" N ARG G 134 " --> pdb=" O GLN E 98 " (cutoff:3.500A) removed outlier: 8.525A pdb=" N THR E 100 " --> pdb=" O ARG G 134 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR E 76 " --> pdb=" O SER E 87 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 77 through 80 Processing sheet with id=AA5, first strand: chain 'C' and resid 126 through 128 removed outlier: 3.721A pdb=" N PHE C 149 " --> pdb=" O VAL C 160 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 134 through 135 removed outlier: 3.681A pdb=" N VAL A 78 " --> pdb=" O VAL A 85 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR A 76 " --> pdb=" O SER A 87 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 126 through 128 removed outlier: 3.676A pdb=" N PHE A 149 " --> pdb=" O VAL A 160 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 126 through 128 removed outlier: 3.594A pdb=" N VAL E 152 " --> pdb=" O ALA E 126 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 76 through 80 removed outlier: 3.714A pdb=" N THR I 76 " --> pdb=" O SER I 87 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'I' and resid 97 through 98 Processing sheet with id=AB2, first strand: chain 'I' and resid 126 through 128 Processing sheet with id=AB3, first strand: chain 'K' and resid 77 through 80 Processing sheet with id=AB4, first strand: chain 'K' and resid 125 through 128 Processing sheet with id=AB5, first strand: chain 'O' and resid 88 through 89 Processing sheet with id=AB6, first strand: chain 'O' and resid 126 through 128 removed outlier: 3.760A pdb=" N ALA O 126 " --> pdb=" O VAL O 152 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE O 149 " --> pdb=" O VAL O 160 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL O 160 " --> pdb=" O PHE O 149 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LEU O 151 " --> pdb=" O TYR O 158 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'M' and resid 76 through 80 Processing sheet with id=AB8, first strand: chain 'M' and resid 149 through 152 Processing sheet with id=AB9, first strand: chain 'Q' and resid 321 through 322 Processing sheet with id=AC1, first strand: chain 'R' and resid 103 through 104 Processing sheet with id=AC2, first strand: chain 'R' and resid 278 through 279 Processing sheet with id=AC3, first strand: chain 'S' and resid 321 through 322 Processing sheet with id=AC4, first strand: chain 'T' and resid 103 through 104 Processing sheet with id=AC5, first strand: chain 'T' and resid 278 through 279 1644 hydrogen bonds defined for protein. 4785 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: 4.91 Time building geometry restraints manager: 3.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6441 1.33 - 1.45: 6693 1.45 - 1.57: 17118 1.57 - 1.69: 0 1.69 - 1.82: 220 Bond restraints: 30472 Sorted by residual: bond pdb=" N ILE C 153 " pdb=" CA ILE C 153 " ideal model delta sigma weight residual 1.459 1.532 -0.073 1.25e-02 6.40e+03 3.39e+01 bond pdb=" N ILE P 97 " pdb=" CA ILE P 97 " ideal model delta sigma weight residual 1.456 1.494 -0.038 1.19e-02 7.06e+03 1.01e+01 bond pdb=" N VAL M 152 " pdb=" CA VAL M 152 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.20e-02 6.94e+03 9.97e+00 bond pdb=" N LEU E 156 " pdb=" CA LEU E 156 " ideal model delta sigma weight residual 1.455 1.493 -0.038 1.29e-02 6.01e+03 8.79e+00 bond pdb=" N ASN C 154 " pdb=" CA ASN C 154 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.23e-02 6.61e+03 8.54e+00 ... (remaining 30467 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.50: 40528 2.50 - 5.00: 512 5.00 - 7.50: 60 7.50 - 10.00: 8 10.00 - 12.50: 6 Bond angle restraints: 41114 Sorted by residual: angle pdb=" C ASP P 96 " pdb=" N ILE P 97 " pdb=" CA ILE P 97 " ideal model delta sigma weight residual 120.49 131.85 -11.36 1.38e+00 5.25e-01 6.78e+01 angle pdb=" N ASP P 96 " pdb=" CA ASP P 96 " pdb=" C ASP P 96 " ideal model delta sigma weight residual 108.19 118.04 -9.85 1.29e+00 6.01e-01 5.83e+01 angle pdb=" N GLU P 93 " pdb=" CA GLU P 93 " pdb=" C GLU P 93 " ideal model delta sigma weight residual 113.38 104.21 9.17 1.23e+00 6.61e-01 5.55e+01 angle pdb=" N ILE B 73 " pdb=" CA ILE B 73 " pdb=" C ILE B 73 " ideal model delta sigma weight residual 113.53 106.56 6.97 9.80e-01 1.04e+00 5.05e+01 angle pdb=" C LYS O 180 " pdb=" N THR O 181 " pdb=" CA THR O 181 " ideal model delta sigma weight residual 120.38 111.44 8.94 1.37e+00 5.33e-01 4.26e+01 ... (remaining 41109 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 16229 17.79 - 35.59: 1729 35.59 - 53.38: 368 53.38 - 71.18: 68 71.18 - 88.97: 33 Dihedral angle restraints: 18427 sinusoidal: 7706 harmonic: 10721 Sorted by residual: dihedral pdb=" CA GLU A 257 " pdb=" C GLU A 257 " pdb=" N TYR A 258 " pdb=" CA TYR A 258 " ideal model delta harmonic sigma weight residual -180.00 -153.38 -26.62 0 5.00e+00 4.00e-02 2.83e+01 dihedral pdb=" C ASP P 96 " pdb=" N ASP P 96 " pdb=" CA ASP P 96 " pdb=" CB ASP P 96 " ideal model delta harmonic sigma weight residual -122.60 -135.83 13.23 0 2.50e+00 1.60e-01 2.80e+01 dihedral pdb=" N ASP P 96 " pdb=" C ASP P 96 " pdb=" CA ASP P 96 " pdb=" CB ASP P 96 " ideal model delta harmonic sigma weight residual 122.80 135.89 -13.09 0 2.50e+00 1.60e-01 2.74e+01 ... (remaining 18424 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.109: 4510 0.109 - 0.217: 90 0.217 - 0.326: 4 0.326 - 0.434: 1 0.434 - 0.543: 2 Chirality restraints: 4607 Sorted by residual: chirality pdb=" CA ASP P 96 " pdb=" N ASP P 96 " pdb=" C ASP P 96 " pdb=" CB ASP P 96 " both_signs ideal model delta sigma weight residual False 2.51 1.97 0.54 2.00e-01 2.50e+01 7.37e+00 chirality pdb=" CA ILE C 153 " pdb=" N ILE C 153 " pdb=" C ILE C 153 " pdb=" CB ILE C 153 " both_signs ideal model delta sigma weight residual False 2.43 2.90 -0.46 2.00e-01 2.50e+01 5.33e+00 chirality pdb=" CA ILE E 153 " pdb=" N ILE E 153 " pdb=" C ILE E 153 " pdb=" CB ILE E 153 " both_signs ideal model delta sigma weight residual False 2.43 2.82 -0.38 2.00e-01 2.50e+01 3.68e+00 ... (remaining 4604 not shown) Planarity restraints: 5208 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR O 175 " 0.017 2.00e-02 2.50e+03 3.52e-02 1.24e+01 pdb=" C THR O 175 " -0.061 2.00e-02 2.50e+03 pdb=" O THR O 175 " 0.023 2.00e-02 2.50e+03 pdb=" N LEU O 176 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU P 94 " 0.017 2.00e-02 2.50e+03 3.37e-02 1.13e+01 pdb=" C GLU P 94 " -0.058 2.00e-02 2.50e+03 pdb=" O GLU P 94 " 0.022 2.00e-02 2.50e+03 pdb=" N HIS P 95 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS O 180 " -0.017 2.00e-02 2.50e+03 3.35e-02 1.12e+01 pdb=" C LYS O 180 " 0.058 2.00e-02 2.50e+03 pdb=" O LYS O 180 " -0.021 2.00e-02 2.50e+03 pdb=" N THR O 181 " -0.020 2.00e-02 2.50e+03 ... (remaining 5205 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 2081 2.72 - 3.27: 36189 3.27 - 3.81: 50684 3.81 - 4.36: 61366 4.36 - 4.90: 94647 Nonbonded interactions: 244967 Sorted by model distance: nonbonded pdb=" O GLN I 184 " pdb=" OG1 THR I 188 " model vdw 2.179 3.040 nonbonded pdb=" OG1 THR A 76 " pdb=" OG SER A 87 " model vdw 2.185 3.040 nonbonded pdb=" O GLN O 185 " pdb=" OG1 THR O 189 " model vdw 2.185 3.040 nonbonded pdb=" O LEU R 184 " pdb=" OG1 THR R 186 " model vdw 2.186 3.040 nonbonded pdb=" O LEU T 184 " pdb=" OG1 THR T 186 " model vdw 2.186 3.040 ... (remaining 244962 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 75 through 164 or resid 172 through 336)) selection = (chain 'C' and (resid 75 through 164 or resid 172 through 336)) selection = (chain 'E' and (resid 75 through 164 or resid 172 through 336)) selection = chain 'G' selection = (chain 'I' and (resid 75 through 164 or resid 172 through 336)) selection = (chain 'K' and (resid 75 through 164 or resid 172 through 336)) selection = (chain 'M' and (resid 75 through 164 or resid 172 through 336)) selection = chain 'O' } ncs_group { reference = (chain 'B' and resid 48 through 97) selection = (chain 'D' and resid 48 through 97) selection = chain 'F' selection = (chain 'H' and resid 48 through 97) selection = (chain 'J' and resid 48 through 97) selection = (chain 'L' and resid 48 through 97) selection = (chain 'N' and resid 48 through 97) selection = (chain 'P' and resid 48 through 97) } ncs_group { reference = chain 'Q' selection = chain 'S' } ncs_group { reference = chain 'R' selection = chain 'T' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.460 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 24.110 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 30472 Z= 0.243 Angle : 0.729 12.504 41114 Z= 0.423 Chirality : 0.046 0.543 4607 Planarity : 0.004 0.066 5208 Dihedral : 15.464 88.973 11469 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 21.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.79 % Favored : 90.21 % Rotamer: Outliers : 0.77 % Allowed : 8.13 % Favored : 91.10 % Cbeta Deviations : 0.03 % 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: -5.14 (0.11), residues: 3585 helix: -3.55 (0.07), residues: 2179 sheet: -3.43 (0.29), residues: 224 loop : -2.60 (0.18), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.031 0.001 ARG Q 107 TYR 0.014 0.002 TYR O 79 PHE 0.017 0.001 PHE Q 223 TRP 0.015 0.001 TRP K 256 HIS 0.005 0.001 HIS A 170 Details of bonding type rmsd covalent geometry : bond 0.00505 (30472) covalent geometry : angle 0.72874 (41114) hydrogen bonds : bond 0.29262 ( 1644) hydrogen bonds : angle 10.52529 ( 4785) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 557 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 532 time to evaluate : 1.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 84 PRO cc_start: 0.8620 (Cg_exo) cc_final: 0.8297 (Cg_endo) REVERT: G 236 LEU cc_start: 0.9022 (tp) cc_final: 0.8727 (tp) REVERT: H 59 LYS cc_start: 0.9315 (tmmt) cc_final: 0.9072 (tttt) REVERT: H 96 ASP cc_start: 0.8188 (p0) cc_final: 0.7979 (p0) REVERT: A 205 GLU cc_start: 0.9092 (tm-30) cc_final: 0.8706 (tm-30) REVERT: A 212 GLU cc_start: 0.8856 (tp30) cc_final: 0.8581 (tp30) REVERT: A 267 THR cc_start: 0.8732 (m) cc_final: 0.8518 (p) REVERT: B 73 ILE cc_start: 0.8368 (mm) cc_final: 0.8052 (mm) REVERT: B 79 TYR cc_start: 0.7363 (t80) cc_final: 0.6961 (t80) REVERT: E 154 ASN cc_start: 0.7987 (OUTLIER) cc_final: 0.7755 (m110) REVERT: E 289 TYR cc_start: 0.8590 (t80) cc_final: 0.7861 (t80) REVERT: E 329 MET cc_start: 0.7957 (tpt) cc_final: 0.7703 (tmm) REVERT: F 79 TYR cc_start: 0.7656 (t80) cc_final: 0.6775 (m-10) REVERT: I 236 LEU cc_start: 0.8938 (mt) cc_final: 0.8638 (tp) REVERT: I 267 THR cc_start: 0.8760 (m) cc_final: 0.8556 (p) REVERT: J 57 LEU cc_start: 0.8943 (mp) cc_final: 0.8705 (mp) REVERT: J 94 GLU cc_start: 0.8893 (pp20) cc_final: 0.8457 (pp20) REVERT: J 98 PHE cc_start: 0.8578 (t80) cc_final: 0.7756 (t80) REVERT: K 172 ASN cc_start: 0.8477 (m110) cc_final: 0.8047 (m-40) REVERT: O 84 PRO cc_start: 0.8500 (Cg_exo) cc_final: 0.8185 (Cg_endo) REVERT: M 113 ARG cc_start: 0.8431 (ttp80) cc_final: 0.8216 (tmm-80) REVERT: M 276 MET cc_start: 0.8160 (ttt) cc_final: 0.7653 (ttt) REVERT: N 79 TYR cc_start: 0.7682 (t80) cc_final: 0.6973 (m-10) REVERT: Q 345 MET cc_start: 0.8782 (mmm) cc_final: 0.8261 (mmm) REVERT: Q 386 MET cc_start: 0.8846 (mmt) cc_final: 0.8519 (mmt) REVERT: Q 396 MET cc_start: 0.9419 (tmm) cc_final: 0.9188 (tmm) REVERT: R 91 MET cc_start: 0.8109 (mmm) cc_final: 0.7796 (mmt) REVERT: R 254 ARG cc_start: 0.9073 (mtt90) cc_final: 0.8732 (mpp80) REVERT: S 209 TYR cc_start: 0.9128 (t80) cc_final: 0.8865 (t80) REVERT: S 345 MET cc_start: 0.8970 (mmm) cc_final: 0.8560 (mmm) REVERT: S 366 ASN cc_start: 0.9046 (p0) cc_final: 0.8839 (p0) REVERT: S 396 MET cc_start: 0.9357 (tmm) cc_final: 0.8629 (tmm) REVERT: T 91 MET cc_start: 0.8293 (mmm) cc_final: 0.8039 (tpp) REVERT: T 278 MET cc_start: 0.8199 (ttm) cc_final: 0.7697 (ttp) outliers start: 25 outliers final: 15 residues processed: 555 average time/residue: 0.2032 time to fit residues: 173.1225 Evaluate side-chains 397 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 381 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 176 LEU Chi-restraints excluded: chain G residue 178 ASP Chi-restraints excluded: chain G residue 179 VAL Chi-restraints excluded: chain G residue 181 THR Chi-restraints excluded: chain G residue 182 LEU Chi-restraints excluded: chain C residue 154 ASN Chi-restraints excluded: chain E residue 154 ASN Chi-restraints excluded: chain K residue 153 ILE Chi-restraints excluded: chain O residue 176 LEU Chi-restraints excluded: chain O residue 179 VAL Chi-restraints excluded: chain M residue 154 ASN Chi-restraints excluded: chain Q residue 213 THR Chi-restraints excluded: chain R residue 376 LEU Chi-restraints excluded: chain S residue 213 THR Chi-restraints excluded: chain T residue 239 PHE Chi-restraints excluded: chain T residue 376 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 0.0670 chunk 183 optimal weight: 0.0570 chunk 298 optimal weight: 1.9990 overall best weight: 0.6240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 184 GLN ** G 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 298 GLN C 159 HIS C 341 HIS A 80 GLN A 81 ASN A 116 GLN A 177 ASN ** E 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 154 ASN E 185 GLN ** E 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 246 GLN E 339 GLN I 80 GLN I 81 ASN I 116 GLN K 114 GLN K 116 GLN K 172 ASN O 184 GLN O 287 GLN O 298 GLN ** O 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 81 ASN ** M 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 222 ASN Q 326 GLN Q 373 ASN Q 385 HIS Q 397 GLN R 88 GLN ** R 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 292 ASN R 365 ASN R 393 ASN S 222 ASN S 247 GLN S 326 GLN S 373 ASN S 397 GLN T 88 GLN ** T 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 292 ASN T 365 ASN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.100325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.074895 restraints weight = 91260.