Starting phenix.real_space_refine on Sat Aug 8 13:39:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ujw_64228/08_2026/9ujw_64228.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ujw_64228/08_2026/9ujw_64228.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ujw_64228/08_2026/9ujw_64228.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ujw_64228/08_2026/9ujw_64228.map" model { file = "/net/cci-nas-00/data/ceres_data/9ujw_64228/08_2026/9ujw_64228.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ujw_64228/08_2026/9ujw_64228.cif" } resolution = 4.21 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= 0.003 sd= 0.042 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 120 5.16 5 C 17613 2.51 5 N 4877 2.21 5 O 5142 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 27752 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2288 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 10, 'TRANS': 278} Chain breaks: 2 Chain: "B" Number of atoms: 2365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2365 Classifications: {'peptide': 298} Link IDs: {'PTRANS': 12, 'TRANS': 285} Chain breaks: 1 Chain: "C" Number of atoms: 2334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2334 Classifications: {'peptide': 294} Link IDs: {'PTRANS': 11, 'TRANS': 282} Chain breaks: 1 Chain: "D" Number of atoms: 2342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2342 Classifications: {'peptide': 295} Link IDs: {'PTRANS': 11, 'TRANS': 283} Chain breaks: 1 Chain: "E" Number of atoms: 2341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2341 Classifications: {'peptide': 295} Link IDs: {'PTRANS': 11, 'TRANS': 283} Chain breaks: 1 Chain: "F" Number of atoms: 2205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2205 Classifications: {'peptide': 277} Link IDs: {'PTRANS': 11, 'TRANS': 265} Chain breaks: 2 Chain: "a" Number of atoms: 2294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2294 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 10, 'TRANS': 278} Chain breaks: 2 Chain: "b" Number of atoms: 2350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2350 Classifications: {'peptide': 296} Link IDs: {'PTRANS': 11, 'TRANS': 284} Chain breaks: 1 Chain: "c" Number of atoms: 2343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2343 Classifications: {'peptide': 295} Link IDs: {'PTRANS': 11, 'TRANS': 283} Chain breaks: 1 Chain: "d" Number of atoms: 2334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2334 Classifications: {'peptide': 294} Link IDs: {'PTRANS': 11, 'TRANS': 282} Chain breaks: 1 Chain: "e" Number of atoms: 2343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2343 Classifications: {'peptide': 295} Link IDs: {'PTRANS': 11, 'TRANS': 283} Chain breaks: 1 Chain: "f" Number of atoms: 2213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2213 Classifications: {'peptide': 278} Link IDs: {'PTRANS': 11, 'TRANS': 266} Chain breaks: 2 Time building chain proxies: 6.25, per 1000 atoms: 0.23 Number of scatterers: 27752 At special positions: 0 Unit cell: (203.816, 150.07, 114.472, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 120 16.00 O 5142 8.00 N 4877 7.00 C 17613 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: 2.25 Conformation dependent library (CDL) restraints added in 1.1 seconds 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6634 Finding SS restraints... Secondary structure from input PDB file: 149 helices and 35 sheets defined 47.5% alpha, 12.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'A' and resid 18 through 23 Processing helix chain 'A' and resid 53 through 63 Processing helix chain 'A' and resid 76 through 88 Processing helix chain 'A' and resid 102 through 107 Processing helix chain 'A' and resid 126 through 133 Processing helix chain 'A' and resid 142 through 146 Processing helix chain 'A' and resid 153 through 160 Processing helix chain 'A' and resid 225 through 233 removed outlier: 4.143A pdb=" N VAL A 231 " --> pdb=" O ASN A 227 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N LYS A 232 " --> pdb=" O ILE A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 262 Processing helix chain 'A' and resid 269 through 282 Processing helix chain 'A' and resid 286 through 294 Processing helix chain 'A' and resid 299 through 315 removed outlier: 4.062A pdb=" N ALA A 304 " --> pdb=" O GLU A 300 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N THR A 305 " --> pdb=" O LEU A 301 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA A 307 " --> pdb=" O ARG A 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 23 Processing helix chain 'B' and resid 50 through 64 Processing helix chain 'B' and resid 76 through 89 removed outlier: 3.717A pdb=" N HIS B 80 " --> pdb=" O GLY B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 107 Processing helix chain 'B' and resid 126 through 134 Processing helix chain 'B' and resid 152 through 160 Processing helix chain 'B' and resid 204 through 209 removed outlier: 4.265A pdb=" N MET B 208 " --> pdb=" O ASN B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 233 Processing helix chain 'B' and resid 238 through 261 removed outlier: 3.754A pdb=" N GLU B 243 " --> pdb=" O ALA B 239 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASN B 261 " --> pdb=" O GLN B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 284 Processing helix chain 'B' and resid 286 through 294 removed outlier: 3.822A pdb=" N PHE B 294 " --> pdb=" O PHE B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 314 removed outlier: 3.693A pdb=" N ALA B 304 " --> pdb=" O GLU B 300 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N THR B 305 " --> pdb=" O LEU B 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 23 Processing helix chain 'C' and resid 50 through 64 Processing helix chain 'C' and resid 78 through 88 Processing helix chain 'C' and resid 102 through 107 Processing helix chain 'C' and resid 126 through 134 Processing helix chain 'C' and resid 147 through 159 removed outlier: 4.357A pdb=" N VAL C 153 " --> pdb=" O ASP C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 209 removed outlier: 3.751A pdb=" N MET C 208 " --> pdb=" O ASN C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 233 removed outlier: 3.536A pdb=" N VAL C 229 " --> pdb=" O GLU C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 262 removed outlier: 3.821A pdb=" N VAL C 251 " --> pdb=" O LYS C 247 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA C 252 " --> pdb=" O MET C 248 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG C 256 " --> pdb=" O ALA C 252 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN C 257 " --> pdb=" O ASP C 253 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ALA C 258 " --> pdb=" O MET C 254 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N PHE C 259 " --> pdb=" O THR C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 279 Processing helix chain 'C' and resid 285 through 290 Processing helix chain 'C' and resid 299 through 315 removed outlier: 4.741A pdb=" N ALA C 304 " --> pdb=" O GLU C 300 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N THR C 305 " --> pdb=" O LEU C 301 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ALA C 313 " --> pdb=" O PHE C 309 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE C 314 " --> pdb=" O TYR C 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 22 Processing helix chain 'D' and resid 50 through 63 Processing helix chain 'D' and resid 76 through 88 Processing helix chain 'D' and resid 126 through 134 Processing helix chain 'D' and resid 147 through 159 removed outlier: 4.400A pdb=" N VAL D 153 " --> pdb=" O ASP D 149 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL D 157 " --> pdb=" O VAL D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 210 Processing helix chain 'D' and resid 221 through 233 Processing helix chain 'D' and resid 234 through 237 Processing helix chain 'D' and resid 238 through 262 removed outlier: 4.156A pdb=" N GLU D 243 " --> pdb=" O ALA D 239 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ILE D 244 " --> pdb=" O GLU D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 284 Processing helix chain 'D' and resid 285 through 294 Processing helix chain 'D' and resid 299 through 301 No H-bonds generated for 'chain 'D' and resid 299 through 301' Processing helix chain 'D' and resid 302 through 315 Processing helix chain 'E' and resid 18 through 23 Processing helix chain 'E' and resid 50 through 63 Processing helix chain 'E' and resid 76 through 88 Processing helix chain 'E' and resid 102 through 107 Processing helix chain 'E' and resid 126 through 134 Processing helix chain 'E' and resid 150 through 160 removed outlier: 4.125A pdb=" N ILE E 154 " --> pdb=" O VAL E 150 " (cutoff:3.500A) Processing helix chain 'E' and resid 221 through 231 Processing helix chain 'E' and resid 238 through 262 removed outlier: 3.540A pdb=" N ARG E 242 " --> pdb=" O ASN E 238 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N GLU E 243 " --> pdb=" O ALA E 239 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ILE E 244 " --> pdb=" O GLU E 240 " (cutoff:3.500A) Processing helix chain 'E' and resid 269 through 284 Processing helix chain 'E' and resid 286 through 294 Processing helix chain 'E' and resid 302 through 315 Processing helix chain 'F' and resid 18 through 23 Processing helix chain 'F' and resid 55 through 63 Processing helix chain 'F' and resid 76 through 89 Processing helix chain 'F' and resid 102 through 108 Processing helix chain 'F' and resid 126 through 133 Processing helix chain 'F' and resid 149 through 159 removed outlier: 4.171A pdb=" N ARG F 156 " --> pdb=" O PHE F 152 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N VAL F 157 " --> pdb=" O VAL F 153 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU F 159 " --> pdb=" O GLN F 155 " (cutoff:3.500A) Processing helix chain 'F' and resid 221 through 233 Processing helix chain 'F' and resid 239 through 261 removed outlier: 4.459A pdb=" N GLU F 243 " --> pdb=" O ALA F 239 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N ILE F 244 " --> pdb=" O GLU F 240 " (cutoff:3.500A) Processing helix chain 'F' and resid 269 through 284 Processing helix chain 'F' and resid 285 through 294 removed outlier: 4.021A pdb=" N PHE F 294 " --> pdb=" O PHE F 290 " (cutoff:3.500A) Processing helix chain 'F' and resid 295 through 298 Processing helix chain 'F' and resid 299 through 301 No H-bonds generated for 'chain 'F' and resid 299 through 301' Processing helix chain 'F' and resid 302 through 315 Processing helix chain 'a' and resid 18 through 23 Processing helix chain 'a' and resid 53 through 63 Processing helix chain 'a' and resid 76 through 88 removed outlier: 3.628A pdb=" N HIS a 80 " --> pdb=" O GLY a 76 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ILE a 81 " --> pdb=" O LYS a 77 " (cutoff:3.500A) Processing helix chain 'a' and resid 102 through 107 Processing helix chain 'a' and resid 126 through 133 Processing helix chain 'a' and resid 152 through 160 removed outlier: 3.801A pdb=" N ARG a 156 " --> pdb=" O PHE a 152 " (cutoff:3.500A) Processing helix chain 'a' and resid 206 through 211 Processing helix chain 'a' and resid 224 through 231 removed outlier: 3.846A pdb=" N ILE a 228 " --> pdb=" O ASN a 224 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N VAL a 231 " --> pdb=" O ASN a 227 " (cutoff:3.500A) Processing helix chain 'a' and resid 238 through 261 Processing helix chain 'a' and resid 269 through 283 removed outlier: 4.053A pdb=" N ALA a 281 " --> pdb=" O ALA a 277 " (cutoff:3.500A) Processing helix chain 'a' and resid 286 through 294 Processing helix chain 'a' and resid 295 through 298 Processing helix chain 'a' and resid 299 through 315 removed outlier: 3.877A pdb=" N ALA a 304 " --> pdb=" O GLU a 300 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N THR a 305 " --> pdb=" O LEU a 301 " (cutoff:3.500A) Processing helix chain 'b' and resid 18 through 23 Processing helix chain 'b' and resid 50 through 63 Processing helix chain 'b' and resid 76 through 89 Processing helix chain 'b' and resid 102 through 107 Processing helix chain 'b' and resid 126 through 133 Processing helix chain 'b' and resid 152 through 160 Processing helix chain 'b' and resid 204 through 209 Processing helix chain 'b' and resid 221 through 232 Processing helix chain 'b' and resid 238 through 262 removed outlier: 3.779A pdb=" N VAL b 251 " --> pdb=" O LYS b 247 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA b 252 " --> pdb=" O MET b 248 " (cutoff:3.500A) Processing helix chain 'b' and resid 271 through 284 removed outlier: 3.845A pdb=" N ALA b 281 " --> pdb=" O ALA b 277 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ILE b 282 " --> pdb=" O GLU b 278 " (cutoff:3.500A) Processing helix chain 'b' and resid 286 through 294 Processing helix chain 'b' and resid 295 through 298 Processing helix chain 'b' and resid 299 through 315 removed outlier: 3.575A pdb=" N THR b 305 " --> pdb=" O LEU b 301 " (cutoff:3.500A) Processing helix chain 'c' and resid 18 through 23 Processing helix chain 'c' and resid 50 through 64 Processing helix chain 'c' and resid 76 through 88 Processing helix chain 'c' and resid 102 through 107 removed outlier: 3.666A pdb=" N LEU c 106 " --> pdb=" O SER c 102 " (cutoff:3.500A) Processing helix chain 'c' and resid 126 through 134 Processing helix chain 'c' and resid 147 through 159 removed outlier: 4.738A pdb=" N VAL c 153 " --> pdb=" O ASP c 149 " (cutoff:3.500A) Processing helix chain 'c' and resid 204 through 210 removed outlier: 3.565A pdb=" N MET c 208 " --> pdb=" O ASN c 204 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ARG c 210 " --> pdb=" O ALA c 206 " (cutoff:3.500A) Processing helix chain 'c' and resid 221 through 233 removed outlier: 3.812A pdb=" N ASN c 227 " --> pdb=" O ASP c 223 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ILE c 228 " --> pdb=" O ASN c 224 " (cutoff:3.500A) Processing helix chain 'c' and resid 241 through 262 removed outlier: 3.808A pdb=" N VAL c 251 " --> pdb=" O LYS c 247 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA c 252 " --> pdb=" O MET c 248 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N THR c 255 " --> pdb=" O VAL c 251 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N ARG c 256 " --> pdb=" O ALA c 252 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N GLN c 257 " --> pdb=" O ASP c 253 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ALA c 258 " --> pdb=" O MET c 254 " (cutoff:3.500A) Processing helix chain 'c' and resid 269 through 284 removed outlier: 3.762A pdb=" N ILE c 274 " --> pdb=" O PRO c 270 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR c 275 " --> pdb=" O ARG c 271 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N ALA c 281 " --> pdb=" O ALA c 277 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ILE c 282 " --> pdb=" O GLU c 278 " (cutoff:3.500A) Processing helix chain 'c' and resid 286 through 294 removed outlier: 3.821A pdb=" N ARG c 291 " --> pdb=" O GLY c 287 " (cutoff:3.500A) Processing helix chain 'c' and resid 295 through 298 Processing helix chain 'c' and resid 299 through 315 removed outlier: 4.110A pdb=" N ALA c 304 " --> pdb=" O GLU c 300 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N THR c 305 " --> pdb=" O LEU c 301 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARG c 312 " --> pdb=" O GLU c 308 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ALA c 313 " --> pdb=" O PHE c 309 " (cutoff:3.500A) Processing helix chain 'd' and resid 18 through 23 Processing helix chain 'd' and resid 50 through 63 Processing helix chain 'd' and resid 76 through 88 Processing helix chain 'd' and resid 126 through 134 Processing helix chain 'd' and resid 152 through 159 removed outlier: 3.510A pdb=" N VAL d 157 " --> pdb=" O VAL d 153 " (cutoff:3.500A) Processing helix chain 'd' and resid 206 through 210 Processing helix chain 'd' and resid 221 through 232 Processing helix chain 'd' and resid 238 through 240 No H-bonds generated for 'chain 'd' and resid 238 through 240' Processing helix chain 'd' and resid 241 through 262 removed outlier: 3.891A pdb=" N LYS d 247 " --> pdb=" O GLU d 243 " (cutoff:3.500A) Processing helix chain 'd' and resid 269 through 284 Processing helix chain 'd' and resid 285 through 294 removed outlier: 3.536A pdb=" N ALA d 289 " --> pdb=" O ASP d 285 " (cutoff:3.500A) Processing helix chain 'd' and resid 302 through 315 Processing helix chain 'e' and resid 18 through 22 Processing helix chain 'e' and resid 50 through 63 Processing helix chain 'e' and resid 76 through 88 Processing helix chain 'e' and resid 102 through 107 Processing helix chain 'e' and resid 126 through 134 Processing helix chain 'e' and resid 150 through 160 removed outlier: 4.204A pdb=" N ILE e 154 " --> pdb=" O VAL e 150 " (cutoff:3.500A) Processing helix chain 'e' and resid 221 through 231 Processing helix chain 'e' and resid 238 through 261 Processing helix chain 'e' and resid 269 through 284 Processing helix chain 'e' and resid 285 through 294 Processing helix chain 'e' and resid 301 through 315 removed outlier: 4.337A pdb=" N THR e 305 " --> pdb=" O LEU e 301 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE e 309 " --> pdb=" O THR e 305 " (cutoff:3.500A) Processing helix chain 'f' and resid 18 through 23 Processing helix chain 'f' and resid 55 through 63 Processing helix chain 'f' and resid 76 through 89 Processing helix