Starting phenix.real_space_refine on Mon Sep 14 10:03:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6wdo_21643/09_2026/6wdo_21643.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wdo_21643/09_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_21643/09_2026/6wdo_21643.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wdo_21643/09_2026/6wdo_21643.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6wdo_21643/09_2026/6wdo_21643.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6wdo_21643/09_2026/6wdo_21643.cif" model { file = "/net/cci-nas-00/data/ceres_data/6wdo_21643/09_2026/6wdo_21643.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wdo_21643/09_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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/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: 6.72, 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: 2.62 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: 0.57 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: 6.17 Time building geometry restraints manager: 3.51 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: 3.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 27.640 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 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/Z covalent geometry : bond 0.00505 / 0.24 (30472) covalent geometry : angle 0.72874 / 0.42 (41114) hydrogen bonds : bond 0.29262 / 19.34 ( 1644) hydrogen bonds : angle 10.52529 / 7.24 ( 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 : 1.525 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: 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: 0.8517 (p) REVERT: B 73 ILE cc_start: 0.8368 (mm) cc_final: 0.8054 (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: 0.8704 (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: 0.8048 (m-40) REVERT: O 84 PRO cc_start: 0.8500 (Cg_exo) cc_final: 0.8186 (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: 0.2019 time to fit residues: 173.5408 Evaluate side-chains 398 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 382 time to evaluate : 1.161 ------------------------------------------------------------------------------- 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... 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 114 GLN E 116 GLN 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: 41 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.100248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.074818 restraints weight = 91277.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.077903 restraints weight = 43015.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.079728 restraints weight = 22592.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.079934 restraints weight = 16396.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.080021 restraints weight = 15069.914| |-----------------------------------------------------------------------------| r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.2312 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= 0.160 Angle : 0.725 12.956 41114 Z= 0.373 Chirality : 0.044 0.228 4607 Planarity : 0.005 0.061 5208 Dihedral : 5.781 56.609 4046 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 2.42 % Allowed : 15.65 % Favored : 81.93 % 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: -2.27 (0.14), residues: 3585 helix: -1.02 (0.10), residues: 2268 sheet: -2.53 (0.33), residues: 190 loop : -2.04 (0.19), residues: 1127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG S 301 TYR 0.024 0.002 TYR P 79 PHE 0.021 0.002 PHE S 383 TRP 0.013 0.001 TRP C 256 HIS 0.006 0.001 HIS R 178 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.16 (30472) covalent geometry : angle 0.72505 / 0.37 (41114) hydrogen bonds : bond 0.05489 / 3.65 ( 1644) hydrogen bonds : angle 5.80581 / 4.04 ( 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 561 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 482 time to evaluate : 1.224 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: symmetry clash revert: symmetry clash REVERT: G 84 PRO cc_start: 0.8594 (Cg_exo) cc_final: 0.8277 (Cg_endo) REVERT: G 249 ILE cc_start: 0.8620 (tt) cc_final: 0.8263 (tt) REVERT: G 276 MET cc_start: 0.8324 (ttp) cc_final: 0.7545 (ttp) REVERT: H 85 SER cc_start: 0.8470 (t) cc_final: 0.8086 (p) REVERT: H 91 LEU cc_start: 0.9184 (tp) cc_final: 0.8957 (tp) REVERT: C 172 ASN cc_start: 0.7882 (m110) cc_final: 0.7576 (m110) REVERT: A 187 TYR cc_start: 0.8549 (t80) cc_final: 0.8258 (t80) REVERT: A 205 GLU cc_start: 0.9050 (tm-30) cc_final: 0.8701 (tm-30) REVERT: A 243 MET cc_start: 0.7793 (ttm) cc_final: 0.7544 (ttm) REVERT: A 267 THR cc_start: 0.8995 (m) cc_final: 0.8720 (p) REVERT: B 57 LEU cc_start: 0.9073 (mm) cc_final: 0.8815 (mp) REVERT: B 79 TYR cc_start: 0.6829 (t80) cc_final: 0.6392 (m-10) REVERT: E 243 MET cc_start: 0.8339 (ttt) cc_final: 0.8037 (ttt) REVERT: E 260 TRP cc_start: 0.8340 (t-100) cc_final: 0.8018 (t-100) REVERT: E 289 TYR cc_start: 0.8600 (t80) cc_final: 0.7809 (t80) REVERT: E 329 MET cc_start: 0.7715 (tpt) cc_final: 0.7285 (tmm) REVERT: F 79 TYR cc_start: 0.7307 (t80) cc_final: 0.6571 (m-10) REVERT: I 161 ARG cc_start: 0.8273 (mmt-90) cc_final: 0.7908 (mmt-90) REVERT: I 187 TYR cc_start: 0.8951 (t80) cc_final: 0.8680 (t80) REVERT: I 200 GLU cc_start: 0.9161 (tm-30) cc_final: 0.8752 (tm-30) REVERT: I 212 GLU cc_start: 0.8777 (tp30) cc_final: 0.8410 (tp30) REVERT: I 236 LEU cc_start: 0.8674 (mt) cc_final: 0.8440 (tt) REVERT: I 246 GLN cc_start: 0.8532 (tp40) cc_final: 0.8245 (tp40) REVERT: I 267 THR cc_start: 0.8970 (m) cc_final: 0.8700 (p) REVERT: J 57 LEU cc_start: 0.8880 (mp) cc_final: 0.8673 (mp) REVERT: J 94 GLU cc_start: 0.8755 (pp20) cc_final: 0.8405 (pp20) REVERT: K 172 ASN cc_start: 0.8383 (m-40) cc_final: 0.8145 (m-40) REVERT: K 209 ASP cc_start: 0.9020 (t0) cc_final: 0.8631 (t0) REVERT: K 242 TYR cc_start: 0.8293 (t80) cc_final: 0.8065 (t80) REVERT: O 84 PRO cc_start: 0.8481 (Cg_exo) cc_final: 0.8131 (Cg_endo) REVERT: O 276 MET cc_start: 0.8378 (ttp) cc_final: 0.7714 (ttp) REVERT: M 329 MET cc_start: 0.8342 (tmm) cc_final: 0.8126 (tmm) REVERT: N 79 TYR cc_start: 0.7363 (t80) cc_final: 0.6622 (m-10) REVERT: Q 240 MET cc_start: 0.9500 (ppp) cc_final: 0.9195 (tmm) REVERT: Q 345 MET cc_start: 0.8787 (mmm) cc_final: 0.8360 (mmm) REVERT: Q 381 LEU cc_start: 0.9426 (tp) cc_final: 0.9155 (tp) REVERT: R 91 MET cc_start: 0.7983 (mmm) cc_final: 0.7541 (tpp) REVERT: R 183 MET cc_start: 0.9266 (tmm) cc_final: 0.8934 (tmm) REVERT: R 256 MET cc_start: 0.8863 (mmm) cc_final: 0.8655 (mtm) REVERT: S 209 TYR cc_start: 0.8938 (t80) cc_final: 0.8607 (t80) REVERT: S 345 MET cc_start: 0.8952 (mmm) cc_final: 0.8562 (mmm) REVERT: S 381 LEU cc_start: 0.9464 (tp) cc_final: 0.9231 (tp) REVERT: S 396 MET cc_start: 0.9434 (tmm) cc_final: 0.8661 (tmm) REVERT: T 91 MET cc_start: 0.8195 (mmm) cc_final: 0.7851 (tpp) REVERT: T 102 TYR cc_start: 0.8807 (m-80) cc_final: 0.8400 (m-80) REVERT: T 109 PHE cc_start: 0.8563 (t80) cc_final: 0.8320 (t80) REVERT: T 183 MET cc_start: 0.9288 (tmm) cc_final: 0.8995 (tmm) REVERT: T 256 MET cc_start: 0.8881 (mmm) cc_final: 0.8577 (mtm) REVERT: T 278 MET cc_start: 0.8224 (ttm) cc_final: 0.7657 (ttp) outliers start: 79 outliers final: 46 residues processed: 534 average time/residue: 0.1823 time to fit residues: 156.4778 Evaluate side-chains 447 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 401 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 179 VAL Chi-restraints excluded: chain G residue 235 VAL 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 A residue 232 THR 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 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 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 Q residue 408 LEU 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 369 THR 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: 0.0570 chunk 341 optimal weight: 9.9990 chunk 344 optimal weight: 8.9990 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: 4.9990 chunk 342 optimal weight: 9.9990 chunk 110 optimal weight: 4.9990 overall best weight: 2.7304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 177 ASN ** E 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 341 HIS Q 222 ASN ** 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.112315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.082965 restraints weight = 99385.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.085552 restraints weight = 45028.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.087225 restraints weight = 26877.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.088308 restraints weight = 19128.