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.077977 restraints weight = 43314.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.079867 restraints weight = 22587.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.080069 restraints weight = 15713.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.080162 restraints weight = 15041.738| |-----------------------------------------------------------------------------| r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.100 30472 Z= 0.162 Angle : 0.730 12.894 41114 Z= 0.375 Chirality : 0.044 0.259 4607 Planarity : 0.005 0.060 5208 Dihedral : 5.783 56.737 4046 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 2.42 % Allowed : 15.62 % Favored : 81.96 % 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: -2.24 (0.14), residues: 3585 helix: -1.00 (0.10), residues: 2261 sheet: -2.52 (0.33), residues: 190 loop : -2.01 (0.19), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 165 TYR 0.025 0.002 TYR P 79 PHE 0.021 0.002 PHE S 383 TRP 0.013 0.001 TRP C 256 HIS 0.007 0.001 HIS R 178 Details of bonding type rmsd covalent geometry : bond 0.00338 (30472) covalent geometry : angle 0.72964 (41114) hydrogen bonds : bond 0.05400 ( 1644) hydrogen bonds : angle 5.78356 ( 4785) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 562 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 483 time to evaluate : 1.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 84 PRO cc_start: 0.8595 (Cg_exo) cc_final: 0.8280 (Cg_endo) REVERT: G 249 ILE cc_start: 0.8642 (tt) cc_final: 0.8279 (tt) REVERT: G 276 MET cc_start: 0.8310 (ttp) cc_final: 0.7557 (ttp) REVERT: H 85 SER cc_start: 0.8451 (t) cc_final: 0.8076 (p) REVERT: H 91 LEU cc_start: 0.9204 (tp) cc_final: 0.8989 (tp) REVERT: C 172 ASN cc_start: 0.7881 (m110) cc_final: 0.7580 (m110) REVERT: A 187 TYR cc_start: 0.8545 (t80) cc_final: 0.8252 (t80) REVERT: A 205 GLU cc_start: 0.9037 (tm-30) cc_final: 0.8626 (tm-30) REVERT: A 243 MET cc_start: 0.7799 (ttm) cc_final: 0.7567 (ttm) REVERT: A 267 THR cc_start: 0.8988 (m) cc_final: 0.8711 (p) REVERT: B 57 LEU cc_start: 0.9073 (mm) cc_final: 0.8819 (mp) REVERT: B 79 TYR cc_start: 0.6832 (t80) cc_final: 0.6406 (m-10) REVERT: E 243 MET cc_start: 0.8331 (ttt) cc_final: 0.8033 (ttt) REVERT: E 260 TRP cc_start: 0.8345 (t-100) cc_final: 0.8024 (t-100) REVERT: E 289 TYR cc_start: 0.8588 (t80) cc_final: 0.7811 (t80) REVERT: E 329 MET cc_start: 0.7722 (tpt) cc_final: 0.7296 (tmm) REVERT: F 79 TYR cc_start: 0.7315 (t80) cc_final: 0.6581 (m-10) REVERT: I 161 ARG cc_start: 0.8227 (mmt-90) cc_final: 0.7921 (mmt-90) REVERT: I 187 TYR cc_start: 0.8952 (t80) cc_final: 0.8669 (t80) REVERT: I 200 GLU cc_start: 0.9160 (tm-30) cc_final: 0.8756 (tm-30) REVERT: I 212 GLU cc_start: 0.8776 (tp30) cc_final: 0.8408 (tp30) REVERT: I 236 LEU cc_start: 0.8677 (mt) cc_final: 0.8439 (tt) REVERT: I 246 GLN cc_start: 0.8535 (tp40) cc_final: 0.8246 (tp40) REVERT: I 267 THR cc_start: 0.8959 (m) cc_final: 0.8689 (p) REVERT: J 94 GLU cc_start: 0.8758 (pp20) cc_final: 0.8405 (pp20) REVERT: K 172 ASN cc_start: 0.8377 (m-40) cc_final: 0.8142 (m-40) REVERT: K 209 ASP cc_start: 0.9004 (t0) cc_final: 0.8613 (t0) REVERT: K 242 TYR cc_start: 0.8302 (t80) cc_final: 0.8100 (t80) REVERT: O 84 PRO cc_start: 0.8486 (Cg_exo) cc_final: 0.8140 (Cg_endo) REVERT: O 276 MET cc_start: 0.8363 (ttp) cc_final: 0.7669 (ttp) REVERT: M 329 MET cc_start: 0.8352 (tmm) cc_final: 0.8135 (tmm) REVERT: N 79 TYR cc_start: 0.7365 (t80) cc_final: 0.6628 (m-10) REVERT: Q 240 MET cc_start: 0.9477 (ppp) cc_final: 0.9200 (tmm) REVERT: Q 345 MET cc_start: 0.8779 (mmm) cc_final: 0.8352 (mmm) REVERT: Q 381 LEU cc_start: 0.9433 (tp) cc_final: 0.9169 (tp) REVERT: R 91 MET cc_start: 0.7986 (mmm) cc_final: 0.7544 (tpp) REVERT: R 183 MET cc_start: 0.9273 (tmm) cc_final: 0.8954 (tmm) REVERT: R 256 MET cc_start: 0.8872 (mmm) cc_final: 0.8666 (mtm) REVERT: S 209 TYR cc_start: 0.8932 (t80) cc_final: 0.8600 (t80) REVERT: S 345 MET cc_start: 0.8946 (mmm) cc_final: 0.8558 (mmm) REVERT: S 381 LEU cc_start: 0.9465 (tp) cc_final: 0.9236 (tp) REVERT: S 396 MET cc_start: 0.9426 (tmm) cc_final: 0.8655 (tmm) REVERT: T 91 MET cc_start: 0.8195 (mmm) cc_final: 0.7855 (tpp) REVERT: T 102 TYR cc_start: 0.8814 (m-80) cc_final: 0.8401 (m-80) REVERT: T 109 PHE cc_start: 0.8563 (t80) cc_final: 0.8319 (t80) REVERT: T 183 MET cc_start: 0.9285 (tmm) cc_final: 0.9001 (tmm) REVERT: T 256 MET cc_start: 0.8886 (mmm) cc_final: 0.8583 (mtm) REVERT: T 278 MET cc_start: 0.8220 (ttm) cc_final: 0.7656 (ttp) outliers start: 79 outliers final: 46 residues processed: 534 average time/residue: 0.1820 time to fit residues: 155.8349 Evaluate side-chains 445 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 399 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 179 VAL Chi-restraints excluded: chain G residue 235 VAL Chi-restraints excluded: chain G residue 267 THR Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 71 PHE Chi-restraints excluded: chain C residue 154 ASN Chi-restraints excluded: chain C residue 249 ILE Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 71 PHE Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 82 THR Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain E residue 81 ASN Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 290 VAL Chi-restraints excluded: chain E residue 312 PHE Chi-restraints excluded: chain I residue 159 HIS Chi-restraints excluded: chain I residue 263 MET Chi-restraints excluded: chain J residue 49 ILE Chi-restraints excluded: chain J residue 65 PHE Chi-restraints excluded: chain K residue 153 ILE Chi-restraints excluded: chain K residue 182 LEU Chi-restraints excluded: chain K residue 267 THR Chi-restraints excluded: chain K residue 314 LEU Chi-restraints excluded: chain L residue 71 PHE Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 91 LEU Chi-restraints excluded: chain O residue 77 VAL Chi-restraints excluded: chain O residue 179 VAL Chi-restraints excluded: chain O residue 267 THR Chi-restraints excluded: chain M residue 81 ASN Chi-restraints excluded: chain M residue 112 LEU Chi-restraints excluded: chain M residue 270 ILE Chi-restraints excluded: chain M residue 312 PHE Chi-restraints excluded: chain Q residue 313 GLU Chi-restraints excluded: chain R residue 132 ILE Chi-restraints excluded: chain R residue 198 PHE Chi-restraints excluded: chain S residue 313 GLU Chi-restraints excluded: chain S residue 385 HIS Chi-restraints excluded: chain S residue 408 LEU Chi-restraints excluded: chain T residue 132 ILE Chi-restraints excluded: chain T residue 198 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 222 optimal weight: 4.9990 chunk 267 optimal weight: 9.9990 chunk 341 optimal weight: 10.0000 chunk 344 optimal weight: 5.9990 chunk 329 optimal weight: 7.9990 chunk 182 optimal weight: 4.9990 chunk 96 optimal weight: 2.9990 chunk 77 optimal weight: 0.5980 chunk 43 optimal weight: 5.9990 chunk 342 optimal weight: 7.9990 chunk 110 optimal weight: 4.9990 overall best weight: 3.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 ASN C 116 GLN A 177 ASN E 114 GLN I 172 ASN K 81 ASN K 213 GLN ** K 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 341 HIS M 213 GLN ** R 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 292 ASN S 222 ASN S 385 HIS ** T 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 292 ASN T 393 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.110801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.081375 restraints weight = 100020.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.083910 restraints weight = 45820.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.085561 restraints weight = 27566.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.086618 restraints weight = 19746.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.087256 restraints weight = 15940.167| |-----------------------------------------------------------------------------| r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.2630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.087 30472 Z= 0.312 Angle : 0.794 10.733 41114 Z= 0.404 Chirality : 0.047 0.179 4607 Planarity : 0.005 0.057 5208 Dihedral : 5.577 57.032 4025 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 15.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.17 % Favored : 91.83 % Rotamer: Outliers : 4.27 % Allowed : 19.85 % Favored : 75.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.81 (0.14), residues: 3585 helix: -0.67 (0.11), residues: 2287 sheet: -2.34 (0.34), residues: 190 loop : -1.85 (0.20), residues: 1108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG I 335 TYR 0.026 0.002 TYR H 79 PHE 0.028 0.002 PHE M 312 TRP 0.014 0.002 TRP C 260 HIS 0.008 0.002 HIS T 384 Details of bonding type rmsd covalent geometry : bond 0.00707 (30472) covalent geometry : angle 0.79393 (41114) hydrogen bonds : bond 0.05177 ( 1644) hydrogen bonds : angle 5.62151 ( 4785) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 389 time to evaluate : 0.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 84 PRO cc_start: 0.8724 (Cg_exo) cc_final: 0.8489 (Cg_endo) REVERT: G 205 GLU cc_start: 0.8768 (mp0) cc_final: 0.8566 (mp0) REVERT: G 253 LEU cc_start: 0.8920 (tp) cc_final: 0.8429 (tp) REVERT: G 276 MET cc_start: 0.8267 (ttp) cc_final: 0.7752 (ttp) REVERT: G 283 VAL cc_start: 0.9411 (OUTLIER) cc_final: 0.9177 (p) REVERT: H 85 SER cc_start: 0.8338 (t) cc_final: 0.8018 (p) REVERT: C 161 ARG cc_start: 0.7981 (OUTLIER) cc_final: 0.7647 (ptt-90) REVERT: A 187 TYR cc_start: 0.8752 (t80) cc_final: 0.8338 (t80) REVERT: A 205 GLU cc_start: 0.8997 (tm-30) cc_final: 0.8533 (tm-30) REVERT: A 212 GLU cc_start: 0.8751 (tp30) cc_final: 0.8487 (tp30) REVERT: A 263 MET cc_start: 0.8259 (OUTLIER) cc_final: 0.7930 (tpp) REVERT: B 79 TYR cc_start: 0.7039 (t80) cc_final: 0.6549 (m-10) REVERT: B 97 ILE cc_start: 0.7956 (mm) cc_final: 0.7719 (mt) REVERT: E 260 TRP cc_start: 0.8335 (t-100) cc_final: 0.7990 (t-100) REVERT: E 289 TYR cc_start: 0.8493 (t80) cc_final: 0.7697 (t80) REVERT: E 329 MET cc_start: 0.7744 (tpt) cc_final: 0.7413 (tmm) REVERT: F 79 TYR cc_start: 0.7326 (t80) cc_final: 0.6811 (m-10) REVERT: I 187 TYR cc_start: 0.8911 (t80) cc_final: 0.8703 (t80) REVERT: I 212 GLU cc_start: 0.8656 (tp30) cc_final: 0.8347 (tp30) REVERT: I 236 LEU cc_start: 0.8893 (mt) cc_final: 0.8587 (tt) REVERT: I 246 GLN cc_start: 0.8651 (tp40) cc_final: 0.8352 (tp40) REVERT: I 267 THR cc_start: 0.8962 (m) cc_final: 0.8720 (p) REVERT: J 94 GLU cc_start: 0.8804 (pp20) cc_final: 0.8440 (pp20) REVERT: K 172 ASN cc_start: 0.8358 (m-40) cc_final: 0.8148 (m-40) REVERT: K 209 ASP cc_start: 0.8892 (t0) cc_final: 0.8543 (t0) REVERT: O 84 PRO cc_start: 0.8635 (Cg_exo) cc_final: 0.8360 (Cg_endo) REVERT: O 276 MET cc_start: 0.8375 (ttp) cc_final: 0.7811 (ttp) REVERT: P 88 PHE cc_start: 0.8651 (t80) cc_final: 0.8396 (t80) REVERT: P 98 PHE cc_start: 0.7759 (OUTLIER) cc_final: 0.6552 (t80) REVERT: N 79 TYR cc_start: 0.7441 (t80) cc_final: 0.6694 (m-10) REVERT: Q 240 MET cc_start: 0.9406 (ppp) cc_final: 0.9153 (tmm) REVERT: Q 345 MET cc_start: 0.8665 (mmm) cc_final: 0.8313 (mmm) REVERT: Q 381 LEU cc_start: 0.9371 (tp) cc_final: 0.9110 (tp) REVERT: Q 396 MET cc_start: 0.9408 (tmm) cc_final: 0.8666 (tmm) REVERT: R 91 MET cc_start: 0.8067 (mmm) cc_final: 0.7739 (tpp) REVERT: R 118 MET cc_start: 0.7352 (ttp) cc_final: 0.6947 (ttt) REVERT: R 182 LYS cc_start: 0.8227 (OUTLIER) cc_final: 0.7936 (mmtm) REVERT: R 183 MET cc_start: 0.9167 (tmm) cc_final: 0.8813 (tmm) REVERT: R 271 PHE cc_start: 0.8197 (OUTLIER) cc_final: 0.7790 (m-80) REVERT: S 209 TYR cc_start: 0.8829 (t80) cc_final: 0.8494 (t80) REVERT: S 330 MET cc_start: 0.8397 (ptp) cc_final: 0.8166 (ptp) REVERT: S 345 MET cc_start: 0.8877 (mmm) cc_final: 0.8536 (mmm) REVERT: S 381 LEU cc_start: 0.9435 (tp) cc_final: 0.9191 (tp) REVERT: S 396 MET cc_start: 0.9391 (tmm) cc_final: 0.8797 (tmm) REVERT: T 91 MET cc_start: 0.8213 (mmm) cc_final: 0.7850 (tpp) REVERT: T 109 PHE cc_start: 0.8627 (t80) cc_final: 0.8415 (t80) REVERT: T 183 MET cc_start: 0.9232 (tmm) cc_final: 0.8989 (tmm) REVERT: T 271 PHE cc_start: 0.8287 (OUTLIER) cc_final: 0.7970 (m-80) outliers start: 139 outliers final: 95 residues processed: 497 average time/residue: 0.1850 time to fit residues: 148.3629 Evaluate side-chains 461 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 359 time to evaluate : 1.