chain 'f' and resid 102 through 108 Processing helix chain 'f' and resid 126 through 133 Processing helix chain 'f' and resid 148 through 159 removed outlier: 3.939A pdb=" N GLU f 159 " --> pdb=" O GLN f 155 " (cutoff:3.500A) Processing helix chain 'f' and resid 205 through 210 removed outlier: 3.786A pdb=" N ARG f 210 " --> pdb=" O ALA f 206 " (cutoff:3.500A) Processing helix chain 'f' and resid 221 through 233 Processing helix chain 'f' and resid 239 through 261 removed outlier: 4.222A pdb=" N GLU f 243 " --> pdb=" O ALA f 239 " (cutoff:3.500A) Processing helix chain 'f' and resid 269 through 284 Processing helix chain 'f' and resid 285 through 294 removed outlier: 4.100A pdb=" N PHE f 294 " --> pdb=" O PHE f 290 " (cutoff:3.500A) Processing helix chain 'f' and resid 295 through 298 removed outlier: 4.090A pdb=" N CYS f 298 " --> pdb=" O LEU f 295 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 295 through 298' Processing helix chain 'f' and resid 299 through 301 No H-bonds generated for 'chain 'f' and resid 299 through 301' Processing helix chain 'f' and resid 302 through 314 Processing sheet with id=AA1, first strand: chain 'A' and resid 14 through 17 Processing sheet with id=AA2, first strand: chain 'A' and resid 92 through 96 removed outlier: 6.542A pdb=" N VAL A 93 " --> pdb=" O VAL A 139 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N ASP A 141 " --> pdb=" O VAL A 93 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N VAL A 95 " --> pdb=" O ASP A 141 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N VAL A 67 " --> pdb=" O LEU A 181 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N MET A 68 " --> pdb=" O THR A 215 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 108 through 115 Processing sheet with id=AA4, first strand: chain 'B' and resid 14 through 17 Processing sheet with id=AA5, first strand: chain 'B' and resid 92 through 95 removed outlier: 6.081A pdb=" N LEU B 138 " --> pdb=" O PHE B 182 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N THR B 184 " --> pdb=" O LEU B 138 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N PHE B 140 " --> pdb=" O THR B 184 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N VAL B 67 " --> pdb=" O ALA B 183 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N ALA B 185 " --> pdb=" O VAL B 67 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N VAL B 69 " --> pdb=" O ALA B 185 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N MET B 68 " --> pdb=" O THR B 215 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 108 through 112 Processing sheet with id=AA7, first strand: chain 'C' and resid 14 through 17 Processing sheet with id=AA8, first strand: chain 'C' and resid 92 through 96 removed outlier: 3.968A pdb=" N VAL C 67 " --> pdb=" O LEU C 181 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N MET C 68 " --> pdb=" O THR C 215 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 108 through 115 Processing sheet with id=AB1, first strand: chain 'C' and resid 164 through 165 Processing sheet with id=AB2, first strand: chain 'D' and resid 14 through 17 Processing sheet with id=AB3, first strand: chain 'D' and resid 92 through 96 removed outlier: 6.632A pdb=" N VAL D 93 " --> pdb=" O VAL D 139 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N ASP D 141 " --> pdb=" O VAL D 93 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N VAL D 95 " --> pdb=" O ASP D 141 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N LEU D 138 " --> pdb=" O PHE D 182 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N THR D 184 " --> pdb=" O LEU D 138 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N PHE D 140 " --> pdb=" O THR D 184 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N VAL D 67 " --> pdb=" O ALA D 183 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N ALA D 185 " --> pdb=" O VAL D 67 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N VAL D 69 " --> pdb=" O ALA D 185 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N MET D 68 " --> pdb=" O THR D 215 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N LEU D 217 " --> pdb=" O MET D 68 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N SER D 70 " --> pdb=" O LEU D 217 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'D' and resid 108 through 115 Processing sheet with id=AB5, first strand: chain 'E' and resid 14 through 17 Processing sheet with id=AB6, first strand: chain 'E' and resid 93 through 96 removed outlier: 6.381A pdb=" N VAL E 93 " --> pdb=" O VAL E 139 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N ASP E 141 " --> pdb=" O VAL E 93 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N VAL E 95 " --> pdb=" O ASP E 141 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N VAL E 67 " --> pdb=" O LEU E 181 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N MET E 68 " --> pdb=" O THR E 215 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N LEU E 217 " --> pdb=" O MET E 68 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N SER E 70 " --> pdb=" O LEU E 217 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 108 through 115 Processing sheet with id=AB8, first strand: chain 'F' and resid 14 through 17 Processing sheet with id=AB9, first strand: chain 'F' and resid 92 through 96 removed outlier: 6.350A pdb=" N LEU F 138 " --> pdb=" O PHE F 182 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N THR F 184 " --> pdb=" O LEU F 138 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N PHE F 140 " --> pdb=" O THR F 184 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N VAL F 67 " --> pdb=" O LEU F 181 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'a' and resid 14 through 17 Processing sheet with id=AC2, first strand: chain 'a' and resid 92 through 96 removed outlier: 6.578A pdb=" N VAL a 67 " --> pdb=" O ALA a 183 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N ALA a 185 " --> pdb=" O VAL a 67 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N VAL a 69 " --> pdb=" O ALA a 185 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N MET a 68 " --> pdb=" O THR a 215 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N LEU a 217 " --> pdb=" O MET a 68 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N SER a 70 " --> pdb=" O LEU a 217 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'a' and resid 108 through 115 Processing sheet with id=AC4, first strand: chain 'b' and resid 14 through 17 Processing sheet with id=AC5, first strand: chain 'b' and resid 92 through 96 removed outlier: 6.319A pdb=" N VAL b 93 " --> pdb=" O VAL b 139 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N ASP b 141 " --> pdb=" O VAL b 93 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N VAL b 95 " --> pdb=" O ASP b 141 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N LEU b 138 " --> pdb=" O PHE b 182 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N THR b 184 " --> pdb=" O LEU b 138 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N PHE b 140 " --> pdb=" O THR b 184 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N VAL b 67 " --> pdb=" O ALA b 183 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N MET b 68 " --> pdb=" O THR b 215 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N LEU b 217 " --> pdb=" O MET b 68 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N SER b 70 " --> pdb=" O LEU b 217 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'b' and resid 108 through 112 Processing sheet with id=AC7, first strand: chain 'c' and resid 14 through 17 Processing sheet with id=AC8, first strand: chain 'c' and resid 92 through 96 removed outlier: 4.070A pdb=" N VAL c 67 " --> pdb=" O LEU c 181 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'c' and resid 108 through 115 Processing sheet with id=AD1, first strand: chain 'd' and resid 14 through 17 Processing sheet with id=AD2, first strand: chain 'd' and resid 92 through 96 removed outlier: 6.593A pdb=" N VAL d 93 " --> pdb=" O VAL d 139 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N ASP d 141 " --> pdb=" O VAL d 93 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N VAL d 95 " --> pdb=" O ASP d 141 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N LEU d 138 " --> pdb=" O PHE d 182 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N THR d 184 " --> pdb=" O LEU d 138 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N PHE d 140 " --> pdb=" O THR d 184 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N VAL d 67 " --> pdb=" O ALA d 183 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'd' and resid 108 through 114 Processing sheet with id=AD4, first strand: chain 'e' and resid 14 through 17 Processing sheet with id=AD5, first strand: chain 'e' and resid 93 through 96 removed outlier: 6.241A pdb=" N VAL e 93 " --> pdb=" O VAL e 139 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N ASP e 141 " --> pdb=" O VAL e 93 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N VAL e 95 " --> pdb=" O ASP e 141 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N LEU e 138 " --> pdb=" O PHE e 182 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N THR e 184 " --> pdb=" O LEU e 138 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N PHE e 140 " --> pdb=" O THR e 184 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL e 67 " --> pdb=" O LEU e 181 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'e' and resid 108 through 115 Processing sheet with id=AD7, first strand: chain 'f' and resid 14 through 17 Processing sheet with id=AD8, first strand: chain 'f' and resid 92 through 96 removed outlier: 6.301A pdb=" N LEU f 138 " --> pdb=" O PHE f 182 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N THR f 184 " --> pdb=" O LEU f 138 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N PHE f 140 " --> pdb=" O THR f 184 " (cutoff:3.500A) 1188 hydrogen bonds defined for protein. 3471 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.69 Time building geometry restraints manager: 2.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9337 1.34 - 1.46: 5784 1.46 - 1.58: 12992 1.58 - 1.70: 1 1.70 - 1.82: 216 Bond restraints: 28330 Sorted by residual: bond pdb=" N ASN b 218 " pdb=" CA ASN b 218 " ideal model delta sigma weight residual 1.460 1.487 -0.027 8.20e-03 1.49e+04 1.08e+01 bond pdb=" N LEU c 220 " pdb=" CA LEU c 220 " ideal model delta sigma weight residual 1.454 1.487 -0.033 1.14e-02 7.69e+03 8.33e+00 bond pdb=" N TYR b 219 " pdb=" CA TYR b 219 " ideal model delta sigma weight residual 1.455 1.490 -0.035 1.25e-02 6.40e+03 8.01e+00 bond pdb=" N TYR B 219 " pdb=" CA TYR B 219 " ideal model delta sigma weight residual 1.455 1.489 -0.034 1.21e-02 6.83e+03 7.91e+00 bond pdb=" N TYR c 219 " pdb=" CA TYR c 219 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.29e-02 6.01e+03 6.52e+00 ... (remaining 28325 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.17: 37937 2.17 - 4.34: 505 4.34 - 6.50: 60 6.50 - 8.67: 17 8.67 - 10.84: 3 Bond angle restraints: 38522 Sorted by residual: angle pdb=" C LEU C 167 " pdb=" CA LEU C 167 " pdb=" CB LEU C 167 " ideal model delta sigma weight residual 116.54 110.46 6.08 1.15e+00 7.56e-01 2.80e+01 angle pdb=" CA PRO a 129 " pdb=" N PRO a 129 " pdb=" CD PRO a 129 " ideal model delta sigma weight residual 112.00 105.01 6.99 1.40e+00 5.10e-01 2.49e+01 angle pdb=" C ASP d 253 " pdb=" N MET d 254 " pdb=" CA MET d 254 " ideal model delta sigma weight residual 121.58 113.36 8.22 1.95e+00 2.63e-01 1.78e+01 angle pdb=" C ASP D 253 " pdb=" N MET D 254 " pdb=" CA MET D 254 " ideal model delta sigma weight residual 121.14 114.60 6.54 1.75e+00 3.27e-01 1.40e+01 angle pdb=" CA LYS A 297 " pdb=" CB LYS A 297 " pdb=" CG LYS A 297 " ideal model delta sigma weight residual 114.10 121.39 -7.29 2.00e+00 2.50e-01 1.33e+01 ... (remaining 38517 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 15213 17.68 - 35.35: 1321 35.35 - 53.03: 241 53.03 - 70.70: 54 70.70 - 88.38: 31 Dihedral angle restraints: 16860 sinusoidal: 6640 harmonic: 10220 Sorted by residual: dihedral pdb=" CA MET d 151 " pdb=" C MET d 151 " pdb=" N PHE d 152 " pdb=" CA PHE d 152 " ideal model delta harmonic sigma weight residual 180.00 158.22 21.78 0 5.00e+00 4.00e-02 1.90e+01 dihedral pdb=" CA TYR d 63 " pdb=" C TYR d 63 " pdb=" N ASN d 64 " pdb=" CA ASN d 64 " ideal model delta harmonic sigma weight residual 180.00 158.59 21.41 0 5.00e+00 4.00e-02 1.83e+01 dihedral pdb=" CA GLU B 317 " pdb=" C GLU B 317 " pdb=" N LEU B 318 " pdb=" CA LEU B 318 " ideal model delta harmonic sigma weight residual -180.00 -160.89 -19.11 0 5.00e+00 4.00e-02 1.46e+01 ... (remaining 16857 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 3142 0.042 - 0.085: 966 0.085 - 0.127: 252 0.127 - 0.169: 19 0.169 - 0.211: 4 Chirality restraints: 4383 Sorted by residual: chirality pdb=" CA PRO a 129 " pdb=" N PRO a 129 " pdb=" C PRO a 129 " pdb=" CB PRO a 129 " both_signs ideal model delta sigma weight residual False 2.72 2.51 0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CB ILE B 154 " pdb=" CA ILE B 154 " pdb=" CG1 ILE B 154 " pdb=" CG2 ILE B 154 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CA MET f 151 " pdb=" N MET f 151 " pdb=" C MET f 151 " pdb=" CB MET f 151 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.09e-01 ... (remaining 4380 not shown) Planarity restraints: 5016 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU a 128 " 0.062 5.00e-02 4.00e+02 9.02e-02 1.30e+01 pdb=" N PRO a 129 " -0.156 5.00e-02 4.00e+02 pdb=" CA PRO a 129 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO a 129 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 130 " 0.017 2.00e-02 2.50e+03 1.62e-02 6.55e+00 pdb=" CG TRP E 130 " -0.044 2.00e-02 2.50e+03 pdb=" CD1 TRP E 130 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP E 130 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP E 130 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP E 130 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP E 130 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 130 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 130 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP E 130 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL F 40 " -0.042 5.00e-02 4.00e+02 6.38e-02 6.51e+00 pdb=" N PRO F 41 " 0.110 5.00e-02 4.00e+02 pdb=" CA PRO F 41 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO F 41 " -0.035 5.00e-02 4.00e+02 ... (remaining 5013 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1826 2.73 - 3.27: 29388 3.27 - 3.82: 46374 3.82 - 4.36: 52712 4.36 - 4.90: 86983 Nonbonded interactions: 217283 Sorted by model distance: nonbonded pdb=" OD1 ASN B 96 " pdb=" N LEU B 97 " model vdw 2.191 3.120 nonbonded pdb=" O ALA A 252 " pdb=" OG1 THR A 255 " model vdw 2.198 3.040 nonbonded pdb=" O ALA d 307 " pdb=" NE2 GLN d 311 " model vdw 2.198 3.120 nonbonded pdb=" O SER F 269 " pdb=" OG1 THR F 272 " model vdw 2.200 3.040 nonbonded pdb=" O ASN B 10 " pdb=" OH TYR B 33 " model vdw 2.201 3.040 ... (remaining 217278 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 10 through 109 or resid 124 through 187 or resid 205 throu \ gh 315)) selection = (chain 'B' and (resid 10 through 109 or resid 124 through 187 or resid 205 throu \ gh 218 or resid 224 through 315)) selection = (chain 'C' and (resid 10 through 109 or resid 124 through 187 or resid 205 throu \ gh 218 or resid 224 through 315)) selection = (chain 'D' and (resid 10 through 109 or resid 124 through 187 or resid 205 throu \ gh 218 or resid 224 through 315)) selection = (chain 'E' and (resid 10 through 109 or resid 124 through 187 or resid 205 throu \ gh 218 or resid 224 through 315)) selection = (chain 'F' and (resid 10 through 187 or resid 205 through 218 or resid 224 throu \ gh 315)) selection = (chain 'a' and (resid 10 through 109 or resid 124 through 187 or resid 205 throu \ gh 218 or resid 224 through 315)) selection = (chain 'b' and (resid 10 through 109 or resid 124 through 187 or resid 205 throu \ gh 218 or resid 224 through 315)) selection = (chain 'c' and (resid 10 through 109 or resid 124 through 187 or resid 205 throu \ gh 218 or resid 224 through 315)) selection = (chain 'd' and (resid 10 through 109 or resid 124 through 187 or resid 205 throu \ gh 218 or resid 224 through 315)) selection = (chain 'e' and (resid 10 through 109 or resid 124 through 187 or resid 205 throu \ gh 218 or resid 224 through 315)) selection = (chain 'f' and (resid 10 through 187 or resid 205 through 218 or resid 224 throu \ gh 315)) } 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: 4.