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.088985 restraints weight = 15386.306| |-----------------------------------------------------------------------------| r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.2646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 30472 Z= 0.243 Angle : 0.729 11.082 41114 Z= 0.372 Chirality : 0.045 0.170 4607 Planarity : 0.005 0.058 5208 Dihedral : 5.410 59.390 4025 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 14.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.50 % Favored : 92.50 % Rotamer: Outliers : 3.62 % Allowed : 19.73 % Favored : 76.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.64 (0.14), residues: 3585 helix: -0.54 (0.11), residues: 2286 sheet: -2.33 (0.34), residues: 190 loop : -1.76 (0.20), residues: 1109 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 134 TYR 0.036 0.002 TYR R 103 PHE 0.025 0.002 PHE R 177 TRP 0.014 0.001 TRP C 260 HIS 0.007 0.001 HIS T 384 Details of bonding type rmsd/Z covalent geometry : bond 0.00549 / 0.24 (30472) covalent geometry : angle 0.72946 / 0.37 (41114) hydrogen bonds : bond 0.04943 / 3.30 ( 1644) hydrogen bonds : angle 5.47197 / 3.81 ( 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 530 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 412 time to evaluate : 1.202 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: G 84 PRO cc_start: 0.8689 (Cg_exo) cc_final: 0.8413 (Cg_endo) REVERT: G 205 GLU cc_start: 0.8865 (mp0) cc_final: 0.8599 (mp0) REVERT: G 249 ILE cc_start: 0.8693 (tt) cc_final: 0.8269 (tt) REVERT: G 253 LEU cc_start: 0.8810 (tp) cc_final: 0.8410 (tp) REVERT: G 276 MET cc_start: 0.8328 (ttp) cc_final: 0.7655 (ttp) REVERT: G 283 VAL cc_start: 0.9325 (OUTLIER) cc_final: 0.9098 (p) REVERT: H 85 SER cc_start: 0.8394 (t) cc_final: 0.8032 (p) REVERT: C 161 ARG cc_start: 0.8145 (OUTLIER) cc_final: 0.7839 (ptt-90) REVERT: C 209 ASP cc_start: 0.9095 (t0) cc_final: 0.8843 (t0) REVERT: A 187 TYR cc_start: 0.8782 (t80) cc_final: 0.8327 (t80) REVERT: A 205 GLU cc_start: 0.9064 (tm-30) cc_final: 0.8711 (tm-30) REVERT: A 212 GLU cc_start: 0.8827 (tp30) cc_final: 0.8506 (tp30) REVERT: B 79 TYR cc_start: 0.6924 (t80) cc_final: 0.6409 (m-10) REVERT: E 260 TRP cc_start: 0.8350 (t-100) cc_final: 0.7984 (t-100) REVERT: E 289 TYR cc_start: 0.8541 (t80) cc_final: 0.7631 (t80) REVERT: E 329 MET cc_start: 0.7758 (tpt) cc_final: 0.7321 (tmm) REVERT: F 79 TYR cc_start: 0.7353 (t80) cc_final: 0.6767 (m-10) REVERT: I 161 ARG cc_start: 0.8239 (mmt-90) cc_final: 0.8038 (mmt-90) REVERT: I 187 TYR cc_start: 0.8975 (t80) cc_final: 0.8731 (t80) REVERT: I 200 GLU cc_start: 0.9186 (tm-30) cc_final: 0.8825 (tm-30) REVERT: I 212 GLU cc_start: 0.8756 (tp30) cc_final: 0.8412 (tp30) REVERT: I 236 LEU cc_start: 0.8809 (mt) cc_final: 0.8531 (tt) REVERT: I 246 GLN cc_start: 0.8603 (tp40) cc_final: 0.8299 (tp40) REVERT: I 267 THR cc_start: 0.8996 (m) cc_final: 0.8723 (p) REVERT: J 57 LEU cc_start: 0.8940 (mp) cc_final: 0.8711 (mp) REVERT: J 94 GLU cc_start: 0.8735 (pp20) cc_final: 0.8404 (pp20) REVERT: K 172 ASN cc_start: 0.8464 (m-40) cc_final: 0.8218 (m-40) REVERT: K 209 ASP cc_start: 0.8991 (t0) cc_final: 0.8643 (t0) REVERT: O 84 PRO cc_start: 0.8636 (Cg_exo) cc_final: 0.8353 (Cg_endo) REVERT: O 276 MET cc_start: 0.8421 (ttp) cc_final: 0.7764 (ttp) REVERT: P 88 PHE cc_start: 0.8793 (t80) cc_final: 0.8533 (t80) REVERT: P 98 PHE cc_start: 0.7689 (OUTLIER) cc_final: 0.7157 (t80) REVERT: M 276 MET cc_start: 0.8287 (ttt) cc_final: 0.7995 (ttt) REVERT: N 79 TYR cc_start: 0.7515 (t80) cc_final: 0.6605 (m-10) REVERT: Q 240 MET cc_start: 0.9458 (ppp) cc_final: 0.9121 (tmm) REVERT: Q 345 MET cc_start: 0.8701 (mmm) cc_final: 0.8324 (mmm) REVERT: Q 381 LEU cc_start: 0.9362 (tp) cc_final: 0.9129 (tp) REVERT: Q 396 MET cc_start: 0.9423 (tmm) cc_final: 0.8630 (tmm) REVERT: R 182 LYS cc_start: 0.8120 (OUTLIER) cc_final: 0.7841 (mmtm) REVERT: R 183 MET cc_start: 0.9222 (tmm) cc_final: 0.8903 (tmm) REVERT: R 256 MET cc_start: 0.8896 (mmm) cc_final: 0.8600 (mtm) REVERT: S 209 TYR cc_start: 0.8863 (t80) cc_final: 0.8526 (t80) REVERT: S 240 MET cc_start: 0.9401 (tmm) cc_final: 0.9149 (tmm) REVERT: S 330 MET cc_start: 0.8469 (ptp) cc_final: 0.8225 (ptp) REVERT: S 345 MET cc_start: 0.8919 (mmm) cc_final: 0.8547 (mmm) REVERT: S 381 LEU cc_start: 0.9462 (tp) cc_final: 0.9205 (tp) REVERT: S 396 MET cc_start: 0.9448 (tmm) cc_final: 0.8846 (tmm) REVERT: T 91 MET cc_start: 0.8211 (mmm) cc_final: 0.7826 (tpp) REVERT: T 102 TYR cc_start: 0.8821 (m-80) cc_final: 0.8168 (m-80) REVERT: T 182 LYS cc_start: 0.8196 (OUTLIER) cc_final: 0.7943 (mmtm) REVERT: T 183 MET cc_start: 0.9219 (tmm) cc_final: 0.8945 (tmm) REVERT: T 256 MET cc_start: 0.8884 (mmm) cc_final: 0.8409 (mtp) REVERT: T 278 MET cc_start: 0.8356 (ttm) cc_final: 0.7897 (ttp) outliers start: 118 outliers final: 83 residues processed: 498 average time/residue: 0.1827 time to fit residues: 147.2411 Evaluate side-chains 464 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 376 time to evaluate : 1.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 235 VAL Chi-restraints excluded: chain G residue 258 TYR 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 48 VAL Chi-restraints excluded: chain H residue 49 ILE Chi-restraints excluded: chain H residue 71 PHE 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 267 THR Chi-restraints excluded: chain C residue 271 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 80 VAL 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 177 ASN Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 263 MET 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 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 250 LEU 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 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 L residue 91 LEU Chi-restraints excluded: chain O residue 77 VAL Chi-restraints excluded: chain O residue 176 LEU 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 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 270 ILE Chi-restraints excluded: chain M residue 284 MET Chi-restraints excluded: chain M residue 312 PHE 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 132 ILE Chi-restraints excluded: chain R residue 182 LYS Chi-restraints excluded: chain R residue 198 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 T residue 132 ILE Chi-restraints excluded: chain T residue 182 LYS Chi-restraints excluded: chain T residue 198 PHE 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: 0.5980 chunk 181 optimal weight: 5.9990 chunk 268 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 230 optimal weight: 0.7980 chunk 272 optimal weight: 0.9990 chunk 344 optimal weight: 8.9990 chunk 231 optimal weight: 2.9990 chunk 264 optimal weight: 0.0770 chunk 130 optimal weight: 0.6980 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 159 HIS K 326 GLN M 81 ASN ** M 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 222 ASN ** R 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 189 ASN ** R 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 365 ASN S 222 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.110616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.085335 restraints weight = 94740.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.087997 restraints weight = 45126.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.090435 restraints weight = 24339.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.090475 restraints weight = 16155.