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain G residue 235 VAL Chi-restraints excluded: chain G residue 258 TYR Chi-restraints excluded: chain G residue 266 VAL Chi-restraints excluded: chain G residue 267 THR Chi-restraints excluded: chain G residue 271 THR Chi-restraints excluded: chain G residue 278 MET Chi-restraints excluded: chain G residue 283 VAL Chi-restraints excluded: chain G residue 290 VAL Chi-restraints excluded: chain H residue 49 ILE Chi-restraints excluded: chain H residue 71 PHE Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 154 ASN Chi-restraints excluded: chain C residue 161 ARG Chi-restraints excluded: chain C residue 249 ILE Chi-restraints excluded: chain C residue 266 VAL Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 296 ASP Chi-restraints excluded: chain C residue 312 PHE Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 71 PHE Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 82 THR Chi-restraints excluded: chain A residue 159 HIS Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 177 ASN Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 263 MET Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain E residue 81 ASN Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain E residue 183 VAL Chi-restraints excluded: chain E residue 232 THR Chi-restraints excluded: chain E residue 266 VAL Chi-restraints excluded: chain E residue 290 VAL Chi-restraints excluded: chain E residue 312 PHE Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain I residue 156 LEU Chi-restraints excluded: chain I residue 159 HIS Chi-restraints excluded: chain I residue 232 THR Chi-restraints excluded: chain I residue 262 ILE Chi-restraints excluded: chain I residue 263 MET Chi-restraints excluded: chain I residue 266 VAL Chi-restraints excluded: chain I residue 316 LYS Chi-restraints excluded: chain I residue 324 ILE Chi-restraints excluded: chain J residue 49 ILE Chi-restraints excluded: chain J residue 65 PHE Chi-restraints excluded: chain J residue 75 ILE Chi-restraints excluded: chain K residue 75 VAL Chi-restraints excluded: chain K residue 125 VAL Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 153 ILE Chi-restraints excluded: chain K residue 182 LEU Chi-restraints excluded: chain K residue 266 VAL Chi-restraints excluded: chain K residue 267 THR Chi-restraints excluded: chain K residue 271 THR Chi-restraints excluded: chain K residue 312 PHE Chi-restraints excluded: chain K residue 314 LEU Chi-restraints excluded: chain L residue 71 PHE Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 82 THR Chi-restraints excluded: chain O residue 77 VAL Chi-restraints excluded: chain O residue 176 LEU Chi-restraints excluded: chain O residue 204 ILE Chi-restraints excluded: chain O residue 266 VAL Chi-restraints excluded: chain O residue 267 THR Chi-restraints excluded: chain O residue 283 VAL Chi-restraints excluded: chain P residue 98 PHE Chi-restraints excluded: chain M residue 112 LEU Chi-restraints excluded: chain M residue 125 VAL Chi-restraints excluded: chain M residue 127 ILE Chi-restraints excluded: chain M residue 133 VAL Chi-restraints excluded: chain M residue 182 LEU Chi-restraints excluded: chain M residue 192 ILE Chi-restraints excluded: chain M residue 232 THR Chi-restraints excluded: chain M residue 270 ILE Chi-restraints excluded: chain M residue 284 MET Chi-restraints excluded: chain M residue 312 PHE Chi-restraints excluded: chain N residue 49 ILE Chi-restraints excluded: chain N residue 68 LEU Chi-restraints excluded: chain N residue 83 LEU Chi-restraints excluded: chain Q residue 313 GLU Chi-restraints excluded: chain Q residue 369 THR Chi-restraints excluded: chain R residue 113 VAL Chi-restraints excluded: chain R residue 132 ILE Chi-restraints excluded: chain R residue 182 LYS Chi-restraints excluded: chain R residue 198 PHE Chi-restraints excluded: chain R residue 271 PHE Chi-restraints excluded: chain R residue 363 SER Chi-restraints excluded: chain S residue 121 TYR Chi-restraints excluded: chain S residue 313 GLU Chi-restraints excluded: chain S residue 369 THR Chi-restraints excluded: chain T residue 113 VAL Chi-restraints excluded: chain T residue 132 ILE Chi-restraints excluded: chain T residue 198 PHE Chi-restraints excluded: chain T residue 271 PHE Chi-restraints excluded: chain T residue 363 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 254 optimal weight: 5.9990 chunk 261 optimal weight: 0.3980 chunk 181 optimal weight: 3.9990 chunk 268 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 230 optimal weight: 0.7980 chunk 272 optimal weight: 6.9990 chunk 344 optimal weight: 7.9990 chunk 231 optimal weight: 0.9980 chunk 264 optimal weight: 0.0370 chunk 130 optimal weight: 0.9980 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 326 GLN Q 222 ASN ** R 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 365 ASN S 222 ASN ** T 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 365 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.109893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.084458 restraints weight = 94972.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.087070 restraints weight = 45115.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.089412 restraints weight = 24412.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.089463 restraints weight = 16452.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.089591 restraints weight = 16045.501| |-----------------------------------------------------------------------------| r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.3094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 30472 Z= 0.136 Angle : 0.666 11.580 41114 Z= 0.335 Chirality : 0.042 0.182 4607 Planarity : 0.004 0.057 5208 Dihedral : 5.187 58.607 4023 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 3.10 % Allowed : 22.64 % Favored : 74.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.20 (0.14), residues: 3585 helix: -0.17 (0.11), residues: 2288 sheet: -1.98 (0.34), residues: 196 loop : -1.68 (0.20), residues: 1101 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG O 113 TYR 0.029 0.002 TYR T 103 PHE 0.029 0.001 PHE R 252 TRP 0.014 0.001 TRP C 256 HIS 0.008 0.001 HIS T 384 Details of bonding type rmsd covalent geometry : bond 0.00293 (30472) covalent geometry : angle 0.66587 (41114) hydrogen bonds : bond 0.04165 ( 1644) hydrogen bonds : angle 5.02244 ( 4785) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 533 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 432 time to evaluate : 1.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 84 PRO cc_start: 0.8594 (Cg_exo) cc_final: 0.8279 (Cg_endo) REVERT: G 249 ILE cc_start: 0.8596 (tt) cc_final: 0.8122 (tt) REVERT: G 276 MET cc_start: 0.8157 (ttp) cc_final: 0.7630 (ttp) REVERT: H 93 GLU cc_start: 0.8715 (pp20) cc_final: 0.8383 (pp20) REVERT: C 209 ASP cc_start: 0.9157 (t0) cc_final: 0.8846 (t0) REVERT: A 187 TYR cc_start: 0.8775 (t80) cc_final: 0.8252 (t80) REVERT: A 205 GLU cc_start: 0.9054 (tm-30) cc_final: 0.8623 (tm-30) REVERT: A 267 THR cc_start: 0.8882 (m) cc_final: 0.8658 (p) REVERT: B 57 LEU cc_start: 0.9003 (mm) cc_final: 0.8704 (mp) REVERT: B 79 TYR cc_start: 0.6806 (t80) cc_final: 0.6454 (m-10) REVERT: E 243 MET cc_start: 0.8366 (ttt) cc_final: 0.8096 (ttt) REVERT: E 260 TRP cc_start: 0.8295 (t-100) cc_final: 0.7959 (t-100) REVERT: E 289 TYR cc_start: 0.8461 (t80) cc_final: 0.7582 (t80) REVERT: E 329 MET cc_start: 0.7725 (tpt) cc_final: 0.7305 (tmm) REVERT: F 79 TYR cc_start: 0.7261 (t80) cc_final: 0.6687 (m-10) REVERT: I 187 TYR cc_start: 0.8932 (t80) cc_final: 0.8713 (t80) REVERT: I 200 GLU cc_start: 0.9195 (tm-30) cc_final: 0.8880 (tm-30) REVERT: I 212 GLU cc_start: 0.8656 (tp30) cc_final: 0.8255 (tp30) REVERT: I 236 LEU cc_start: 0.8718 (mt) cc_final: 0.8411 (tt) REVERT: I 246 GLN cc_start: 0.8430 (tp40) cc_final: 0.8175 (tp40) REVERT: I 267 THR cc_start: 0.8914 (m) cc_final: 0.8669 (p) REVERT: J 79 TYR cc_start: 0.6607 (t80) cc_final: 0.5903 (m-10) REVERT: J 94 GLU cc_start: 0.8637 (pp20) cc_final: 0.8329 (pp20) REVERT: K 172 ASN cc_start: 0.8382 (m-40) cc_final: 0.8116 (m-40) REVERT: K 209 ASP cc_start: 0.9006 (t0) cc_final: 0.8613 (t0) REVERT: K 263 MET cc_start: 0.7862 (tpp) cc_final: 0.7567 (ttm) REVERT: O 84 PRO cc_start: 0.8540 (Cg_exo) cc_final: 0.8230 (Cg_endo) REVERT: O 243 MET cc_start: 0.7906 (ttm) cc_final: 0.7366 (ttm) REVERT: O 276 MET cc_start: 0.8302 (ttp) cc_final: 0.7727 (ttp) REVERT: P 98 PHE cc_start: 0.7500 (OUTLIER) cc_final: 0.7059 (t80) REVERT: N 79 TYR cc_start: 0.7471 (t80) cc_final: 0.6684 (m-10) REVERT: Q 216 LEU cc_start: 0.9023 (tp) cc_final: 0.8782 (mt) REVERT: Q 240 MET cc_start: 0.9466 (ppp) cc_final: 0.9131 (tmm) REVERT: Q 334 TYR cc_start: 0.8626 (t80) cc_final: 0.8395 (t80) REVERT: Q 345 MET cc_start: 0.8702 (mmm) cc_final: 0.8297 (mmm) REVERT: Q 396 MET cc_start: 0.9459 (tmm) cc_final: 0.8788 (tmm) REVERT: R 118 MET cc_start: 0.7386 (ttp) cc_final: 0.6904 (ttt) REVERT: R 161 THR cc_start: 0.9070 (m) cc_final: 0.8769 (t) REVERT: R 182 LYS cc_start: 0.8202 (OUTLIER) cc_final: 0.7855 (mmtm) REVERT: R 183 MET cc_start: 0.9189 (tmm) cc_final: 0.8895 (tmm) REVERT: R 271 PHE cc_start: 0.8041 (OUTLIER) cc_final: 0.7791 (m-80) REVERT: S 209 TYR cc_start: 0.8849 (t80) cc_final: 0.8576 (t80) REVERT: S 345 MET cc_start: 0.8877 (mmm) cc_final: 0.8504 (mmm) REVERT: S 381 LEU cc_start: 0.9438 (tp) cc_final: 0.9148 (tp) REVERT: S 396 MET cc_start: 0.9465 (tmm) cc_final: 0.8933 (tmm) REVERT: T 91 MET cc_start: 0.8224 (mmm) cc_final: 0.7938 (mmm) REVERT: T 102 TYR cc_start: 0.8805 (m-80) cc_final: 0.8026 (m-80) REVERT: T 183 MET cc_start: 0.9184 (tmm) cc_final: 0.8952 (tmm) REVERT: T 256 MET cc_start: 0.8856 (mmm) cc_final: 0.8594 (mtm) REVERT: T 335 MET cc_start: 0.8627 (mmm) cc_final: 0.8300 (mmp) REVERT: T 391 LEU cc_start: 0.9394 (OUTLIER) cc_final: 0.9145 (mm) outliers start: 101 outliers final: 67 residues processed: 501 average time/residue: 0.1750 time to fit residues: 142.6744 Evaluate side-chains 454 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 383 time to evaluate : 1.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 258 TYR Chi-restraints excluded: chain G residue 267 THR Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 71 PHE Chi-restraints excluded: chain C residue 154 ASN Chi-restraints excluded: chain C residue 249 ILE Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 296 ASP Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 71 PHE Chi-restraints excluded: chain D residue 82 THR Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain A residue 159 HIS Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 263 MET Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain E residue 81 ASN Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain E residue 270 ILE Chi-restraints excluded: chain E residue 312 PHE Chi-restraints excluded: chain E residue 324 ILE Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain I residue 159 HIS Chi-restraints excluded: chain I residue 262 ILE Chi-restraints excluded: chain I residue 263 MET Chi-restraints excluded: chain I residue 300 LEU Chi-restraints excluded: chain I residue 316 LYS Chi-restraints excluded: chain J residue 65 PHE Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain K residue 75 VAL Chi-restraints excluded: chain K residue 125 VAL Chi-restraints excluded: chain K residue 153 ILE Chi-restraints excluded: chain K residue 182 LEU Chi-restraints excluded: chain K residue 267 THR Chi-restraints excluded: chain K residue 312 PHE Chi-restraints excluded: chain L residue 71 PHE Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 82 THR Chi-restraints excluded: chain O residue 77 VAL Chi-restraints excluded: chain O residue 125 VAL Chi-restraints excluded: chain O residue 176 LEU Chi-restraints excluded: chain O residue 245 THR Chi-restraints excluded: chain O residue 267 THR Chi-restraints excluded: chain P residue 98 PHE Chi-restraints excluded: chain M residue 112 LEU Chi-restraints excluded: chain M residue 204 ILE Chi-restraints excluded: chain M residue 312 PHE Chi-restraints excluded: chain M residue 324 ILE Chi-restraints excluded: chain N residue 68 LEU Chi-restraints excluded: chain N residue 83 LEU Chi-restraints excluded: chain Q residue 313 GLU Chi-restraints excluded: chain Q residue 369 THR Chi-restraints excluded: chain Q residue 385 HIS Chi-restraints excluded: chain R residue 182 LYS Chi-restraints excluded: chain R residue 198 PHE Chi-restraints excluded: chain R residue 271 PHE Chi-restraints excluded: chain R residue 363 SER Chi-restraints excluded: chain R residue 365 ASN Chi-restraints excluded: chain S residue 111 VAL Chi-restraints excluded: chain S residue 121 TYR Chi-restraints excluded: chain S residue 313 GLU Chi-restraints excluded: chain S residue 369 THR Chi-restraints excluded: chain S residue 385 HIS Chi-restraints excluded: chain T residue 198 PHE Chi-restraints excluded: chain T residue 363 SER Chi-restraints excluded: chain T residue 365 ASN Chi-restraints excluded: chain T residue 391 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 309 optimal weight: 20.0000 chunk 246 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 332 optimal weight: 0.8980 chunk 173 optimal weight: 4.9990 chunk 129 optimal weight: 0.5980 chunk 118 optimal weight: 5.9990 chunk 232 optimal weight: 0.2980 chunk 349 optimal weight: 8.9990 chunk 330 optimal weight: 3.9990 chunk 137 optimal weight: 5.