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.620 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 23.550 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.040 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:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6804 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.092 28330 Z= 0.147 Angle : 0.608 10.838 38522 Z= 0.333 Chirality : 0.042 0.211 4383 Planarity : 0.004 0.090 5016 Dihedral : 14.143 88.376 10226 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 14.92 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.44 % Favored : 94.45 % Rotamer: Outliers : 0.34 % Allowed : 0.37 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.15), residues: 3439 helix: 0.65 (0.14), residues: 1477 sheet: -0.05 (0.23), residues: 491 loop : -0.99 (0.17), residues: 1471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG d 210 TYR 0.019 0.001 TYR b 219 PHE 0.037 0.002 PHE f 152 TRP 0.044 0.002 TRP E 130 HIS 0.005 0.000 HIS f 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.15 (28330) covalent geometry : angle 0.60809 / 0.33 (38522) hydrogen bonds : bond 0.13681 / 9.36 ( 1188) hydrogen bonds : angle 6.63494 / 4.80 ( 3471) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 926 residues out of total 2985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 916 time to evaluate : 0.975 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: 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: 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: A 208 MET cc_start: 0.8290 (mmp) cc_final: 0.8076 (mmp) REVERT: B 28 MET cc_start: 0.4758 (ptm) cc_final: 0.4546 (ptm) REVERT: B 80 HIS cc_start: 0.7581 (m90) cc_final: 0.7079 (m90) REVERT: B 98 ASP cc_start: 0.7721 (p0) cc_final: 0.7203 (p0) REVERT: B 100 HIS cc_start: 0.7792 (m90) cc_final: 0.7512 (m90) REVERT: B 103 ARG cc_start: 0.8504 (ttm-80) cc_final: 0.8216 (ttm-80) REVERT: B 168 ASP cc_start: 0.7548 (p0) cc_final: 0.7155 (p0) REVERT: B 211 TRP cc_start: 0.7048 (m100) cc_final: 0.6647 (m100) REVERT: B 232 LYS cc_start: 0.9209 (tptt) cc_final: 0.8702 (tptt) REVERT: C 68 MET cc_start: 0.6839 (ttp) cc_final: 0.6448 (ttp) REVERT: C 105 ASP cc_start: 0.8483 (m-30) cc_final: 0.8244 (m-30) REVERT: C 151 MET cc_start: 0.8069 (mmp) cc_final: 0.7656 (mmt) REVERT: C 155 GLN cc_start: 0.8489 (OUTLIER) cc_final: 0.8128 (mp-120) REVERT: C 303 ARG cc_start: 0.8880 (mmm-85) cc_final: 0.8614 (mmm-85) REVERT: C 309 PHE cc_start: 0.8493 (m-80) cc_final: 0.8291 (m-80) REVERT: C 310 TYR cc_start: 0.7943 (t80) cc_final: 0.7213 (t80) REVERT: C 314 PHE cc_start: 0.8156 (m-10) cc_final: 0.7914 (m-10) REVERT: D 29 MET cc_start: 0.6275 (mmp) cc_final: 0.5922 (mmp) REVERT: D 87 ARG cc_start: 0.8120 (mtp85) cc_final: 0.7457 (mtp180) REVERT: D 151 MET cc_start: 0.8103 (tpt) cc_final: 0.7517 (tpt) REVERT: D 155 GLN cc_start: 0.8699 (mt0) cc_final: 0.8303 (mt0) REVERT: D 244 ILE cc_start: 0.8492 (mt) cc_final: 0.7873 (mt) REVERT: D 248 MET cc_start: 0.8181 (mmp) cc_final: 0.7978 (mmp) REVERT: E 10 ASN cc_start: 0.8810 (m-40) cc_final: 0.8538 (m-40) REVERT: E 127 ILE cc_start: 0.7381 (mm) cc_final: 0.7113 (mm) REVERT: E 134 HIS cc_start: 0.7126 (m170) cc_final: 0.6880 (m170) REVERT: E 181 LEU cc_start: 0.7821 (tp) cc_final: 0.7546 (tp) REVERT: E 244 ILE cc_start: 0.9512 (mp) cc_final: 0.8999 (mp) REVERT: E 297 LYS cc_start: 0.8422 (mtmm) cc_final: 0.7954 (mtmm) REVERT: E 309 PHE cc_start: 0.9126 (m-10) cc_final: 0.8875 (m-10) REVERT: F 29 MET cc_start: 0.6714 (mmp) cc_final: 0.6392 (mmp) REVERT: F 68 MET cc_start: 0.5549 (ppp) cc_final: 0.5285 (ppp) REVERT: F 73 HIS cc_start: 0.7449 (t-90) cc_final: 0.7175 (t-90) REVERT: F 80 HIS cc_start: 0.8305 (m90) cc_final: 0.8086 (m90) REVERT: F 87 ARG cc_start: 0.7840 (mmp80) cc_final: 0.7526 (mmp80) REVERT: F 151 MET cc_start: 0.8558 (mtm) cc_final: 0.8301 (mtm) REVERT: F 176 HIS cc_start: 0.8347 (t-170) cc_final: 0.7819 (t-170) REVERT: F 214 VAL cc_start: 0.7311 (t) cc_final: 0.6901 (t) REVERT: F 234 LYS cc_start: 0.8944 (mppt) cc_final: 0.8717 (mmtm) REVERT: F 248 MET cc_start: 0.8388 (mmp) cc_final: 0.8162 (mmp) REVERT: F 278 GLU cc_start: 0.8543 (pt0) cc_final: 0.8269 (pt0) REVERT: F 314 PHE cc_start: 0.7707 (m-80) cc_final: 0.7400 (m-80) REVERT: a 29 MET cc_start: 0.6780 (mmp) cc_final: 0.6559 (mmp) REVERT: a 33 TYR cc_start: 0.7481 (m-80) cc_final: 0.6752 (m-80) REVERT: a 109 LYS cc_start: 0.8700 (tmtt) cc_final: 0.8488 (tptp) REVERT: a 204 ASN cc_start: 0.8452 (p0) cc_final: 0.8104 (p0) REVERT: a 309 PHE cc_start: 0.7253 (m-80) cc_final: 0.6885 (m-80) REVERT: b 68 MET cc_start: 0.7328 (mmm) cc_final: 0.6989 (mmm) REVERT: b 100 HIS cc_start: 0.8133 (m90) cc_final: 0.7772 (m90) REVERT: b 141 ASP cc_start: 0.6860 (t70) cc_final: 0.6547 (t70) REVERT: b 168 ASP cc_start: 0.7751 (p0) cc_final: 0.7368 (p0) REVERT: b 180 ARG cc_start: 0.6707 (mpt180) cc_final: 0.6347 (mpt180) REVERT: b 208 MET cc_start: 0.7802 (mtm) cc_final: 0.7186 (mtt) REVERT: b 234 LYS cc_start: 0.7459 (mppt) cc_final: 0.6961 (mppt) REVERT: b 235 HIS cc_start: 0.7892 (t-90) cc_final: 0.7623 (t-90) REVERT: b 251 VAL cc_start: 0.8388 (p) cc_final: 0.8113 (m) REVERT: b 254 MET cc_start: 0.8777 (ppp) cc_final: 0.8419 (ppp) REVERT: b 299 ASP cc_start: 0.7307 (t0) cc_final: 0.7035 (t0) REVERT: c 11 LEU cc_start: 0.8712 (mt) cc_final: 0.8508 (mt) REVERT: c 55 LEU cc_start: 0.9166 (mt) cc_final: 0.8936 (mt) REVERT: c 68 MET cc_start: 0.6607 (tmm) cc_final: 0.5987 (tmm) REVERT: c 75 THR cc_start: 0.9081 (p) cc_final: 0.8839 (p) REVERT: c 103 ARG cc_start: 0.8826 (mmm-85) cc_final: 0.8607 (mmm-85) REVERT: c 151 MET cc_start: 0.8011 (mtm) cc_final: 0.7481 (mtt) REVERT: c 164 LEU cc_start: 0.8097 (tp) cc_final: 0.7891 (tp) REVERT: c 168 ASP cc_start: 0.8584 (t0) cc_final: 0.8166 (t0) REVERT: c 174 ARG cc_start: 0.7171 (tmm160) cc_final: 0.6887 (tmm160) REVERT: c 209 ASP cc_start: 0.8045 (t0) cc_final: 0.7744 (t0) REVERT: c 224 ASN cc_start: 0.7926 (t0) cc_final: 0.7707 (t0) REVERT: c 295 LEU cc_start: 0.8341 (tp) cc_final: 0.8057 (tp) REVERT: d 28 MET cc_start: 0.4439 (ptp) cc_final: 0.4229 (ptp) REVERT: d 65 ARG cc_start: 0.8037 (mmm-85) cc_final: 0.7734 (mmm-85) REVERT: d 68 MET cc_start: 0.7155 (ttt) cc_final: 0.6948 (ttt) REVERT: d 82 GLU cc_start: 0.8313 (pt0) cc_final: 0.8031 (pt0) REVERT: d 124 LYS cc_start: 0.8707 (tmmt) cc_final: 0.8392 (tmmt) REVERT: d 128 LEU cc_start: 0.9213 (mt) cc_final: 0.8984 (mt) REVERT: d 166 LEU cc_start: 0.8290 (tp) cc_final: 0.8074 (tp) REVERT: d 248 MET cc_start: 0.7933 (ptt) cc_final: 0.7599 (ptt) REVERT: e 10 ASN cc_start: 0.8599 (m-40) cc_final: 0.8292 (m-40) REVERT: e 164 LEU cc_start: 0.8352 (tt) cc_final: 0.8107 (tt) REVERT: e 227 ASN cc_start: 0.8680 (m110) cc_final: 0.8401 (m110) REVERT: e 296 ASN cc_start: 0.7379 (t160) cc_final: 0.7049 (t0) REVERT: f 42 GLU cc_start: 0.7881 (pp20) cc_final: 0.7603 (pp20) REVERT: f 43 LEU cc_start: 0.8688 (mm) cc_final: 0.8454 (mm) REVERT: f 68 MET cc_start: 0.6589 (tpt) cc_final: 0.6071 (tpt) REVERT: f 243 GLU cc_start: 0.9091 (pm20) cc_final: 0.8824 (pm20) REVERT: f 254 MET cc_start: 0.8026 (ppp) cc_final: 0.7584 (ppp) REVERT: f 278 GLU cc_start: 0.8247 (mt-10) cc_final: 0.7702 (mt-10) REVERT: f 309 PHE cc_start: 0.8865 (m-80) cc_final: 0.8654 (m-80) outliers start: 10 outliers final: 3 residues processed: 926 average time/residue: 0.2044 time to fit residues: 286.2878 Evaluate side-chains 903 residues out of total 2985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 899 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 8.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 0.8980 chunk 298 optimal weight: 0.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 83 GLN C 155 GLN C 224 ASN C 246 ASN C 257 GLN D 176 HIS ** E 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 296 ASN F 155 GLN ** F 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 135 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.159963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.127575 restraints weight = 59754.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.132700 restraints weight = 37411.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.136490 restraints weight = 26502.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.139122 restraints weight = 20271.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.140986 restraints weight = 16430.665| |-----------------------------------------------------------------------------| r_work (final): 0.3950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6896 moved from start: 0.1139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 28330 Z= 0.165 Angle : 0.558 9.628 38522 Z= 0.298 Chirality : 0.042 0.161 4383 Planarity : 0.005 0.056 5016 Dihedral : 4.270 24.201 3838 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.35 % Favored : 94.56 % Rotamer: Outliers : 0.40 % Allowed : 5.53 % Favored : 94.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.15), residues: 3439 helix: 0.63 (0.14), residues: 1514 sheet: -0.00 (0.24), residues: 448 loop : -1.06 (0.17), residues: 1477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG d 65 TYR 0.015 0.001 TYR C 143 PHE 0.028 0.002 PHE A 259 TRP 0.025 0.002 TRP E 130 HIS 0.004 0.001 HIS f 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.16 (28330) covalent geometry : angle 0.55765 / 0.30 (38522) hydrogen bonds : bond 0.03829 / 2.59 ( 1188) hydrogen bonds : angle 5.48777 / 3.94 ( 3471) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 974 residues out of total 2985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 962 time to evaluate : 0.956 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 ASN cc_start: 0.8319 (t0) cc_final: 0.7799 (t0) REVERT: A 65 ARG cc_start: 0.8041 (mmm-85) cc_final: 0.7792 (mtp85) REVERT: B 16 VAL cc_start: 0.7994 (p) cc_final: 0.7690 (p) REVERT: B 80 HIS cc_start: 0.7851 (m90) cc_final: 0.7410 (m90) REVERT: B 89 ASN cc_start: 0.7822 (t0) cc_final: 0.7590 (t0) REVERT: B 100 HIS cc_start: 0.8031 (m90) cc_final: 0.7724 (m90) REVERT: B 130 TRP cc_start: 0.8793 (t60) cc_final: 0.8583 (t60) REVERT: B 232 LYS cc_start: 0.9341 (tptt) cc_final: 0.8941 (tptt) REVERT: B 317 GLU cc_start: 0.6869 (tm-30) cc_final: 0.6525 (tm-30) REVERT: C 68 MET cc_start: 0.7060 (ttp) cc_final: 0.6637 (ttp) REVERT: C 105 ASP cc_start: 0.8521 (m-30) cc_final: 0.8230 (m-30) REVERT: C 155 GLN cc_start: 0.8545 (mp10) cc_final: 0.8323 (mp10) REVERT: C 179 PHE cc_start: 0.8245 (t80) cc_final: 0.8039 (t80) REVERT: C 295 LEU cc_start: 0.8354 (mp) cc_final: 0.8053 (mp) REVERT: C 303 ARG cc_start: 0.8805 (mmm-85) cc_final: 0.8583 (mmm160) REVERT: C 310 TYR cc_start: 0.7667 (t80) cc_final: 0.7127 (t80) REVERT: C 314 PHE cc_start: 0.8043 (m-10) cc_final: 0.7801 (m-10) REVERT: D 29 MET cc_start: 0.6219 (mmp) cc_final: 0.5892 (mmp) REVERT: D 135 ASN cc_start: 0.8097 (p0) cc_final: 0.7779 (p0) REVERT: D 151 MET cc_start: 0.8291 (tpt) cc_final: 0.7724 (tpt) REVERT: D 155 GLN cc_start: 0.8862 (mt0) cc_final: 0.8423 (mt0) REVERT: D 244 ILE cc_start: 0.8609 (mt) cc_final: 0.8044 (mt) REVERT: D 248 MET cc_start: 0.8277 (mmp) cc_final: 0.8065 (mmp) REVERT: D 310 TYR cc_start: 0.8752 (t80) cc_final: 0.7965 (t80) REVERT: E 147 ARG cc_start: 0.8190 (ttp-110) cc_final: 0.7614 (ttp-110) REVERT: E 158 LEU cc_start: 0.9030 (tp) cc_final: 0.8804 (tp) REVERT: E 168 ASP cc_start: 0.6852 (t0) cc_final: 0.6503 (t0) REVERT: E 176 HIS cc_start: 0.7808 (t-90) cc_final: 0.7412 (t-90) REVERT: E 271 ARG cc_start: 0.8530 (ptt90) cc_final: 0.8220 (ttp80) REVERT: E 296 ASN cc_start: 0.8175 (t0) cc_final: 0.7944 (t0) REVERT: E 297 LYS cc_start: 0.8629 (mtmm) cc_final: 0.8281 (mtmm) REVERT: E 309 PHE cc_start: 0.9136 (m-10) cc_final: 0.8840 (m-10) REVERT: F 68 MET cc_start: 0.5927 (ppp) cc_final: 0.5599 (ppp) REVERT: F 73 HIS cc_start: 0.7860 (t-90) cc_final: 0.7590 (t-90) REVERT: F 80 HIS cc_start: 0.8461 (m90) cc_final: 0.8185 (m90) REVERT: F 87 ARG cc_start: 0.7634 (mmp80) cc_final: 0.7413 (mmp80) REVERT: F 138 LEU cc_start: 0.7674 (tp) cc_final: 0.7455 (tp) REVERT: F 151 MET cc_start: 0.8595 (mtm) cc_final: 0.8343 (mtm) REVERT: F 176 HIS cc_start: 0.8368 (t-170) cc_final: 0.7939 (t-170) REVERT: F 229 VAL cc_start: 0.9239 (p) cc_final: 0.9013 (m) REVERT: F 234 LYS cc_start: 0.8948 (mppt) cc_final: 0.8669 (mmtm) REVERT: F 242 ARG cc_start: 0.8590 (tpp-160) cc_final: 0.7393 (tpp-160) REVERT: F 248 MET cc_start: 0.8624 (mmp) cc_final: 0.8369 (mmp) REVERT: F 257 GLN cc_start: 0.8837 (tp40) cc_final: 0.8536 (tp-100) REVERT: a 10 ASN cc_start: 0.8994 (t0) cc_final: 0.8774 (t0) REVERT: a 29 MET cc_start: 0.6725 (mmp) cc_final: 0.6438 (mmp) REVERT: a 33 TYR cc_start: 0.7629 (m-80) cc_final: 0.6752 (m-80) REVERT: a 151 MET cc_start: 0.8713 (pmm) cc_final: 0.8137 (pmm) REVERT: a 155 GLN cc_start: 0.8852 (mt0) cc_final: 0.8450 (mt0) REVERT: a 204 ASN cc_start: 0.8373 (p0) cc_final: 0.8013 (p0) REVERT: a 291 ARG cc_start: 0.8161 (ptp-110) cc_final: 0.7293 (mtm110) REVERT: b 68 MET cc_start: 0.7417 (mmm) cc_final: 0.6789 (mmm) REVERT: b 80 HIS cc_start: 0.7844 (m90) cc_final: 0.7141 (m90) REVERT: b 93 VAL cc_start: 0.8496 (t) cc_final: 0.8221 (p) REVERT: b 100 HIS cc_start: 0.8298 (m90) cc_final: 0.7969 (m90) REVERT: b 106 LEU cc_start: 0.8950 (mm) cc_final: 0.8745 (mm) REVERT: b 141 ASP cc_start: 0.7137 (t70) cc_final: 0.6818 (t70) REVERT: b 168 ASP cc_start: 0.7847 (p0) cc_final: 0.7469 (p0) REVERT: b 180 ARG cc_start: 0.6698 (mpt180) cc_final: 0.6337 (mpt180) REVERT: b 208 MET cc_start: 0.7742 (mtm) cc_final: 0.7098 (mtt) REVERT: b 234 LYS cc_start: 0.7613 (mppt) cc_final: 0.6965 (mppt) REVERT: b 235 HIS cc_start: 0.7973 (t-90) cc_final: 0.7676 (t-90) REVERT: b 247 LYS cc_start: 0.5972 (tptt) cc_final: 0.5765 (tptt) REVERT: b 254 MET cc_start: 0.8817 (ppp) cc_final: 0.8536 (ppp) REVERT: b 256 ARG cc_start: 0.8409 (ttm-80) cc_final: 0.8122 (ttm-80) REVERT: b 299 ASP cc_start: 0.7296 (t0) cc_final: 0.7044 (t0) REVERT: b 309 PHE cc_start: 0.6985 (m-80) cc_final: 0.6693 (m-80) REVERT: c 11 LEU cc_start: 0.8783 (mt) cc_final: 0.8579 (mt) REVERT: c 55 LEU cc_start: 0.9125 (mt) cc_final: 0.8845 (mt) REVERT: c 68 MET cc_start: 0.6705 (tmm) cc_final: 0.5865 (tmm) REVERT: c 103 ARG cc_start: 0.8750 (mmm-85) cc_final: 0.8413 (mmm-85) REVERT: c 109 LYS cc_start: 0.8893 (tptp) cc_final: 0.8324 (tptp) REVERT: c 149 ASP cc_start: 0.8023 (t0) cc_final: 0.7635 (t0) REVERT: c 151 MET cc_start: 0.8022 (mtm) cc_final: 0.7655 (mtt) REVERT: c 164 LEU cc_start: 0.7960 (tp) cc_final: 0.7757 (tp) REVERT: c 174 ARG cc_start: 0.7277 (tmm160) cc_final: 0.6858 (tmm160) REVERT: c 209 ASP cc_start: 0.8054 (t0) cc_final: 0.7774 (t0) REVERT: c 295 LEU cc_start: 0.8191 (tp) cc_final: 0.7854 (tp) REVERT: c 309 PHE cc_start: 0.7855 (m-10) cc_final: 0.7531 (m-80) REVERT: d 10 ASN cc_start: 0.8638 (t0) cc_final: 0.8311 (t0) REVERT: d 65 ARG cc_start: 0.8307 (mmm-85) cc_final: 0.8080 (mmm-85) REVERT: d 68 MET cc_start: 0.7164 (ttt) cc_final: 0.6932 (ttt) REVERT: d 69 VAL cc_start: 0.8746 (t) cc_final: 0.8215 (m) REVERT: d 82 GLU cc_start: 0.8489 (pt0) cc_final: 0.8199 (pt0) REVERT: d 124 LYS cc_start: 0.8825 (tmmt) cc_final: 0.8504 (tmmt) REVERT: d 128 LEU cc_start: 0.9288 (mt) cc_final: 0.9071 (mt) REVERT: d 138 LEU cc_start: 0.8122 (tp) cc_final: 0.7893 (tp) REVERT: d 211 TRP cc_start: 0.8260 (m100) cc_final: 0.7817 (m100) REVERT: d 245 VAL cc_start: 0.8248 (p) cc_final: 0.8025 (m) REVERT: d 248 MET cc_start: 0.7963 (ptt) cc_final: 0.7658 (ptt) REVERT: d 311 GLN cc_start: 0.9111 (mp10) cc_final: 0.8771 (mm-40) REVERT: d 314 PHE cc_start: 0.8497 (m-10) cc_final: 0.8216 (m-10) REVERT: e 10 ASN cc_start: 0.8620 (m-40) cc_final: 0.8416 (m-40) REVERT: e 16 VAL cc_start: 0.8314 (t) cc_final: 0.8027 (t) REVERT: e 44 ASP cc_start: 0.8268 (t0) cc_final: 0.8052 (t0) REVERT: e 87 ARG cc_start: 0.8401 (mmp-170) cc_final: 0.8028 (mmp-170) REVERT: e 158 LEU cc_start: 0.9250 (tp) cc_final: 0.8981 (tp) REVERT: e 164 LEU cc_start: 0.8559 (tt) cc_final: 0.8264 (tt) REVERT: e 165 THR cc_start: 0.6993 (t) cc_final: 0.6744 (t) REVERT: e 174 ARG cc_start: 0.8058 (mmm160) cc_final: 0.7781 (mmm160) REVERT: e 227 ASN cc_start: 0.8661 (m110) cc_final: 0.8366 (m110) REVERT: e 244 ILE cc_start: 0.9391 (OUTLIER) cc_final: 0.9129 (mp) REVERT: e 296 ASN cc_start: 0.7700 (t0) cc_final: 0.7347 (t0) REVERT: f 42 GLU cc_start: 0.7887 (pp20) cc_final: 0.7611 (tm-30) REVERT: f 43 LEU cc_start: 0.8785 (mm) cc_final: 0.8202 (mm) REVERT: f 68 MET cc_start: 0.6875 (tpt) cc_final: 0.6532 (tpt) REVERT: f 182 PHE cc_start: 0.8306 (m-80) cc_final: 0.8023 (m-80) REVERT: f 243 GLU cc_start: 0.9147 (pm20) cc_final: 0.8866 (pm20) REVERT: f 254 MET cc_start: 0.8338 (ppp) cc_final: 0.7998 (ppp) REVERT: f 278 GLU cc_start: 0.8331 (mt-10) cc_final: 0.7864 (mt-10) REVERT: f 309 PHE cc_start: 0.9059 (m-80) cc_final: 0.8690 (m-80) outliers start: 12 outliers final: 0 residues processed: 966 average time/residue: 0.2030 time to fit residues: 297.5502 Evaluate side-chains 931 residues out of total 2985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 930 time to evaluate : 1.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 184 optimal weight: 7.9990 chunk 132 optimal weight: 0.8980 chunk 205 optimal weight: 3.9990 chunk 257 optimal weight: 5.9990 chunk 240 optimal weight: 0.5980 chunk 92 optimal weight: 9.9990 chunk 238 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 203 optimal weight: 0.1980 chunk 235 optimal weight: 1.9990 chunk 116 optimal weight: 0.0040 overall best weight: 0.7394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 169 GLN ** D 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 176 HIS ** F 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 135 ASN e 83 GLN e 205 GLN f 83 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.161953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.129889 restraints weight = 59251.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.135087 restraints weight = 36997.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.138926 restraints weight = 26064.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.141708 restraints weight = 19710.