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.090603 restraints weight = 15732.930| |-----------------------------------------------------------------------------| r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.3166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 30472 Z= 0.131 Angle : 0.657 11.905 41114 Z= 0.330 Chirality : 0.042 0.194 4607 Planarity : 0.004 0.057 5208 Dihedral : 5.096 56.875 4023 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 3.07 % Allowed : 21.66 % Favored : 75.27 % 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: -1.10 (0.14), residues: 3585 helix: -0.10 (0.11), residues: 2288 sheet: -1.97 (0.35), residues: 196 loop : -1.62 (0.20), residues: 1101 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG N 52 TYR 0.028 0.001 TYR R 103 PHE 0.019 0.001 PHE R 289 TRP 0.014 0.001 TRP C 256 HIS 0.011 0.001 HIS K 159 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 (30472) covalent geometry : angle 0.65747 / 0.33 (41114) hydrogen bonds : bond 0.04067 / 2.69 ( 1644) hydrogen bonds : angle 4.94853 / 3.44 ( 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 538 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 438 time to evaluate : 1.230 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: 0.8514 (Cg_exo) cc_final: 0.8197 (Cg_endo) REVERT: G 249 ILE cc_start: 0.8443 (tt) cc_final: 0.7985 (tt) REVERT: G 276 MET cc_start: 0.8120 (ttp) cc_final: 0.7662 (ttp) REVERT: G 296 ASP cc_start: 0.8531 (m-30) cc_final: 0.8008 (p0) REVERT: H 93 GLU cc_start: 0.8728 (pp20) cc_final: 0.8390 (pp20) REVERT: C 209 ASP cc_start: 0.9185 (t0) cc_final: 0.8894 (t0) REVERT: A 187 TYR cc_start: 0.8756 (t80) cc_final: 0.8201 (t80) REVERT: A 205 GLU cc_start: 0.9062 (tm-30) cc_final: 0.8634 (tm-30) REVERT: A 267 THR cc_start: 0.8909 (m) cc_final: 0.8671 (p) REVERT: B 57 LEU cc_start: 0.8996 (mm) cc_final: 0.8752 (mp) REVERT: E 243 MET cc_start: 0.8333 (ttt) cc_final: 0.8053 (ttt) REVERT: E 260 TRP cc_start: 0.8314 (t-100) cc_final: 0.8016 (t-100) REVERT: E 289 TYR cc_start: 0.8523 (t80) cc_final: 0.7664 (t80) REVERT: E 329 MET cc_start: 0.7686 (tpt) cc_final: 0.7269 (tmm) REVERT: F 79 TYR cc_start: 0.7199 (t80) cc_final: 0.6614 (m-10) REVERT: I 187 TYR cc_start: 0.8965 (t80) cc_final: 0.8720 (t80) REVERT: I 200 GLU cc_start: 0.9199 (tm-30) cc_final: 0.8907 (tm-30) REVERT: I 212 GLU cc_start: 0.8675 (tp30) cc_final: 0.8283 (tp30) REVERT: I 236 LEU cc_start: 0.8666 (mt) cc_final: 0.8370 (tt) REVERT: I 246 GLN cc_start: 0.8379 (tp40) cc_final: 0.8159 (tp40) REVERT: I 267 THR cc_start: 0.8943 (m) cc_final: 0.8659 (p) REVERT: J 57 LEU cc_start: 0.8913 (mp) cc_final: 0.8670 (mp) REVERT: J 94 GLU cc_start: 0.8595 (pp20) cc_final: 0.8290 (pp20) REVERT: K 172 ASN cc_start: 0.8406 (m-40) cc_final: 0.7809 (m-40) REVERT: K 209 ASP cc_start: 0.9060 (t0) cc_final: 0.8678 (t0) REVERT: K 243 MET cc_start: 0.7975 (ttm) cc_final: 0.6979 (ttt) REVERT: L 96 ASP cc_start: 0.7657 (m-30) cc_final: 0.7185 (m-30) REVERT: O 84 PRO cc_start: 0.8421 (Cg_exo) cc_final: 0.8084 (Cg_endo) REVERT: O 263 MET cc_start: 0.8348 (tpp) cc_final: 0.7959 (tpt) REVERT: O 276 MET cc_start: 0.8280 (ttp) cc_final: 0.7895 (ttp) REVERT: P 98 PHE cc_start: 0.7769 (OUTLIER) cc_final: 0.6773 (t80) REVERT: N 79 TYR cc_start: 0.7447 (t80) cc_final: 0.6638 (m-10) REVERT: Q 216 LEU cc_start: 0.9025 (tp) cc_final: 0.8795 (mt) REVERT: Q 240 MET cc_start: 0.9480 (ppp) cc_final: 0.9139 (tmm) REVERT: Q 334 TYR cc_start: 0.8639 (t80) cc_final: 0.8439 (t80) REVERT: Q 345 MET cc_start: 0.8756 (mmm) cc_final: 0.8331 (mmm) REVERT: Q 396 MET cc_start: 0.9457 (tmm) cc_final: 0.8814 (tmm) REVERT: R 161 THR cc_start: 0.9057 (m) cc_final: 0.8757 (t) REVERT: R 182 LYS cc_start: 0.8118 (OUTLIER) cc_final: 0.7733 (mmtm) REVERT: R 183 MET cc_start: 0.9197 (tmm) cc_final: 0.8991 (tmm) REVERT: R 256 MET cc_start: 0.8885 (mmm) cc_final: 0.8681 (mtm) REVERT: R 271 PHE cc_start: 0.8052 (OUTLIER) cc_final: 0.7834 (m-80) REVERT: S 209 TYR cc_start: 0.8861 (t80) cc_final: 0.8592 (t80) REVERT: S 216 LEU cc_start: 0.9232 (tp) cc_final: 0.8939 (mt) REVERT: S 240 MET cc_start: 0.9418 (tmm) cc_final: 0.9151 (tmm) REVERT: S 345 MET cc_start: 0.8904 (mmm) cc_final: 0.8543 (mmm) REVERT: S 381 LEU cc_start: 0.9436 (tp) cc_final: 0.9173 (tp) REVERT: S 396 MET cc_start: 0.9468 (tmm) cc_final: 0.8947 (tmm) REVERT: T 91 MET cc_start: 0.8225 (mmm) cc_final: 0.7820 (tpp) REVERT: T 102 TYR cc_start: 0.8767 (m-80) cc_final: 0.8239 (m-80) REVERT: T 161 THR cc_start: 0.9165 (m) cc_final: 0.8903 (t) REVERT: T 183 MET cc_start: 0.9183 (tmm) cc_final: 0.8975 (tmm) REVERT: T 256 MET cc_start: 0.8858 (mmm) cc_final: 0.8612 (mtm) REVERT: T 278 MET cc_start: 0.8318 (ttm) cc_final: 0.7842 (ttp) REVERT: T 391 LEU cc_start: 0.9389 (OUTLIER) cc_final: 0.9142 (mm) outliers start: 100 outliers final: 62 residues processed: 511 average time/residue: 0.1814 time to fit residues: 150.9087 Evaluate side-chains 453 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 387 time to evaluate : 1.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 135 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 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 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 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 156 LEU Chi-restraints excluded: chain I residue 159 HIS Chi-restraints excluded: chain I residue 263 MET Chi-restraints excluded: chain I residue 316 LYS Chi-restraints excluded: chain J residue 49 ILE 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 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 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 267 THR Chi-restraints excluded: chain P residue 98 PHE Chi-restraints excluded: chain M residue 81 ASN Chi-restraints excluded: chain M residue 112 LEU Chi-restraints excluded: chain M residue 202 GLU 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 189 ASN 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 385 HIS Chi-restraints excluded: chain T residue 182 LYS 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: 5.9990 chunk 48 optimal weight: 2.9990 chunk 332 optimal weight: 0.9990 chunk 173 optimal weight: 4.9990 chunk 129 optimal weight: 5.9990 chunk 118 optimal weight: 5.9990 chunk 232 optimal weight: 0.8980 chunk 349 optimal weight: 8.9990 chunk 330 optimal weight: 6.9990 chunk 137 optimal weight: 5.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 326 GLN K 159 HIS K 194 GLN Q 222 ASN ** R 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 222 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 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 365 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.106683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.078731 restraints weight = 97695.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.081371 restraints weight = 44360.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.083077 restraints weight = 26736.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.084121 restraints weight = 19199.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.084804 restraints weight = 15585.621| |-----------------------------------------------------------------------------| r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.3189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.090 30472 Z= 0.266 Angle : 0.735 10.950 41114 Z= 0.369 Chirality : 0.045 0.217 4607 Planarity : 0.004 0.056 5208 Dihedral : 5.236 58.513 4023 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 14.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 4.66 % Allowed : 22.58 % Favored : 72.75 % 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: -1.03 (0.14), residues: 3585 helix: -0.05 (0.11), residues: 2274 sheet: -2.04 (0.35), residues: 190 loop : -1.54 (0.20), residues: 1121 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG M 311 TYR 0.024 0.002 TYR P 79 PHE 0.028 0.002 PHE A 149 TRP 0.016 0.002 TRP K 256 HIS 0.008 0.001 HIS R 384 Details of bonding type rmsd/Z covalent geometry : bond 0.00604 / 0.27 (30472) covalent geometry : angle 0.73531 / 0.37 (41114) hydrogen bonds : bond 0.04256 / 2.83 ( 1644) hydrogen bonds : angle 5.05624 / 3.50 ( 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 546 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 394 time to evaluate : 1.281 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: G 84 PRO cc_start: 0.8824 (Cg_exo) cc_final: 0.8621 (Cg_endo) REVERT: G 276 MET cc_start: 0.8288 (ttp) cc_final: 0.7730 (ttp) REVERT: G 283 VAL cc_start: 0.9327 (OUTLIER) cc_final: 0.9101 (p) REVERT: G 303 PHE cc_start: 0.8644 (t80) cc_final: 0.8338 (t80) REVERT: C 161 ARG cc_start: 0.8147 (OUTLIER) cc_final: 0.7734 (ptt-90) REVERT: C 209 ASP cc_start: 0.9098 (t0) cc_final: 0.8807 (t0) REVERT: C 326 GLN cc_start: 0.8859 (tp40) cc_final: 0.8615 (tp-100) REVERT: A 187 TYR cc_start: 0.8839 (t80) cc_final: 0.8352 (t80) REVERT: A 263 MET cc_start: 0.8201 (OUTLIER) cc_final: 0.7986 (tpp) REVERT: A 267 THR cc_start: 0.8963 (m) cc_final: 0.8689 (p) REVERT: B 57 LEU cc_start: 0.9107 (mm) cc_final: 0.8831 (mp) REVERT: B 79 TYR cc_start: 0.6939 (t80) cc_final: 0.6433 (m-10) REVERT: B 98 PHE cc_start: 0.8350 (t80) cc_final: 0.8028 (t80) REVERT: E 260 TRP cc_start: 0.8362 (t-100) cc_final: 0.8018 (t-100) REVERT: E 289 TYR cc_start: 0.8506 (t80) cc_final: 0.7580 (t80) REVERT: E 329 MET cc_start: 0.7772 (tpt) cc_final: 0.7459 (tmm) REVERT: F 79 TYR cc_start: 0.7278 (t80) cc_final: 0.6690 (m-10) REVERT: I 212 GLU cc_start: 0.8619 (tp30) cc_final: 0.8330 (tp30) REVERT: I 236 LEU cc_start: 0.8794 (mt) cc_final: 0.8453 (tt) REVERT: I 246 GLN cc_start: 0.8563 (tp40) cc_final: 0.8242 (tp40) REVERT: I 263 MET cc_start: 0.8054 (OUTLIER) cc_final: 0.7824 (tpp) REVERT: I 267 THR cc_start: 0.8941 (m) cc_final: 0.8678 (p) REVERT: J 57 LEU cc_start: 0.8972 (mp) cc_final: 0.8705 (mp) REVERT: J 94 GLU cc_start: 0.8724 (pp20) cc_final: 0.8316 (pp20) REVERT: J 97 ILE cc_start: 0.7843 (mm) cc_final: 0.7570 (mt) REVERT: K 172 ASN cc_start: 0.8383 (m-40) cc_final: 0.8134 (m-40) REVERT: K 209 ASP cc_start: 0.8971 (t0) cc_final: 0.8604 (t0) REVERT: L 96 ASP cc_start: 0.7431 (m-30) cc_final: 0.6966 (m-30) REVERT: O 84 PRO cc_start: 0.8614 (Cg_exo) cc_final: 0.8331 (Cg_endo) REVERT: O 276 MET cc_start: 0.8401 (ttp) cc_final: 0.7823 (ttp) REVERT: P 98 PHE cc_start: 0.7826 (OUTLIER) cc_final: 0.7002 (t80) REVERT: N 79 TYR cc_start: 0.7561 (t80) cc_final: 0.6744 (m-10) REVERT: Q 240 MET cc_start: 0.9455 (ppp) cc_final: 0.9108 (tmm) REVERT: Q 334 TYR cc_start: 0.8676 (t80) cc_final: 0.8297 (t80) REVERT: Q 345 MET cc_start: 0.8778 (mmm) cc_final: 0.8400 (mmm) REVERT: Q 381 LEU cc_start: 0.9360 (tp) cc_final: 0.9098 (tp) REVERT: Q 396 MET cc_start: 0.9486 (tmm) cc_final: 0.8841 (tmm) REVERT: R 161 THR cc_start: 0.9070 (m) cc_final: 0.8788 (t) REVERT: R 182 LYS cc_start: 0.8183 (OUTLIER) cc_final: 0.7764 (mmtm) REVERT: R 183 MET cc_start: 0.9223 (tmm) cc_final: 0.8967 (tmm) REVERT: R 271 PHE cc_start: 0.8022 (OUTLIER) cc_final: 0.7693 (m-80) REVERT: R 335 MET cc_start: 0.8732 (mmm) cc_final: 0.8524 (mmm) REVERT: S 209 TYR cc_start: 0.8796 (t80) cc_final: 0.8520 (t80) REVERT: S 216 LEU cc_start: 0.9196 (tp) cc_final: 0.8941 (mt) REVERT: S 240 MET cc_start: 0.9413 (tmm) cc_final: 0.9108 (tmm) REVERT: S 345 MET cc_start: 0.8879 (mmm) cc_final: 0.8510 (mmm) REVERT: S 381 LEU cc_start: 0.9442 (tp) cc_final: 0.9151 (tp) REVERT: S 396 MET cc_start: 0.9463 (tmm) cc_final: 0.8949 (tmm) REVERT: T 91 MET cc_start: 0.8222 (mmm) cc_final: 0.7801 (tpp) REVERT: T 102 TYR cc_start: 0.8753 (m-80) cc_final: 0.8244 (m-80) REVERT: T 118 MET cc_start: 0.6559 (ttt) cc_final: 0.6346 (ttt) REVERT: T 161 THR cc_start: 0.9183 (m) cc_final: 0.8944 (t) REVERT: T 183 MET cc_start: 0.9216 (tmm) cc_final: 0.9002 (tmm) REVERT: T 256 MET cc_start: 0.8867 (mmm) cc_final: 0.8597 (mtm) REVERT: T 271 PHE cc_start: 0.8346 (OUTLIER) cc_final: 0.7899 (m-10) outliers start: 152 outliers final: 109 residues processed: 503 average time/residue: 0.1734 time to fit residues: 143.2840 Evaluate side-chains 495 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 378 time to evaluate : 1.167 ------------------------------------------------------------------------------- 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 267 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 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 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 112 LEU Chi-restraints excluded: chain E residue 135 VAL 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 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 56 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 197 LEU Chi-restraints excluded: chain I residue 232 THR Chi-restraints excluded: chain I residue 254 THR Chi-restraints excluded: chain I residue 263 MET Chi-restraints excluded: chain I residue 276 MET Chi-restraints excluded: chain I residue 290 VAL Chi-restraints excluded: chain I residue 300 LEU Chi-restraints excluded: chain J residue 49 ILE 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 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 125 VAL Chi-restraints excluded: chain O residue 235 VAL Chi-restraints excluded: chain O residue 245 THR Chi-restraints excluded: chain O residue 266 VAL 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 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 224 ILE Chi-restraints excluded: chain M residue 232 THR 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 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 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 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 182 LYS 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 364 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 78 optimal weight: 2.9990 chunk 92 optimal weight: 4.9990 chunk 74 optimal weight: 4.9990 chunk 26 optimal weight: 0.0170 chunk 54 optimal weight: 3.9990 chunk 14 optimal weight: 9.9990 chunk 41 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 111 optimal weight: 4.9990 chunk 303 optimal weight: 9.9990 chunk 323 optimal weight: 0.8980 overall best weight: 1.1822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 172 ASN M 81 ASN Q 222 ASN ** R 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.117766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.088541 restraints weight = 98423.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.091277 restraints weight = 43982.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.093041 restraints weight = 25969.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.094153 restraints weight = 18412.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.094879 restraints weight = 14759.696| |-----------------------------------------------------------------------------| r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.3499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 30472 Z= 0.146 Angle : 0.659 11.576 41114 Z= 0.329 Chirality : 0.042 0.204 4607 Planarity : 0.004 0.056 5208 Dihedral : 5.064 58.296 4023 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 3.68 % Allowed : 24.18 % Favored : 72.14 % 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: -0.80 (0.14), residues: 3585 helix: 0.15 (0.11), residues: 2298 sheet: -1.74 (0.36), residues: 196 loop : -1.57 (0.20), residues: 1091 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG M 311 TYR 0.030 0.001 TYR I 187 PHE 0.025 0.001 PHE A 149 TRP 0.014 0.001 TRP C 256 HIS 0.007 0.001 HIS R 384 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.15 (30472) covalent geometry : angle 0.65870 / 0.33 (41114) hydrogen bonds : bond 0.03817 / 2.52 ( 1644) hydrogen bonds : angle 4.78676 / 3.32 ( 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 530 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 410 time to evaluate : 1.205 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: G 84 PRO cc_start: 0.8767 (Cg_exo) cc_final: 0.8539 (Cg_endo) REVERT: G 263 MET cc_start: 0.8398 (tpp) cc_final: 0.8056 (tpp) REVERT: G 276 MET cc_start: 0.8182 (ttp) cc_final: 0.7725 (ttp) REVERT: G 283 VAL cc_start: 0.9295 (OUTLIER) cc_final: 0.9070 (p) REVERT: C 161 ARG cc_start: 0.8164 (OUTLIER) cc_final: 0.7709 (ptt-90) REVERT: C 209 ASP cc_start: 0.9098 (t0) cc_final: 0.8785 (t0) REVERT: C 326 GLN cc_start: 0.8932 (tp40) cc_final: 0.8681 (tp-100) REVERT: A 187 TYR cc_start: 0.8818 (t80) cc_final: 0.8273 (t80) REVERT: A 205 GLU cc_start: 0.9027 (tm-30) cc_final: 0.8603 (tm-30) REVERT: B 57 LEU cc_start: 0.9053 (mm) cc_final: 0.8770 (mp) REVERT: B 71 PHE cc_start: 0.8406 (m-80) cc_final: 0.8021 (m-80) REVERT: B 98 PHE cc_start: 0.8347 (t80) cc_final: 0.7970 (t80) REVERT: E 260 TRP cc_start: 0.8328 (t-100) cc_final: 0.8015 (t-100) REVERT: E 289 TYR cc_start: 0.8462 (t80) cc_final: 0.7596 (t80) REVERT: E 303 PHE cc_start: 0.8541 (t80) cc_final: 0.8279 (t80) REVERT: E 329 MET cc_start: 0.7529 (tpt) cc_final: 0.7279 (tmm) REVERT: F 79 TYR cc_start: 0.7031 (t80) cc_final: 0.6510 (m-10) REVERT: I 161 ARG cc_start: 0.8125 (mmt-90) cc_final: 0.7924 (mmt-90) REVERT: I 212 GLU cc_start: 0.8619 (tp30) cc_final: 0.8270 (tp30) REVERT: I 236 LEU cc_start: 0.8749 (mt) cc_final: 0.8417 (tt) REVERT: I 246 GLN cc_start: 0.8403 (tp40) cc_final: 0.8164 (tp40) REVERT: J 57 LEU cc_start: 0.8954 (mp) cc_final: 0.8700 (mp) REVERT: J 79 TYR cc_start: 0.6474 (t80) cc_final: 0.5956 (m-10) REVERT: J 97 ILE cc_start: 0.7763 (mm) cc_final: 0.7463 (mt) REVERT: K 172 ASN cc_start: 0.8383 (m-40) cc_final: 0.8122 (m-40) REVERT: K 209 ASP cc_start: 0.8956 (t0) cc_final: 0.8567 (t0) REVERT: K 243 MET cc_start: 0.7979 (ttm) cc_final: 0.7023 (ttt) REVERT: L 96 ASP cc_start: 0.7512 (m-30) cc_final: 0.7044 (m-30) REVERT: O 84 PRO cc_start: 0.8507 (Cg_exo) cc_final: 0.8210 (Cg_endo) REVERT: O 192 ILE cc_start: 0.8941 (OUTLIER) cc_final: 0.8721 (tt) REVERT: O 276 MET cc_start: 0.8294 (ttp) cc_final: 0.7966 (ttp) REVERT: P 98 PHE cc_start: 0.7690 (OUTLIER) cc_final: 0.6964 (t80) REVERT: N 79 TYR cc_start: 0.7455 (t80) cc_final: 0.6803 (m-10) REVERT: Q 240 MET cc_start: 0.9434 (ppp) cc_final: 0.9073 (tmm) REVERT: Q 334 TYR cc_start: 0.8646 (t80) cc_final: 0.8437 (t80) REVERT: Q 345 MET cc_start: 0.8779 (mmm) cc_final: 0.8391 (mmm) REVERT: Q 381 LEU cc_start: 0.9301 (tp) cc_final: 0.9020 (tp) REVERT: Q 396 MET cc_start: 0.9474 (tmm) cc_final: 0.8894 (tmm) REVERT: R 91 MET cc_start: 0.7910 (tpp) cc_final: 0.7612 (tpp) REVERT: R 161 THR cc_start: 0.9061 (m) cc_final: 0.8772 (t) REVERT: R 182 LYS cc_start: 0.8207 (OUTLIER) cc_final: 0.7989 (mmtm) REVERT: R 183 MET cc_start: 0.9177 (tmm) cc_final: 0.8954 (tmm) REVERT: R 271 PHE cc_start: 0.8044 (OUTLIER) cc_final: 0.7784 (m-10) REVERT: R 278 MET cc_start: 0.8276 (tmm) cc_final: 0.8067 (tmm) REVERT: R 305 GLU cc_start: 0.8815 (mp0) cc_final: 0.8564 (mp0) REVERT: R 335 MET cc_start: 0.8706 (mmm) cc_final: 0.8479 (mmm) REVERT: S 209 TYR cc_start: 0.8744 (t80) cc_final: 0.8462 (t80) REVERT: S 216 LEU cc_start: 0.9179 (tp) cc_final: 0.8952 (mt) REVERT: S 240 MET cc_start: 0.9381 (tmm) cc_final: 0.9078 (tmm) REVERT: S 305 HIS cc_start: 0.9491 (t-90) cc_final: 0.9066 (t-90) REVERT: S 345 MET cc_start: 0.8824 (mmm) cc_final: 0.8488 (mmm) REVERT: S 396 MET cc_start: 0.9419 (tmm) cc_final: 0.8932 (tmm) REVERT: T 91 MET cc_start: 0.8201 (mmm) cc_final: 0.7801 (tpp) REVERT: T 102 TYR cc_start: 0.8757 (m-80) cc_final: 0.8161 (m-80) REVERT: T 118 MET cc_start: 0.6532 (ttt) cc_final: 0.6317 (ttt) REVERT: T 161 THR cc_start: 0.9180 (m) cc_final: 0.8946 (t) REVERT: T 256 MET cc_start: 0.8828 (mmm) cc_final: 0.8608 (mtm) REVERT: T 271 PHE cc_start: 0.8241 (OUTLIER) cc_final: 0.7805 (m-10) REVERT: T 335 MET cc_start: 0.8662 (mmm) cc_final: 0.8293 (mmm) REVERT: T 391 LEU cc_start: 0.9346 (OUTLIER) cc_final: 0.9113 (mm) outliers start: 120 outliers final: 86 residues processed: 497 average time/residue: 0.1834 time to fit residues: 149.1447 Evaluate side-chains 484 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 390 time to evaluate : 1.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 135 VAL 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 48 VAL Chi-restraints excluded: chain H residue 71 PHE Chi-restraints excluded: chain C residue 125 VAL 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 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 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 182 LEU Chi-restraints excluded: chain E residue 266 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 300 LEU Chi-restraints excluded: chain I residue 331 LEU Chi-restraints excluded: chain J residue 49 ILE 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 159 HIS Chi-restraints excluded: chain K residue 182 LEU Chi-restraints excluded: chain K residue 267 THR Chi-restraints excluded: chain K residue 271 THR 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 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 P residue 98 PHE 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 204 ILE Chi-restraints excluded: chain M residue 232 THR 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 182 LYS 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 222 ASN 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 182 LYS 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 320 optimal weight: 0.0980 chunk 282 optimal weight: 9.9990 chunk 62 optimal weight: 0.8980 chunk 15 optimal weight: 4.9990 chunk 3 optimal weight: 6.9990 chunk 109 optimal weight: 0.9990 chunk 278 optimal weight: 4.9990 chunk 178 optimal weight: 3.9990 chunk 291 optimal weight: 10.0000 chunk 136 optimal weight: 0.5980 chunk 31 optimal weight: 4.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 222 ASN R 189 ASN ** R 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 222 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.119659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.093944 restraints weight = 84426.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.096127 restraints weight = 42114.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.098164 restraints weight = 22935.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.098006 restraints weight = 18279.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.098156 restraints weight = 16215.601| |-----------------------------------------------------------------------------| r_work (final): 0.3858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.3636 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= 0.151 Angle : 0.674 11.406 41114 Z= 0.335 Chirality : 0.042 0.175 4607 Planarity : 0.004 0.055 5208 Dihedral : 5.014 58.510 4023 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 4.45 % Allowed : 23.81 % Favored : 71.74 % 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: -0.63 (0.14), residues: 3585 helix: 0.26 (0.11), residues: 2299 sheet: -1.61 (0.40), residues: 176 loop : -1.47 (0.20), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 52 TYR 0.028 0.001 TYR I 187 PHE 0.019 0.001 PHE R 289 TRP 0.014 0.001 TRP T 286 HIS 0.009 0.001 HIS R 384 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 (30472) covalent geometry : angle 0.67421 / 0.33 (41114) hydrogen bonds : bond 0.03745 / 2.48 ( 1644) hydrogen bonds : angle 4.74940 / 3.29 ( 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 542 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 397 time to evaluate : 1.183 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: G 84 PRO cc_start: 0.8884 (Cg_exo) cc_final: 0.8668 (Cg_endo) REVERT: G 276 MET cc_start: 0.8108 (ttp) cc_final: 0.7762 (ttp) REVERT: G 283 VAL cc_start: 0.9262 (OUTLIER) cc_final: 0.9039 (p) REVERT: C 161 ARG cc_start: 0.8144 (OUTLIER) cc_final: 0.7707 (ptt-90) REVERT: C 209 ASP cc_start: 0.9048 (t0) cc_final: 0.8740 (t0) REVERT: C 311 ARG cc_start: 0.8624 (mmp80) cc_final: 0.8404 (mmp80) REVERT: C 326 GLN cc_start: 0.8953 (tp40) cc_final: 0.8719 (tp-100) REVERT: A 187 TYR cc_start: 0.8736 (t80) cc_final: 0.8108 (t80) REVERT: A 205 GLU cc_start: 0.8905 (tm-30) cc_final: 0.8521 (tm-30) REVERT: A 212 GLU cc_start: 0.8725 (tp30) cc_final: 0.8419 (tp30) REVERT: B 57 LEU cc_start: 0.9024 (mm) cc_final: 0.8751 (mp) REVERT: B 71 PHE cc_start: 0.8360 (m-80) cc_final: 0.8061 (m-80) REVERT: B 98 PHE cc_start: 0.8265 (t80) cc_final: 0.7979 (t80) REVERT: E 260 TRP cc_start: 0.8309 (t-100) cc_final: 0.7987 (t-100) REVERT: E 289 TYR cc_start: 0.8446 (t80) cc_final: 0.7660 (t80) REVERT: E 303 PHE cc_start: 0.8460 (t80) cc_final: 0.8216 (t80) REVERT: I 161 ARG cc_start: 0.8156 (mmt-90) cc_final: 0.7939 (mmt-90) REVERT: I 212 GLU cc_start: 0.8541 (tp30) cc_final: 0.8236 (tp30) REVERT: I 236 LEU cc_start: 0.8781 (mt) cc_final: 0.8429 (tt) REVERT: I 246 GLN cc_start: 0.8404 (tp40) cc_final: 0.8198 (tp40) REVERT: I 253 LEU cc_start: 0.9130 (OUTLIER) cc_final: 0.8792 (tt) REVERT: J 57 LEU cc_start: 0.8939 (mp) cc_final: 0.8711 (mp) REVERT: J 79 TYR cc_start: 0.6518 (t80) cc_final: 0.6045 (m-10) REVERT: K 172 ASN cc_start: 0.8343 (m-40) cc_final: 0.8095 (m-40) REVERT: K 209 ASP cc_start: 0.8881 (t0) cc_final: 0.8493 (t0) REVERT: K 243 MET cc_start: 0.8008 (ttm) cc_final: 0.7181 (ttt) REVERT: K 252 ARG cc_start: 0.6431 (mpt180) cc_final: 0.6153 (mmt180) REVERT: L 96 ASP cc_start: 0.7402 (m-30) cc_final: 0.6922 (m-30) REVERT: O 84 PRO cc_start: 0.8568 (Cg_exo) cc_final: 0.8284 (Cg_endo) REVERT: O 192 ILE cc_start: 0.9049 (OUTLIER) cc_final: 0.8814 (tt) REVERT: O 276 MET cc_start: 0.8303 (ttp) cc_final: 0.8078 (ttp) REVERT: P 98 PHE cc_start: 0.7616 (OUTLIER) cc_final: 0.7015 (t80) REVERT: N 79 TYR cc_start: 0.7426 (t80) cc_final: 0.6823 (m-10) REVERT: N 92 LEU cc_start: 0.8755 (tp) cc_final: 0.8542 (tt) REVERT: Q 240 MET cc_start: 0.9326 (ppp) cc_final: 0.8952 (tmm) REVERT: Q 345 MET cc_start: 0.8701 (mmm) cc_final: 0.8343 (mmm) REVERT: Q 381 LEU cc_start: 0.9186 (tp) cc_final: 0.8912 (tp) REVERT: Q 396 MET cc_start: 0.9381 (tmm) cc_final: 0.8821 (tmm) REVERT: R 91 MET cc_start: 0.7812 (tpp) cc_final: 0.7425 (tpp) REVERT: R 161 THR cc_start: 0.8995 (m) cc_final: 0.8705 (t) REVERT: R 183 MET cc_start: 0.9066 (tmm) cc_final: 0.8837 (tmm) REVERT: R 258 ASN cc_start: 0.8723 (p0) cc_final: 0.8510 (p0) REVERT: R 271 PHE cc_start: 0.8000 (OUTLIER) cc_final: 0.7740 (m-80) REVERT: R 278 MET cc_start: 0.8358 (tmm) cc_final: 0.8138 (tmm) REVERT: S 240 MET cc_start: 0.9287 (tmm) cc_final: 0.8979 (tmm) REVERT: S 305 HIS cc_start: 0.9376 (t-90) cc_final: 0.8963 (t-90) REVERT: S 345 MET cc_start: 0.8764 (mmm) cc_final: 0.8558 (mmm) REVERT: S 396 MET cc_start: 0.9261 (tmm) cc_final: 0.8834 (tmm) REVERT: T 91 MET cc_start: 0.8138 (mmm) cc_final: 0.7778 (tpp) REVERT: T 102 TYR cc_start: 0.8670 (m-80) cc_final: 0.8137 (m-80) REVERT: T 103 TYR cc_start: 0.6195 (m-80) cc_final: 0.5872 (t80) REVERT: T 161 THR cc_start: 0.9123 (m) cc_final: 0.8889 (t) REVERT: T 271 PHE cc_start: 0.8207 (OUTLIER) cc_final: 0.7753 (m-10) REVERT: T 278 MET cc_start: 0.8108 (tmm) cc_final: 0.7892 (tmm) REVERT: T 391 LEU cc_start: 0.9274 (OUTLIER) cc_final: 0.9071 (mm) outliers start: 145 outliers final: 108 residues processed: 508 average time/residue: 0.1809 time to fit residues: 150.3402 Evaluate side-chains 504 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 388 time to evaluate : 1.