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 326 GLN ** E 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 159 HIS R 189 ASN ** R 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 264 GLN ** R 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 365 ASN S 222 ASN ** T 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 264 GLN T 365 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.108769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.083272 restraints weight = 96167.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.086314 restraints weight = 44955.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.088656 restraints weight = 23673.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.088828 restraints weight = 15834.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.088765 restraints weight = 14833.506| |-----------------------------------------------------------------------------| r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.3343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 30472 Z= 0.143 Angle : 0.664 11.839 41114 Z= 0.332 Chirality : 0.042 0.176 4607 Planarity : 0.004 0.056 5208 Dihedral : 5.084 59.364 4023 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 4.05 % Allowed : 23.07 % Favored : 72.88 % 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: -0.91 (0.14), residues: 3585 helix: 0.04 (0.11), residues: 2287 sheet: -1.77 (0.35), residues: 196 loop : -1.55 (0.20), residues: 1102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG M 311 TYR 0.024 0.001 TYR P 79 PHE 0.046 0.001 PHE R 252 TRP 0.013 0.001 TRP C 256 HIS 0.009 0.001 HIS K 159 Details of bonding type rmsd covalent geometry : bond 0.00318 (30472) covalent geometry : angle 0.66439 (41114) hydrogen bonds : bond 0.03932 ( 1644) hydrogen bonds : angle 4.85079 ( 4785) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 549 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 417 time to evaluate : 1.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 84 PRO cc_start: 0.8771 (Cg_exo) cc_final: 0.8522 (Cg_endo) REVERT: G 276 MET cc_start: 0.8097 (ttp) cc_final: 0.7748 (ttp) REVERT: G 283 VAL cc_start: 0.9290 (OUTLIER) cc_final: 0.9063 (p) REVERT: H 93 GLU cc_start: 0.8658 (pp20) cc_final: 0.8378 (pp20) REVERT: C 161 ARG cc_start: 0.8124 (OUTLIER) cc_final: 0.7665 (ptt-90) REVERT: C 209 ASP cc_start: 0.9152 (t0) cc_final: 0.8845 (t0) REVERT: A 187 TYR cc_start: 0.8773 (t80) cc_final: 0.8244 (t80) REVERT: A 205 GLU cc_start: 0.9053 (tm-30) cc_final: 0.8637 (tm-30) REVERT: B 57 LEU cc_start: 0.9032 (mm) cc_final: 0.8726 (mp) REVERT: B 79 TYR cc_start: 0.6850 (t80) cc_final: 0.6499 (m-10) REVERT: B 98 PHE cc_start: 0.8364 (t80) cc_final: 0.8015 (t80) REVERT: E 260 TRP cc_start: 0.8306 (t-100) cc_final: 0.7965 (t-100) REVERT: E 289 TYR cc_start: 0.8486 (t80) cc_final: 0.7644 (t80) REVERT: E 329 MET cc_start: 0.7586 (tpt) cc_final: 0.7323 (tmm) REVERT: F 79 TYR cc_start: 0.7240 (t80) cc_final: 0.6684 (m-10) REVERT: I 161 ARG cc_start: 0.8172 (mmt-90) cc_final: 0.7936 (mmt-90) REVERT: I 187 TYR cc_start: 0.8945 (t80) cc_final: 0.8701 (t80) REVERT: I 200 GLU cc_start: 0.9198 (tm-30) cc_final: 0.8942 (tm-30) REVERT: I 236 LEU cc_start: 0.8707 (mt) cc_final: 0.8402 (tt) REVERT: I 246 GLN cc_start: 0.8443 (tp40) cc_final: 0.8133 (tp40) REVERT: J 79 TYR cc_start: 0.6606 (t80) cc_final: 0.5919 (m-10) REVERT: J 94 GLU cc_start: 0.8663 (pp20) cc_final: 0.8286 (pp20) REVERT: J 97 ILE cc_start: 0.7813 (mm) cc_final: 0.7547 (mt) REVERT: K 172 ASN cc_start: 0.8421 (m-40) cc_final: 0.8160 (m-40) REVERT: K 209 ASP cc_start: 0.8999 (t0) cc_final: 0.8591 (t0) REVERT: O 84 PRO cc_start: 0.8486 (Cg_exo) cc_final: 0.8170 (Cg_endo) REVERT: O 263 MET cc_start: 0.8301 (tpp) cc_final: 0.8005 (tpp) REVERT: O 276 MET cc_start: 0.8291 (ttp) cc_final: 0.7742 (ttp) REVERT: P 98 PHE cc_start: 0.7888 (OUTLIER) cc_final: 0.7117 (t80) REVERT: N 79 TYR cc_start: 0.7457 (t80) cc_final: 0.6631 (m-10) REVERT: Q 240 MET cc_start: 0.9464 (ppp) cc_final: 0.9134 (tmm) REVERT: Q 334 TYR cc_start: 0.8626 (t80) cc_final: 0.8291 (t80) REVERT: Q 345 MET cc_start: 0.8770 (mmm) cc_final: 0.8404 (mmm) REVERT: Q 381 LEU cc_start: 0.9357 (tp) cc_final: 0.9100 (tp) REVERT: Q 396 MET cc_start: 0.9487 (tmm) cc_final: 0.8851 (tmm) REVERT: R 161 THR cc_start: 0.9059 (m) cc_final: 0.8768 (t) REVERT: R 183 MET cc_start: 0.9106 (tmm) cc_final: 0.8858 (tmm) REVERT: R 305 GLU cc_start: 0.8875 (mp0) cc_final: 0.8620 (mp0) REVERT: S 209 TYR cc_start: 0.8811 (t80) cc_final: 0.8533 (t80) REVERT: S 216 LEU cc_start: 0.9193 (tp) cc_final: 0.8941 (mt) REVERT: S 345 MET cc_start: 0.8864 (mmm) cc_final: 0.8504 (mmm) REVERT: S 396 MET cc_start: 0.9438 (tmm) cc_final: 0.8934 (tmm) REVERT: T 91 MET cc_start: 0.8190 (mmm) cc_final: 0.7789 (tpp) REVERT: T 102 TYR cc_start: 0.8766 (m-80) cc_final: 0.8221 (m-80) REVERT: T 118 MET cc_start: 0.6498 (ttt) cc_final: 0.6273 (ttt) REVERT: T 161 THR cc_start: 0.9159 (m) cc_final: 0.8912 (t) REVERT: T 183 MET cc_start: 0.9147 (tmm) cc_final: 0.8907 (tmm) REVERT: T 256 MET cc_start: 0.8846 (mmm) cc_final: 0.8578 (mtm) REVERT: T 391 LEU cc_start: 0.9363 (OUTLIER) cc_final: 0.9114 (mm) outliers start: 132 outliers final: 95 residues processed: 506 average time/residue: 0.1826 time to fit residues: 150.0671 Evaluate side-chains 488 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 389 time to evaluate : 1.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain G residue 235 VAL Chi-restraints excluded: chain G residue 253 LEU Chi-restraints excluded: chain G residue 283 VAL Chi-restraints excluded: chain G residue 290 VAL Chi-restraints excluded: chain G residue 334 LEU Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 49 ILE Chi-restraints excluded: chain H residue 71 PHE Chi-restraints excluded: chain C residue 154 ASN Chi-restraints excluded: chain C residue 161 ARG Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 296 ASP Chi-restraints excluded: chain C residue 312 PHE Chi-restraints excluded: chain D residue 71 PHE Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 263 MET Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain E residue 81 ASN Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain E residue 266 VAL Chi-restraints excluded: chain E residue 270 ILE Chi-restraints excluded: chain E residue 312 PHE Chi-restraints excluded: chain E residue 324 ILE Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 92 LEU Chi-restraints excluded: chain I residue 159 HIS Chi-restraints excluded: chain I residue 262 ILE Chi-restraints excluded: chain I residue 263 MET Chi-restraints excluded: chain I residue 266 VAL Chi-restraints excluded: chain I residue 290 VAL Chi-restraints excluded: chain I residue 300 LEU Chi-restraints excluded: chain I residue 331 LEU Chi-restraints excluded: chain J residue 65 PHE Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain K residue 75 VAL Chi-restraints excluded: chain K residue 125 VAL Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 153 ILE Chi-restraints excluded: chain K residue 182 LEU Chi-restraints excluded: chain K residue 254 THR Chi-restraints excluded: chain K residue 267 THR Chi-restraints excluded: chain K residue 312 PHE Chi-restraints excluded: chain L residue 71 PHE Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 82 THR Chi-restraints excluded: chain O residue 77 VAL Chi-restraints excluded: chain O residue 125 VAL Chi-restraints excluded: chain O residue 157 THR Chi-restraints excluded: chain O residue 176 LEU Chi-restraints excluded: chain O residue 235 VAL Chi-restraints excluded: chain O residue 245 THR Chi-restraints excluded: chain O residue 267 THR Chi-restraints excluded: chain O residue 278 MET Chi-restraints excluded: chain O residue 283 VAL Chi-restraints excluded: chain P residue 98 PHE Chi-restraints excluded: chain M residue 112 LEU Chi-restraints excluded: chain M residue 127 ILE Chi-restraints excluded: chain M residue 133 VAL Chi-restraints excluded: chain M residue 204 ILE Chi-restraints excluded: chain M residue 270 ILE Chi-restraints excluded: chain M residue 312 PHE Chi-restraints excluded: chain M residue 324 ILE Chi-restraints excluded: chain N residue 68 LEU Chi-restraints excluded: chain N residue 83 LEU Chi-restraints excluded: chain Q residue 279 THR Chi-restraints excluded: chain Q residue 313 GLU Chi-restraints excluded: chain Q residue 369 THR Chi-restraints excluded: chain Q residue 385 HIS Chi-restraints excluded: chain R residue 189 ASN Chi-restraints excluded: chain R residue 198 PHE Chi-restraints excluded: chain R residue 363 SER Chi-restraints excluded: chain R residue 364 ASN Chi-restraints excluded: chain R residue 382 LEU Chi-restraints excluded: chain R residue 391 LEU Chi-restraints excluded: chain S residue 111 VAL Chi-restraints excluded: chain S residue 121 TYR Chi-restraints excluded: chain S residue 222 ASN Chi-restraints excluded: chain S residue 279 THR Chi-restraints excluded: chain S residue 313 GLU Chi-restraints excluded: chain S residue 315 HIS Chi-restraints excluded: chain S residue 369 THR Chi-restraints excluded: chain S residue 385 HIS Chi-restraints excluded: chain T residue 198 PHE Chi-restraints excluded: chain T residue 363 SER Chi-restraints excluded: chain T residue 364 ASN Chi-restraints excluded: chain T residue 391 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 78 optimal weight: 3.9990 chunk 92 optimal weight: 10.0000 chunk 74 optimal weight: 5.9990 chunk 26 optimal weight: 4.9990 chunk 54 optimal weight: 4.9990 chunk 14 optimal weight: 9.9990 chunk 41 optimal weight: 2.9990 chunk 33 optimal weight: 0.2980 chunk 111 optimal weight: 0.9980 chunk 303 optimal weight: 5.9990 chunk 323 optimal weight: 0.0010 overall best weight: 1.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 189 ASN ** R 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 365 ASN S 373 ASN ** T 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 365 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.108720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.081275 restraints weight = 96282.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.083990 restraints weight = 43071.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.085711 restraints weight = 25598.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.086800 restraints weight = 18260.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.087477 restraints weight = 14711.381| |-----------------------------------------------------------------------------| r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.3468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 30472 Z= 0.166 Angle : 0.673 11.768 41114 Z= 0.336 Chirality : 0.043 0.227 4607 Planarity : 0.004 0.064 5208 Dihedral : 5.060 58.131 4023 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 4.36 % Allowed : 23.69 % Favored : 71.95 % 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: -0.74 (0.14), residues: 3585 helix: 0.18 (0.11), residues: 2295 sheet: -1.61 (0.36), residues: 196 loop : -1.54 (0.20), residues: 1094 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG N 52 TYR 0.023 0.001 TYR P 79 PHE 0.040 0.001 PHE R 252 TRP 0.014 0.001 TRP C 256 HIS 0.007 0.001 HIS R 384 Details of bonding type rmsd covalent geometry : bond 0.00377 (30472) covalent geometry : angle 0.67350 (41114) hydrogen bonds : bond 0.03832 ( 1644) hydrogen bonds : angle 4.79199 ( 4785) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 547 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 405 time to evaluate : 1.