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.143414 restraints weight = 15818.425| |-----------------------------------------------------------------------------| r_work (final): 0.3995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6825 moved from start: 0.1400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 28330 Z= 0.108 Angle : 0.536 10.582 38522 Z= 0.281 Chirality : 0.042 0.157 4383 Planarity : 0.004 0.049 5016 Dihedral : 4.189 21.610 3838 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.71 % Favored : 95.20 % Rotamer: Outliers : 0.40 % Allowed : 3.32 % Favored : 96.28 % 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: -0.24 (0.15), residues: 3439 helix: 0.62 (0.14), residues: 1505 sheet: 0.04 (0.24), residues: 445 loop : -0.98 (0.17), residues: 1489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG b 210 TYR 0.020 0.001 TYR E 219 PHE 0.046 0.002 PHE f 152 TRP 0.026 0.002 TRP E 130 HIS 0.007 0.001 HIS b 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 (28330) covalent geometry : angle 0.53620 / 0.28 (38522) hydrogen bonds : bond 0.03204 / 2.16 ( 1188) hydrogen bonds : angle 5.20442 / 3.73 ( 3471) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 963 residues out of total 2985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 951 time to evaluate : 1.055 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 ASN cc_start: 0.8408 (t0) cc_final: 0.7845 (t0) REVERT: A 29 MET cc_start: 0.6984 (mmp) cc_final: 0.6594 (mmp) REVERT: A 65 ARG cc_start: 0.7858 (mmm-85) cc_final: 0.7577 (mtp85) REVERT: A 109 LYS cc_start: 0.8506 (ttpp) cc_final: 0.8123 (ttpp) REVERT: A 138 LEU cc_start: 0.7730 (tp) cc_final: 0.7255 (tp) REVERT: A 140 PHE cc_start: 0.8004 (m-80) cc_final: 0.7468 (m-80) REVERT: A 181 LEU cc_start: 0.8180 (tp) cc_final: 0.7754 (tp) REVERT: B 16 VAL cc_start: 0.8024 (p) cc_final: 0.7716 (p) REVERT: B 80 HIS cc_start: 0.7812 (m90) cc_final: 0.7436 (m90) REVERT: B 89 ASN cc_start: 0.7834 (t0) cc_final: 0.7556 (t0) REVERT: B 100 HIS cc_start: 0.7958 (m90) cc_final: 0.7636 (m90) REVERT: B 130 TRP cc_start: 0.8757 (t60) cc_final: 0.8492 (t60) REVERT: B 168 ASP cc_start: 0.7530 (p0) cc_final: 0.7119 (p0) REVERT: B 211 TRP cc_start: 0.7216 (m100) cc_final: 0.6454 (m100) REVERT: B 232 LYS cc_start: 0.9333 (tptt) cc_final: 0.8936 (tptt) REVERT: C 55 LEU cc_start: 0.9036 (mt) cc_final: 0.8823 (mt) REVERT: C 68 MET cc_start: 0.7032 (ttp) cc_final: 0.6632 (ttp) REVERT: C 105 ASP cc_start: 0.8427 (m-30) cc_final: 0.8187 (m-30) REVERT: C 155 GLN cc_start: 0.8497 (mp10) cc_final: 0.8275 (mp10) REVERT: C 248 MET cc_start: 0.8452 (ttp) cc_final: 0.8235 (ttp) REVERT: C 295 LEU cc_start: 0.8284 (mp) cc_final: 0.7969 (mp) REVERT: C 303 ARG cc_start: 0.8780 (mmm-85) cc_final: 0.8579 (mmm160) REVERT: C 310 TYR cc_start: 0.7659 (t80) cc_final: 0.7161 (t80) REVERT: C 314 PHE cc_start: 0.8003 (m-10) cc_final: 0.7718 (m-10) REVERT: D 29 MET cc_start: 0.6170 (mmp) cc_final: 0.5836 (mmp) REVERT: D 138 LEU cc_start: 0.7766 (tp) cc_final: 0.7523 (tp) REVERT: D 151 MET cc_start: 0.8192 (tpt) cc_final: 0.7693 (tpt) REVERT: D 155 GLN cc_start: 0.8778 (mt0) cc_final: 0.8449 (mt0) REVERT: D 248 MET cc_start: 0.8279 (mmp) cc_final: 0.8075 (mmp) REVERT: D 282 ILE cc_start: 0.7770 (OUTLIER) cc_final: 0.7533 (mp) REVERT: D 306 VAL cc_start: 0.9115 (t) cc_final: 0.8793 (m) REVERT: D 314 PHE cc_start: 0.8818 (m-10) cc_final: 0.8432 (m-10) REVERT: E 147 ARG cc_start: 0.8110 (ttp-110) cc_final: 0.7561 (ttp-110) REVERT: E 168 ASP cc_start: 0.6933 (t0) cc_final: 0.6616 (t0) REVERT: E 176 HIS cc_start: 0.7840 (t-90) cc_final: 0.7439 (t-90) REVERT: E 182 PHE cc_start: 0.7261 (m-10) cc_final: 0.6931 (m-80) REVERT: E 271 ARG cc_start: 0.8485 (ptt90) cc_final: 0.8164 (ttp80) REVERT: E 297 LYS cc_start: 0.8622 (mtmm) cc_final: 0.8149 (mtmm) REVERT: E 309 PHE cc_start: 0.9117 (m-10) cc_final: 0.8829 (m-10) REVERT: E 314 PHE cc_start: 0.7753 (m-10) cc_final: 0.7529 (m-10) REVERT: F 68 MET cc_start: 0.5958 (ppp) cc_final: 0.5209 (ppp) REVERT: F 73 HIS cc_start: 0.7805 (t-90) cc_final: 0.7576 (t-90) REVERT: F 80 HIS cc_start: 0.8448 (m90) cc_final: 0.8062 (m90) REVERT: F 83 GLN cc_start: 0.8113 (tm-30) cc_final: 0.7315 (tm-30) REVERT: F 87 ARG cc_start: 0.7597 (mmp80) cc_final: 0.7392 (mmp80) REVERT: F 151 MET cc_start: 0.8463 (mtm) cc_final: 0.8234 (mtm) REVERT: F 176 HIS cc_start: 0.8372 (t-170) cc_final: 0.7907 (t-170) REVERT: F 214 VAL cc_start: 0.7306 (t) cc_final: 0.7096 (t) REVERT: F 229 VAL cc_start: 0.9246 (p) cc_final: 0.9022 (m) REVERT: F 242 ARG cc_start: 0.8536 (tpp-160) cc_final: 0.7349 (tpp-160) REVERT: F 248 MET cc_start: 0.8572 (mmp) cc_final: 0.8358 (mmp) REVERT: F 257 GLN cc_start: 0.8824 (tp40) cc_final: 0.8511 (tp-100) REVERT: a 10 ASN cc_start: 0.9020 (t0) cc_final: 0.8779 (t0) REVERT: a 22 PHE cc_start: 0.7331 (m-80) cc_final: 0.7111 (m-80) REVERT: a 29 MET cc_start: 0.6720 (mmp) cc_final: 0.6390 (mmp) REVERT: a 33 TYR cc_start: 0.7500 (m-80) cc_final: 0.6650 (m-80) REVERT: a 138 LEU cc_start: 0.7755 (tp) cc_final: 0.7548 (tp) REVERT: a 151 MET cc_start: 0.8610 (pmm) cc_final: 0.8187 (pmm) REVERT: a 155 GLN cc_start: 0.8786 (mt0) cc_final: 0.8376 (mt0) REVERT: a 204 ASN cc_start: 0.8471 (p0) cc_final: 0.8118 (p0) REVERT: a 211 TRP cc_start: 0.8356 (m100) cc_final: 0.8133 (m100) REVERT: a 291 ARG cc_start: 0.8129 (ptp-110) cc_final: 0.7220 (mtm110) REVERT: b 68 MET cc_start: 0.7480 (mmm) cc_final: 0.6874 (mmm) REVERT: b 93 VAL cc_start: 0.8519 (t) cc_final: 0.8244 (p) REVERT: b 100 HIS cc_start: 0.8219 (m90) cc_final: 0.7890 (m90) REVERT: b 104 ILE cc_start: 0.8470 (tp) cc_final: 0.8264 (tp) REVERT: b 106 LEU cc_start: 0.8922 (mm) cc_final: 0.8714 (mm) REVERT: b 141 ASP cc_start: 0.7051 (t70) cc_final: 0.6780 (t70) REVERT: b 154 ILE cc_start: 0.8717 (mm) cc_final: 0.8470 (mm) REVERT: b 168 ASP cc_start: 0.7910 (p0) cc_final: 0.7473 (p0) REVERT: b 180 ARG cc_start: 0.6600 (mpt180) cc_final: 0.6299 (mpt180) REVERT: b 208 MET cc_start: 0.7651 (mtm) cc_final: 0.7079 (mtt) REVERT: b 234 LYS cc_start: 0.7606 (mppt) cc_final: 0.6976 (mppt) REVERT: b 235 HIS cc_start: 0.7975 (t-90) cc_final: 0.7666 (t-90) REVERT: b 242 ARG cc_start: 0.8901 (tpt170) cc_final: 0.8518 (tpt170) REVERT: b 251 VAL cc_start: 0.8443 (p) cc_final: 0.8123 (m) REVERT: b 254 MET cc_start: 0.8737 (ppp) cc_final: 0.8516 (ppp) REVERT: b 256 ARG cc_start: 0.8263 (ttm-80) cc_final: 0.7986 (ttm-80) REVERT: b 299 ASP cc_start: 0.7248 (t0) cc_final: 0.6981 (t0) REVERT: b 309 PHE cc_start: 0.6945 (m-80) cc_final: 0.6661 (m-80) REVERT: c 11 LEU cc_start: 0.8703 (mt) cc_final: 0.8489 (mt) REVERT: c 55 LEU cc_start: 0.9096 (mt) cc_final: 0.8811 (mt) REVERT: c 68 MET cc_start: 0.6691 (tmm) cc_final: 0.5877 (tmm) REVERT: c 75 THR cc_start: 0.9177 (p) cc_final: 0.8973 (p) REVERT: c 103 ARG cc_start: 0.8695 (mmm-85) cc_final: 0.8247 (mmm-85) REVERT: c 109 LYS cc_start: 0.8834 (tptp) cc_final: 0.8263 (tptp) REVERT: c 149 ASP cc_start: 0.7958 (t0) cc_final: 0.7419 (t0) REVERT: c 151 MET cc_start: 0.7967 (mtm) cc_final: 0.7585 (mtt) REVERT: c 164 LEU cc_start: 0.7913 (tp) cc_final: 0.7682 (tp) REVERT: c 168 ASP cc_start: 0.8421 (t0) cc_final: 0.8188 (t0) REVERT: c 174 ARG cc_start: 0.7319 (tmm160) cc_final: 0.6774 (tmm160) REVERT: c 209 ASP cc_start: 0.8063 (t0) cc_final: 0.7764 (t0) REVERT: c 295 LEU cc_start: 0.8125 (tp) cc_final: 0.7813 (tp) REVERT: c 309 PHE cc_start: 0.7790 (m-10) cc_final: 0.7484 (m-80) REVERT: d 65 ARG cc_start: 0.8269 (mmm-85) cc_final: 0.7986 (mmm-85) REVERT: d 68 MET cc_start: 0.7047 (ttt) cc_final: 0.6824 (ttt) REVERT: d 69 VAL cc_start: 0.8730 (t) cc_final: 0.8225 (m) REVERT: d 82 GLU cc_start: 0.8444 (pt0) cc_final: 0.8128 (pt0) REVERT: d 124 LYS cc_start: 0.8842 (tmmt) cc_final: 0.8481 (tmmt) REVERT: d 128 LEU cc_start: 0.9239 (mt) cc_final: 0.9012 (mt) REVERT: d 138 LEU cc_start: 0.8201 (tp) cc_final: 0.7939 (tp) REVERT: d 248 MET cc_start: 0.7920 (ptt) cc_final: 0.7613 (ptt) REVERT: d 314 PHE cc_start: 0.8545 (m-10) cc_final: 0.8240 (m-10) REVERT: e 10 ASN cc_start: 0.8600 (m-40) cc_final: 0.8383 (m-40) REVERT: e 16 VAL cc_start: 0.8308 (t) cc_final: 0.8037 (t) REVERT: e 158 LEU cc_start: 0.9204 (tp) cc_final: 0.8897 (tp) REVERT: e 164 LEU cc_start: 0.8584 (tt) cc_final: 0.8302 (tt) REVERT: e 165 THR cc_start: 0.7114 (t) cc_final: 0.6894 (t) REVERT: e 171 ARG cc_start: 0.6548 (ttp-170) cc_final: 0.6335 (ttp-170) REVERT: e 174 ARG cc_start: 0.7786 (mmm160) cc_final: 0.7563 (mmm160) REVERT: e 227 ASN cc_start: 0.8658 (m110) cc_final: 0.8381 (m110) REVERT: e 244 ILE cc_start: 0.9398 (OUTLIER) cc_final: 0.9120 (mp) REVERT: e 248 MET cc_start: 0.8773 (mmt) cc_final: 0.8568 (mmt) REVERT: e 257 GLN cc_start: 0.8226 (tp-100) cc_final: 0.7412 (tp-100) REVERT: e 296 ASN cc_start: 0.7630 (t0) cc_final: 0.7340 (t0) REVERT: f 42 GLU cc_start: 0.7905 (pp20) cc_final: 0.7614 (tm-30) REVERT: f 68 MET cc_start: 0.6860 (tpt) cc_final: 0.6541 (tpt) REVERT: f 182 PHE cc_start: 0.8220 (m-80) cc_final: 0.8019 (m-80) REVERT: f 243 GLU cc_start: 0.9117 (pm20) cc_final: 0.8811 (pm20) REVERT: f 278 GLU cc_start: 0.8256 (mt-10) cc_final: 0.7799 (mt-10) REVERT: f 309 PHE cc_start: 0.9018 (m-80) cc_final: 0.8758 (m-80) outliers start: 12 outliers final: 0 residues processed: 955 average time/residue: 0.2021 time to fit residues: 292.6597 Evaluate side-chains 927 residues out of total 2985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 925 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 18 optimal weight: 0.9990 chunk 127 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 chunk 163 optimal weight: 0.7980 chunk 194 optimal weight: 9.9990 chunk 243 optimal weight: 9.9990 chunk 325 optimal weight: 6.9990 chunk 72 optimal weight: 7.9990 chunk 205 optimal weight: 0.4980 chunk 66 optimal weight: 0.0870 chunk 238 optimal weight: 10.0000 overall best weight: 0.6762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 279 ASN ** F 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 96 ASN ** b 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 135 ASN ** e 83 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 = 0.4262 r_free = 0.4262 target = 0.162857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.130225 restraints weight = 59695.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.135354 restraints weight = 37530.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.139178 restraints weight = 26598.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.141835 restraints weight = 20344.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.143673 restraints weight = 16486.102| |-----------------------------------------------------------------------------| r_work (final): 0.3985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6834 moved from start: 0.1589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 28330 Z= 0.103 Angle : 0.529 7.622 38522 Z= 0.277 Chirality : 0.042 0.177 4383 Planarity : 0.004 0.053 5016 Dihedral : 4.132 21.637 3838 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.71 % Favored : 95.20 % Rotamer: Outliers : 0.23 % Allowed : 2.98 % Favored : 96.78 % 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: 3439 helix: 0.62 (0.14), residues: 1506 sheet: -0.16 (0.24), residues: 451 loop : -0.94 (0.17), residues: 1482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 210 TYR 0.029 0.001 TYR E 219 PHE 0.039 0.001 PHE f 152 TRP 0.027 0.002 TRP E 130 HIS 0.009 0.001 HIS c 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.10 (28330) covalent geometry : angle 0.52946 / 0.28 (38522) hydrogen bonds : bond 0.03022 / 2.02 ( 1188) hydrogen bonds : angle 5.09306 / 3.65 ( 3471) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 946 residues out of total 2985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 939 time to evaluate : 1.117 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 ASN cc_start: 0.8407 (t0) cc_final: 0.7794 (t0) REVERT: A 22 PHE cc_start: 0.7814 (m-80) cc_final: 0.7519 (m-80) REVERT: A 65 ARG cc_start: 0.7789 (mmm-85) cc_final: 0.7540 (mtp85) REVERT: A 68 MET cc_start: 0.8270 (ttm) cc_final: 0.8048 (ttm) REVERT: B 16 VAL cc_start: 0.7976 (p) cc_final: 0.7689 (p) REVERT: B 68 MET cc_start: 0.7262 (mmm) cc_final: 0.6983 (mmm) REVERT: B 80 HIS cc_start: 0.7795 (m90) cc_final: 0.7339 (m90) REVERT: B 89 ASN cc_start: 0.7828 (t0) cc_final: 0.7487 (t0) REVERT: B 100 HIS cc_start: 0.7932 (m90) cc_final: 0.7590 (m90) REVERT: B 130 TRP cc_start: 0.8762 (t60) cc_final: 0.8397 (t60) REVERT: B 232 LYS cc_start: 0.9347 (tptt) cc_final: 0.8918 (tptt) REVERT: C 68 MET cc_start: 0.6938 (ttp) cc_final: 0.6575 (ttp) REVERT: C 105 ASP cc_start: 0.8443 (m-30) cc_final: 0.8198 (m-30) REVERT: C 155 GLN cc_start: 0.8449 (mp10) cc_final: 0.8229 (mp10) REVERT: C 303 ARG cc_start: 0.8777 (mmm-85) cc_final: 0.8458 (mmm-85) REVERT: C 310 TYR cc_start: 0.7691 (t80) cc_final: 0.7184 (t80) REVERT: C 314 PHE cc_start: 0.8026 (m-10) cc_final: 0.7704 (m-10) REVERT: D 10 ASN cc_start: 0.8661 (t0) cc_final: 0.8405 (t0) REVERT: D 29 MET cc_start: 0.6207 (mmp) cc_final: 0.5906 (mmp) REVERT: D 94 ARG cc_start: 0.8454 (ptp-170) cc_final: 0.8102 (ptp-170) REVERT: D 109 LYS cc_start: 0.9065 (ttpp) cc_final: 0.8508 (ttpp) REVERT: D 135 ASN cc_start: 0.7981 (p0) cc_final: 0.7666 (p0) REVERT: D 138 LEU cc_start: 0.7785 (tp) cc_final: 0.7551 (tp) REVERT: D 151 MET cc_start: 0.8230 (tpt) cc_final: 0.7646 (tpt) REVERT: D 155 GLN cc_start: 0.8756 (mt0) cc_final: 0.8246 (mt0) REVERT: D 248 MET cc_start: 0.8305 (mmp) cc_final: 0.8099 (mmp) REVERT: D 282 ILE cc_start: 0.7754 (mp) cc_final: 0.7475 (mp) REVERT: D 314 PHE cc_start: 0.8834 (m-10) cc_final: 0.8458 (m-10) REVERT: E 28 MET cc_start: 0.5913 (mtm) cc_final: 0.5708 (mtm) REVERT: E 66 ARG cc_start: 0.6480 (mmt90) cc_final: 0.5931 (mtt180) REVERT: E 147 ARG cc_start: 0.8100 (ttp-110) cc_final: 0.7526 (ttp-110) REVERT: E 158 LEU cc_start: 0.9065 (tp) cc_final: 0.8843 (tp) REVERT: E 168 ASP cc_start: 0.6913 (t0) cc_final: 0.6607 (t0) REVERT: E 176 HIS cc_start: 0.7805 (t-90) cc_final: 0.7405 (t-90) REVERT: E 182 PHE cc_start: 0.7082 (m-10) cc_final: 0.6600 (m-80) REVERT: E 271 ARG cc_start: 0.8512 (ptt90) cc_final: 0.8157 (ttp80) REVERT: E 297 LYS cc_start: 0.8636 (mtmm) cc_final: 0.8164 (mtmm) REVERT: E 309 PHE cc_start: 0.9114 (m-10) cc_final: 0.8817 (m-10) REVERT: E 314 PHE cc_start: 0.7771 (m-10) cc_final: 0.7546 (m-10) REVERT: F 68 MET cc_start: 0.5914 (ppp) cc_final: 0.5182 (ppp) REVERT: F 73 HIS cc_start: 0.7842 (t-90) cc_final: 0.7572 (t-90) REVERT: F 80 HIS cc_start: 0.8432 (m90) cc_final: 0.8080 (m90) REVERT: F 83 GLN cc_start: 0.8066 (tm-30) cc_final: 0.7329 (tm-30) REVERT: F 87 ARG cc_start: 0.7599 (mmp80) cc_final: 0.7398 (mmp80) REVERT: F 151 MET cc_start: 0.8526 (mtm) cc_final: 0.8182 (mtm) REVERT: F 176 HIS cc_start: 0.8379 (t-170) cc_final: 0.7875 (t-170) REVERT: F 229 VAL cc_start: 0.9262 (p) cc_final: 0.9034 (m) REVERT: F 234 LYS cc_start: 0.8813 (mppt) cc_final: 0.8553 (mmtm) REVERT: F 242 ARG cc_start: 0.8533 (tpp-160) cc_final: 0.7353 (tpp-160) REVERT: F 248 MET cc_start: 0.8591 (mmp) cc_final: 0.8376 (mmp) REVERT: F 257 GLN cc_start: 0.8845 (tp40) cc_final: 0.8277 (tp-100) REVERT: F 261 ASN cc_start: 0.8538 (m110) cc_final: 0.7996 (m110) REVERT: a 10 ASN cc_start: 0.9035 (t0) cc_final: 0.8783 (t0) REVERT: a 22 PHE cc_start: 0.7446 (m-80) cc_final: 0.7208 (m-80) REVERT: a 29 MET cc_start: 0.6658 (mmp) cc_final: 0.6318 (mmp) REVERT: a 33 TYR cc_start: 0.7477 (m-80) cc_final: 0.6648 (m-80) REVERT: a 138 LEU cc_start: 0.7675 (tp) cc_final: 0.7420 (tp) REVERT: a 140 PHE cc_start: 0.7987 (m-80) cc_final: 0.7688 (m-80) REVERT: a 151 MET cc_start: 0.8616 (pmm) cc_final: 0.8367 (pmm) REVERT: a 155 GLN cc_start: 0.8820 (mt0) cc_final: 0.8399 (mt0) REVERT: a 204 ASN cc_start: 0.8465 (p0) cc_final: 0.8138 (p0) REVERT: a 211 TRP cc_start: 0.8358 (m100) cc_final: 0.8074 (m100) REVERT: a 268 MET cc_start: 0.7111 (tpp) cc_final: 0.6639 (mmm) REVERT: a 291 ARG cc_start: 0.8149 (ptp-110) cc_final: 0.7212 (mtm110) REVERT: b 28 MET cc_start: 0.3437 (ptp) cc_final: 0.3226 (ptp) REVERT: b 80 HIS cc_start: 0.7811 (m90) cc_final: 0.7413 (m90) REVERT: b 100 HIS cc_start: 0.8227 (m90) cc_final: 0.7891 (m90) REVERT: b 104 ILE cc_start: 0.8467 (tp) cc_final: 0.8242 (tp) REVERT: b 141 ASP cc_start: 0.7077 (t70) cc_final: 0.6786 (t70) REVERT: b 154 ILE cc_start: 0.8766 (mm) cc_final: 0.8468 (mm) REVERT: b 168 ASP cc_start: 0.7884 (p0) cc_final: 0.7425 (p0) REVERT: b 180 ARG cc_start: 0.6634 (mpt180) cc_final: 0.6378 (mpt180) REVERT: b 208 MET cc_start: 0.7650 (mtm) cc_final: 0.6995 (mtt) REVERT: b 215 THR cc_start: 0.8394 (m) cc_final: 0.8014 (t) REVERT: b 234 LYS cc_start: 0.7636 (mppt) cc_final: 0.7003 (mppt) REVERT: b 235 HIS cc_start: 0.8001 (t-90) cc_final: 0.7701 (t-90) REVERT: b 242 ARG cc_start: 0.8875 (tpt170) cc_final: 0.8522 (tpt170) REVERT: b 256 ARG cc_start: 0.8271 (ttm-80) cc_final: 0.7955 (ttm-80) REVERT: b 299 ASP cc_start: 0.7219 (t0) cc_final: 0.6996 (t0) REVERT: b 309 PHE cc_start: 0.6786 (m-80) cc_final: 0.6528 (m-80) REVERT: c 11 LEU cc_start: 0.8700 (mt) cc_final: 0.8483 (mt) REVERT: c 28 MET cc_start: 0.7304 (mtm) cc_final: 0.7050 (mtm) REVERT: c 55 LEU cc_start: 0.9101 (mt) cc_final: 0.8872 (mt) REVERT: c 68 MET cc_start: 0.6711 (tmm) cc_final: 0.5881 (tmm) REVERT: c 97 LEU cc_start: 0.8651 (mp) cc_final: 0.8332 (mp) REVERT: c 103 ARG cc_start: 0.8714 (mmm-85) cc_final: 0.8333 (mmm-85) REVERT: c 109 LYS cc_start: 0.8849 (tptp) cc_final: 0.8316 (tptp) REVERT: c 149 ASP cc_start: 0.7985 (t0) cc_final: 0.7411 (t0) REVERT: c 151 MET cc_start: 0.7953 (mtm) cc_final: 0.7628 (mtt) REVERT: c 164 LEU cc_start: 0.7901 (tp) cc_final: 0.7641 (tp) REVERT: c 174 ARG cc_start: 0.7374 (tmm160) cc_final: 0.6841 (tmm160) REVERT: c 209 ASP cc_start: 0.8111 (t0) cc_final: 0.7794 (t0) REVERT: c 295 LEU cc_start: 0.8159 (tp) cc_final: 0.7842 (tp) REVERT: c 309 PHE cc_start: 0.7779 (m-10) cc_final: 0.7485 (m-80) REVERT: d 33 TYR cc_start: 0.6072 (m-80) cc_final: 0.5714 (m-80) REVERT: d 65 ARG cc_start: 0.8239 (mmm-85) cc_final: 0.7934 (mmm-85) REVERT: d 68 MET cc_start: 0.7065 (ttt) cc_final: 0.6823 (ttt) REVERT: d 69 VAL cc_start: 0.8715 (t) cc_final: 0.8184 (m) REVERT: d 82 GLU cc_start: 0.8431 (pt0) cc_final: 0.8116 (pt0) REVERT: d 124 LYS cc_start: 0.8854 (tmmt) cc_final: 0.8489 (tmmt) REVERT: d 128 LEU cc_start: 0.9247 (mt) cc_final: 0.9013 (mt) REVERT: d 130 TRP cc_start: 0.8385 (t60) cc_final: 0.8138 (t60) REVERT: d 138 LEU cc_start: 0.8228 (tp) cc_final: 0.7916 (tp) REVERT: d 248 MET cc_start: 0.7929 (ptt) cc_final: 0.7631 (ptt) REVERT: d 282 ILE cc_start: 0.7632 (mt) cc_final: 0.7417 (mt) REVERT: d 314 PHE cc_start: 0.8582 (m-10) cc_final: 0.8256 (m-10) REVERT: e 10 ASN cc_start: 0.8590 (m-40) cc_final: 0.8363 (m-40) REVERT: e 80 HIS cc_start: 0.8639 (t70) cc_final: 0.8234 (t70) REVERT: e 83 GLN cc_start: 0.8611 (pt0) cc_final: 0.8335 (pp30) REVERT: e 87 ARG cc_start: 0.8379 (mmp-170) cc_final: 0.8107 (mmp-170) REVERT: e 158 LEU cc_start: 0.9212 (tp) cc_final: 0.8943 (tp) REVERT: e 171 ARG cc_start: 0.6632 (ttp-170) cc_final: 0.6385 (ttp-170) REVERT: e 227 ASN cc_start: 0.8663 (m110) cc_final: 0.8401 (m110) REVERT: e 244 ILE cc_start: 0.9414 (OUTLIER) cc_final: 0.9170 (mp) REVERT: e 276 TRP cc_start: 0.6951 (t60) cc_final: 0.6721 (t60) REVERT: e 296 ASN cc_start: 0.7620 (t0) cc_final: 0.7364 (t0) REVERT: f 42 GLU cc_start: 0.7943 (pp20) cc_final: 0.7605 (tm-30) REVERT: f 141 ASP cc_start: 0.6581 (t0) cc_final: 0.6369 (t0) REVERT: f 243 GLU cc_start: 0.9116 (pm20) cc_final: 0.8817 (pm20) REVERT: f 278 GLU cc_start: 0.8279 (mt-10) cc_final: 0.7800 (mt-10) REVERT: f 309 PHE cc_start: 0.9039 (m-80) cc_final: 0.8742 (m-80) outliers start: 7 outliers final: 0 residues processed: 942 average time/residue: 0.2125 time to fit residues: 302.9246 Evaluate side-chains 922 residues out of total 2985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 921 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 39 optimal weight: 10.0000 chunk 186 optimal weight: 3.9990 chunk 338 optimal weight: 2.9990 chunk 55 optimal weight: 7.9990 chunk 27 optimal weight: 0.9980 chunk 217 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 218 optimal weight: 0.0040 chunk 170 optimal weight: 4.9990 chunk 83 optimal weight: 4.9990 chunk 204 optimal weight: 4.9990 overall best weight: 2.