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 135 VAL 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 48 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 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 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 C residue 314 LEU 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 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 232 THR Chi-restraints excluded: chain E residue 266 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 250 LEU Chi-restraints excluded: chain I residue 253 LEU 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 I residue 331 LEU Chi-restraints excluded: chain J residue 49 ILE 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 159 HIS 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 271 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 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 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 232 THR 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 167 LEU 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 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 385 HIS Chi-restraints excluded: chain T residue 105 THR Chi-restraints excluded: chain T residue 109 PHE Chi-restraints excluded: chain T residue 182 LYS 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 281 optimal weight: 9.9990 chunk 68 optimal weight: 1.9990 chunk 82 optimal weight: 0.8980 chunk 75 optimal weight: 0.3980 chunk 153 optimal weight: 5.9990 chunk 282 optimal weight: 0.0980 chunk 19 optimal weight: 4.9990 chunk 204 optimal weight: 3.9990 chunk 218 optimal weight: 1.9990 chunk 339 optimal weight: 4.9990 chunk 145 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 222 ASN R 189 ASN ** R 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 222 ASN 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 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.103364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.077032 restraints weight = 91471.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.079953 restraints weight = 44666.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.082465 restraints weight = 24907.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.082620 restraints weight = 16034.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.082766 restraints weight = 14957.326| |-----------------------------------------------------------------------------| r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.3813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.099 30472 Z= 0.140 Angle : 0.679 15.710 41114 Z= 0.335 Chirality : 0.043 0.274 4607 Planarity : 0.004 0.055 5208 Dihedral : 4.965 57.714 4023 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 4.36 % Allowed : 24.21 % Favored : 71.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.15), residues: 3585 helix: 0.40 (0.11), residues: 2285 sheet: -1.62 (0.36), residues: 196 loop : -1.47 (0.20), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG S 107 TYR 0.027 0.001 TYR Q 334 PHE 0.030 0.001 PHE T 252 TRP 0.019 0.001 TRP T 286 HIS 0.008 0.001 HIS C 159 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 (30472) covalent geometry : angle 0.67898 / 0.34 (41114) hydrogen bonds : bond 0.03658 / 2.41 ( 1644) hydrogen bonds : angle 4.66887 / 3.24 ( 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: 142 poor density : 404 time to evaluate : 1.234 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: 0.8900 (Cg_exo) cc_final: 0.8671 (Cg_endo) REVERT: G 276 MET cc_start: 0.8117 (ttp) cc_final: 0.7677 (ttp) REVERT: G 283 VAL cc_start: 0.9256 (OUTLIER) cc_final: 0.9037 (p) REVERT: C 161 ARG cc_start: 0.8230 (OUTLIER) cc_final: 0.7804 (ptt-90) REVERT: C 209 ASP cc_start: 0.9189 (t0) cc_final: 0.8878 (t0) REVERT: C 263 MET cc_start: 0.8103 (ttm) cc_final: 0.7843 (ttm) REVERT: C 326 GLN cc_start: 0.9049 (tp40) cc_final: 0.8586 (tp-100) REVERT: A 187 TYR cc_start: 0.8825 (t80) cc_final: 0.8155 (t80) REVERT: A 205 GLU cc_start: 0.9116 (tm-30) cc_final: 0.8659 (tm-30) REVERT: A 212 GLU cc_start: 0.8894 (tp30) cc_final: 0.8606 (tp30) REVERT: B 57 LEU cc_start: 0.9059 (mm) cc_final: 0.8702 (mp) REVERT: B 71 PHE cc_start: 0.8362 (m-80) cc_final: 0.8011 (m-80) REVERT: B 83 LEU cc_start: 0.7579 (mt) cc_final: 0.7316 (tt) REVERT: B 98 PHE cc_start: 0.8353 (t80) cc_final: 0.7940 (t80) REVERT: E 260 TRP cc_start: 0.8295 (t-100) cc_final: 0.7971 (t-100) REVERT: E 276 MET cc_start: 0.7940 (OUTLIER) cc_final: 0.7737 (mmt) REVERT: E 289 TYR cc_start: 0.8547 (t80) cc_final: 0.7675 (t80) REVERT: E 303 PHE cc_start: 0.8482 (t80) cc_final: 0.8245 (t80) REVERT: E 329 MET cc_start: 0.8108 (tmm) cc_final: 0.7502 (tmm) REVERT: I 156 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8251 (tt) REVERT: I 161 ARG cc_start: 0.8188 (mmt-90) cc_final: 0.7910 (mmt-90) REVERT: I 212 GLU cc_start: 0.8716 (tp30) cc_final: 0.8386 (tp30) REVERT: I 236 LEU cc_start: 0.8635 (mt) cc_final: 0.8333 (tt) REVERT: I 246 GLN cc_start: 0.8407 (tp40) cc_final: 0.8125 (tp40) REVERT: I 253 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8590 (tt) REVERT: I 255 TRP cc_start: 0.7665 (OUTLIER) cc_final: 0.7037 (m100) REVERT: J 57 LEU cc_start: 0.8943 (mp) cc_final: 0.8658 (mp) REVERT: J 79 TYR cc_start: 0.6650 (t80) cc_final: 0.5938 (m-10) REVERT: K 172 ASN cc_start: 0.8350 (m-40) cc_final: 0.8081 (m-40) REVERT: K 209 ASP cc_start: 0.9062 (t0) cc_final: 0.8673 (t0) REVERT: K 243 MET cc_start: 0.7839 (ttm) cc_final: 0.6613 (ttt) REVERT: L 96 ASP cc_start: 0.7533 (m-30) cc_final: 0.7044 (m-30) REVERT: O 84 PRO cc_start: 0.8565 (Cg_exo) cc_final: 0.8247 (Cg_endo) REVERT: O 192 ILE cc_start: 0.8742 (OUTLIER) cc_final: 0.8513 (tt) REVERT: O 263 MET cc_start: 0.8320 (tpp) cc_final: 0.8024 (tpp) REVERT: O 276 MET cc_start: 0.8367 (ttp) cc_final: 0.7793 (ttp) REVERT: M 243 MET cc_start: 0.7707 (ttt) cc_final: 0.7457 (ttt) REVERT: M 260 TRP cc_start: 0.8247 (t-100) cc_final: 0.7705 (t-100) REVERT: N 79 TYR cc_start: 0.7498 (t80) cc_final: 0.6794 (m-10) REVERT: Q 240 MET cc_start: 0.9491 (ppp) cc_final: 0.9140 (tmm) REVERT: Q 345 MET cc_start: 0.8811 (mmm) cc_final: 0.8394 (mmm) REVERT: Q 381 LEU cc_start: 0.9288 (tp) cc_final: 0.9009 (tp) REVERT: Q 396 MET cc_start: 0.9488 (tmm) cc_final: 0.8916 (tmm) REVERT: R 91 MET cc_start: 0.7872 (tpp) cc_final: 0.7510 (tpp) REVERT: R 161 THR cc_start: 0.9072 (m) cc_final: 0.8796 (t) REVERT: R 183 MET cc_start: 0.9143 (tmm) cc_final: 0.8929 (tmm) REVERT: R 236 MET cc_start: 0.8574 (mpp) cc_final: 0.8316 (mpp) REVERT: R 258 ASN cc_start: 0.8635 (p0) cc_final: 0.8431 (p0) REVERT: R 271 PHE cc_start: 0.8022 (OUTLIER) cc_final: 0.7789 (m-80) REVERT: R 278 MET cc_start: 0.8367 (tmm) cc_final: 0.8113 (tmm) REVERT: R 335 MET cc_start: 0.8695 (mmm) cc_final: 0.8456 (mmm) REVERT: S 107 ARG cc_start: 0.6034 (mmm160) cc_final: 0.5319 (tpp80) REVERT: S 240 MET cc_start: 0.9424 (tmm) cc_final: 0.9144 (tmm) REVERT: S 305 HIS cc_start: 0.9504 (t-90) cc_final: 0.9099 (t-90) REVERT: S 345 MET cc_start: 0.8821 (mmm) cc_final: 0.8570 (mmm) REVERT: S 396 MET cc_start: 0.9401 (tmm) cc_final: 0.9039 (tmm) REVERT: S 437 MET cc_start: 0.9164 (mmp) cc_final: 0.8902 (mmp) REVERT: T 91 MET cc_start: 0.8190 (mmm) cc_final: 0.7775 (tpp) REVERT: T 102 TYR cc_start: 0.8731 (m-80) cc_final: 0.8039 (m-80) REVERT: T 161 THR cc_start: 0.9165 (m) cc_final: 0.8930 (t) REVERT: T 271 PHE cc_start: 0.8278 (OUTLIER) cc_final: 0.7866 (m-80) REVERT: T 391 LEU cc_start: 0.9319 (OUTLIER) cc_final: 0.9086 (mm) outliers start: 142 outliers final: 111 residues processed: 513 average time/residue: 0.1783 time to fit residues: 151.2069 Evaluate side-chains 511 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 390 time to evaluate : 1.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 135 VAL 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 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 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 C residue 314 LEU 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 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 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 276 MET 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 156 LEU Chi-restraints excluded: chain I residue 159 HIS Chi-restraints excluded: chain I residue 250 LEU Chi-restraints excluded: chain I residue 253 LEU Chi-restraints excluded: chain I residue 255 TRP Chi-restraints excluded: chain I residue 263 MET Chi-restraints excluded: chain I residue 316 LYS Chi-restraints excluded: chain I residue 331 LEU Chi-restraints excluded: chain J residue 49 ILE 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 159 HIS 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 271 THR 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 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 P residue 71 PHE 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 204 ILE Chi-restraints excluded: chain M residue 232 THR Chi-restraints excluded: chain M residue 257 GLU 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 315 HIS 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 271 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 109 PHE Chi-restraints excluded: chain T residue 167 LEU Chi-restraints excluded: chain T residue 182 LYS 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 177 optimal weight: 2.9990 chunk 106 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 212 optimal weight: 6.9990 chunk 239 optimal weight: 0.5980 chunk 23 optimal weight: 0.9990 chunk 36 optimal weight: 4.9990 chunk 234 optimal weight: 0.8980 chunk 290 optimal weight: 10.0000 chunk 95 optimal weight: 5.9990 chunk 201 optimal weight: 3.