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 84 PRO cc_start: 0.8835 (Cg_exo) cc_final: 0.8610 (Cg_endo) REVERT: G 276 MET cc_start: 0.8165 (ttp) cc_final: 0.7789 (ttp) REVERT: G 283 VAL cc_start: 0.9255 (OUTLIER) cc_final: 0.9026 (p) REVERT: C 161 ARG cc_start: 0.8192 (OUTLIER) cc_final: 0.7737 (ptt-90) REVERT: C 209 ASP cc_start: 0.9088 (t0) cc_final: 0.8783 (t0) REVERT: A 187 TYR cc_start: 0.8825 (t80) cc_final: 0.8290 (t80) REVERT: A 205 GLU cc_start: 0.9025 (tm-30) cc_final: 0.8574 (tm-30) REVERT: A 267 THR cc_start: 0.8895 (m) cc_final: 0.8691 (p) REVERT: B 57 LEU cc_start: 0.9057 (mm) cc_final: 0.8800 (mp) REVERT: B 71 PHE cc_start: 0.8394 (m-80) cc_final: 0.7951 (m-80) REVERT: B 79 TYR cc_start: 0.6872 (t80) cc_final: 0.6451 (m-10) REVERT: B 98 PHE cc_start: 0.8400 (t80) cc_final: 0.8076 (t80) REVERT: E 260 TRP cc_start: 0.8320 (t-100) cc_final: 0.7966 (t-100) REVERT: E 289 TYR cc_start: 0.8456 (t80) cc_final: 0.7539 (t80) REVERT: E 303 PHE cc_start: 0.8579 (t80) cc_final: 0.8320 (t80) REVERT: E 329 MET cc_start: 0.7554 (tpt) cc_final: 0.7283 (tmm) REVERT: F 79 TYR cc_start: 0.7080 (t80) cc_final: 0.6531 (m-10) REVERT: I 187 TYR cc_start: 0.8975 (t80) cc_final: 0.8764 (t80) REVERT: I 212 GLU cc_start: 0.8769 (tp30) cc_final: 0.8508 (tp30) REVERT: I 236 LEU cc_start: 0.8735 (mt) cc_final: 0.8419 (tt) REVERT: I 246 GLN cc_start: 0.8440 (tp40) cc_final: 0.8175 (tp40) REVERT: I 265 PRO cc_start: 0.8928 (Cg_exo) cc_final: 0.8707 (Cg_endo) REVERT: J 79 TYR cc_start: 0.6634 (t80) cc_final: 0.5941 (m-10) REVERT: K 172 ASN cc_start: 0.8388 (m-40) cc_final: 0.8138 (m-40) REVERT: K 209 ASP cc_start: 0.8944 (t0) cc_final: 0.8541 (t0) REVERT: L 96 ASP cc_start: 0.7340 (m-30) cc_final: 0.6985 (m-30) REVERT: O 84 PRO cc_start: 0.8581 (Cg_exo) cc_final: 0.8290 (Cg_endo) REVERT: O 192 ILE cc_start: 0.8930 (OUTLIER) cc_final: 0.8712 (tt) REVERT: O 263 MET cc_start: 0.8312 (tpp) cc_final: 0.8026 (tpp) REVERT: O 276 MET cc_start: 0.8319 (ttp) cc_final: 0.7769 (ttp) REVERT: P 98 PHE cc_start: 0.7729 (OUTLIER) cc_final: 0.7106 (t80) REVERT: M 243 MET cc_start: 0.8142 (ttt) cc_final: 0.7868 (ttt) REVERT: N 79 TYR cc_start: 0.7460 (t80) cc_final: 0.6649 (m-10) REVERT: Q 240 MET cc_start: 0.9454 (ppp) cc_final: 0.9106 (tmm) REVERT: Q 334 TYR cc_start: 0.8675 (t80) cc_final: 0.8444 (t80) REVERT: Q 345 MET cc_start: 0.8783 (mmm) cc_final: 0.8396 (mmm) REVERT: Q 396 MET cc_start: 0.9518 (tmm) cc_final: 0.8905 (tmm) REVERT: R 118 MET cc_start: 0.7351 (ttp) cc_final: 0.7006 (ttt) REVERT: R 161 THR cc_start: 0.9056 (m) cc_final: 0.8786 (t) REVERT: R 183 MET cc_start: 0.9094 (tmm) cc_final: 0.8888 (tmm) REVERT: R 271 PHE cc_start: 0.8014 (OUTLIER) cc_final: 0.7788 (m-80) REVERT: R 278 MET cc_start: 0.8252 (tmm) cc_final: 0.8045 (tmm) REVERT: R 305 GLU cc_start: 0.8821 (mp0) cc_final: 0.8568 (mp0) REVERT: S 209 TYR cc_start: 0.8759 (t80) cc_final: 0.8485 (t80) REVERT: S 216 LEU cc_start: 0.9176 (tp) cc_final: 0.8962 (mt) REVERT: S 305 HIS cc_start: 0.9493 (t-90) cc_final: 0.9057 (t-90) REVERT: S 345 MET cc_start: 0.8832 (mmm) cc_final: 0.8489 (mmm) REVERT: S 396 MET cc_start: 0.9413 (tmm) cc_final: 0.8933 (tmm) REVERT: T 91 MET cc_start: 0.8201 (mmm) cc_final: 0.7795 (tpp) REVERT: T 102 TYR cc_start: 0.8703 (m-80) cc_final: 0.8116 (m-80) REVERT: T 103 TYR cc_start: 0.6134 (m-80) cc_final: 0.5918 (t80) REVERT: T 161 THR cc_start: 0.9166 (m) cc_final: 0.8936 (t) REVERT: T 183 MET cc_start: 0.9144 (tmm) cc_final: 0.8919 (tmm) REVERT: T 256 MET cc_start: 0.8838 (mmm) cc_final: 0.8616 (mtm) outliers start: 142 outliers final: 109 residues processed: 506 average time/residue: 0.1778 time to fit residues: 148.3994 Evaluate side-chains 501 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 387 time to evaluate : 1.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain G residue 235 VAL Chi-restraints excluded: chain G residue 236 LEU Chi-restraints excluded: chain G residue 253 LEU Chi-restraints excluded: chain G residue 267 THR Chi-restraints excluded: chain G residue 270 ILE Chi-restraints excluded: chain G residue 283 VAL Chi-restraints excluded: chain G residue 290 VAL Chi-restraints excluded: chain G residue 334 LEU Chi-restraints excluded: chain H residue 49 ILE Chi-restraints excluded: chain H residue 71 PHE Chi-restraints excluded: chain C residue 154 ASN Chi-restraints excluded: chain C residue 161 ARG Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 296 ASP Chi-restraints excluded: chain C residue 312 PHE Chi-restraints excluded: chain D residue 71 PHE Chi-restraints excluded: chain D residue 82 THR Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 263 MET Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain E residue 81 ASN Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain E residue 250 LEU Chi-restraints excluded: chain E residue 266 VAL Chi-restraints excluded: chain E residue 270 ILE Chi-restraints excluded: chain E residue 312 PHE Chi-restraints excluded: chain E residue 324 ILE Chi-restraints excluded: chain F residue 63 MET Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 92 LEU Chi-restraints excluded: chain I residue 156 LEU Chi-restraints excluded: chain I residue 159 HIS Chi-restraints excluded: chain I residue 254 THR Chi-restraints excluded: chain I residue 262 ILE Chi-restraints excluded: chain I residue 263 MET Chi-restraints excluded: chain I residue 266 VAL Chi-restraints excluded: chain I residue 290 VAL Chi-restraints excluded: chain I residue 300 LEU Chi-restraints excluded: chain I residue 331 LEU Chi-restraints excluded: chain J residue 65 PHE Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain K residue 75 VAL Chi-restraints excluded: chain K residue 125 VAL Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 153 ILE Chi-restraints excluded: chain K residue 182 LEU Chi-restraints excluded: chain K residue 190 LEU Chi-restraints excluded: chain K residue 254 THR Chi-restraints excluded: chain K residue 267 THR Chi-restraints excluded: chain K residue 312 PHE Chi-restraints excluded: chain L residue 71 PHE Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 82 THR Chi-restraints excluded: chain O residue 77 VAL Chi-restraints excluded: chain O residue 125 VAL Chi-restraints excluded: chain O residue 157 THR Chi-restraints excluded: chain O residue 176 LEU Chi-restraints excluded: chain O residue 192 ILE Chi-restraints excluded: chain O residue 207 LEU Chi-restraints excluded: chain O residue 235 VAL Chi-restraints excluded: chain O residue 245 THR Chi-restraints excluded: chain O residue 267 THR Chi-restraints excluded: chain O residue 278 MET Chi-restraints excluded: chain O residue 283 VAL Chi-restraints excluded: chain P residue 71 PHE Chi-restraints excluded: chain P residue 98 PHE Chi-restraints excluded: chain M residue 78 VAL Chi-restraints excluded: chain M residue 104 ILE Chi-restraints excluded: chain M residue 112 LEU Chi-restraints excluded: chain M residue 127 ILE Chi-restraints excluded: chain M residue 133 VAL Chi-restraints excluded: chain M residue 192 ILE Chi-restraints excluded: chain M residue 204 ILE Chi-restraints excluded: chain M residue 270 ILE Chi-restraints excluded: chain M residue 312 PHE Chi-restraints excluded: chain M residue 324 ILE Chi-restraints excluded: chain N residue 49 ILE Chi-restraints excluded: chain N residue 68 LEU Chi-restraints excluded: chain N residue 83 LEU Chi-restraints excluded: chain Q residue 279 THR Chi-restraints excluded: chain Q residue 313 GLU Chi-restraints excluded: chain Q residue 369 THR Chi-restraints excluded: chain Q residue 385 HIS Chi-restraints excluded: chain Q residue 411 HIS Chi-restraints excluded: chain R residue 132 ILE Chi-restraints excluded: chain R residue 189 ASN Chi-restraints excluded: chain R residue 198 PHE Chi-restraints excluded: chain R residue 271 PHE Chi-restraints excluded: chain R residue 365 ASN Chi-restraints excluded: chain R residue 391 LEU Chi-restraints excluded: chain S residue 111 VAL Chi-restraints excluded: chain S residue 121 TYR Chi-restraints excluded: chain S residue 313 GLU Chi-restraints excluded: chain S residue 315 HIS Chi-restraints excluded: chain S residue 369 THR Chi-restraints excluded: chain S residue 385 HIS Chi-restraints excluded: chain T residue 132 ILE Chi-restraints excluded: chain T residue 198 PHE Chi-restraints excluded: chain T residue 365 ASN Chi-restraints excluded: chain T residue 382 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 320 optimal weight: 1.9990 chunk 282 optimal weight: 9.9990 chunk 62 optimal weight: 0.7980 chunk 15 optimal weight: 4.9990 chunk 3 optimal weight: 5.9990 chunk 109 optimal weight: 0.9990 chunk 278 optimal weight: 3.9990 chunk 178 optimal weight: 2.9990 chunk 291 optimal weight: 1.9990 chunk 136 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 159 HIS ** R 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 373 ASN ** T 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.108965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.081977 restraints weight = 91405.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.084687 restraints weight = 41290.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.086418 restraints weight = 24781.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.087525 restraints weight = 17851.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.088209 restraints weight = 14461.079| |-----------------------------------------------------------------------------| r_work (final): 0.3643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.3619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.093 30472 Z= 0.152 Angle : 0.679 12.498 41114 Z= 0.335 Chirality : 0.043 0.248 4607 Planarity : 0.004 0.055 5208 Dihedral : 5.028 57.140 4023 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 4.42 % Allowed : 24.09 % Favored : 71.49 % 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: -0.66 (0.14), residues: 3585 helix: 0.24 (0.11), residues: 2314 sheet: -1.58 (0.36), residues: 196 loop : -1.54 (0.20), residues: 1075 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 52 TYR 0.022 0.001 TYR P 79 PHE 0.038 0.001 PHE R 252 TRP 0.027 0.001 TRP K 256 HIS 0.009 0.001 HIS T 384 Details of bonding type rmsd covalent geometry : bond 0.00345 (30472) covalent geometry : angle 0.67852 (41114) hydrogen bonds : bond 0.03723 ( 1644) hydrogen bonds : angle 4.75539 ( 4785) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 551 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 407 time to evaluate : 1.079 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 276 MET cc_start: 0.8161 (ttp) cc_final: 0.7719 (ttp) REVERT: G 283 VAL cc_start: 0.9255 (OUTLIER) cc_final: 0.9032 (p) REVERT: C 161 ARG cc_start: 0.8277 (OUTLIER) cc_final: 0.7814 (ptt-90) REVERT: C 209 ASP cc_start: 0.9148 (t0) cc_final: 0.8821 (t0) REVERT: A 187 TYR cc_start: 0.8828 (t80) cc_final: 0.8216 (t80) REVERT: A 205 GLU cc_start: 0.9100 (tm-30) cc_final: 0.8650 (tm-30) REVERT: A 267 THR cc_start: 0.8857 (m) cc_final: 0.8650 (p) REVERT: B 57 LEU cc_start: 0.9086 (mm) cc_final: 0.8767 (mp) REVERT: B 71 PHE cc_start: 0.8331 (m-80) cc_final: 0.8012 (m-80) REVERT: B 98 PHE cc_start: 0.8398 (t80) cc_final: 0.8025 (t80) REVERT: E 260 TRP cc_start: 0.8320 (t-100) cc_final: 0.7971 (t-100) REVERT: E 276 MET cc_start: 0.8143 (tpp) cc_final: 0.7735 (tpp) REVERT: E 289 TYR cc_start: 0.8508 (t80) cc_final: 0.7614 (t80) REVERT: E 329 MET cc_start: 0.7543 (tpt) cc_final: 0.7208 (tmm) REVERT: F 79 TYR cc_start: 0.7050 (t80) cc_final: 0.6747 (m-10) REVERT: I 187 TYR cc_start: 0.8985 (t80) cc_final: 0.8770 (t80) REVERT: I 236 LEU cc_start: 0.8713 (mt) cc_final: 0.8398 (tt) REVERT: I 246 GLN cc_start: 0.8367 (tp40) cc_final: 0.8105 (tp40) REVERT: I 265 PRO cc_start: 0.8933 (Cg_exo) cc_final: 0.8692 (Cg_endo) REVERT: J 79 TYR cc_start: 0.6606 (t80) cc_final: 0.5899 (m-10) REVERT: J 97 ILE cc_start: 0.7816 (mm) cc_final: 0.7545 (mt) REVERT: K 172 ASN cc_start: 0.8403 (m-40) cc_final: 0.8148 (m-40) REVERT: K 209 ASP cc_start: 0.9009 (t0) cc_final: 0.8593 (t0) REVERT: K 243 MET cc_start: 0.7936 (ttm) cc_final: 0.6734 (ttt) REVERT: K 263 MET cc_start: 0.7790 (ttm) cc_final: 0.7514 (ttm) REVERT: L 96 ASP cc_start: 0.7454 (m-30) cc_final: 0.7102 (m-30) REVERT: O 84 PRO cc_start: 0.8600 (Cg_exo) cc_final: 0.8296 (Cg_endo) REVERT: O 192 ILE cc_start: 0.8771 (OUTLIER) cc_final: 0.8556 (tt) REVERT: O 263 MET cc_start: 0.8427 (tpp) cc_final: 0.8113 (tpp) REVERT: O 276 MET cc_start: 0.8322 (ttp) cc_final: 0.7656 (ttp) REVERT: P 98 PHE cc_start: 0.7722 (OUTLIER) cc_final: 0.7030 (t80) REVERT: M 243 MET cc_start: 0.8318 (ttt) cc_final: 0.8096 (ttt) REVERT: N 79 TYR cc_start: 0.7552 (t80) cc_final: 0.6809 (m-10) REVERT: Q 240 MET cc_start: 0.9462 (ppp) cc_final: 0.9119 (tmm) REVERT: Q 334 TYR cc_start: 0.8693 (t80) cc_final: 0.8445 (t80) REVERT: Q 345 MET cc_start: 0.8792 (mmm) cc_final: 0.8388 (mmm) REVERT: Q 396 MET cc_start: 0.9495 (tmm) cc_final: 0.8901 (tmm) REVERT: R 118 MET cc_start: 0.7325 (ttp) cc_final: 0.7106 (ttt) REVERT: R 161 THR cc_start: 0.9048 (m) cc_final: 0.8785 (t) REVERT: R 271 PHE cc_start: 0.8008 (OUTLIER) cc_final: 0.7780 (m-80) REVERT: R 278 MET cc_start: 0.8338 (tmm) cc_final: 0.8100 (tmm) REVERT: R 305 GLU cc_start: 0.8807 (mp0) cc_final: 0.8553 (mp0) REVERT: S 209 TYR cc_start: 0.8746 (t80) cc_final: 0.8487 (t80) REVERT: S 216 LEU cc_start: 0.9179 (tp) cc_final: 0.8955 (mt) REVERT: S 305 HIS cc_start: 0.9499 (t-90) cc_final: 0.9071 (t-90) REVERT: S 345 MET cc_start: 0.8841 (mmm) cc_final: 0.8596 (mmm) REVERT: S 396 MET cc_start: 0.9416 (tmm) cc_final: 0.9012 (tmm) REVERT: T 91 MET cc_start: 0.8198 (mmm) cc_final: 0.7790 (tpp) REVERT: T 102 TYR cc_start: 0.8714 (m-80) cc_final: 0.8100 (m-80) REVERT: T 161 THR cc_start: 0.9165 (m) cc_final: 0.8936 (t) REVERT: T 278 MET cc_start: 0.8079 (tmm) cc_final: 0.7859 (tmm) REVERT: T 391 LEU cc_start: 0.9326 (OUTLIER) cc_final: 0.9091 (mm) outliers start: 144 outliers final: 115 residues processed: 509 average time/residue: 0.1887 time to fit residues: 156.0137 Evaluate side-chains 509 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 388 time to evaluate : 1.