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 169 GLN E 296 ASN ** F 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 155 GLN ** c 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 227 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.157435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.125201 restraints weight = 59681.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.130211 restraints weight = 37517.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.133914 restraints weight = 26634.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.136402 restraints weight = 20314.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.138519 restraints weight = 16577.774| |-----------------------------------------------------------------------------| r_work (final): 0.3916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6945 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.097 28330 Z= 0.194 Angle : 0.603 10.936 38522 Z= 0.321 Chirality : 0.043 0.163 4383 Planarity : 0.005 0.108 5016 Dihedral : 4.507 24.866 3838 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.32 % Favored : 94.59 % Rotamer: Outliers : 0.13 % Allowed : 2.71 % Favored : 97.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.14), residues: 3439 helix: 0.42 (0.13), residues: 1530 sheet: -0.43 (0.24), residues: 459 loop : -1.05 (0.17), residues: 1450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 256 TYR 0.019 0.001 TYR e 132 PHE 0.023 0.002 PHE f 152 TRP 0.035 0.002 TRP E 130 HIS 0.007 0.001 HIS c 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.19 (28330) covalent geometry : angle 0.60285 / 0.32 (38522) hydrogen bonds : bond 0.03638 / 2.42 ( 1188) hydrogen bonds : angle 5.30723 / 3.80 ( 3471) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 991 residues out of total 2985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 987 time to evaluate : 1.062 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: 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: 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: A 10 ASN cc_start: 0.8533 (t0) cc_final: 0.7926 (t0) REVERT: A 22 PHE cc_start: 0.7819 (m-80) cc_final: 0.7542 (m-80) REVERT: A 29 MET cc_start: 0.6947 (mmp) cc_final: 0.6547 (mmp) REVERT: A 65 ARG cc_start: 0.8054 (mmm-85) cc_final: 0.7682 (mtp-110) REVERT: A 68 MET cc_start: 0.8317 (ttm) cc_final: 0.8032 (ttm) REVERT: A 97 LEU cc_start: 0.8058 (mt) cc_final: 0.7839 (mt) REVERT: A 138 LEU cc_start: 0.7995 (tp) cc_final: 0.7548 (tp) REVERT: A 140 PHE cc_start: 0.7964 (m-80) cc_final: 0.7489 (m-80) REVERT: A 181 LEU cc_start: 0.8273 (tp) cc_final: 0.7916 (tp) REVERT: A 268 MET cc_start: 0.7630 (mmm) cc_final: 0.6914 (mpp) REVERT: B 66 ARG cc_start: 0.7198 (mpt-90) cc_final: 0.6848 (mpt-90) REVERT: B 68 MET cc_start: 0.7467 (mmm) cc_final: 0.7106 (mmm) REVERT: B 80 HIS cc_start: 0.7936 (m90) cc_final: 0.7641 (m90) REVERT: B 82 GLU cc_start: 0.8723 (pt0) cc_final: 0.8166 (pt0) REVERT: B 89 ASN cc_start: 0.7881 (t0) cc_final: 0.7482 (t0) REVERT: B 96 ASN cc_start: 0.8551 (t0) cc_final: 0.7869 (t0) REVERT: B 98 ASP cc_start: 0.7648 (p0) cc_final: 0.7151 (p0) REVERT: B 100 HIS cc_start: 0.8018 (m90) cc_final: 0.7720 (m90) REVERT: B 130 TRP cc_start: 0.8834 (t60) cc_final: 0.8549 (t60) REVERT: B 278 GLU cc_start: 0.8274 (pt0) cc_final: 0.8038 (pt0) REVERT: C 68 MET cc_start: 0.7146 (ttp) cc_final: 0.6749 (ttp) REVERT: C 97 LEU cc_start: 0.8710 (mp) cc_final: 0.8493 (mp) REVERT: C 105 ASP cc_start: 0.8490 (m-30) cc_final: 0.8256 (m-30) REVERT: C 186 ASN cc_start: 0.7457 (m110) cc_final: 0.7197 (m110) REVERT: C 303 ARG cc_start: 0.8852 (mmm-85) cc_final: 0.8600 (mmm-85) REVERT: C 314 PHE cc_start: 0.8123 (m-10) cc_final: 0.7719 (m-10) REVERT: D 10 ASN cc_start: 0.8684 (t0) cc_final: 0.8419 (t0) REVERT: D 29 MET cc_start: 0.6286 (mmp) cc_final: 0.5959 (mmp) REVERT: D 39 TYR cc_start: 0.8629 (m-80) cc_final: 0.8378 (m-80) REVERT: D 95 VAL cc_start: 0.8413 (t) cc_final: 0.7762 (m) REVERT: D 106 LEU cc_start: 0.8482 (mp) cc_final: 0.8226 (mp) REVERT: D 135 ASN cc_start: 0.7995 (p0) cc_final: 0.7744 (p0) REVERT: D 151 MET cc_start: 0.8198 (tpt) cc_final: 0.7696 (tpt) REVERT: D 152 PHE cc_start: 0.8509 (t80) cc_final: 0.8303 (t80) REVERT: D 155 GLN cc_start: 0.8805 (mt0) cc_final: 0.8359 (mt0) REVERT: D 168 ASP cc_start: 0.8072 (t0) cc_final: 0.7869 (t0) REVERT: D 248 MET cc_start: 0.8265 (mmp) cc_final: 0.8063 (mmp) REVERT: D 306 VAL cc_start: 0.9078 (t) cc_final: 0.8877 (t) REVERT: D 314 PHE cc_start: 0.8826 (m-10) cc_final: 0.8417 (m-10) REVERT: E 28 MET cc_start: 0.5841 (mtm) cc_final: 0.5600 (mtm) REVERT: E 130 TRP cc_start: 0.8661 (t60) cc_final: 0.8392 (t60) REVERT: E 147 ARG cc_start: 0.8241 (ttp-110) cc_final: 0.7621 (ttp-110) REVERT: E 157 VAL cc_start: 0.8674 (p) cc_final: 0.8446 (m) REVERT: E 158 LEU cc_start: 0.9050 (tp) cc_final: 0.8818 (tp) REVERT: E 168 ASP cc_start: 0.7170 (t0) cc_final: 0.6903 (t0) REVERT: E 176 HIS cc_start: 0.7943 (t-90) cc_final: 0.7501 (t-90) REVERT: E 182 PHE cc_start: 0.7074 (m-10) cc_final: 0.6500 (m-10) REVERT: E 244 ILE cc_start: 0.9538 (mp) cc_final: 0.8965 (mp) REVERT: E 271 ARG cc_start: 0.8554 (ptt90) cc_final: 0.8213 (ttp80) REVERT: E 276 TRP cc_start: 0.7188 (t60) cc_final: 0.6549 (t60) REVERT: E 297 LYS cc_start: 0.8641 (mtmm) cc_final: 0.8149 (mtmm) REVERT: E 309 PHE cc_start: 0.9121 (m-10) cc_final: 0.8814 (m-10) REVERT: E 314 PHE cc_start: 0.7891 (m-10) cc_final: 0.7471 (m-10) REVERT: F 73 HIS cc_start: 0.8001 (t-90) cc_final: 0.7761 (t-90) REVERT: F 80 HIS cc_start: 0.8492 (m90) cc_final: 0.8113 (m90) REVERT: F 83 GLN cc_start: 0.7936 (tm-30) cc_final: 0.7384 (tm-30) REVERT: F 151 MET cc_start: 0.8525 (mtm) cc_final: 0.8219 (mtm) REVERT: F 176 HIS cc_start: 0.8463 (t-170) cc_final: 0.8027 (t-170) REVERT: F 229 VAL cc_start: 0.9326 (p) cc_final: 0.9104 (m) REVERT: F 242 ARG cc_start: 0.8644 (tpp-160) cc_final: 0.7504 (tpp-160) REVERT: F 257 GLN cc_start: 0.8862 (tp40) cc_final: 0.8538 (tp-100) REVERT: F 268 MET cc_start: 0.7147 (mmp) cc_final: 0.6894 (mmt) REVERT: F 309 PHE cc_start: 0.8766 (m-80) cc_final: 0.8360 (m-80) REVERT: F 310 TYR cc_start: 0.7704 (t80) cc_final: 0.7431 (t80) REVERT: F 312 ARG cc_start: 0.8398 (mmt-90) cc_final: 0.8139 (mmt-90) REVERT: a 10 ASN cc_start: 0.9063 (t0) cc_final: 0.8798 (t0) REVERT: a 22 PHE cc_start: 0.7497 (m-80) cc_final: 0.7249 (m-80) REVERT: a 29 MET cc_start: 0.6718 (mmp) cc_final: 0.6293 (mmp) REVERT: a 109 LYS cc_start: 0.8732 (tmtt) cc_final: 0.8503 (tptp) REVERT: a 151 MET cc_start: 0.8729 (pmm) cc_final: 0.8325 (pmm) REVERT: a 155 GLN cc_start: 0.8834 (mt0) cc_final: 0.8433 (mt0) REVERT: a 186 ASN cc_start: 0.8246 (m110) cc_final: 0.7979 (m110) REVERT: a 204 ASN cc_start: 0.8404 (p0) cc_final: 0.8046 (p0) REVERT: a 291 ARG cc_start: 0.8200 (ptp-110) cc_final: 0.7753 (mtm110) REVERT: b 80 HIS cc_start: 0.7968 (m90) cc_final: 0.7478 (m90) REVERT: b 100 HIS cc_start: 0.8316 (m90) cc_final: 0.8035 (m90) REVERT: b 106 LEU cc_start: 0.9008 (mm) cc_final: 0.8798 (mm) REVERT: b 141 ASP cc_start: 0.7329 (t70) cc_final: 0.7051 (t70) REVERT: b 154 ILE cc_start: 0.8929 (mm) cc_final: 0.8426 (tp) REVERT: b 168 ASP cc_start: 0.7854 (p0) cc_final: 0.7522 (p0) REVERT: b 180 ARG cc_start: 0.6714 (mpt180) cc_final: 0.6357 (mpt180) REVERT: b 208 MET cc_start: 0.7587 (mtm) cc_final: 0.7048 (mtt) REVERT: b 215 THR cc_start: 0.8474 (m) cc_final: 0.7978 (t) REVERT: b 235 HIS cc_start: 0.8031 (t-90) cc_final: 0.7753 (t-90) REVERT: b 254 MET cc_start: 0.8851 (ppp) cc_final: 0.8625 (ppp) REVERT: b 256 ARG cc_start: 0.8300 (ttm-80) cc_final: 0.7968 (ttm-80) REVERT: b 299 ASP cc_start: 0.7389 (t0) cc_final: 0.7109 (t0) REVERT: b 309 PHE cc_start: 0.7048 (m-80) cc_final: 0.6682 (m-80) REVERT: c 11 LEU cc_start: 0.8814 (mt) cc_final: 0.8604 (mt) REVERT: c 28 MET cc_start: 0.7383 (mtm) cc_final: 0.7145 (mtm) REVERT: c 55 LEU cc_start: 0.9099 (mt) cc_final: 0.8875 (mt) REVERT: c 68 MET cc_start: 0.6780 (tmm) cc_final: 0.5958 (tmm) REVERT: c 103 ARG cc_start: 0.8783 (mmm-85) cc_final: 0.8406 (mmm-85) REVERT: c 141 ASP cc_start: 0.6015 (p0) cc_final: 0.5590 (p0) REVERT: c 149 ASP cc_start: 0.8045 (t0) cc_final: 0.7451 (t0) REVERT: c 151 MET cc_start: 0.7927 (mtm) cc_final: 0.7491 (mtt) REVERT: c 156 ARG cc_start: 0.8908 (tpt90) cc_final: 0.8609 (tpt170) REVERT: c 174 ARG cc_start: 0.7452 (tmm160) cc_final: 0.6905 (tmm160) REVERT: c 209 ASP cc_start: 0.8138 (t0) cc_final: 0.7815 (t0) REVERT: c 295 LEU cc_start: 0.8138 (tp) cc_final: 0.7812 (tp) REVERT: c 309 PHE cc_start: 0.7955 (m-10) cc_final: 0.7629 (m-80) REVERT: d 65 ARG cc_start: 0.8292 (mmm-85) cc_final: 0.8066 (mmm-85) REVERT: d 68 MET cc_start: 0.7089 (ttt) cc_final: 0.6859 (ttt) REVERT: d 69 VAL cc_start: 0.8788 (t) cc_final: 0.8261 (m) REVERT: d 82 GLU cc_start: 0.8565 (pt0) cc_final: 0.8252 (pt0) REVERT: d 124 LYS cc_start: 0.8880 (tmmt) cc_final: 0.8541 (tmmt) REVERT: d 130 TRP cc_start: 0.8520 (t60) cc_final: 0.8264 (t60) REVERT: d 138 LEU cc_start: 0.8161 (tp) cc_final: 0.7894 (tp) REVERT: d 152 PHE cc_start: 0.7354 (m-80) cc_final: 0.7057 (m-80) REVERT: d 211 TRP cc_start: 0.8411 (m100) cc_final: 0.7978 (m100) REVERT: d 242 ARG cc_start: 0.7974 (mmm-85) cc_final: 0.7705 (mmm-85) REVERT: d 245 VAL cc_start: 0.8357 (p) cc_final: 0.7956 (m) REVERT: d 248 MET cc_start: 0.7961 (ptt) cc_final: 0.7605 (ptt) REVERT: d 282 ILE cc_start: 0.7704 (mt) cc_final: 0.7499 (mt) REVERT: d 314 PHE cc_start: 0.8613 (m-10) cc_final: 0.8285 (m-10) REVERT: e 16 VAL cc_start: 0.8268 (t) cc_final: 0.8005 (t) REVERT: e 68 MET cc_start: 0.7412 (mtt) cc_final: 0.7134 (mtt) REVERT: e 87 ARG cc_start: 0.8382 (mmp-170) cc_final: 0.8125 (mmp-170) REVERT: e 93 VAL cc_start: 0.8739 (t) cc_final: 0.8359 (m) REVERT: e 155 GLN cc_start: 0.8382 (tp40) cc_final: 0.7924 (tp40) REVERT: e 158 LEU cc_start: 0.9287 (tp) cc_final: 0.9000 (tp) REVERT: e 164 LEU cc_start: 0.8595 (tt) cc_final: 0.8373 (tt) REVERT: e 176 HIS cc_start: 0.8075 (t-90) cc_final: 0.7660 (t-90) REVERT: e 227 ASN cc_start: 0.8653 (m110) cc_final: 0.8380 (m110) REVERT: e 244 ILE cc_start: 0.9389 (OUTLIER) cc_final: 0.9137 (mp) REVERT: e 276 TRP cc_start: 0.7094 (t60) cc_final: 0.6871 (t60) REVERT: e 296 ASN cc_start: 0.7943 (t0) cc_final: 0.7574 (t0) REVERT: f 42 GLU cc_start: 0.7979 (pp20) cc_final: 0.7720 (pp20) REVERT: f 43 LEU cc_start: 0.8796 (mm) cc_final: 0.8256 (mm) REVERT: f 68 MET cc_start: 0.6974 (tpt) cc_final: 0.6681 (tpt) REVERT: f 73 HIS cc_start: 0.7874 (t-90) cc_final: 0.7603 (t-90) REVERT: f 278 GLU cc_start: 0.8338 (mt-10) cc_final: 0.7907 (mt-10) REVERT: f 309 PHE cc_start: 0.9115 (m-80) cc_final: 0.8726 (m-80) outliers start: 4 outliers final: 0 residues processed: 988 average time/residue: 0.2125 time to fit residues: 318.1605 Evaluate side-chains 950 residues out of total 2985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 949 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 158 optimal weight: 50.0000 chunk 221 optimal weight: 0.8980 chunk 107 optimal weight: 0.9980 chunk 231 optimal weight: 0.3980 chunk 62 optimal weight: 9.9990 chunk 120 optimal weight: 7.9990 chunk 337 optimal weight: 7.9990 chunk 31 optimal weight: 0.4980 chunk 206 optimal weight: 0.7980 chunk 223 optimal weight: 0.6980 chunk 141 optimal weight: 10.0000 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 204 ASN ** F 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 52 GLN ** b 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 155 GLN ** b 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 83 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.160833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.128578 restraints weight = 58744.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.133728 restraints weight = 36618.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.137448 restraints weight = 25772.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.140325 restraints weight = 19637.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.141894 restraints weight = 15725.113| |-----------------------------------------------------------------------------| r_work (final): 0.3963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6861 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 28330 Z= 0.108 Angle : 0.559 10.890 38522 Z= 0.289 Chirality : 0.043 0.177 4383 Planarity : 0.004 0.073 5016 Dihedral : 4.325 23.342 3838 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.51 % Favored : 95.41 % Rotamer: Outliers : 0.03 % Allowed : 2.24 % Favored : 97.