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 222 ASN R 189 ASN ** R 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 222 ASN ** S 295 ASN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.103265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.077662 restraints weight = 91268.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.080449 restraints weight = 42328.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.082776 restraints weight = 22491.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.082411 restraints weight = 17904.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.082514 restraints weight = 15945.616| |-----------------------------------------------------------------------------| r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.3917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.099 30472 Z= 0.147 Angle : 0.692 13.743 41114 Z= 0.339 Chirality : 0.043 0.234 4607 Planarity : 0.004 0.054 5208 Dihedral : 4.954 57.284 4023 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 4.20 % Allowed : 24.85 % Favored : 70.94 % 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: -0.41 (0.15), residues: 3585 helix: 0.47 (0.11), residues: 2289 sheet: -1.61 (0.37), residues: 196 loop : -1.44 (0.20), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG S 107 TYR 0.029 0.002 TYR P 79 PHE 0.044 0.001 PHE T 252 TRP 0.022 0.001 TRP T 286 HIS 0.012 0.001 HIS C 159 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 (30472) covalent geometry : angle 0.69182 / 0.34 (41114) hydrogen bonds : bond 0.03643 / 2.41 ( 1644) hydrogen bonds : angle 4.65375 / 3.24 ( 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 534 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 397 time to evaluate : 1.244 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: 0.8933 (Cg_exo) cc_final: 0.8716 (Cg_endo) REVERT: G 276 MET cc_start: 0.8095 (ttp) cc_final: 0.7672 (ttp) REVERT: G 283 VAL cc_start: 0.9268 (OUTLIER) cc_final: 0.9048 (p) REVERT: C 161 ARG cc_start: 0.8226 (OUTLIER) cc_final: 0.7912 (ptt-90) REVERT: C 209 ASP cc_start: 0.9175 (t0) cc_final: 0.8850 (t0) REVERT: C 326 GLN cc_start: 0.9070 (tp40) cc_final: 0.8591 (tp-100) REVERT: A 187 TYR cc_start: 0.8804 (t80) cc_final: 0.8124 (t80) REVERT: A 205 GLU cc_start: 0.9109 (tm-30) cc_final: 0.8654 (tm-30) REVERT: A 212 GLU cc_start: 0.8880 (tp30) cc_final: 0.8664 (tp30) REVERT: B 57 LEU cc_start: 0.9028 (mm) cc_final: 0.8652 (mp) REVERT: B 71 PHE cc_start: 0.8296 (m-80) cc_final: 0.8072 (m-80) REVERT: B 98 PHE cc_start: 0.8179 (t80) cc_final: 0.7777 (t80) REVERT: E 289 TYR cc_start: 0.8534 (t80) cc_final: 0.7705 (t80) REVERT: E 303 PHE cc_start: 0.8466 (t80) cc_final: 0.8238 (t80) REVERT: E 329 MET cc_start: 0.7947 (tmm) cc_final: 0.7515 (tmm) REVERT: I 161 ARG cc_start: 0.8211 (mmt-90) cc_final: 0.7927 (mmt-90) REVERT: I 212 GLU cc_start: 0.8700 (tp30) cc_final: 0.8407 (tp30) REVERT: I 236 LEU cc_start: 0.8645 (mt) cc_final: 0.8346 (tt) REVERT: I 246 GLN cc_start: 0.8414 (tp40) cc_final: 0.8125 (tp40) REVERT: I 255 TRP cc_start: 0.7646 (OUTLIER) cc_final: 0.7026 (m100) REVERT: J 57 LEU cc_start: 0.8950 (mp) cc_final: 0.8662 (mp) REVERT: J 79 TYR cc_start: 0.6647 (t80) cc_final: 0.5931 (m-10) REVERT: K 172 ASN cc_start: 0.8348 (m-40) cc_final: 0.8087 (m-40) REVERT: K 209 ASP cc_start: 0.9054 (t0) cc_final: 0.8664 (t0) REVERT: K 243 MET cc_start: 0.7793 (ttm) cc_final: 0.6609 (ttt) REVERT: L 96 ASP cc_start: 0.7470 (m-30) cc_final: 0.7006 (m-30) REVERT: O 84 PRO cc_start: 0.8568 (Cg_exo) cc_final: 0.8255 (Cg_endo) REVERT: O 192 ILE cc_start: 0.8739 (OUTLIER) cc_final: 0.8508 (tt) REVERT: O 263 MET cc_start: 0.8321 (tpp) cc_final: 0.8074 (tpp) REVERT: O 276 MET cc_start: 0.8345 (ttp) cc_final: 0.7757 (ttp) REVERT: M 193 GLU cc_start: 0.8078 (pm20) cc_final: 0.7695 (pm20) REVERT: M 243 MET cc_start: 0.7773 (ttt) cc_final: 0.7521 (ttt) REVERT: N 79 TYR cc_start: 0.7481 (t80) cc_final: 0.6794 (m-10) REVERT: Q 240 MET cc_start: 0.9478 (ppp) cc_final: 0.9115 (tmm) REVERT: Q 345 MET cc_start: 0.8810 (mmm) cc_final: 0.8387 (mmm) REVERT: Q 381 LEU cc_start: 0.9284 (tp) cc_final: 0.9004 (tp) REVERT: Q 396 MET cc_start: 0.9481 (tmm) cc_final: 0.8877 (tmm) REVERT: R 91 MET cc_start: 0.7870 (tpp) cc_final: 0.7501 (tpp) REVERT: R 161 THR cc_start: 0.9084 (m) cc_final: 0.8813 (t) REVERT: R 183 MET cc_start: 0.9134 (tmm) cc_final: 0.8918 (tmm) REVERT: R 236 MET cc_start: 0.8611 (mpp) cc_final: 0.8321 (mpp) REVERT: R 258 ASN cc_start: 0.8651 (p0) cc_final: 0.8444 (p0) REVERT: R 301 LYS cc_start: 0.9563 (ptpt) cc_final: 0.9145 (tptp) REVERT: R 335 MET cc_start: 0.8697 (mmm) cc_final: 0.8460 (mmm) REVERT: S 107 ARG cc_start: 0.5996 (mmm160) cc_final: 0.5217 (tpp80) REVERT: S 240 MET cc_start: 0.9409 (tmm) cc_final: 0.9134 (tmm) REVERT: S 305 HIS cc_start: 0.9496 (t-90) cc_final: 0.9093 (t-90) REVERT: S 345 MET cc_start: 0.8819 (mmm) cc_final: 0.8567 (mmm) REVERT: S 396 MET cc_start: 0.9377 (tmm) cc_final: 0.9043 (tmm) REVERT: T 91 MET cc_start: 0.8166 (mmm) cc_final: 0.7758 (tpp) REVERT: T 102 TYR cc_start: 0.8621 (m-80) cc_final: 0.8065 (m-80) REVERT: T 161 THR cc_start: 0.9145 (m) cc_final: 0.8910 (t) REVERT: T 271 PHE cc_start: 0.8252 (OUTLIER) cc_final: 0.7801 (m-80) REVERT: T 391 LEU cc_start: 0.9298 (OUTLIER) cc_final: 0.9067 (mm) outliers start: 137 outliers final: 118 residues processed: 503 average time/residue: 0.1798 time to fit residues: 148.5793 Evaluate side-chains 514 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 390 time to evaluate : 1.498 ------------------------------------------------------------------------------- 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 267 THR Chi-restraints excluded: chain G residue 270 ILE Chi-restraints excluded: chain G residue 271 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 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 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 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 C residue 314 LEU 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 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 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 232 THR Chi-restraints excluded: chain E residue 250 LEU Chi-restraints excluded: chain E residue 266 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 250 LEU Chi-restraints excluded: chain I residue 255 TRP 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 49 ILE 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 159 HIS 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 271 THR 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 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 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 204 ILE Chi-restraints excluded: chain M residue 232 THR 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 315 HIS 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 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 105 THR Chi-restraints excluded: chain T residue 167 LEU Chi-restraints excluded: chain T residue 182 LYS 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: 4.9990 chunk 7 optimal weight: 0.8980 chunk 85 optimal weight: 1.9990 chunk 231 optimal weight: 0.7980 chunk 321 optimal weight: 7.9990 chunk 310 optimal weight: 4.9990 chunk 117 optimal weight: 3.9990 chunk 347 optimal weight: 5.9990 chunk 44 optimal weight: 0.9990 chunk 130 optimal weight: 0.0770 chunk 190 optimal weight: 1.9990 overall best weight: 0.9542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 222 ASN ** S 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 373 ASN ** 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 = 0.3889 r_free = 0.3889 target = 0.103949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.078813 restraints weight = 90837.