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain G residue 235 VAL Chi-restraints excluded: chain G residue 236 LEU Chi-restraints excluded: chain G residue 253 LEU Chi-restraints excluded: chain G residue 267 THR Chi-restraints excluded: chain G residue 270 ILE Chi-restraints excluded: chain G residue 283 VAL Chi-restraints excluded: chain G residue 290 VAL Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 49 ILE Chi-restraints excluded: chain H residue 71 PHE Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 154 ASN Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 161 ARG Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 296 ASP Chi-restraints excluded: chain C residue 312 PHE Chi-restraints excluded: chain D residue 71 PHE Chi-restraints excluded: chain D residue 82 THR Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 159 HIS Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 263 MET Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain E residue 81 ASN Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain E residue 250 LEU Chi-restraints excluded: chain E residue 266 VAL Chi-restraints excluded: chain E residue 270 ILE Chi-restraints excluded: chain E residue 290 VAL Chi-restraints excluded: chain E residue 312 PHE Chi-restraints excluded: chain E residue 324 ILE Chi-restraints excluded: chain F residue 63 MET Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 92 LEU Chi-restraints excluded: chain I residue 159 HIS Chi-restraints excluded: chain I residue 262 ILE Chi-restraints excluded: chain I residue 263 MET Chi-restraints excluded: chain I residue 266 VAL Chi-restraints excluded: chain I residue 290 VAL Chi-restraints excluded: chain I residue 300 LEU Chi-restraints excluded: chain I residue 316 LYS Chi-restraints excluded: chain I residue 331 LEU Chi-restraints excluded: chain J residue 65 PHE Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain K residue 75 VAL Chi-restraints excluded: chain K residue 125 VAL Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 153 ILE Chi-restraints excluded: chain K residue 182 LEU Chi-restraints excluded: chain K residue 190 LEU Chi-restraints excluded: chain K residue 250 LEU Chi-restraints excluded: chain K residue 254 THR Chi-restraints excluded: chain K residue 267 THR Chi-restraints excluded: chain K residue 312 PHE Chi-restraints excluded: chain L residue 71 PHE Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 82 THR Chi-restraints excluded: chain O residue 77 VAL Chi-restraints excluded: chain O residue 125 VAL Chi-restraints excluded: chain O residue 157 THR Chi-restraints excluded: chain O residue 176 LEU Chi-restraints excluded: chain O residue 192 ILE Chi-restraints excluded: chain O residue 207 LEU Chi-restraints excluded: chain O residue 235 VAL Chi-restraints excluded: chain O residue 245 THR Chi-restraints excluded: chain O residue 267 THR Chi-restraints excluded: chain O residue 283 VAL Chi-restraints excluded: chain P residue 71 PHE Chi-restraints excluded: chain P residue 98 PHE Chi-restraints excluded: chain M residue 78 VAL Chi-restraints excluded: chain M residue 112 LEU Chi-restraints excluded: chain M residue 127 ILE Chi-restraints excluded: chain M residue 133 VAL Chi-restraints excluded: chain M residue 192 ILE Chi-restraints excluded: chain M residue 204 ILE Chi-restraints excluded: chain M residue 270 ILE Chi-restraints excluded: chain M residue 312 PHE Chi-restraints excluded: chain M residue 324 ILE Chi-restraints excluded: chain N residue 68 LEU Chi-restraints excluded: chain N residue 83 LEU Chi-restraints excluded: chain Q residue 279 THR Chi-restraints excluded: chain Q residue 313 GLU Chi-restraints excluded: chain Q residue 315 HIS Chi-restraints excluded: chain Q residue 369 THR Chi-restraints excluded: chain Q residue 385 HIS Chi-restraints excluded: chain Q residue 411 HIS Chi-restraints excluded: chain R residue 105 THR Chi-restraints excluded: chain R residue 132 ILE Chi-restraints excluded: chain R residue 198 PHE Chi-restraints excluded: chain R residue 271 PHE Chi-restraints excluded: chain R residue 363 SER Chi-restraints excluded: chain R residue 364 ASN Chi-restraints excluded: chain R residue 391 LEU Chi-restraints excluded: chain S residue 111 VAL Chi-restraints excluded: chain S residue 121 TYR Chi-restraints excluded: chain S residue 279 THR Chi-restraints excluded: chain S residue 313 GLU Chi-restraints excluded: chain S residue 315 HIS Chi-restraints excluded: chain S residue 369 THR Chi-restraints excluded: chain S residue 385 HIS Chi-restraints excluded: chain T residue 105 THR Chi-restraints excluded: chain T residue 132 ILE Chi-restraints excluded: chain T residue 198 PHE Chi-restraints excluded: chain T residue 363 SER Chi-restraints excluded: chain T residue 364 ASN Chi-restraints excluded: chain T residue 391 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 281 optimal weight: 7.9990 chunk 68 optimal weight: 1.9990 chunk 82 optimal weight: 0.6980 chunk 75 optimal weight: 0.7980 chunk 153 optimal weight: 0.0020 chunk 282 optimal weight: 5.9990 chunk 19 optimal weight: 4.9990 chunk 204 optimal weight: 3.9990 chunk 218 optimal weight: 3.9990 chunk 339 optimal weight: 5.9990 chunk 145 optimal weight: 3.9990 overall best weight: 1.4992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 172 ASN K 194 GLN R 189 ASN ** R 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 373 ASN T 174 HIS ** T 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 327 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.109204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.083023 restraints weight = 95129.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.085758 restraints weight = 43226.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.087492 restraints weight = 26042.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.088587 restraints weight = 18779.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.089276 restraints weight = 15266.187| |-----------------------------------------------------------------------------| r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.3776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 30472 Z= 0.158 Angle : 0.702 15.804 41114 Z= 0.344 Chirality : 0.043 0.230 4607 Planarity : 0.004 0.055 5208 Dihedral : 5.037 55.741 4023 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 4.54 % Allowed : 24.24 % Favored : 71.22 % 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: -0.52 (0.15), residues: 3585 helix: 0.36 (0.11), residues: 2302 sheet: -1.58 (0.36), residues: 196 loop : -1.47 (0.20), residues: 1087 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG S 107 TYR 0.022 0.001 TYR Q 209 PHE 0.041 0.001 PHE R 252 TRP 0.022 0.001 TRP K 256 HIS 0.008 0.001 HIS T 384 Details of bonding type rmsd covalent geometry : bond 0.00362 (30472) covalent geometry : angle 0.70181 (41114) hydrogen bonds : bond 0.03695 ( 1644) hydrogen bonds : angle 4.70915 ( 4785) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 546 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 398 time to evaluate : 1.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 276 MET cc_start: 0.8151 (ttp) cc_final: 0.7700 (ttp) REVERT: G 283 VAL cc_start: 0.9262 (OUTLIER) cc_final: 0.9040 (p) REVERT: G 303 PHE cc_start: 0.8588 (t80) cc_final: 0.8186 (t80) REVERT: C 161 ARG cc_start: 0.8242 (OUTLIER) cc_final: 0.7800 (ptt-90) REVERT: C 209 ASP cc_start: 0.9163 (t0) cc_final: 0.8839 (t0) REVERT: A 187 TYR cc_start: 0.8836 (t80) cc_final: 0.8222 (t80) REVERT: A 205 GLU cc_start: 0.9131 (tm-30) cc_final: 0.8663 (tm-30) REVERT: A 267 THR cc_start: 0.8846 (m) cc_final: 0.8646 (p) REVERT: B 57 LEU cc_start: 0.9078 (mm) cc_final: 0.8716 (mp) REVERT: B 71 PHE cc_start: 0.8388 (m-80) cc_final: 0.8018 (m-80) REVERT: B 83 LEU cc_start: 0.7511 (mt) cc_final: 0.7214 (tt) REVERT: B 98 PHE cc_start: 0.8397 (t80) cc_final: 0.7941 (t80) REVERT: E 260 TRP cc_start: 0.8326 (t-100) cc_final: 0.7986 (t-100) REVERT: E 276 MET cc_start: 0.8025 (tpp) cc_final: 0.7686 (tpp) REVERT: E 289 TYR cc_start: 0.8535 (t80) cc_final: 0.7644 (t80) REVERT: F 79 TYR cc_start: 0.6987 (t80) cc_final: 0.6657 (m-10) REVERT: I 187 TYR cc_start: 0.8974 (t80) cc_final: 0.8755 (t80) REVERT: I 236 LEU cc_start: 0.8669 (mt) cc_final: 0.8372 (tt) REVERT: I 246 GLN cc_start: 0.8440 (tp40) cc_final: 0.8164 (tp40) REVERT: I 265 PRO cc_start: 0.8913 (Cg_exo) cc_final: 0.8704 (Cg_endo) REVERT: J 79 TYR cc_start: 0.6648 (t80) cc_final: 0.5936 (m-10) REVERT: J 97 ILE cc_start: 0.7806 (mm) cc_final: 0.7546 (mt) REVERT: K 172 ASN cc_start: 0.8427 (m-40) cc_final: 0.8161 (m-40) REVERT: K 209 ASP cc_start: 0.9022 (t0) cc_final: 0.8619 (t0) REVERT: K 243 MET cc_start: 0.7922 (ttm) cc_final: 0.6618 (ttt) REVERT: L 96 ASP cc_start: 0.7475 (m-30) cc_final: 0.7098 (m-30) REVERT: O 84 PRO cc_start: 0.8798 (Cg_exo) cc_final: 0.8522 (Cg_endo) REVERT: O 192 ILE cc_start: 0.8756 (OUTLIER) cc_final: 0.8531 (tt) REVERT: O 263 MET cc_start: 0.8435 (tpp) cc_final: 0.8129 (tpp) REVERT: O 276 MET cc_start: 0.8363 (ttp) cc_final: 0.7618 (ttp) REVERT: M 243 MET cc_start: 0.8359 (ttt) cc_final: 0.8106 (ttt) REVERT: N 79 TYR cc_start: 0.7531 (t80) cc_final: 0.6815 (m-10) REVERT: Q 240 MET cc_start: 0.9471 (ppp) cc_final: 0.9129 (tmm) REVERT: Q 345 MET cc_start: 0.8802 (mmm) cc_final: 0.8382 (mmm) REVERT: Q 396 MET cc_start: 0.9495 (tmm) cc_final: 0.8935 (tmm) REVERT: R 161 THR cc_start: 0.9047 (m) cc_final: 0.8785 (t) REVERT: R 256 MET cc_start: 0.8117 (OUTLIER) cc_final: 0.7883 (mtm) REVERT: R 271 PHE cc_start: 0.8064 (OUTLIER) cc_final: 0.7841 (m-80) REVERT: R 305 GLU cc_start: 0.8789 (mp0) cc_final: 0.8533 (mp0) REVERT: S 107 ARG cc_start: 0.6001 (mmm160) cc_final: 0.5460 (tpp80) REVERT: S 209 TYR cc_start: 0.8713 (t80) cc_final: 0.8465 (t80) REVERT: S 216 LEU cc_start: 0.9182 (tp) cc_final: 0.8967 (mt) REVERT: S 305 HIS cc_start: 0.9495 (t-90) cc_final: 0.9071 (t-90) REVERT: S 345 MET cc_start: 0.8843 (mmm) cc_final: 0.8588 (mmm) REVERT: S 396 MET cc_start: 0.9394 (tmm) cc_final: 0.9044 (tmm) REVERT: S 437 MET cc_start: 0.9177 (mmp) cc_final: 0.8870 (mmp) REVERT: T 91 MET cc_start: 0.8176 (mmm) cc_final: 0.7752 (tpp) REVERT: T 102 TYR cc_start: 0.8600 (m-80) cc_final: 0.8032 (m-80) REVERT: T 158 ILE cc_start: 0.9156 (mm) cc_final: 0.8889 (mp) REVERT: T 161 THR cc_start: 0.9159 (m) cc_final: 0.8939 (t) REVERT: T 391 LEU cc_start: 0.9315 (OUTLIER) cc_final: 0.9083 (mm) outliers start: 148 outliers final: 124 residues processed: 503 average time/residue: 0.1873 time to fit residues: 154.5160 Evaluate side-chains 513 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 383 time to evaluate : 1.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain G residue 235 VAL Chi-restraints excluded: chain G residue 236 LEU Chi-restraints excluded: chain G residue 245 THR Chi-restraints excluded: chain G residue 253 LEU Chi-restraints excluded: chain G residue 267 THR Chi-restraints excluded: chain G residue 270 ILE Chi-restraints excluded: chain G residue 283 VAL Chi-restraints excluded: chain G residue 290 VAL Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 49 ILE Chi-restraints excluded: chain H residue 71 PHE Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 154 ASN Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 161 ARG Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 296 ASP Chi-restraints excluded: chain C residue 312 PHE Chi-restraints excluded: chain D residue 71 PHE Chi-restraints excluded: chain D residue 82 THR Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 159 HIS Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 170 HIS Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 263 MET Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain E residue 81 ASN Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 182 LEU Chi-restraints excluded: chain E residue 250 LEU Chi-restraints excluded: chain E residue 266 VAL Chi-restraints excluded: chain E residue 270 ILE Chi-restraints excluded: chain E residue 290 VAL Chi-restraints excluded: chain E residue 312 PHE Chi-restraints excluded: chain E residue 324 ILE Chi-restraints excluded: chain F residue 63 MET Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 92 LEU Chi-restraints excluded: chain I residue 159 HIS Chi-restraints excluded: chain I residue 262 ILE Chi-restraints excluded: chain I residue 263 MET Chi-restraints excluded: chain I residue 266 VAL Chi-restraints excluded: chain I residue 290 VAL Chi-restraints excluded: chain I residue 300 LEU Chi-restraints excluded: chain I residue 316 LYS Chi-restraints excluded: chain I residue 331 