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.15), residues: 3439 helix: 0.52 (0.13), residues: 1521 sheet: -0.41 (0.24), residues: 469 loop : -0.93 (0.17), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 256 TYR 0.020 0.001 TYR E 219 PHE 0.036 0.001 PHE f 152 TRP 0.025 0.002 TRP E 130 HIS 0.005 0.001 HIS c 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 (28330) covalent geometry : angle 0.55931 / 0.29 (38522) hydrogen bonds : bond 0.03049 / 2.04 ( 1188) hydrogen bonds : angle 5.11530 / 3.66 ( 3471) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 952 residues out of total 2985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 951 time to evaluate : 1.031 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 ASN cc_start: 0.8527 (t0) cc_final: 0.7920 (t0) REVERT: A 22 PHE cc_start: 0.7808 (m-80) cc_final: 0.7557 (m-80) REVERT: A 29 MET cc_start: 0.6952 (mmp) cc_final: 0.6597 (mmp) REVERT: A 65 ARG cc_start: 0.7810 (mmm-85) cc_final: 0.7441 (mtp-110) REVERT: A 68 MET cc_start: 0.8296 (ttm) cc_final: 0.8049 (ttm) REVERT: A 94 ARG cc_start: 0.8401 (mtp180) cc_final: 0.8184 (mtm180) REVERT: A 268 MET cc_start: 0.7455 (mmm) cc_final: 0.6452 (mpp) REVERT: B 28 MET cc_start: 0.5344 (ptp) cc_final: 0.5070 (ptp) REVERT: B 68 MET cc_start: 0.7414 (mmm) cc_final: 0.5580 (mmm) REVERT: B 80 HIS cc_start: 0.7850 (m90) cc_final: 0.7358 (m90) REVERT: B 89 ASN cc_start: 0.7844 (t0) cc_final: 0.7440 (t0) REVERT: B 96 ASN cc_start: 0.8570 (t0) cc_final: 0.7879 (t0) REVERT: B 98 ASP cc_start: 0.7571 (p0) cc_final: 0.7081 (p0) REVERT: B 100 HIS cc_start: 0.7955 (m90) cc_final: 0.7585 (m90) REVERT: B 130 TRP cc_start: 0.8811 (t60) cc_final: 0.8482 (t60) REVERT: B 211 TRP cc_start: 0.7337 (m100) cc_final: 0.6410 (m100) REVERT: B 213 ILE cc_start: 0.7857 (mp) cc_final: 0.7551 (mp) REVERT: B 215 THR cc_start: 0.8038 (m) cc_final: 0.7829 (t) REVERT: B 278 GLU cc_start: 0.8157 (pt0) cc_final: 0.7952 (pt0) REVERT: C 68 MET cc_start: 0.7010 (ttp) cc_final: 0.6621 (ttp) REVERT: C 97 LEU cc_start: 0.8404 (mp) cc_final: 0.8033 (mp) REVERT: C 103 ARG cc_start: 0.8604 (mtp-110) cc_final: 0.8372 (mtp180) REVERT: C 105 ASP cc_start: 0.8448 (m-30) cc_final: 0.8223 (m-30) REVERT: C 151 MET cc_start: 0.8148 (mmp) cc_final: 0.7649 (mmt) REVERT: C 248 MET cc_start: 0.8694 (ttm) cc_final: 0.8238 (ttm) REVERT: C 303 ARG cc_start: 0.8834 (mmm-85) cc_final: 0.8453 (mmm-85) REVERT: C 314 PHE cc_start: 0.8015 (m-10) cc_final: 0.7555 (m-10) REVERT: D 10 ASN cc_start: 0.8633 (t0) cc_final: 0.8392 (t0) REVERT: D 29 MET cc_start: 0.6269 (mmp) cc_final: 0.5954 (mmp) REVERT: D 39 TYR cc_start: 0.8615 (m-80) cc_final: 0.8286 (m-80) REVERT: D 94 ARG cc_start: 0.8500 (ptp-170) cc_final: 0.7914 (ptp-170) REVERT: D 95 VAL cc_start: 0.8360 (t) cc_final: 0.7706 (m) REVERT: D 106 LEU cc_start: 0.8369 (mp) cc_final: 0.8097 (mp) REVERT: D 135 ASN cc_start: 0.8130 (p0) cc_final: 0.7740 (p0) REVERT: D 151 MET cc_start: 0.8172 (tpt) cc_final: 0.7620 (tpt) REVERT: D 152 PHE cc_start: 0.8441 (t80) cc_final: 0.8202 (t80) REVERT: D 155 GLN cc_start: 0.8762 (mt0) cc_final: 0.8273 (mt0) REVERT: D 314 PHE cc_start: 0.8812 (m-10) cc_final: 0.8403 (m-10) REVERT: E 28 MET cc_start: 0.5875 (mtm) cc_final: 0.5673 (mtm) REVERT: E 66 ARG cc_start: 0.6567 (mmt90) cc_final: 0.5894 (mtt90) REVERT: E 68 MET cc_start: 0.7635 (mmm) cc_final: 0.7349 (mmp) REVERT: E 147 ARG cc_start: 0.8144 (ttp-110) cc_final: 0.7415 (ttp-110) REVERT: E 149 ASP cc_start: 0.7674 (t0) cc_final: 0.6872 (t0) REVERT: E 168 ASP cc_start: 0.7078 (t0) cc_final: 0.6760 (t0) REVERT: E 176 HIS cc_start: 0.7881 (t-90) cc_final: 0.7465 (t-90) REVERT: E 182 PHE cc_start: 0.7037 (m-10) cc_final: 0.6531 (m-80) REVERT: E 271 ARG cc_start: 0.8498 (ptt90) cc_final: 0.8131 (ttp80) REVERT: E 297 LYS cc_start: 0.8688 (mtmm) cc_final: 0.8238 (mtmm) REVERT: E 309 PHE cc_start: 0.9105 (m-10) cc_final: 0.8775 (m-10) REVERT: E 314 PHE cc_start: 0.7824 (m-10) cc_final: 0.7607 (m-10) REVERT: F 68 MET cc_start: 0.6132 (ppp) cc_final: 0.5579 (ppp) REVERT: F 80 HIS cc_start: 0.8421 (m90) cc_final: 0.8062 (m90) REVERT: F 83 GLN cc_start: 0.8009 (tm-30) cc_final: 0.7430 (tm-30) REVERT: F 151 MET cc_start: 0.8418 (mtm) cc_final: 0.8147 (mtm) REVERT: F 176 HIS cc_start: 0.8404 (t-170) cc_final: 0.7922 (t-170) REVERT: F 229 VAL cc_start: 0.9304 (p) cc_final: 0.9073 (m) REVERT: F 242 ARG cc_start: 0.8617 (tpp-160) cc_final: 0.7455 (tpp-160) REVERT: F 248 MET cc_start: 0.8645 (mmp) cc_final: 0.8420 (mmp) REVERT: F 257 GLN cc_start: 0.8848 (tp40) cc_final: 0.8223 (tp-100) REVERT: F 261 ASN cc_start: 0.8528 (m110) cc_final: 0.7950 (m110) REVERT: F 268 MET cc_start: 0.6956 (mmp) cc_final: 0.6753 (mmt) REVERT: F 295 LEU cc_start: 0.7589 (mp) cc_final: 0.7092 (mp) REVERT: F 309 PHE cc_start: 0.8714 (m-80) cc_final: 0.8327 (m-80) REVERT: F 312 ARG cc_start: 0.8413 (mmt-90) cc_final: 0.8123 (mmt-90) REVERT: a 10 ASN cc_start: 0.9030 (t0) cc_final: 0.8730 (t0) REVERT: a 22 PHE cc_start: 0.7447 (m-80) cc_final: 0.7211 (m-80) REVERT: a 29 MET cc_start: 0.6737 (mmp) cc_final: 0.6353 (mmp) REVERT: a 52 GLN cc_start: 0.6735 (OUTLIER) cc_final: 0.6295 (tm130) REVERT: a 151 MET cc_start: 0.8622 (pmm) cc_final: 0.8286 (pmm) REVERT: a 155 GLN cc_start: 0.8791 (mt0) cc_final: 0.8364 (mt0) REVERT: a 186 ASN cc_start: 0.8215 (m110) cc_final: 0.7957 (m110) REVERT: a 204 ASN cc_start: 0.8424 (p0) cc_final: 0.8077 (p0) REVERT: a 268 MET cc_start: 0.7415 (tpp) cc_final: 0.6222 (mmm) REVERT: a 278 GLU cc_start: 0.8327 (mp0) cc_final: 0.8081 (mp0) REVERT: a 291 ARG cc_start: 0.8129 (ptp-110) cc_final: 0.7219 (mtm110) REVERT: a 309 PHE cc_start: 0.7333 (m-80) cc_final: 0.7017 (m-80) REVERT: b 68 MET cc_start: 0.7387 (mmm) cc_final: 0.7115 (tpt) REVERT: b 80 HIS cc_start: 0.7955 (m90) cc_final: 0.7390 (m90) REVERT: b 100 HIS cc_start: 0.8275 (m90) cc_final: 0.7924 (m90) REVERT: b 106 LEU cc_start: 0.8989 (mm) cc_final: 0.8753 (mm) REVERT: b 141 ASP cc_start: 0.7225 (t70) cc_final: 0.6990 (t70) REVERT: b 154 ILE cc_start: 0.8894 (mm) cc_final: 0.8399 (tp) REVERT: b 168 ASP cc_start: 0.7946 (p0) cc_final: 0.7537 (p0) REVERT: b 180 ARG cc_start: 0.6662 (mpt180) cc_final: 0.6290 (mpt180) REVERT: b 208 MET cc_start: 0.7563 (mtm) cc_final: 0.6935 (mtt) REVERT: b 215 THR cc_start: 0.8420 (m) cc_final: 0.8065 (t) REVERT: b 235 HIS cc_start: 0.8015 (t-90) cc_final: 0.7717 (t-90) REVERT: b 242 ARG cc_start: 0.8889 (tpt170) cc_final: 0.8526 (tpt170) REVERT: b 299 ASP cc_start: 0.7230 (t0) cc_final: 0.6965 (t0) REVERT: b 309 PHE cc_start: 0.6867 (m-80) cc_final: 0.6562 (m-80) REVERT: c 11 LEU cc_start: 0.8701 (mt) cc_final: 0.8489 (mt) REVERT: c 28 MET cc_start: 0.7351 (mtm) cc_final: 0.7092 (mtm) REVERT: c 55 LEU cc_start: 0.9073 (mt) cc_final: 0.8850 (mt) REVERT: c 68 MET cc_start: 0.6772 (tmm) cc_final: 0.5946 (tmm) REVERT: c 103 ARG cc_start: 0.8681 (mmm-85) cc_final: 0.8149 (mmm-85) REVERT: c 141 ASP cc_start: 0.5839 (p0) cc_final: 0.5380 (p0) REVERT: c 149 ASP cc_start: 0.8063 (t0) cc_final: 0.7440 (t0) REVERT: c 151 MET cc_start: 0.7839 (mtm) cc_final: 0.7369 (mtt) REVERT: c 168 ASP cc_start: 0.8495 (t0) cc_final: 0.8278 (t0) REVERT: c 174 ARG cc_start: 0.7381 (tmm160) cc_final: 0.6802 (tmm160) REVERT: c 209 ASP cc_start: 0.8138 (t0) cc_final: 0.7800 (t0) REVERT: c 295 LEU cc_start: 0.8100 (tp) cc_final: 0.7796 (tp) REVERT: c 309 PHE cc_start: 0.7883 (m-10) cc_final: 0.7533 (m-80) REVERT: d 10 ASN cc_start: 0.8424 (t0) cc_final: 0.8016 (t0) REVERT: d 33 TYR cc_start: 0.6160 (m-80) cc_final: 0.5954 (m-80) REVERT: d 65 ARG cc_start: 0.8217 (mmm-85) cc_final: 0.7969 (mmm-85) REVERT: d 68 MET cc_start: 0.6973 (ttt) cc_final: 0.6726 (ttt) REVERT: d 69 VAL cc_start: 0.8690 (t) cc_final: 0.8133 (m) REVERT: d 82 GLU cc_start: 0.8467 (pt0) cc_final: 0.8143 (pt0) REVERT: d 124 LYS cc_start: 0.8869 (tmmt) cc_final: 0.8507 (tmmt) REVERT: d 128 LEU cc_start: 0.9280 (mt) cc_final: 0.9021 (mt) REVERT: d 130 TRP cc_start: 0.8483 (t60) cc_final: 0.8094 (t60) REVERT: d 138 LEU cc_start: 0.8164 (tp) cc_final: 0.7852 (tp) REVERT: d 156 ARG cc_start: 0.8454 (mmm-85) cc_final: 0.8031 (mmm-85) REVERT: d 166 LEU cc_start: 0.8384 (tp) cc_final: 0.8089 (tp) REVERT: d 211 TRP cc_start: 0.8368 (m100) cc_final: 0.7953 (m100) REVERT: d 242 ARG cc_start: 0.7938 (mmm-85) cc_final: 0.7639 (mmm-85) REVERT: d 248 MET cc_start: 0.7955 (ptt) cc_final: 0.7604 (ptt) REVERT: d 282 ILE cc_start: 0.7643 (mt) cc_final: 0.7431 (mt) REVERT: d 314 PHE cc_start: 0.8574 (m-10) cc_final: 0.8247 (m-10) REVERT: e 10 ASN cc_start: 0.8612 (m-40) cc_final: 0.8407 (m-40) REVERT: e 16 VAL cc_start: 0.8205 (t) cc_final: 0.7915 (t) REVERT: e 68 MET cc_start: 0.7416 (mtt) cc_final: 0.6874 (mtt) REVERT: e 80 HIS cc_start: 0.8618 (t70) cc_final: 0.8181 (t70) REVERT: e 83 GLN cc_start: 0.8592 (pt0) cc_final: 0.8351 (pp30) REVERT: e 87 ARG cc_start: 0.8414 (mmp-170) cc_final: 0.8127 (mmp-170) REVERT: e 93 VAL cc_start: 0.8724 (t) cc_final: 0.8367 (p) REVERT: e 158 LEU cc_start: 0.9227 (tp) cc_final: 0.8959 (tp) REVERT: e 164 LEU cc_start: 0.8515 (tt) cc_final: 0.8299 (tt) REVERT: e 165 THR cc_start: 0.7582 (t) cc_final: 0.7346 (t) REVERT: e 176 HIS cc_start: 0.8003 (t-90) cc_final: 0.7594 (t-90) REVERT: e 227 ASN cc_start: 0.8684 (m110) cc_final: 0.8420 (m110) REVERT: e 244 ILE cc_start: 0.9364 (mp) cc_final: 0.9083 (mp) REVERT: e 248 MET cc_start: 0.8827 (mmm) cc_final: 0.8132 (mmt) REVERT: e 257 GLN cc_start: 0.8228 (tp-100) cc_final: 0.7314 (tp-100) REVERT: e 296 ASN cc_start: 0.7850 (t0) cc_final: 0.7565 (t0) REVERT: e 299 ASP cc_start: 0.7241 (t0) cc_final: 0.7037 (t0) REVERT: f 42 GLU cc_start: 0.8009 (pp20) cc_final: 0.7630 (pp20) REVERT: f 68 MET cc_start: 0.6932 (tpt) cc_final: 0.6568 (tpt) REVERT: f 80 HIS cc_start: 0.8321 (m90) cc_final: 0.8110 (m90) REVERT: f 182 PHE cc_start: 0.8342 (m-80) cc_final: 0.8125 (m-80) REVERT: f 278 GLU cc_start: 0.8273 (mt-10) cc_final: 0.7831 (mt-10) REVERT: f 309 PHE cc_start: 0.9079 (m-80) cc_final: 0.8726 (m-80) outliers start: 1 outliers final: 0 residues processed: 952 average time/residue: 0.2152 time to fit residues: 309.3236 Evaluate side-chains 926 residues out of total 2985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 925 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 157 optimal weight: 0.5980 chunk 192 optimal weight: 7.9990 chunk 1 optimal weight: 5.9990 chunk 239 optimal weight: 10.0000 chunk 112 optimal weight: 10.0000 chunk 197 optimal weight: 0.6980 chunk 140 optimal weight: 6.9990 chunk 205 optimal weight: 9.9990 chunk 15 optimal weight: 10.0000 chunk 204 optimal weight: 2.9990 chunk 291 optimal weight: 3.9990 overall best weight: 2.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 52 GLN E 296 ASN F 52 GLN ** F 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 80 HIS a 169 GLN ** b 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 83 GLN ** 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 = 0.4165 r_free = 0.4165 target = 0.155337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.123363 restraints weight = 59188.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.128331 restraints weight = 36903.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.132010 restraints weight = 26120.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.134721 restraints weight = 19836.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.136278 restraints weight = 15931.342| |-----------------------------------------------------------------------------| r_work (final): 0.3887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6990 moved from start: 0.2506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.124 28330 Z= 0.245 Angle : 0.666 13.778 38522 Z= 0.359 Chirality : 0.045 0.224 4383 Planarity : 0.005 0.090 5016 Dihedral : 4.761 25.499 3838 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 15.07 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.84 % Favored : 94.07 % Rotamer: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.14), residues: 3439 helix: 0.11 (0.13), residues: 1532 sheet: -0.62 (0.25), residues: 443 loop : -1.12 (0.17), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 291 TYR 0.024 0.002 TYR e 132 PHE 0.031 0.002 PHE f 152 TRP 0.045 0.003 TRP E 130 HIS 0.006 0.001 HIS f 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00484 / 0.25 (28330) covalent geometry : angle 0.66574 / 0.36 (38522) hydrogen bonds : bond 0.04022 / 2.69 ( 1188) hydrogen bonds : angle 5.53730 / 3.95 ( 3471) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 989 residues out of total 2985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 989 time to evaluate : 1.005 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 ASN cc_start: 0.8646 (t0) cc_final: 0.8030 (t0) REVERT: A 22 PHE cc_start: 0.7765 (m-80) cc_final: 0.7543 (m-80) REVERT: A 65 ARG cc_start: 0.8156 (mmm-85) cc_final: 0.7816 (mtp-110) REVERT: A 68 MET cc_start: 0.8290 (ttm) cc_final: 0.7933 (ttm) REVERT: A 97 LEU cc_start: 0.8084 (mt) cc_final: 0.7856 (mt) REVERT: A 109 LYS cc_start: 0.8481 (ttpp) cc_final: 0.8123 (ttpp) REVERT: A 138 LEU cc_start: 0.8066 (tp) cc_final: 0.7677 (tp) REVERT: A 140 PHE cc_start: 0.7978 (m-80) cc_final: 0.7586 (m-80) REVERT: A 164 LEU cc_start: 0.8354 (tp) cc_final: 0.8025 (tp) REVERT: A 181 LEU cc_start: 0.8307 (tp) cc_final: 0.8001 (tp) REVERT: A 268 MET cc_start: 0.7569 (mmm) cc_final: 0.6787 (mpp) REVERT: B 28 MET cc_start: 0.5360 (ptp) cc_final: 0.5047 (ptp) REVERT: B 68 MET cc_start: 0.7630 (mmm) cc_final: 0.7254 (mmm) REVERT: B 80 HIS cc_start: 0.8022 (m90) cc_final: 0.7696 (m90) REVERT: B 89 ASN cc_start: 0.7853 (t0) cc_final: 0.7429 (t0) REVERT: B 98 ASP cc_start: 0.7715 (p0) cc_final: 0.7355 (p0) REVERT: B 100 HIS cc_start: 0.8078 (m90) cc_final: 0.7692 (m90) REVERT: B 130 TRP cc_start: 0.8864 (t60) cc_final: 0.8588 (t60) REVERT: B 278 GLU cc_start: 0.8290 (pt0) cc_final: 0.8064 (pt0) REVERT: C 28 MET cc_start: 0.7375 (mtm) cc_final: 0.7132 (mtm) REVERT: C 68 MET cc_start: 0.7192 (ttp) cc_final: 0.6770 (ttp) REVERT: C 75 THR cc_start: 0.8799 (p) cc_final: 0.8553 (p) REVERT: C 105 ASP cc_start: 0.8505 (m-30) cc_final: 0.8279 (m-30) REVERT: C 151 MET cc_start: 0.7994 (mmp) cc_final: 0.7787 (mmt) REVERT: C 186 ASN cc_start: 0.7366 (m110) cc_final: 0.7135 (m110) REVERT: C 248 MET cc_start: 0.8636 (ttm) cc_final: 0.8150 (ttm) REVERT: C 303 ARG cc_start: 0.8867 (mmm-85) cc_final: 0.8511 (mmm-85) REVERT: C 314 PHE cc_start: 0.8158 (m-10) cc_final: 0.7753 (m-10) REVERT: D 10 ASN cc_start: 0.8663 (t0) cc_final: 0.8396 (t0) REVERT: D 29 MET cc_start: 0.6318 (mmp) cc_final: 0.6065 (mmp) REVERT: D 39 TYR cc_start: 0.8538 (m-80) cc_final: 0.8309 (m-80) REVERT: D 63 TYR cc_start: 0.8460 (m-80) cc_final: 0.8249 (m-80) REVERT: D 95 VAL cc_start: 0.8734 (t) cc_final: 0.8221 (m) REVERT: D 128 LEU cc_start: 0.9203 (mt) cc_final: 0.8997 (mt) REVERT: D 135 ASN cc_start: 0.8074 (p0) cc_final: 0.7711 (p0) REVERT: D 151 MET cc_start: 0.8218 (tpt) cc_final: 0.7736 (tpt) REVERT: D 152 PHE cc_start: 0.8499 (t80) cc_final: 0.8208 (t80) REVERT: D 155 GLN cc_start: 0.8845 (mt0) cc_final: 0.8368 (mt0) REVERT: D 229 VAL cc_start: 0.8903 (p) cc_final: 0.8702 (m) REVERT: D 248 MET cc_start: 0.8271 (mmp) cc_final: 0.8020 (mmp) REVERT: D 314 PHE cc_start: 0.8813 (m-10) cc_final: 0.8408 (m-10) REVERT: E 28 MET cc_start: 0.5913 (mtm) cc_final: 0.5710 (mtm) REVERT: E 66 ARG cc_start: 0.6902 (mmt90) cc_final: 0.6666 (mmm-85) REVERT: E 68 MET cc_start: 0.7828 (mmm) cc_final: 0.7545 (mmm) REVERT: E 93 VAL cc_start: 0.8621 (t) cc_final: 0.8252 (p) REVERT: E 130 TRP cc_start: 0.8740 (t60) cc_final: 0.8309 (t60) REVERT: E 147 ARG cc_start: 0.8316 (ttp-110) cc_final: 0.7594 (ttp-110) REVERT: E 149 ASP cc_start: 0.7727 (t0) cc_final: 0.6898 (t0) REVERT: E 158 LEU cc_start: 0.9214 (tp) cc_final: 0.9010 (tp) REVERT: E 168 ASP cc_start: 0.7304 (t0) cc_final: 0.7019 (t0) REVERT: E 176 HIS cc_start: 0.8046 (t-90) cc_final: 0.7639 (t-90) REVERT: E 182 PHE cc_start: 0.7137 (m-10) cc_final: 0.6561 (m-80) REVERT: E 244 ILE cc_start: 0.9544 (mp) cc_final: 0.9084 (mp) REVERT: E 276 TRP cc_start: 0.7222 (t60) cc_final: 0.6555 (t60) REVERT: E 297 LYS cc_start: 0.8666 (mtmm) cc_final: 0.8156 (mtmm) REVERT: E 309 PHE cc_start: 0.9117 (m-10) cc_final: 0.8795 (m-10) REVERT: E 314 PHE cc_start: 0.7897 (m-10) cc_final: 0.7521 (m-10) REVERT: F 68 MET cc_start: 0.6393 (ppp) cc_final: 0.5539 (ppp) REVERT: F 80 HIS cc_start: 0.8503 (m90) cc_final: 0.8164 (m90) REVERT: F 83 GLN cc_start: 0.7904 (tm-30) cc_final: 0.7311 (tm-30) REVERT: F 151 MET cc_start: 0.8491 (mtm) cc_final: 0.8149 (mtm) REVERT: F 176 HIS cc_start: 0.8518 (t-170) cc_final: 0.8080 (t-170) REVERT: F 214 VAL cc_start: 0.7622 (p) cc_final: 0.6762 (p) REVERT: F 242 ARG cc_start: 0.8678 (tpp-160) cc_final: 0.7567 (tpp-160) REVERT: F 248 MET cc_start: 0.8677 (mmp) cc_final: 0.8445 (mmp) REVERT: F 257 GLN cc_start: 0.8844 (tp40) cc_final: 0.8528 (tp-100) REVERT: F 309 PHE cc_start: 0.8882 (m-80) cc_final: 0.8470 (m-80) REVERT: F 312 ARG cc_start: 0.8493 (mmt-90) cc_final: 0.8219 (mmt-90) REVERT: a 22 PHE cc_start: 0.7529 (m-80) cc_final: 0.7284 (m-80) REVERT: a 29 MET cc_start: 0.6703 (mmp) cc_final: 0.6340 (mmp) REVERT: a 33 TYR cc_start: 0.7562 (m-80) cc_final: 0.7059 (m-80) REVERT: a 94 ARG cc_start: 0.8415 (mtp180) cc_final: 0.8132 (mtm180) REVERT: a 109 LYS cc_start: 0.8760 (tmtt) cc_final: 0.8542 (tptp) REVERT: a 151 MET cc_start: 0.8725 (pmm) cc_final: 0.8402 (pmm) REVERT: a 155 GLN cc_start: 0.8843 (mt0) cc_final: 0.8445 (mt0) REVERT: a 186 ASN cc_start: 0.8271 (m110) cc_final: 0.7951 (m110) REVERT: a 204 ASN cc_start: 0.8437 (p0) cc_final: 0.8071 (p0) REVERT: a 268 MET cc_start: 0.7839 (tpp) cc_final: 0.6272 (mmm) REVERT: a 291 ARG cc_start: 0.8233 (ptp-110) cc_final: 0.7325 (mtm110) REVERT: a 309 PHE cc_start: 0.7469 (m-80) cc_final: 0.7128 (m-80) REVERT: b 80 HIS cc_start: 0.8074 (m90) cc_final: 0.7513 (m90) REVERT: b 100 HIS cc_start: 0.8341 (m90) cc_final: 0.8088 (m90) REVERT: b 141 ASP cc_start: 0.7478 (t70) cc_final: 0.7154 (t70) REVERT: b 154 ILE cc_start: 0.9041 (mm) cc_final: 0.8639 (tp) REVERT: b 168 ASP cc_start: 0.7940 (p0) cc_final: 0.7593 (p0) REVERT: b 208 MET cc_start: 0.7619 (mtm) cc_final: 0.7052 (mtt) REVERT: b 215 THR cc_start: 0.8567 (m) cc_final: 0.8025 (t) REVERT: b 235 HIS cc_start: 0.8074 (t-90) cc_final: 0.7820 (t-90) REVERT: b 254 MET cc_start: 0.8859 (ppp) cc_final: 0.8631 (ppp) REVERT: b 261 ASN cc_start: 0.8148 (m110) cc_final: 0.7854 (m110) REVERT: b 299 ASP cc_start: 0.7428 (t0) cc_final: 0.7155 (t0) REVERT: b 309 PHE cc_start: 0.7085 (m-80) cc_final: 0.6675 (m-80) REVERT: c 28 MET cc_start: 0.7492 (mtm) cc_final: 0.7194 (mtm) REVERT: c 55 LEU cc_start: 0.9082 (mt) cc_final: 0.8851 (mt) REVERT: c 68 MET cc_start: 0.6892 (tmm) cc_final: 0.6466 (tmm) REVERT: c 103 ARG cc_start: 0.8743 (mmm-85) cc_final: 0.8237 (mmm-85) REVERT: c 149 ASP cc_start: 0.8087 (t0) cc_final: 0.7460 (t0) REVERT: c 151 MET cc_start: 0.7932 (mtm) cc_final: 0.7522 (mtt) REVERT: c 156 ARG cc_start: 0.9072 (tpt170) cc_final: 0.8864 (tpt170) REVERT: c 174 ARG cc_start: 0.7458 (tmm160) cc_final: 0.6942 (tmm160) REVERT: c 268 MET cc_start: 0.8034 (tpt) cc_final: 0.7794 (tpt) REVERT: c 295 LEU cc_start: 0.8119 (tp) cc_final: 0.7789 (tp) REVERT: d 10 ASN cc_start: 0.8523 (t0) cc_final: 0.8177 (t0) REVERT: d 65 ARG cc_start: 0.8303 (mmm-85) cc_final: 0.7637 (mmt180) REVERT: d 69 VAL cc_start: 0.8796 (t) cc_final: 0.8296 (m) REVERT: d 82 GLU cc_start: 0.8620 (pt0) cc_final: 0.8333 (pt0) REVERT: d 95 VAL cc_start: 0.9052 (t) cc_final: 0.8703 (p) REVERT: d 100 HIS cc_start: 0.7872 (m90) cc_final: 0.7671 (m90) REVERT: d 106 LEU cc_start: 0.8719 (mp) cc_final: 0.8485 (mp) REVERT: d 124 LYS cc_start: 0.8880 (tmmt) cc_final: 0.8549 (tmmt) REVERT: d 128 LEU cc_start: 0.9317 (mt) cc_final: 0.9112 (mt) REVERT: d 130 TRP cc_start: 0.8595 (t60) cc_final: 0.8126 (t60) REVERT: d 138 LEU cc_start: 0.8171 (tp) cc_final: 0.7898 (tp) REVERT: d 142 GLU cc_start: 0.7320 (mp0) cc_final: 0.6955 (mp0) REVERT: d 242 ARG cc_start: 0.8086 (mmm-85) cc_final: 0.7742 (mmm-85) REVERT: d 245 VAL cc_start: 0.8343 (p) cc_final: 0.7880 (m) REVERT: d 248 MET cc_start: 0.7981 (ptt) cc_final: 0.7624 (ptt) REVERT: d 314 PHE cc_start: 0.8586 (m-10) cc_final: 0.8237 (m-10) REVERT: e 16 VAL cc_start: 0.8249 (t) cc_final: 0.8042 (t) REVERT: e 69 VAL cc_start: 0.8700 (t) cc_final: 0.8265 (p) REVERT: e 87 ARG cc_start: 0.8416 (mmp-170) cc_final: 0.8135 (mmp-170) REVERT: e 90 TRP cc_start: 0.7589 (t-100) cc_final: 0.6552 (t-100) REVERT: e 155 GLN cc_start: 0.8433 (tp40) cc_final: 0.7993 (tp40) REVERT: e 158 LEU cc_start: 0.9283 (tp) cc_final: 0.9022 (tp) REVERT: e 164 LEU cc_start: 0.8567 (tt) cc_final: 0.8236 (tt) REVERT: e 176 HIS cc_start: 0.8114 (t-90) cc_final: 0.7721 (t-90) REVERT: e 227 ASN cc_start: 0.8685 (m110) cc_final: 0.8400 (m110) REVERT: e 244 ILE cc_start: 0.9371 (mp) cc_final: 0.9090 (mp) REVERT: e 248 MET cc_start: 0.8878 (mmm) cc_final: 0.8137 (mmt) REVERT: e 276 TRP cc_start: 0.7350 (t60) cc_final: 0.6798 (t60) REVERT: e 296 ASN cc_start: 0.8038 (t0) cc_final: 0.7593 (t0) REVERT: f 42 GLU cc_start: 0.8109 (pp20) cc_final: 0.7731 (pp20) REVERT: f 68 MET cc_start: 0.7186 (tpt) cc_final: 0.6881 (tpt) REVERT: f 73 HIS cc_start: 0.7920 (t-90) cc_final: 0.7643 (t-90) REVERT: f 103 ARG cc_start: 0.8346 (mtt-85) cc_final: 0.7966 (mtt-85) REVERT: f 152 PHE cc_start: 0.8632 (m-80) cc_final: 0.8392 (m-80) REVERT: f 155 GLN cc_start: 0.8644 (mp10) cc_final: 0.8383 (mp10) REVERT: f 248 MET cc_start: 0.8765 (ptp) cc_final: 0.8545 (ptp) REVERT: f 274 ILE cc_start: 0.8796 (mt) cc_final: 0.8361 (mt) REVERT: f 278 GLU cc_start: 0.8404 (mt-10) cc_final: 0.8009 (mt-10) REVERT: f 309 PHE cc_start: 0.9167 (m-80) cc_final: 0.8781 (m-80) outliers start: 0 outliers final: 0 residues processed: 989 average time/residue: 0.2095 time to fit residues: 313.7945 Evaluate side-chains 950 residues out of total 2985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 950 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 327 optimal weight: 2.9990 chunk 240 optimal weight: 1.9990 chunk 100 optimal weight: 0.0770 chunk 332 optimal weight: 7.9990 chunk 52 optimal weight: 6.9990 chunk 101 optimal weight: 0.3980 chunk 182 optimal weight: 6.9990 chunk 198 optimal weight: 9.9990 chunk 72 optimal weight: 0.9980 chunk 88 optimal weight: 0.9990 chunk 223 optimal weight: 0.3980 overall best weight: 0.5740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 169 GLN ** b 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.160589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.127616 restraints weight = 59508.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.132768 restraints weight = 37253.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.136561 restraints weight = 26390.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.139167 restraints weight = 20201.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.141010 restraints weight = 16416.856| |-----------------------------------------------------------------------------| r_work (final): 0.3951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6883 moved from start: 0.2433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 28330 Z= 0.114 Angle : 0.603 9.782 38522 Z= 0.313 Chirality : 0.044 0.215 4383 Planarity : 0.005 0.170 5016 Dihedral : 4.464 23.695 3838 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.68 % Favored : 95.20 % Rotamer: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % 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: -0.54 (0.15), residues: 3439 helix: 0.33 (0.13), residues: 1515 sheet: -0.39 (0.25), residues: 449 loop : -0.97 (0.17), residues: 1475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 256 TYR 0.022 0.001 TYR B 219 PHE 0.031 0.002 PHE f 152 TRP 0.038 0.002 TRP e 276 HIS 0.005 0.001 HIS c 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 (28330) covalent geometry : angle 0.60261 / 0.31 (38522) hydrogen bonds : bond 0.03180 / 2.13 ( 1188) hydrogen bonds : angle 5.19952 / 3.72 ( 3471) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 951 residues out of total 2985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 951 time to evaluate : 0.924 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: 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: 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: A 10 ASN cc_start: 0.8577 (t0) cc_final: 0.7947 (t0) REVERT: A 22 PHE cc_start: 0.7722 (m-80) cc_final: 0.7500 (m-80) REVERT: A 29 MET cc_start: 0.6910 (mmp) cc_final: 0.6470 (mmp) REVERT: A 65 ARG cc_start: 0.7835 (mmm-85) cc_final: 0.7499 (mtp85) REVERT: A 68 MET cc_start: 0.8288 (ttm) cc_final: 0.7985 (ttm) REVERT: A 94 ARG cc_start: 0.8516 (mtp180) cc_final: 0.8293 (mtm180) REVERT: A 97 LEU cc_start: 0.8078 (mt) cc_final: 0.7857 (mt) REVERT: A 109 LYS cc_start: 0.8433 (ttpp) cc_final: 0.8059 (ttpp) REVERT: A 249 VAL cc_start: 0.7113 (t) cc_final: 0.6815 (p) REVERT: A 268 MET cc_start: 0.7378 (mmm) cc_final: 0.6487 (mpp) REVERT: B 28 MET cc_start: 0.5391 (ptp) cc_final: 0.5058 (ptp) REVERT: B 68 MET cc_start: 0.7581 (mmm) cc_final: 0.7351 (mmm) REVERT: B 80 HIS cc_start: 0.7862 (m90) cc_final: 0.7545 (m90) REVERT: B 89 ASN cc_start: 0.7825 (t0) cc_final: 0.7442 (t0) REVERT: B 96 ASN cc_start: 0.8595 (t0) cc_final: 0.7922 (t0) REVERT: B 98 ASP cc_start: 0.7584 (p0) cc_final: 0.7077 (p0) REVERT: B 100 HIS cc_start: 0.7941 (m90) cc_final: 0.7543 (m90) REVERT: B 130 TRP cc_start: 0.8790 (t60) cc_final: 0.8405 (t60) REVERT: B 168 ASP cc_start: 0.7421 (p0) cc_final: 0.6955 (p0) REVERT: B 317 GLU cc_start: 0.6700 (tm-30) cc_final: 0.6162 (tm-30) REVERT: C 28 MET cc_start: 0.7348 (mtm) cc_final: 0.7142 (mtm) REVERT: C 68 MET cc_start: 0.7007 (ttp) cc_final: 0.6699 (ttp) REVERT: C 97 LEU cc_start: 0.8479 (mp) cc_final: 0.8132 (mp) REVERT: C 105 ASP cc_start: 0.8432 (m-30) cc_final: 0.8134 (m-30) REVERT: C 151 MET cc_start: 0.8061 (mmp) cc_final: 0.7767 (mmt) REVERT: C 186 ASN cc_start: 0.7330 (m110) cc_final: 0.7073 (m110) REVERT: C 248 MET cc_start: 0.8508 (ttm) cc_final: 0.8118 (ttm) REVERT: C 303 ARG cc_start: 0.8858 (mmm-85) cc_final: 0.8582 (mmm-85) REVERT: C 314 PHE cc_start: 0.8048 (m-10) cc_final: 0.7645 (m-10) REVERT: D 10 ASN cc_start: 0.8603 (t0) cc_final: 0.8355 (t0) REVERT: D 29 MET cc_start: 0.6311 (mmp) cc_final: 0.6111 (mmp) REVERT: D 39 TYR cc_start: 0.8609 (m-80) cc_final: 0.8219 (m-80) REVERT: D 95 VAL cc_start: 0.8673 (t) cc_final: 0.8076 (m) REVERT: D 106 LEU cc_start: 0.8342 (mp) cc_final: 0.8074 (mp) REVERT: D 135 ASN cc_start: 0.8101 (p0) cc_final: 0.7710 (p0) REVERT: D 147 ARG cc_start: 0.8279 (tpt170) cc_final: 0.8042 (tpm170) REVERT: D 151 MET cc_start: 0.8172 (tpt) cc_final: 0.7591 (tpt) REVERT: D 152 PHE cc_start: 0.8423 (t80) cc_final: 0.8145 (t80) REVERT: D 155 GLN cc_start: 0.8738 (mt0) cc_final: 0.8254 (mt0) REVERT: D 168 ASP cc_start: 0.7991 (t70) cc_final: 0.7735 (t0) REVERT: D 248 MET cc_start: 0.8282 (mmp) cc_final: 0.8061 (mmp) REVERT: D 314 PHE cc_start: 0.8864 (m-10) cc_final: 0.8447 (m-10) REVERT: E 28 MET cc_start: 0.5909 (mtm) cc_final: 0.5701 (mtm) REVERT: E 66 ARG cc_start: 0.6721 (mmt90) cc_final: 0.6442 (mmm-85) REVERT: E 68 MET cc_start: 0.7763 (mmm) cc_final: 0.7496 (mmm) REVERT: E 97 LEU cc_start: 0.8879 (mm) cc_final: 0.8624 (mm) REVERT: E 127 ILE cc_start: 0.7165 (mm) cc_final: 0.6881 (mm) REVERT: E 156 ARG cc_start: 0.8576 (mmm-85) cc_final: 0.8335 (mmm-85) REVERT: E 158 LEU cc_start: 0.9176 (tp) cc_final: 0.8967 (tp) REVERT: E 166 LEU cc_start: 0.8686 (mm) cc_final: 0.8354 (mm) REVERT: E 168 ASP cc_start: 0.7177 (t0) cc_final: 0.6842 (t0) REVERT: E 176 HIS cc_start: 0.7930 (t-90) cc_final: 0.7537 (t-90) REVERT: E 181 LEU cc_start: 0.7810 (tp) cc_final: 0.7603 (tp) REVERT: E 182 PHE cc_start: 0.7088 (m-10) cc_final: 0.6515 (m-80) REVERT: E 297 LYS cc_start: 0.8712 (mtmm) cc_final: 0.8246 (mtmm) REVERT: E 309 PHE cc_start: 0.9111 (m-10) cc_final: 0.8777 (m-10) REVERT: E 314 PHE cc_start: 0.7810 (m-10) cc_final: 0.7571 (m-10) REVERT: F 68 MET cc_start: 0.6274 (ppp) cc_final: 0.6049 (ppp) REVERT: F 80 HIS cc_start: 0.8425 (m90) cc_final: 0.8068 (m90) REVERT: F 83 GLN cc_start: 0.7989 (tm-30) cc_final: 0.7255 (tm-30) REVERT: F 87 ARG cc_start: 0.7755 (mmp80) cc_final: 0.7327 (mmp80) REVERT: F 151 MET cc_start: 0.8333 (mtm) cc_final: 0.8076 (mtm) REVERT: F 176 HIS cc_start: 0.8442 (t-170) cc_final: 0.8001 (t-170) REVERT: F 229 VAL cc_start: 0.9322 (p) cc_final: 0.9082 (m) REVERT: F 257 GLN cc_start: 0.8847 (tp40) cc_final: 0.8562 (tp-100) REVERT: F 309 PHE cc_start: 0.8822 (m-80) cc_final: 0.8354 (m-80) REVERT: F 310 TYR cc_start: 0.7760 (t80) cc_final: 0.7500 (t80) REVERT: F 312 ARG cc_start: 0.8457 (mmt-90) cc_final: 0.8137 (mmt-90) REVERT: a 10 ASN cc_start: 0.8713 (t0) cc_final: 0.8422 (t0) REVERT: a 22 PHE cc_start: 0.7521 (m-80) cc_final: 0.7312 (m-80) REVERT: a 29 MET cc_start: 0.6744 (mmp) cc_final: 0.6355 (mmp) REVERT: a 94 ARG cc_start: 0.8337 (mtp180) cc_final: 0.7997 (mtm180) REVERT: a 109 LYS cc_start: 0.8783 (tmtt) cc_final: 0.8582 (tptp) REVERT: a 138 LEU cc_start: 0.7656 (tp) cc_final: 0.7448 (tp) REVERT: a 151 MET cc_start: 0.8727 (pmm) cc_final: 0.8236 (pmm) REVERT: a 155 GLN cc_start: 0.8807 (mt0) cc_final: 0.8315 (mt0) REVERT: a 186 ASN cc_start: 0.8246 (m110) cc_final: 0.7964 (m110) REVERT: a 204 ASN cc_start: 0.8445 (p0) cc_final: 0.8104 (p0) REVERT: a 268 MET cc_start: 0.7504 (tpp) cc_final: 0.6567 (mmm) REVERT: a 309 PHE cc_start: 0.7386 (m-80) cc_final: 0.7067 (m-80) REVERT: b 28 MET cc_start: 0.3068 (ptm) cc_final: 0.2731 (ptm) REVERT: b 80 HIS cc_start: 0.7995 (m90) cc_final: 0.7420 (m90) REVERT: b 100 HIS cc_start: 0.8302 (m90) cc_final: 0.7970 (m90) REVERT: b 106 LEU cc_start: 0.8982 (mm) cc_final: 0.8776 (mm) REVERT: b 141 ASP cc_start: 0.7299 (t70) cc_final: 0.7031 (t70) REVERT: b 152 PHE cc_start: 0.7372 (t80) cc_final: 0.7172 (t80) REVERT: b 154 ILE cc_start: 0.8936 (mm) cc_final: 0.8550 (tt) REVERT: b 168 ASP cc_start: 0.7843 (p0) cc_final: 0.7551 (p0) REVERT: b 180 ARG cc_start: 0.6645 (mpt180) cc_final: 0.6240 (mpt180) REVERT: b 208 MET cc_start: 0.7636 (mtm) cc_final: 0.7040 (mtt) REVERT: b 215 THR cc_start: 0.8499 (m) cc_final: 0.8219 (t) REVERT: b 235 HIS cc_start: 0.8070 (t-90) cc_final: 0.7780 (t-90) REVERT: b 242 ARG cc_start: 0.8894 (tpt170) cc_final: 0.8529 (tpt170) REVERT: b 309 PHE cc_start: 0.6935 (m-80) cc_final: 0.6584 (m-80) REVERT: c 11 LEU cc_start: 0.8645 (mt) cc_final: 0.8429 (mt) REVERT: c 28 MET cc_start: 0.7412 (mtm) cc_final: 0.7146 (mtm) REVERT: c 55 LEU cc_start: 0.9061 (mt) cc_final: 0.8830 (mt) REVERT: c 68 MET cc_start: 0.6868 (tmm) cc_final: 0.6067 (tmm) REVERT: c 97 LEU cc_start: 0.8701 (mp) cc_final: 0.8480 (mp) REVERT: c 103 ARG cc_start: 0.8668 (mmm-85) cc_final: 0.8141 (mmm-85) REVERT: c 149 ASP cc_start: 0.7977 (t0) cc_final: 0.7451 (t0) REVERT: c 174 ARG cc_start: 0.7432 (tmm160) cc_final: 0.6890 (tmm160) REVERT: c 209 ASP cc_start: 0.8190 (t0) cc_final: 0.7792 (t0) REVERT: c 295 LEU cc_start: 0.8036 (tp) cc_final: 0.7709 (tp) REVERT: d 10 ASN cc_start: 0.8466 (t0) cc_final: 0.8032 (t0) REVERT: d 65 ARG cc_start: 0.8175 (mmm-85) cc_final: 0.7390 (mmt180) REVERT: d 68 MET cc_start: 0.6905 (ttt) cc_final: 0.6619 (ttt) REVERT: d 82 GLU cc_start: 0.8490 (pt0) cc_final: 0.8162 (pt0) REVERT: d 95 VAL cc_start: 0.9052 (t) cc_final: 0.8700 (p) REVERT: d 106 LEU cc_start: 0.8660 (mp) cc_final: 0.8439 (mp) REVERT: d 124 LYS cc_start: 0.8839 (tmmt) cc_final: 0.8479 (tmmt) REVERT: d 128 LEU cc_start: 0.9274 (mt) cc_final: 0.9039 (mt) REVERT: d 130 TRP cc_start: 0.8516 (t60) cc_final: 0.8018 (t60) REVERT: d 138 LEU cc_start: 0.8241 (tp) cc_final: 0.7884 (tp) REVERT: d 142 GLU cc_start: 0.7177 (mp0) cc_final: 0.6690 (mp0) REVERT: d 154 ILE cc_start: 0.8673 (mt) cc_final: 0.8465 (mt) REVERT: d 157 VAL cc_start: 0.9082 (m) cc_final: 0.8803 (p) REVERT: d 211 TRP cc_start: 0.8381 (m100) cc_final: 0.7765 (m100) REVERT: d 221 PRO cc_start: 0.7007 (Cg_exo) cc_final: 0.6786 (Cg_endo) REVERT: d 242 ARG cc_start: 0.8035 (mmm-85) cc_final: 0.7712 (mmm-85) REVERT: d 248 MET cc_start: 0.7957 (ptt) cc_final: 0.7604 (ptt) REVERT: d 312 ARG cc_start: 0.8717 (ttm170) cc_final: 0.8362 (ttm170) REVERT: d 314 PHE cc_start: 0.8541 (m-10) cc_final: 0.8235 (m-80) REVERT: e 10 ASN cc_start: 0.8605 (m-40) cc_final: 0.8405 (m-40) REVERT: e 67 VAL cc_start: 0.7331 (t) cc_final: 0.7014 (p) REVERT: e 68 MET cc_start: 0.7510 (mtt) cc_final: 0.7097 (mtt) REVERT: e 80 HIS cc_start: 0.8655 (t70) cc_final: 0.8220 (t70) REVERT: e 93 VAL cc_start: 0.8748 (t) cc_final: 0.8447 (p) REVERT: e 103 ARG cc_start: 0.8727 (tmt170) cc_final: 0.8471 (ttt-90) REVERT: e 155 GLN cc_start: 0.8445 (tp40) cc_final: 0.7974 (tp40) REVERT: e 158 LEU cc_start: 0.9228 (tp) cc_final: 0.8904 (tp) REVERT: e 227 ASN cc_start: 0.8685 (m110) cc_final: 0.8426 (m110) REVERT: e 244 ILE cc_start: 0.9375 (mp) cc_final: 0.9115 (mp) REVERT: e 267 VAL cc_start: 0.8172 (m) cc_final: 0.7785 (t) REVERT: e 296 ASN cc_start: 0.7806 (t0) cc_final: 0.7536 (t0) REVERT: f 42 GLU cc_start: 0.8068 (pp20) cc_final: 0.7669 (pp20) REVERT: f 68 MET cc_start: 0.7034 (tpt) cc_final: 0.6675 (tpt) REVERT: f 73 HIS cc_start: 0.7778 (t-90) cc_final: 0.7412 (t-90) REVERT: f 103 ARG cc_start: 0.8224 (mtt-85) cc_final: 0.7832 (mtt-85) REVERT: f 176 HIS cc_start: 0.7982 (t-90) cc_final: 0.7703 (t-90) REVERT: f 248 MET cc_start: 0.8738 (ptp) cc_final: 0.8514 (ptp) REVERT: f 278 GLU cc_start: 0.8297 (mt-10) cc_final: 0.7828 (mt-10) REVERT: f 309 PHE cc_start: 0.9129 (m-80) cc_final: 0.8763 (m-80) outliers start: 0 outliers final: 0 residues processed: 951 average time/residue: 0.2141 time to fit residues: 308.0044 Evaluate side-chains 928 residues out of total 2985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 928 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 207 optimal weight: 3.9990 chunk 213 optimal weight: 0.8980 chunk 202 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 chunk 187 optimal weight: 6.9990 chunk 197 optimal weight: 0.5980 chunk 322 optimal weight: 0.6980 chunk 149 optimal weight: 1.9990 chunk 139 optimal weight: 7.9990 chunk 41 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 222 HIS ** D 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 296 ASN ** F 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 169 GLN b 52 GLN ** b 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.160310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.127987 restraints weight = 58897.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.133126 restraints weight = 36756.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.136812 restraints weight = 25894.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.139432 restraints weight = 19838.