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.081111 restraints weight = 43470.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.083131 restraints weight = 23841.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.083156 restraints weight = 18116.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.083217 restraints weight = 16099.061| |-----------------------------------------------------------------------------| r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.4039 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= 0.136 Angle : 0.688 13.150 41114 Z= 0.336 Chirality : 0.043 0.223 4607 Planarity : 0.004 0.054 5208 Dihedral : 4.879 57.571 4023 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 3.80 % Allowed : 25.28 % Favored : 70.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.15), residues: 3585 helix: 0.60 (0.11), residues: 2273 sheet: -1.60 (0.36), residues: 196 loop : -1.40 (0.20), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG N 52 TYR 0.028 0.001 TYR R 249 PHE 0.054 0.001 PHE T 252 TRP 0.025 0.001 TRP T 286 HIS 0.012 0.001 HIS C 159 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 (30472) covalent geometry : angle 0.68766 / 0.34 (41114) hydrogen bonds : bond 0.03548 / 2.35 ( 1644) hydrogen bonds : angle 4.59152 / 3.19 ( 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 531 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 407 time to evaluate : 1.185 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: 0.8933 (Cg_exo) cc_final: 0.8717 (Cg_endo) REVERT: G 276 MET cc_start: 0.8038 (ttp) cc_final: 0.7643 (ttp) REVERT: G 283 VAL cc_start: 0.9274 (OUTLIER) cc_final: 0.9060 (p) REVERT: G 303 PHE cc_start: 0.8619 (t80) cc_final: 0.8259 (t80) REVERT: C 161 ARG cc_start: 0.8168 (OUTLIER) cc_final: 0.7912 (ptt-90) REVERT: C 209 ASP cc_start: 0.9185 (t0) cc_final: 0.8870 (t0) REVERT: C 326 GLN cc_start: 0.9066 (tp40) cc_final: 0.8582 (tp-100) REVERT: A 187 TYR cc_start: 0.8783 (t80) cc_final: 0.8090 (t80) REVERT: A 205 GLU cc_start: 0.9100 (tm-30) cc_final: 0.8645 (tm-30) REVERT: B 57 LEU cc_start: 0.9020 (mm) cc_final: 0.8635 (mp) REVERT: B 71 PHE cc_start: 0.8321 (m-80) cc_final: 0.7993 (m-80) REVERT: B 98 PHE cc_start: 0.8121 (t80) cc_final: 0.7670 (t80) REVERT: E 289 TYR cc_start: 0.8517 (t80) cc_final: 0.7677 (t80) REVERT: E 303 PHE cc_start: 0.8438 (t80) cc_final: 0.8203 (t80) REVERT: E 329 MET cc_start: 0.7929 (tmm) cc_final: 0.7479 (tmm) REVERT: I 187 TYR cc_start: 0.8624 (t80) cc_final: 0.8406 (t80) REVERT: I 212 GLU cc_start: 0.8695 (tp30) cc_final: 0.8417 (tp30) REVERT: I 236 LEU cc_start: 0.8631 (mt) cc_final: 0.8319 (tt) REVERT: I 246 GLN cc_start: 0.8347 (tp40) cc_final: 0.8069 (tp40) REVERT: I 253 LEU cc_start: 0.8962 (OUTLIER) cc_final: 0.8579 (tt) REVERT: I 255 TRP cc_start: 0.7625 (OUTLIER) cc_final: 0.7006 (m100) REVERT: J 57 LEU cc_start: 0.8946 (mp) cc_final: 0.8660 (mp) REVERT: J 79 TYR cc_start: 0.6636 (t80) cc_final: 0.5917 (m-10) REVERT: K 172 ASN cc_start: 0.8351 (m-40) cc_final: 0.8106 (m-40) REVERT: K 209 ASP cc_start: 0.9051 (t0) cc_final: 0.8663 (t0) REVERT: K 243 MET cc_start: 0.7744 (ttm) cc_final: 0.6542 (ttt) REVERT: L 96 ASP cc_start: 0.7634 (m-30) cc_final: 0.7234 (m-30) REVERT: O 84 PRO cc_start: 0.8497 (Cg_exo) cc_final: 0.8172 (Cg_endo) REVERT: O 192 ILE cc_start: 0.8719 (OUTLIER) cc_final: 0.8490 (tt) REVERT: O 263 MET cc_start: 0.8473 (tpp) cc_final: 0.8185 (tpp) REVERT: O 276 MET cc_start: 0.8328 (ttp) cc_final: 0.7744 (ttp) REVERT: M 243 MET cc_start: 0.7899 (ttt) cc_final: 0.7691 (ttt) REVERT: M 311 ARG cc_start: 0.8975 (tpp80) cc_final: 0.8737 (mmm160) REVERT: N 79 TYR cc_start: 0.7462 (t80) cc_final: 0.6736 (m-10) REVERT: Q 240 MET cc_start: 0.9509 (ppp) cc_final: 0.9240 (tmm) REVERT: Q 345 MET cc_start: 0.8805 (mmm) cc_final: 0.8469 (mmm) REVERT: Q 381 LEU cc_start: 0.9270 (tp) cc_final: 0.8985 (tp) REVERT: Q 396 MET cc_start: 0.9478 (tmm) cc_final: 0.8895 (tmm) REVERT: R 91 MET cc_start: 0.7992 (tpp) cc_final: 0.7626 (tpp) REVERT: R 102 TYR cc_start: 0.8682 (m-80) cc_final: 0.8182 (m-80) REVERT: R 161 THR cc_start: 0.9080 (m) cc_final: 0.8811 (t) REVERT: R 183 MET cc_start: 0.9138 (tmm) cc_final: 0.8933 (tmm) REVERT: R 236 MET cc_start: 0.8616 (mpp) cc_final: 0.8352 (mpp) REVERT: R 301 LYS cc_start: 0.9606 (ptpt) cc_final: 0.9143 (tptp) REVERT: R 335 MET cc_start: 0.8678 (mmm) cc_final: 0.8447 (mmm) REVERT: S 107 ARG cc_start: 0.5889 (mmm160) cc_final: 0.4996 (tpp80) REVERT: S 240 MET cc_start: 0.9414 (tmm) cc_final: 0.9139 (tmm) REVERT: S 305 HIS cc_start: 0.9491 (t-90) cc_final: 0.9092 (t-90) REVERT: S 345 MET cc_start: 0.8815 (mmm) cc_final: 0.8559 (mmm) REVERT: S 396 MET cc_start: 0.9361 (tmm) cc_final: 0.9143 (tmm) REVERT: T 91 MET cc_start: 0.8172 (mmm) cc_final: 0.7769 (tpp) REVERT: T 102 TYR cc_start: 0.8659 (m-80) cc_final: 0.8027 (m-80) REVERT: T 161 THR cc_start: 0.9140 (m) cc_final: 0.8906 (t) REVERT: T 271 PHE cc_start: 0.8247 (OUTLIER) cc_final: 0.7767 (m-80) REVERT: T 391 LEU cc_start: 0.9234 (OUTLIER) cc_final: 0.9032 (mm) outliers start: 124 outliers final: 110 residues processed: 499 average time/residue: 0.1711 time to fit residues: 139.7197 Evaluate side-chains 511 residues out of total 3267 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 394 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain G residue 267 THR Chi-restraints excluded: chain G residue 271 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 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 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 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 C residue 314 LEU 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 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 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 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 250 LEU Chi-restraints excluded: chain I residue 253 LEU Chi-restraints excluded: chain I residue 255 TRP Chi-restraints excluded: chain I residue 300 LEU Chi-restraints excluded: chain I residue 331 LEU Chi-restraints excluded: chain J residue 49 ILE 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 159 HIS 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 271 THR 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 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 O residue 283 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 204 ILE Chi-restraints excluded: chain M residue 232 THR 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 315 HIS 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 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 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 182 LYS 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: 4.9990 chunk 98 optimal weight: 2.9990 chunk 279 optimal weight: 0.3980 chunk 13 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 205 optimal weight: 0.8980 chunk 198 optimal weight: 1.9990 chunk 176 optimal weight: 0.7980 chunk 319 optimal weight: 0.8980 chunk 36 optimal weight: 0.0980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 159 HIS ** I 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.104037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.078504 restraints weight = 91622.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.081322 restraints weight = 42556.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.083762 restraints weight = 22279.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.083386 restraints weight = 17424.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.083461 restraints weight = 15560.505| |-----------------------------------------------------------------------------| r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.4048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.102 30472 Z= 0.157 Angle : 0.781 59.121 41114 Z= 0.409 Chirality : 0.051 1.989 4607 Planarity : 0.004 0.060 5208 Dihedral : 4.879 57.586 4023 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 3.71 % Allowed : 25.59 % Favored : 70.70 % 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: -0.26 (0.15), residues: 3585 helix: 0.61 (0.11), residues: 2273 sheet: -1.60 (0.36), residues: 196 loop : -1.40 (0.20), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG S 107 TYR 0.024 0.001 TYR T 103 PHE 0.053 0.001 PHE T 252 TRP 0.021 0.001 TRP T 286 HIS 0.011 0.001 HIS C 159 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.16 (30472) covalent geometry : angle 0.78067 / 0.41 (41114) hydrogen bonds : bond 0.03547 / 2.35 ( 1644) hydrogen bonds : angle 4.59140 / 3.20 ( 4785) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5581.73 seconds wall clock time: 97 minutes 30.88 seconds (5850.88 seconds total)