LEU Chi-restraints excluded: chain J residue 65 PHE Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain K residue 75 VAL Chi-restraints excluded: chain K residue 125 VAL Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 153 ILE Chi-restraints excluded: chain K residue 182 LEU Chi-restraints excluded: chain K residue 190 LEU Chi-restraints excluded: chain K residue 250 LEU Chi-restraints excluded: chain K residue 254 THR Chi-restraints excluded: chain K residue 267 THR Chi-restraints excluded: chain K residue 312 PHE Chi-restraints excluded: chain L residue 61 VAL Chi-restraints excluded: chain L residue 71 PHE Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 82 THR Chi-restraints excluded: chain L residue 85 SER Chi-restraints excluded: chain O residue 77 VAL Chi-restraints excluded: chain O residue 125 VAL Chi-restraints excluded: chain O residue 135 VAL Chi-restraints excluded: chain O residue 157 THR Chi-restraints excluded: chain O residue 192 ILE Chi-restraints excluded: chain O residue 207 LEU Chi-restraints excluded: chain O residue 235 VAL Chi-restraints excluded: chain O residue 245 THR Chi-restraints excluded: chain O residue 267 THR Chi-restraints excluded: chain O residue 283 VAL Chi-restraints excluded: chain P residue 71 PHE Chi-restraints excluded: chain M residue 78 VAL Chi-restraints excluded: chain M residue 104 ILE Chi-restraints excluded: chain M residue 112 LEU Chi-restraints excluded: chain M residue 125 VAL Chi-restraints excluded: chain M residue 127 ILE Chi-restraints excluded: chain M residue 133 VAL Chi-restraints excluded: chain M residue 192 ILE Chi-restraints excluded: chain M residue 204 ILE Chi-restraints excluded: chain M residue 257 GLU Chi-restraints excluded: chain M residue 270 ILE Chi-restraints excluded: chain M residue 312 PHE Chi-restraints excluded: chain M residue 324 ILE Chi-restraints excluded: chain N residue 49 ILE Chi-restraints excluded: chain N residue 68 LEU Chi-restraints excluded: chain N residue 83 LEU Chi-restraints excluded: chain Q residue 279 THR Chi-restraints excluded: chain Q residue 313 GLU Chi-restraints excluded: chain Q residue 315 HIS Chi-restraints excluded: chain Q residue 369 THR Chi-restraints excluded: chain Q residue 385 HIS Chi-restraints excluded: chain Q residue 411 HIS Chi-restraints excluded: chain R residue 105 THR Chi-restraints excluded: chain R residue 132 ILE Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 189 ASN Chi-restraints excluded: chain R residue 198 PHE Chi-restraints excluded: chain R residue 256 MET Chi-restraints excluded: chain R residue 271 PHE Chi-restraints excluded: chain R residue 363 SER Chi-restraints excluded: chain R residue 391 LEU Chi-restraints excluded: chain S residue 111 VAL Chi-restraints excluded: chain S residue 121 TYR Chi-restraints excluded: chain S residue 313 GLU Chi-restraints excluded: chain S residue 315 HIS Chi-restraints excluded: chain S residue 369 THR Chi-restraints excluded: chain S residue 385 HIS Chi-restraints excluded: chain T residue 105 THR Chi-restraints excluded: chain T residue 132 ILE Chi-restraints excluded: chain T residue 167 LEU Chi-restraints excluded: chain T residue 198 PHE Chi-restraints excluded: chain T residue 363 SER Chi-restraints excluded: chain T residue 391 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 177 optimal weight: 2.9990 chunk 106 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 212 optimal weight: 6.9990 chunk 239 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 234 optimal weight: 0.9990 chunk 290 optimal weight: 3.9990 chunk 95 optimal weight: 4.9990 chunk 201 optimal weight: 0.7980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 189 ASN ** R 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 295 ASN S 373 ASN ** T 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.103308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.077255 restraints weight = 91555.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.080103 restraints weight = 44587.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.083230 restraints weight = 25002.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.082887 restraints weight = 14739.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.082918 restraints weight = 14836.146| |-----------------------------------------------------------------------------| r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.3953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.098 30472 Z= 0.136 Angle : 0.708 14.912 41114 Z= 0.343 Chirality : 0.043 0.206 4607 Planarity : 0.004 0.054 5208 Dihedral : 4.962 56.888 4023 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 4.23 % Allowed : 24.88 % Favored : 70.88 % 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: -0.37 (0.15), residues: 3585 helix: 0.53 (0.11), residues: 2274 sheet: -1.55 (0.36), residues: 196 loop : -1.49 (0.20), residues: 1115 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG S 107 TYR 0.033 0.001 TYR R 102 PHE 0.043 0.001 PHE T 252 TRP 0.028 0.001 TRP K 256 HIS 0.011 0.001 HIS C 159 Details of bonding type rmsd covalent geometry : bond 0.00308 (30472) covalent geometry : angle 0.70791 (41114) hydrogen bonds : bond 0.03607 ( 1644) hydrogen bonds : angle 4.64138 ( 4785) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 540 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 402 time to evaluate : 1.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 276 MET cc_start: 0.8052 (ttp) cc_final: 0.7611 (ttp) REVERT: G 283 VAL cc_start: 0.9252 (OUTLIER) cc_final: 0.9033 (p) REVERT: C 161 ARG cc_start: 0.8184 (OUTLIER) cc_final: 0.7898 (ptt-90) REVERT: C 209 ASP cc_start: 0.9178 (t0) cc_final: 0.8860 (t0) REVERT: A 187 TYR cc_start: 0.8808 (t80) cc_final: 0.8119 (t80) REVERT: A 205 GLU cc_start: 0.9118 (tm-30) cc_final: 0.8659 (tm-30) REVERT: B 57 LEU cc_start: 0.9067 (mm) cc_final: 0.8702 (mp) REVERT: B 71 PHE cc_start: 0.8290 (m-80) cc_final: 0.8037 (m-80) REVERT: B 98 PHE cc_start: 0.8175 (t80) cc_final: 0.7709 (t80) REVERT: E 260 TRP cc_start: 0.8292 (t-100) cc_final: 0.7956 (t-100) REVERT: E 289 TYR cc_start: 0.8518 (t80) cc_final: 0.7659 (t80) REVERT: I 187 TYR cc_start: 0.8957 (t80) cc_final: 0.8746 (t80) REVERT: I 236 LEU cc_start: 0.8626 (mt) cc_final: 0.8323 (tt) REVERT: I 246 GLN cc_start: 0.8362 (tp40) cc_final: 0.8072 (tp40) REVERT: J 79 TYR cc_start: 0.6639 (t80) cc_final: 0.5946 (m-10) REVERT: J 97 ILE cc_start: 0.7778 (mm) cc_final: 0.7524 (mt) REVERT: K 172 ASN cc_start: 0.8352 (m-40) cc_final: 0.8093 (m-40) REVERT: K 209 ASP cc_start: 0.9018 (t0) cc_final: 0.8610 (t0) REVERT: K 243 MET cc_start: 0.7843 (ttm) cc_final: 0.6537 (ttt) REVERT: L 96 ASP cc_start: 0.7588 (m-30) cc_final: 0.7210 (m-30) REVERT: O 84 PRO cc_start: 0.8713 (Cg_exo) cc_final: 0.8452 (Cg_endo) REVERT: O 192 ILE cc_start: 0.8696 (OUTLIER) cc_final: 0.8450 (tt) REVERT: O 263 MET cc_start: 0.8402 (tpp) cc_final: 0.8134 (tpp) REVERT: O 276 MET cc_start: 0.8311 (ttp) cc_final: 0.7580 (ttp) REVERT: M 243 MET cc_start: 0.8290 (ttt) cc_final: 0.8028 (ttt) REVERT: N 79 TYR cc_start: 0.7496 (t80) cc_final: 0.6793 (m-10) REVERT: Q 240 MET cc_start: 0.9464 (ppp) cc_final: 0.9118 (tmm) REVERT: Q 345 MET cc_start: 0.8802 (mmm) cc_final: 0.8379 (mmm) REVERT: Q 396 MET cc_start: 0.9482 (tmm) cc_final: 0.8902 (tmm) REVERT: R 161 THR cc_start: 0.8994 (m) cc_final: 0.8728 (t) REVERT: R 301 LYS cc_start: 0.9304 (tptp) cc_final: 0.8772 (tptp) REVERT: S 107 ARG cc_start: 0.5996 (mmm160) cc_final: 0.5214 (tpp80) REVERT: S 209 TYR cc_start: 0.8710 (t80) cc_final: 0.8479 (t80) REVERT: S 305 HIS cc_start: 0.9477 (t-90) cc_final: 0.9062 (t-90) REVERT: S 345 MET cc_start: 0.8813 (mmm) cc_final: 0.8566 (mmm) REVERT: S 396 MET cc_start: 0.9353 (tmm) cc_final: 0.9135 (tmm) REVERT: T 91 MET cc_start: 0.8174 (mmm) cc_final: 0.7771 (tpp) REVERT: T 102 TYR cc_start: 0.8646 (m-80) cc_final: 0.7998 (m-80) REVERT: T 161 THR cc_start: 0.9096 (m) cc_final: 0.8865 (t) REVERT: T 271 PHE cc_start: 0.8172 (OUTLIER) cc_final: 0.7696 (m-80) REVERT: T 391 LEU cc_start: 0.9282 (OUTLIER) cc_final: 0.9051 (mm) outliers start: 138 outliers final: 110 residues processed: 500 average time/residue: 0.1901 time to fit residues: 153.8346 Evaluate side-chains 500 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 385 time to evaluate : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 125 VAL Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain G residue 242 TYR Chi-restraints excluded: chain G residue 245 THR Chi-restraints excluded: chain G residue 253 LEU Chi-restraints excluded: chain G residue 263 MET Chi-restraints excluded: chain G residue 267 THR Chi-restraints excluded: chain G residue 283 VAL Chi-restraints excluded: chain G residue 290 VAL Chi-restraints excluded: chain G residue 329 MET Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 49 ILE Chi-restraints excluded: chain H residue 61 VAL Chi-restraints excluded: chain H residue 71 PHE Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 154 ASN Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 161 ARG Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 296 ASP Chi-restraints excluded: chain C residue 312 PHE Chi-restraints excluded: chain D residue 71 PHE Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 263 MET Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain E residue 81 ASN Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 250 LEU Chi-restraints excluded: chain E residue 266 VAL Chi-restraints excluded: chain E residue 270 ILE Chi-restraints excluded: chain E residue 290 VAL Chi-restraints excluded: chain E residue 312 PHE Chi-restraints excluded: chain E residue 324 ILE Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 92 LEU Chi-restraints excluded: chain I residue 159 HIS Chi-restraints excluded: chain I residue 263 MET Chi-restraints excluded: chain I residue 266 VAL Chi-restraints excluded: chain I residue 290 VAL Chi-restraints excluded: chain I residue 300 LEU Chi-restraints excluded: chain I residue 316 LYS Chi-restraints excluded: chain I residue 331 LEU Chi-restraints excluded: chain J residue 61 VAL Chi-restraints excluded: chain J residue 65 PHE Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain K residue 75 VAL Chi-restraints excluded: chain K residue 125 VAL Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 153 ILE Chi-restraints excluded: chain K residue 182 LEU Chi-restraints excluded: chain K residue 190 LEU Chi-restraints excluded: chain K residue 250 LEU Chi-restraints excluded: chain K residue 254 THR Chi-restraints excluded: chain K residue 267 THR Chi-restraints excluded: chain K residue 312 PHE Chi-restraints excluded: chain L residue 61 VAL Chi-restraints excluded: chain L residue 71 PHE Chi-restraints excluded: chain L residue 80 VAL Chi-restraints excluded: chain L residue 82 THR Chi-restraints excluded: chain L residue 85 SER Chi-restraints excluded: chain O residue 77 VAL Chi-restraints excluded: chain O residue 125 VAL Chi-restraints excluded: chain O residue 135 VAL Chi-restraints excluded: chain O residue 157 THR Chi-restraints excluded: chain O residue 192 ILE Chi-restraints excluded: chain O residue 207 LEU Chi-restraints excluded: chain O residue 245 THR Chi-restraints excluded: chain O residue 267 THR Chi-restraints excluded: chain M residue 78 VAL Chi-restraints excluded: chain M residue 104 ILE Chi-restraints excluded: chain M residue 125 VAL Chi-restraints excluded: chain M residue 127 ILE Chi-restraints excluded: chain M residue 133 VAL Chi-restraints excluded: chain M residue 192 ILE Chi-restraints excluded: chain M residue 204 ILE Chi-restraints excluded: chain M residue 257 GLU Chi-restraints excluded: chain M residue 270 ILE Chi-restraints excluded: chain M residue 312 PHE Chi-restraints excluded: chain M residue 324 ILE Chi-restraints excluded: chain N residue 68 LEU Chi-restraints excluded: chain N residue 83 LEU Chi-restraints excluded: chain Q residue 313 GLU Chi-restraints excluded: chain Q residue 369 THR Chi-restraints excluded: chain Q residue 385 HIS Chi-restraints excluded: chain R residue 105 THR Chi-restraints excluded: chain R residue 132 ILE Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 189 ASN Chi-restraints excluded: chain R residue 198 PHE Chi-restraints excluded: chain R residue 323 HIS Chi-restraints excluded: chain R residue 363 SER Chi-restraints excluded: chain R residue 391 LEU Chi-restraints excluded: chain S residue 111 VAL Chi-restraints excluded: chain S residue 121 TYR Chi-restraints excluded: chain S residue 279 THR Chi-restraints excluded: chain S residue 313 GLU Chi-restraints excluded: chain S residue 315 HIS Chi-restraints excluded: chain S residue 369 THR Chi-restraints excluded: chain S residue 385 HIS Chi-restraints excluded: chain T residue 105 THR Chi-restraints excluded: chain T residue 132 ILE Chi-restraints excluded: chain T residue 167 LEU Chi-restraints excluded: chain T residue 198 PHE Chi-restraints excluded: chain T residue 271 PHE Chi-restraints excluded: chain T residue 363 SER Chi-restraints excluded: chain T residue 391 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 330 optimal weight: 7.9990 chunk 7 optimal weight: 1.9990 chunk 85 optimal weight: 5.9990 chunk 231 optimal weight: 0.9990 chunk 321 optimal weight: 10.0000 chunk 310 optimal weight: 6.9990 chunk 117 optimal weight: 0.9980 chunk 347 optimal weight: 6.9990 chunk 44 optimal weight: 0.8980 chunk 130 optimal weight: 9.9990 chunk 190 optimal weight: 5.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 159 HIS Q 411 HIS ** R 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 365 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.101167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.074689 restraints weight = 91674.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.077293 restraints weight = 42616.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.078962 restraints weight = 25957.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.080018 restraints weight = 18757.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.080651 restraints weight = 15242.844| |-----------------------------------------------------------------------------| r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.3938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.093 30472 Z= 0.201 Angle : 0.748 15.385 41114 Z= 0.365 Chirality : 0.045 0.282 4607 Planarity : 0.004 0.053 5208 Dihedral : 5.037 54.863 4023 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 4.11 % Allowed : 25.16 % Favored : 70.73 % 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: -0.39 (0.15), residues: 3585 helix: 0.51 (0.11), residues: 2260 sheet: -1.67 (0.37), residues: 190 loop : -1.43 (0.20), residues: 1135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG N 52 TYR 0.030 0.002 TYR R 102 PHE 0.056 0.002 PHE T 252 TRP 0.021 0.001 TRP T 286 HIS 0.013 0.001 HIS C 159 Details of bonding type rmsd covalent geometry : bond 0.00465 (30472) covalent geometry : angle 0.74779 (41114) hydrogen bonds : bond 0.03740 ( 1644) hydrogen bonds : angle 4.76993 ( 4785) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7170 Ramachandran restraints generated. 3585 Oldfield, 0 Emsley, 3585 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 516 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 382 time to evaluate : 1.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 276 MET cc_start: 0.8149 (ttp) cc_final: 0.7677 (ttp) REVERT: C 161 ARG cc_start: 0.8231 (OUTLIER) cc_final: 0.7917 (ptt-90) REVERT: C 209 ASP cc_start: 0.9163 (t0) cc_final: 0.8841 (t0) REVERT: D 86 LYS cc_start: 0.8026 (OUTLIER) cc_final: 0.7821 (ttmm) REVERT: A 187 TYR cc_start: 0.8866 (t80) cc_final: 0.8304 (t80) REVERT: A 205 GLU cc_start: 0.9145 (tm-30) cc_final: 0.8660 (tm-30) REVERT: A 263 MET cc_start: 0.8207 (OUTLIER) cc_final: 0.7972 (tpp) REVERT: B 71 PHE cc_start: 0.8340 (m-80) cc_final: 0.7988 (m-80) REVERT: B 98 PHE cc_start: 0.8327 (t80) cc_final: 0.7924 (t80) REVERT: E 260 TRP cc_start: 0.8361 (t-100) cc_final: 0.7994 (t-100) REVERT: E 276 MET cc_start: 0.8077 (tpp) cc_final: 0.7757 (tpp) REVERT: E 289 TYR cc_start: 0.8544 (t80) cc_final: 0.7590 (t80) REVERT: I 187 TYR cc_start: 0.9009 (t80) cc_final: 0.8773 (t80) REVERT: I 236 LEU cc_start: 0.8657 (mt) cc_final: 0.8377 (tt) REVERT: I 246 GLN cc_start: 0.8454 (tp40) cc_final: 0.8180 (tp40) REVERT: J 79 TYR cc_start: 0.6663 (t80) cc_final: 0.5976 (m-10) REVERT: J 97 ILE cc_start: 0.7780 (mm) cc_final: 0.7526 (mt) REVERT: K 172 ASN cc_start: 0.8349 (m-40) cc_final: 0.8101 (m-40) REVERT: K 209 ASP cc_start: 0.9014 (t0) cc_final: 0.8618 (t0) REVERT: L 96 ASP cc_start: 0.7522 (m-30) cc_final: 0.7142 (m-30) REVERT: O 192 ILE cc_start: 0.8786 (OUTLIER) cc_final: 0.8558 (tt) REVERT: O 263 MET cc_start: 0.8478 (tpp) cc_final: 0.8188 (tpp) REVERT: O 276 MET cc_start: 0.8310 (ttp) cc_final: 0.7826 (ttm) REVERT: M 243 MET cc_start: 0.8414 (ttt) cc_final: 0.8134 (ttt) REVERT: M 303 PHE cc_start: 0.8467 (t80) cc_final: 0.8260 (t80) REVERT: M 311 ARG cc_start: 0.8958 (tpp80) cc_final: 0.8708 (mmm160) REVERT: N 79 TYR cc_start: 0.7520 (t80) cc_final: 0.6827 (m-10) REVERT: Q 240 MET cc_start: 0.9449 (ppp) cc_final: 0.9089 (tmm) REVERT: Q 345 MET cc_start: 0.8809 (mmm) cc_final: 0.8483 (mmm) REVERT: Q 396 MET cc_start: 0.9479 (tmm) cc_final: 0.8895 (tmm) REVERT: R 161 THR cc_start: 0.8999 (m) cc_final: 0.8739 (t) REVERT: R 256 MET cc_start: 0.8092 (OUTLIER) cc_final: 0.7852 (mtm) REVERT: S 107 ARG cc_start: 0.5909 (mmm160) cc_final: 0.5048 (tpp80) REVERT: S 209 TYR cc_start: 0.8727 (t80) cc_final: 0.8481 (t80) REVERT: S 240 MET cc_start: 0.9451 (tmm) cc_final: 0.9198 (tpp) REVERT: S 305 HIS cc_start: 0.9495 (t-90) cc_final: 0.9024 (t70) REVERT: S 345 MET cc_start: 0.8850 (mmm) cc_final: 0.8587 (mmm) REVERT: S 396 MET cc_start: 0.9367 (tmm) cc_final: 0.9142 (tmm) REVERT: T 91 MET cc_start: 0.8186 (mmm) cc_final: 0.7754 (tpp) REVERT: T 102 TYR cc_start: 0.8650 (m-80) cc_final: 0.7980 (m-80) REVERT: T 161 THR cc_start: 0.9149 (m) cc_final: 0.8938 (t) REVERT: T 271 PHE cc_start: 0.8235 (OUTLIER) cc_final: 0.7747 (m-80) REVERT: T 391 LEU cc_start: 0.9261 (OUTLIER) cc_final: 0.9030 (mm) outliers start: 134 outliers final: 122 residues processed: 482 average time/residue: 0.1890 time to fit residues: 149.2112 Evaluate side-chains 506 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 377 time to evaluate : 1.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 125 VAL Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain G residue 188 THR Chi-restraints excluded: chain G residue 235 VAL Chi-restraints excluded: chain G residue 245 THR Chi-restraints excluded: chain G residue 253 LEU Chi-restraints excluded: chain G residue 267 THR Chi-restraints excluded: chain G residue 270 ILE Chi-restraints excluded: chain G residue 283 VAL Chi-restraints excluded: chain G residue 290 VAL Chi-restraints excluded: chain G residue 329 MET Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 49 ILE Chi-restraints excluded: chain H residue 61 VAL Chi-restraints excluded: chain H residue 71 PHE Chi-restraints excluded: chain C residue 110 VAL Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 154 ASN Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 161 ARG Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain C residue 267 THR Chi-restraints excluded: chain C residue 296 ASP Chi-restraints excluded: chain C residue 312 PHE Chi-restraints excluded: chain D residue 71 PHE Chi-restraints excluded: chain D residue 82 THR Chi-restraints excluded: chain D residue 86 LYS Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 159 HIS Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 170 HIS Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 263 MET Chi-restraints excluded: chain A residue 276 MET Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 324 ILE Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain E residue 81 ASN Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 135 VAL Chi-restraints excluded: chain E residue 250 LEU Chi-restraints excluded: chain E residue 266 VAL Chi-restraints excluded: chain E residue 270 ILE Chi-restraints excluded: chain E residue 290 VAL Chi-restraints excluded: chain E residue 312 PHE Chi-restraints excluded: chain E residue 324 ILE Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 92 LEU Chi-restraints excluded: chain I residue 263 MET Chi-restraints excluded: chain I residue 266 VAL Chi-restraints excluded: chain I residue 290 VAL Chi-restraints excluded: chain I residue 300 LEU Chi-restraints excluded: chain I residue 316 LYS Chi-restraints excluded: chain I residue 331 LEU Chi-restraints excluded: chain J residue 61 VAL Chi-restraints excluded: chain J residue 65 PHE Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain K residue 75 VAL Chi-restraints excluded: chain K residue 110 VAL Chi-restraints excluded: chain K residue 125 VAL Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 153 ILE Chi-restraints excluded: chain K residue 182 LEU Chi-restraints excluded: chain K residue 190 LEU Chi-restraints excluded: chain K residue 250 LEU Chi-restraints excluded: chain K residue 254 THR Chi-restraints excluded: chain K residue 259 SER Chi-restraints excluded: chain K residue 266 VAL Chi-restraints excluded: chain K residue 267 THR Chi-restraints excluded: chain K residue 271 THR Chi-restraints excluded: chain K residue 312 PHE Chi-restraints excluded: chain L residue 61 VAL Chi-restraints excluded: chain L residue 71 PHE Chi-restraints excluded: chain L residue 82 THR Chi-restraints excluded: chain L residue 85 SER Chi-restraints excluded: chain O residue 77 VAL Chi-restraints excluded: chain O residue 125 VAL Chi-restraints excluded: chain O residue 135 VAL Chi-restraints excluded: chain O residue 157 THR Chi-restraints excluded: chain O residue 192 ILE Chi-restraints excluded: chain O residue 207 LEU Chi-restraints excluded: chain O residue 245 THR Chi-restraints excluded: chain O residue 267 THR Chi-restraints excluded: chain M residue 78 VAL Chi-restraints excluded: chain M residue 104 ILE Chi-restraints excluded: chain M residue 125 VAL Chi-restraints excluded: chain M residue 127 ILE Chi-restraints excluded: chain M residue 133 VAL Chi-restraints excluded: chain M residue 192 ILE Chi-restraints excluded: chain M residue 204 ILE Chi-restraints excluded: chain M residue 257 GLU Chi-restraints excluded: chain M residue 270 ILE Chi-restraints excluded: chain M residue 312 PHE Chi-restraints excluded: chain M residue 324 ILE Chi-restraints excluded: chain N residue 68 LEU Chi-restraints excluded: chain N residue 83 LEU Chi-restraints excluded: chain Q residue 313 GLU Chi-restraints excluded: chain Q residue 369 THR Chi-restraints excluded: chain Q residue 385 HIS Chi-restraints excluded: chain Q residue 411 HIS Chi-restraints excluded: chain R residue 105 THR Chi-restraints excluded: chain R residue 132 ILE Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 198 PHE Chi-restraints excluded: chain R residue 256 MET Chi-restraints excluded: chain R residue 323 HIS Chi-restraints excluded: chain R residue 363 SER Chi-restraints excluded: chain R residue 391 LEU Chi-restraints excluded: chain S residue 111 VAL Chi-restraints excluded: chain S residue 121 TYR Chi-restraints excluded: chain S residue 279 THR Chi-restraints excluded: chain S residue 313 GLU Chi-restraints excluded: chain S residue 315 HIS Chi-restraints excluded: chain S residue 369 THR Chi-restraints excluded: chain S residue 385 HIS Chi-restraints excluded: chain T residue 105 THR Chi-restraints excluded: chain T residue 132 ILE Chi-restraints excluded: chain T residue 167 LEU Chi-restraints excluded: chain T residue 174 HIS Chi-restraints excluded: chain T residue 198 PHE Chi-restraints excluded: chain T residue 271 PHE Chi-restraints excluded: chain T residue 363 SER Chi-restraints excluded: chain T residue 365 ASN Chi-restraints excluded: chain T residue 391 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 117 optimal weight: 0.8980 chunk 98 optimal weight: 0.8980 chunk 279 optimal weight: 0.5980 chunk 13 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 205 optimal weight: 0.4980 chunk 198 optimal weight: 0.8980 chunk 176 optimal weight: 0.8980 chunk 319 optimal weight: 0.6980 chunk 36 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.101316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.074822 restraints weight = 92401.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.077444 restraints weight = 42786.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.079139 restraints weight = 26015.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.080211 restraints weight = 18737.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.080902 restraints weight = 15178.793| |-----------------------------------------------------------------------------| r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.3959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.123 30472 Z= 0.217 Angle : 0.902 59.157 41114 Z= 0.503 Chirality : 0.054 2.085 4607 Planarity : 0.005 0.132 5208 Dihedral : 5.062 54.808 4023 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 15.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 4.17 % Allowed : 25.50 % Favored : 70.33 % Cbeta Deviations : 0.06 % 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 (0.15), residues: 3585 helix: 0.52 (0.11), residues: 2264 sheet: -1.68 (0.36), residues: 190 loop : -1.43 (0.20), residues: 1131 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG S 107 TYR 0.057 0.002 TYR T 103 PHE 0.055 0.002 PHE T 252 TRP 0.017 0.001 TRP T 286 HIS 0.186 0.003 HIS Q 411 Details of bonding type rmsd covalent geometry : bond 0.00461 (30472) covalent geometry : angle 0.90248 (41114) hydrogen bonds : bond 0.03734 ( 1644) hydrogen bonds : angle 4.76698 ( 4785) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5793.31 seconds wall clock time: 100 minutes 58.21 seconds (6058.21 seconds total)