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.141278 restraints weight = 16035.514| |-----------------------------------------------------------------------------| r_work (final): 0.3962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6872 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 28330 Z= 0.115 Angle : 0.592 10.511 38522 Z= 0.307 Chirality : 0.043 0.194 4383 Planarity : 0.005 0.174 5016 Dihedral : 4.384 22.793 3838 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.83 % Favored : 95.09 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.15), residues: 3439 helix: 0.34 (0.13), residues: 1523 sheet: -0.43 (0.25), residues: 469 loop : -0.96 (0.17), residues: 1447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 256 TYR 0.028 0.001 TYR B 219 PHE 0.031 0.002 PHE f 152 TRP 0.042 0.003 TRP e 276 HIS 0.007 0.001 HIS f 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.11 (28330) covalent geometry : angle 0.59174 / 0.31 (38522) hydrogen bonds : bond 0.03139 / 2.10 ( 1188) hydrogen bonds : angle 5.16150 / 3.69 ( 3471) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 942 residues out of total 2985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 942 time to evaluate : 1.011 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 ASN cc_start: 0.8628 (t0) cc_final: 0.7980 (t0) REVERT: A 22 PHE cc_start: 0.7760 (m-80) cc_final: 0.7538 (m-80) REVERT: A 29 MET cc_start: 0.6908 (mmp) cc_final: 0.6492 (mmp) REVERT: A 65 ARG cc_start: 0.7864 (mmm-85) cc_final: 0.7533 (mtp85) REVERT: A 87 ARG cc_start: 0.8685 (mpt180) cc_final: 0.8114 (mpt180) REVERT: A 94 ARG cc_start: 0.8528 (mtp180) cc_final: 0.8273 (mtm180) REVERT: A 97 LEU cc_start: 0.8070 (mt) cc_final: 0.7850 (mt) REVERT: A 268 MET cc_start: 0.7436 (mmm) cc_final: 0.6556 (mpp) REVERT: B 28 MET cc_start: 0.5320 (ptp) cc_final: 0.5015 (ptp) REVERT: B 68 MET cc_start: 0.7459 (mmm) cc_final: 0.6933 (tpt) REVERT: B 80 HIS cc_start: 0.7870 (m90) cc_final: 0.7337 (m90) REVERT: B 89 ASN cc_start: 0.7823 (t0) cc_final: 0.7456 (t0) REVERT: B 96 ASN cc_start: 0.8590 (t0) cc_final: 0.7883 (t0) REVERT: B 98 ASP cc_start: 0.7521 (p0) cc_final: 0.6989 (p0) REVERT: B 100 HIS cc_start: 0.7978 (m90) cc_final: 0.7587 (m90) REVERT: B 124 LYS cc_start: 0.7493 (tmmt) cc_final: 0.7283 (tmmt) REVERT: B 130 TRP cc_start: 0.8808 (t60) cc_final: 0.8392 (t60) REVERT: B 168 ASP cc_start: 0.7505 (p0) cc_final: 0.7053 (p0) REVERT: B 211 TRP cc_start: 0.7138 (m100) cc_final: 0.6221 (m100) REVERT: B 213 ILE cc_start: 0.7924 (tp) cc_final: 0.7687 (tp) REVERT: B 248 MET cc_start: 0.8624 (mtm) cc_final: 0.8373 (mtm) REVERT: B 317 GLU cc_start: 0.6743 (tm-30) cc_final: 0.6195 (tm-30) REVERT: C 68 MET cc_start: 0.6991 (ttp) cc_final: 0.6698 (ttp) REVERT: C 97 LEU cc_start: 0.8394 (mp) cc_final: 0.8059 (mp) REVERT: C 98 ASP cc_start: 0.6905 (t0) cc_final: 0.6694 (t0) REVERT: C 105 ASP cc_start: 0.8429 (m-30) cc_final: 0.8109 (m-30) REVERT: C 151 MET cc_start: 0.8086 (mmp) cc_final: 0.7879 (mmt) REVERT: C 186 ASN cc_start: 0.7357 (m110) cc_final: 0.7085 (m110) REVERT: C 248 MET cc_start: 0.8474 (ttm) cc_final: 0.8059 (ttm) REVERT: C 294 PHE cc_start: 0.8291 (t80) cc_final: 0.8012 (t80) REVERT: C 303 ARG cc_start: 0.8843 (mmm-85) cc_final: 0.8435 (mmm-85) REVERT: C 314 PHE cc_start: 0.8066 (m-10) cc_final: 0.7651 (m-10) REVERT: D 10 ASN cc_start: 0.8592 (t0) cc_final: 0.8371 (t0) REVERT: D 39 TYR cc_start: 0.8605 (m-80) cc_final: 0.8189 (m-80) REVERT: D 95 VAL cc_start: 0.8691 (t) cc_final: 0.8105 (m) REVERT: D 106 LEU cc_start: 0.8333 (mp) cc_final: 0.8089 (mp) REVERT: D 109 LYS cc_start: 0.9075 (tmmt) cc_final: 0.8621 (ttpp) REVERT: D 135 ASN cc_start: 0.8006 (p0) cc_final: 0.7748 (p0) REVERT: D 151 MET cc_start: 0.8172 (tpt) cc_final: 0.7573 (tpt) REVERT: D 152 PHE cc_start: 0.8427 (t80) cc_final: 0.8159 (t80) REVERT: D 155 GLN cc_start: 0.8733 (mt0) cc_final: 0.8214 (mt0) REVERT: D 163 ARG cc_start: 0.7035 (mpp80) cc_final: 0.6319 (mpp80) REVERT: D 168 ASP cc_start: 0.8034 (t70) cc_final: 0.7720 (t0) REVERT: D 248 MET cc_start: 0.8278 (mmp) cc_final: 0.8046 (mmp) REVERT: D 314 PHE cc_start: 0.8836 (m-10) cc_final: 0.8437 (m-10) REVERT: E 66 ARG cc_start: 0.6701 (mmt90) cc_final: 0.6094 (mtt90) REVERT: E 97 LEU cc_start: 0.8869 (mm) cc_final: 0.8629 (mm) REVERT: E 130 TRP cc_start: 0.8567 (t60) cc_final: 0.8258 (t60) REVERT: E 156 ARG cc_start: 0.8555 (mmm-85) cc_final: 0.8342 (mmm-85) REVERT: E 166 LEU cc_start: 0.8695 (mm) cc_final: 0.8467 (mm) REVERT: E 168 ASP cc_start: 0.7213 (t0) cc_final: 0.6850 (t0) REVERT: E 176 HIS cc_start: 0.7919 (t-90) cc_final: 0.7571 (t-90) REVERT: E 181 LEU cc_start: 0.7801 (tp) cc_final: 0.7585 (tp) REVERT: E 182 PHE cc_start: 0.7017 (m-10) cc_final: 0.6449 (m-80) REVERT: E 271 ARG cc_start: 0.8517 (ptt90) cc_final: 0.8126 (ttp80) REVERT: E 297 LYS cc_start: 0.8686 (mtmm) cc_final: 0.8439 (mtmm) REVERT: E 309 PHE cc_start: 0.9130 (m-10) cc_final: 0.8793 (m-10) REVERT: E 314 PHE cc_start: 0.7865 (m-10) cc_final: 0.7656 (m-10) REVERT: F 68 MET cc_start: 0.6220 (ppp) cc_final: 0.5490 (ppp) REVERT: F 80 HIS cc_start: 0.8394 (m90) cc_final: 0.8054 (m90) REVERT: F 83 GLN cc_start: 0.8022 (tm-30) cc_final: 0.7316 (tm-30) REVERT: F 87 ARG cc_start: 0.7727 (mmp80) cc_final: 0.7299 (mmp80) REVERT: F 151 MET cc_start: 0.8423 (mtm) cc_final: 0.8103 (mtm) REVERT: F 176 HIS cc_start: 0.8431 (t-170) cc_final: 0.7986 (t-170) REVERT: F 229 VAL cc_start: 0.9318 (p) cc_final: 0.9084 (m) REVERT: F 242 ARG cc_start: 0.8671 (tpp-160) cc_final: 0.7528 (tpp-160) REVERT: F 248 MET cc_start: 0.8657 (mmp) cc_final: 0.8419 (mmp) REVERT: F 257 GLN cc_start: 0.8934 (tp40) cc_final: 0.8643 (tp-100) REVERT: F 309 PHE cc_start: 0.8789 (m-80) cc_final: 0.8301 (m-80) REVERT: F 310 TYR cc_start: 0.7755 (t80) cc_final: 0.7495 (t80) REVERT: F 312 ARG cc_start: 0.8448 (mmt-90) cc_final: 0.8110 (mmt-90) REVERT: a 29 MET cc_start: 0.6724 (mmp) cc_final: 0.6354 (mmp) REVERT: a 33 TYR cc_start: 0.7157 (m-80) cc_final: 0.6936 (m-80) REVERT: a 94 ARG cc_start: 0.8348 (mtp180) cc_final: 0.7995 (mtm180) REVERT: a 109 LYS cc_start: 0.8776 (tmtt) cc_final: 0.8572 (tptp) REVERT: a 138 LEU cc_start: 0.7634 (tp) cc_final: 0.7418 (tp) REVERT: a 151 MET cc_start: 0.8688 (pmm) cc_final: 0.8283 (pmm) REVERT: a 155 GLN cc_start: 0.8827 (mt0) cc_final: 0.8407 (mt0) REVERT: a 186 ASN cc_start: 0.8249 (m110) cc_final: 0.7974 (m110) REVERT: a 204 ASN cc_start: 0.8438 (p0) cc_final: 0.8093 (p0) REVERT: a 248 MET cc_start: 0.8807 (mtm) cc_final: 0.8591 (mtm) REVERT: a 268 MET cc_start: 0.7459 (tpp) cc_final: 0.6660 (mmm) REVERT: a 278 GLU cc_start: 0.8345 (mp0) cc_final: 0.8121 (mp0) REVERT: a 309 PHE cc_start: 0.7360 (m-80) cc_final: 0.7057 (m-80) REVERT: b 68 MET cc_start: 0.7318 (tpt) cc_final: 0.6877 (tpt) REVERT: b 80 HIS cc_start: 0.8025 (m90) cc_final: 0.7394 (m90) REVERT: b 100 HIS cc_start: 0.8287 (m90) cc_final: 0.7976 (m90) REVERT: b 106 LEU cc_start: 0.8975 (mm) cc_final: 0.8752 (mm) REVERT: b 141 ASP cc_start: 0.7300 (t70) cc_final: 0.7031 (t70) REVERT: b 154 ILE cc_start: 0.8861 (mm) cc_final: 0.8483 (tt) REVERT: b 168 ASP cc_start: 0.7810 (p0) cc_final: 0.7485 (p0) REVERT: b 208 MET cc_start: 0.7639 (mtm) cc_final: 0.7103 (mtt) REVERT: b 215 THR cc_start: 0.8479 (m) cc_final: 0.8167 (t) REVERT: b 235 HIS cc_start: 0.8083 (t-90) cc_final: 0.7794 (t-90) REVERT: b 242 ARG cc_start: 0.8887 (tpt170) cc_final: 0.8520 (tpt170) REVERT: b 254 MET cc_start: 0.8770 (ppp) cc_final: 0.8552 (ppp) REVERT: b 309 PHE cc_start: 0.6960 (m-80) cc_final: 0.6597 (m-80) REVERT: c 28 MET cc_start: 0.7441 (mtm) cc_final: 0.7166 (mtm) REVERT: c 55 LEU cc_start: 0.9074 (mt) cc_final: 0.8844 (mt) REVERT: c 68 MET cc_start: 0.6857 (tmm) cc_final: 0.6039 (tmm) REVERT: c 103 ARG cc_start: 0.8676 (mmm-85) cc_final: 0.8151 (mmm-85) REVERT: c 141 ASP cc_start: 0.5934 (p0) cc_final: 0.5396 (p0) REVERT: c 149 ASP cc_start: 0.8007 (t0) cc_final: 0.7489 (t0) REVERT: c 174 ARG cc_start: 0.7465 (tmm160) cc_final: 0.6920 (tmm160) REVERT: c 209 ASP cc_start: 0.8181 (t0) cc_final: 0.7770 (t0) REVERT: c 295 LEU cc_start: 0.8005 (tp) cc_final: 0.7684 (tp) REVERT: d 10 ASN cc_start: 0.8517 (t0) cc_final: 0.8100 (t0) REVERT: d 65 ARG cc_start: 0.8179 (mmm-85) cc_final: 0.7469 (mmt180) REVERT: d 82 GLU cc_start: 0.8489 (pt0) cc_final: 0.8199 (pt0) REVERT: d 95 VAL cc_start: 0.9075 (t) cc_final: 0.8753 (p) REVERT: d 106 LEU cc_start: 0.8612 (mp) cc_final: 0.8385 (mp) REVERT: d 124 LYS cc_start: 0.8847 (tmmt) cc_final: 0.8473 (tmmt) REVERT: d 128 LEU cc_start: 0.9302 (mt) cc_final: 0.9064 (mt) REVERT: d 130 TRP cc_start: 0.8491 (t60) cc_final: 0.7980 (t60) REVERT: d 138 LEU cc_start: 0.8177 (tp) cc_final: 0.7842 (tp) REVERT: d 154 ILE cc_start: 0.8700 (mt) cc_final: 0.8492 (mt) REVERT: d 157 VAL cc_start: 0.9062 (m) cc_final: 0.8820 (p) REVERT: d 208 MET cc_start: 0.7527 (pmm) cc_final: 0.7060 (pmm) REVERT: d 221 PRO cc_start: 0.7056 (Cg_exo) cc_final: 0.6834 (Cg_endo) REVERT: d 242 ARG cc_start: 0.8014 (mmm-85) cc_final: 0.7709 (mmm-85) REVERT: d 248 MET cc_start: 0.7939 (ptt) cc_final: 0.7590 (ptt) REVERT: d 282 ILE cc_start: 0.7731 (mt) cc_final: 0.7530 (mt) REVERT: d 312 ARG cc_start: 0.8718 (ttm170) cc_final: 0.8370 (ttm170) REVERT: d 314 PHE cc_start: 0.8540 (m-10) cc_final: 0.8229 (m-80) REVERT: e 16 VAL cc_start: 0.8235 (t) cc_final: 0.8010 (t) REVERT: e 67 VAL cc_start: 0.7416 (t) cc_final: 0.7083 (p) REVERT: e 68 MET cc_start: 0.7528 (mtt) cc_final: 0.7154 (mtt) REVERT: e 80 HIS cc_start: 0.8509 (t70) cc_final: 0.8193 (t70) REVERT: e 87 ARG cc_start: 0.8421 (mmp-170) cc_final: 0.8150 (mmp-170) REVERT: e 93 VAL cc_start: 0.8732 (t) cc_final: 0.8441 (p) REVERT: e 103 ARG cc_start: 0.8662 (tmt170) cc_final: 0.8191 (tmt-80) REVERT: e 155 GLN cc_start: 0.8481 (tp40) cc_final: 0.8026 (tp40) REVERT: e 158 LEU cc_start: 0.9235 (tp) cc_final: 0.8946 (tp) REVERT: e 176 HIS cc_start: 0.7962 (t-90) cc_final: 0.7571 (t-90) REVERT: e 227 ASN cc_start: 0.8696 (m110) cc_final: 0.8427 (m110) REVERT: e 244 ILE cc_start: 0.9372 (mp) cc_final: 0.9166 (mp) REVERT: e 276 TRP cc_start: 0.7194 (t60) cc_final: 0.6840 (t60) REVERT: e 296 ASN cc_start: 0.7813 (t0) cc_final: 0.7569 (t0) REVERT: f 42 GLU cc_start: 0.8060 (pp20) cc_final: 0.7648 (pp20) REVERT: f 51 ARG cc_start: 0.7858 (mtt90) cc_final: 0.7479 (mtt90) REVERT: f 68 MET cc_start: 0.7069 (tpt) cc_final: 0.6684 (tpt) REVERT: f 103 ARG cc_start: 0.8197 (mtt-85) cc_final: 0.7949 (mtt-85) REVERT: f 176 HIS cc_start: 0.7981 (t-90) cc_final: 0.7686 (t-90) REVERT: f 248 MET cc_start: 0.8740 (ptp) cc_final: 0.8491 (ptp) REVERT: f 278 GLU cc_start: 0.8283 (mt-10) cc_final: 0.7825 (mt-10) REVERT: f 309 PHE cc_start: 0.9119 (m-80) cc_final: 0.8749 (m-80) outliers start: 0 outliers final: 0 residues processed: 942 average time/residue: 0.2130 time to fit residues: 302.9350 Evaluate side-chains 922 residues out of total 2985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 922 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 290 optimal weight: 0.7980 chunk 284 optimal weight: 8.9990 chunk 328 optimal weight: 4.9990 chunk 286 optimal weight: 0.7980 chunk 295 optimal weight: 0.0060 chunk 146 optimal weight: 0.6980 chunk 319 optimal weight: 0.9980 chunk 259 optimal weight: 0.0770 chunk 262 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 chunk 221 optimal weight: 7.9990 overall best weight: 0.4754 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 296 ASN ** F 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 169 GLN ** b 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 83 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.161147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.128498 restraints weight = 58872.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.133680 restraints weight = 36998.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.137404 restraints weight = 26191.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.140339 restraints weight = 19928.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.141986 restraints weight = 16017.362| |-----------------------------------------------------------------------------| r_work (final): 0.3984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6849 moved from start: 0.2519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.069 28330 Z= 0.108 Angle : 0.592 10.409 38522 Z= 0.307 Chirality : 0.043 0.224 4383 Planarity : 0.004 0.054 5016 Dihedral : 4.340 28.606 3838 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.89 % Favored : 95.03 % Rotamer: Outliers : 0.03 % Allowed : 0.40 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.15), residues: 3439 helix: 0.33 (0.13), residues: 1526 sheet: -0.45 (0.24), residues: 485 loop : -0.96 (0.17), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG e 174 TYR 0.021 0.001 TYR a 132 PHE 0.031 0.001 PHE f 152 TRP 0.041 0.002 TRP e 276 HIS 0.004 0.001 HIS d 176 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 (28330) covalent geometry : angle 0.59167 / 0.31 (38522) hydrogen bonds : bond 0.03088 / 2.07 ( 1188) hydrogen bonds : angle 5.13077 / 3.67 ( 3471) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 939 residues out of total 2985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 938 time to evaluate : 0.997 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 ASN cc_start: 0.8617 (t0) cc_final: 0.7970 (t0) REVERT: A 22 PHE cc_start: 0.7756 (m-80) cc_final: 0.7541 (m-80) REVERT: A 29 MET cc_start: 0.6932 (mmp) cc_final: 0.6520 (mmp) REVERT: A 65 ARG cc_start: 0.7771 (mmm-85) cc_final: 0.7411 (mtp85) REVERT: A 87 ARG cc_start: 0.8680 (mpt180) cc_final: 0.8334 (mpt180) REVERT: A 94 ARG cc_start: 0.8536 (mtp180) cc_final: 0.8294 (mtm180) REVERT: A 268 MET cc_start: 0.7360 (mmm) cc_final: 0.6386 (mpp) REVERT: B 28 MET cc_start: 0.5305 (ptp) cc_final: 0.5024 (ptp) REVERT: B 68 MET cc_start: 0.7214 (mmm) cc_final: 0.6869 (mmm) REVERT: B 80 HIS cc_start: 0.7851 (m90) cc_final: 0.7345 (m90) REVERT: B 89 ASN cc_start: 0.7772 (t0) cc_final: 0.7426 (t0) REVERT: B 96 ASN cc_start: 0.8574 (t0) cc_final: 0.7876 (t0) REVERT: B 98 ASP cc_start: 0.7498 (p0) cc_final: 0.6970 (p0) REVERT: B 100 HIS cc_start: 0.7938 (m90) cc_final: 0.7558 (m90) REVERT: B 124 LYS cc_start: 0.7473 (tmmt) cc_final: 0.7232 (tmmt) REVERT: B 130 TRP cc_start: 0.8797 (t60) cc_final: 0.8336 (t60) REVERT: B 152 PHE cc_start: 0.7004 (t80) cc_final: 0.6784 (t80) REVERT: B 168 ASP cc_start: 0.7467 (p0) cc_final: 0.7009 (p0) REVERT: B 317 GLU cc_start: 0.6376 (tm-30) cc_final: 0.5791 (tm-30) REVERT: C 68 MET cc_start: 0.6924 (ttp) cc_final: 0.6600 (ttp) REVERT: C 97 LEU cc_start: 0.8309 (mp) cc_final: 0.8003 (mp) REVERT: C 98 ASP cc_start: 0.6761 (t0) cc_final: 0.6498 (t0) REVERT: C 105 ASP cc_start: 0.8401 (m-30) cc_final: 0.8079 (m-30) REVERT: C 109 LYS cc_start: 0.8822 (tmtt) cc_final: 0.8365 (tmtt) REVERT: C 141 ASP cc_start: 0.6558 (p0) cc_final: 0.4808 (p0) REVERT: C 186 ASN cc_start: 0.7358 (m110) cc_final: 0.7078 (m110) REVERT: C 248 MET cc_start: 0.8459 (ttm) cc_final: 0.8034 (ttm) REVERT: C 294 PHE cc_start: 0.8237 (t80) cc_final: 0.8011 (t80) REVERT: C 303 ARG cc_start: 0.8880 (mmm-85) cc_final: 0.8625 (mmm-85) REVERT: C 314 PHE cc_start: 0.8048 (m-10) cc_final: 0.7630 (m-10) REVERT: D 10 ASN cc_start: 0.8577 (t0) cc_final: 0.8363 (t0) REVERT: D 29 MET cc_start: 0.6207 (mmp) cc_final: 0.5813 (mmp) REVERT: D 68 MET cc_start: 0.6584 (mmp) cc_final: 0.6370 (tpp) REVERT: D 95 VAL cc_start: 0.8642 (t) cc_final: 0.8063 (m) REVERT: D 109 LYS cc_start: 0.9075 (tmmt) cc_final: 0.8605 (ttpp) REVERT: D 135 ASN cc_start: 0.8141 (p0) cc_final: 0.7747 (p0) REVERT: D 151 MET cc_start: 0.8180 (tpt) cc_final: 0.7560 (tpt) REVERT: D 152 PHE cc_start: 0.8432 (t80) cc_final: 0.8090 (t80) REVERT: D 155 GLN cc_start: 0.8692 (mt0) cc_final: 0.8190 (mt0) REVERT: D 163 ARG cc_start: 0.7069 (mpp80) cc_final: 0.6245 (mpp80) REVERT: D 168 ASP cc_start: 0.8010 (t70) cc_final: 0.7706 (t0) REVERT: D 314 PHE cc_start: 0.8848 (m-10) cc_final: 0.8413 (m-10) REVERT: E 66 ARG cc_start: 0.6588 (mmt90) cc_final: 0.5960 (mtt180) REVERT: E 97 LEU cc_start: 0.8841 (mm) cc_final: 0.8589 (mm) REVERT: E 130 TRP cc_start: 0.8518 (t60) cc_final: 0.8282 (t60) REVERT: E 158 LEU cc_start: 0.9059 (tp) cc_final: 0.8781 (tp) REVERT: E 166 LEU cc_start: 0.8697 (mm) cc_final: 0.8490 (mm) REVERT: E 168 ASP cc_start: 0.7188 (t0) cc_final: 0.6867 (t0) REVERT: E 176 HIS cc_start: 0.7890 (t-90) cc_final: 0.7566 (t-90) REVERT: E 182 PHE cc_start: 0.6836 (m-10) cc_final: 0.6299 (m-80) REVERT: E 297 LYS cc_start: 0.8696 (mtmm) cc_final: 0.8438 (mtmm) REVERT: E 309 PHE cc_start: 0.9115 (m-10) cc_final: 0.8795 (m-10) REVERT: E 314 PHE cc_start: 0.7931 (m-10) cc_final: 0.7652 (m-10) REVERT: F 68 MET cc_start: 0.6173 (ppp) cc_final: 0.5451 (ppp) REVERT: F 80 HIS cc_start: 0.8343 (m90) cc_final: 0.8033 (m90) REVERT: F 83 GLN cc_start: 0.8057 (tm-30) cc_final: 0.7355 (tm-30) REVERT: F 87 ARG cc_start: 0.7707 (mmp80) cc_final: 0.7276 (mmp80) REVERT: F 176 HIS cc_start: 0.8401 (t-170) cc_final: 0.7954 (t-170) REVERT: F 229 VAL cc_start: 0.9317 (p) cc_final: 0.9083 (m) REVERT: F 242 ARG cc_start: 0.8680 (tpp-160) cc_final: 0.7515 (tpp-160) REVERT: F 248 MET cc_start: 0.8639 (mmp) cc_final: 0.8376 (mmp) REVERT: F 257 GLN cc_start: 0.8928 (tp40) cc_final: 0.8630 (tp-100) REVERT: F 309 PHE cc_start: 0.8741 (m-80) cc_final: 0.8245 (m-80) REVERT: F 312 ARG cc_start: 0.8433 (mmt-90) cc_final: 0.8097 (mmt-90) REVERT: a 10 ASN cc_start: 0.8677 (t0) cc_final: 0.8445 (t0) REVERT: a 29 MET cc_start: 0.6753 (mmp) cc_final: 0.6415 (mmp) REVERT: a 94 ARG cc_start: 0.8326 (mtp180) cc_final: 0.7951 (mtm180) REVERT: a 109 LYS cc_start: 0.8777 (tmtt) cc_final: 0.8563 (tptp) REVERT: a 151 MET cc_start: 0.8651 (pmm) cc_final: 0.8258 (pmm) REVERT: a 155 GLN cc_start: 0.8809 (mt0) cc_final: 0.8356 (mt0) REVERT: a 186 ASN cc_start: 0.8247 (m110) cc_final: 0.8011 (m110) REVERT: a 204 ASN cc_start: 0.8426 (p0) cc_final: 0.8086 (p0) REVERT: a 268 MET cc_start: 0.7369 (tpp) cc_final: 0.6556 (mmm) REVERT: a 309 PHE cc_start: 0.7337 (m-80) cc_final: 0.7045 (m-80) REVERT: b 28 MET cc_start: 0.3351 (ptm) cc_final: 0.2470 (ptm) REVERT: b 29 MET cc_start: 0.5009 (mmp) cc_final: 0.4403 (tpp) REVERT: b 68 MET cc_start: 0.7244 (tpt) cc_final: 0.6801 (tpt) REVERT: b 80 HIS cc_start: 0.7941 (m90) cc_final: 0.7321 (m90) REVERT: b 100 HIS cc_start: 0.8265 (m90) cc_final: 0.7912 (m90) REVERT: b 106 LEU cc_start: 0.8968 (mm) cc_final: 0.8742 (mm) REVERT: b 141 ASP cc_start: 0.7278 (t70) cc_final: 0.7007 (t70) REVERT: b 151 MET cc_start: 0.7132 (mtm) cc_final: 0.6880 (mtm) REVERT: b 152 PHE cc_start: 0.7278 (t80) cc_final: 0.7043 (t80) REVERT: b 154 ILE cc_start: 0.8838 (mm) cc_final: 0.8438 (tt) REVERT: b 168 ASP cc_start: 0.7747 (p0) cc_final: 0.7380 (p0) REVERT: b 180 ARG cc_start: 0.6641 (mpt180) cc_final: 0.6203 (mpt180) REVERT: b 208 MET cc_start: 0.7542 (mtm) cc_final: 0.6943 (mtt) REVERT: b 235 HIS cc_start: 0.8083 (t-90) cc_final: 0.7799 (t-90) REVERT: b 242 ARG cc_start: 0.8874 (tpt170) cc_final: 0.8497 (tpt170) REVERT: b 309 PHE cc_start: 0.6827 (m-80) cc_final: 0.6484 (m-80) REVERT: c 55 LEU cc_start: 0.9066 (mt) cc_final: 0.8791 (mt) REVERT: c 68 MET cc_start: 0.6831 (tmm) cc_final: 0.5991 (tmm) REVERT: c 97 LEU cc_start: 0.8670 (mp) cc_final: 0.8456 (mp) REVERT: c 103 ARG cc_start: 0.8662 (mmm-85) cc_final: 0.8140 (mmm-85) REVERT: c 141 ASP cc_start: 0.5974 (p0) cc_final: 0.5507 (p0) REVERT: c 149 ASP cc_start: 0.8015 (t0) cc_final: 0.7471 (t0) REVERT: c 151 MET cc_start: 0.7893 (mtm) cc_final: 0.7540 (mtt) REVERT: c 174 ARG cc_start: 0.7465 (tmm160) cc_final: 0.6887 (tmm160) REVERT: c 209 ASP cc_start: 0.8171 (t0) cc_final: 0.7738 (t0) REVERT: c 295 LEU cc_start: 0.7983 (tp) cc_final: 0.7656 (tp) REVERT: c 314 PHE cc_start: 0.7200 (m-80) cc_final: 0.6851 (m-80) REVERT: d 10 ASN cc_start: 0.8526 (t0) cc_final: 0.8014 (t0) REVERT: d 65 ARG cc_start: 0.8128 (mmm-85) cc_final: 0.7390 (mmt180) REVERT: d 68 MET cc_start: 0.6961 (ttt) cc_final: 0.6496 (ttt) REVERT: d 82 GLU cc_start: 0.8459 (pt0) cc_final: 0.8195 (pt0) REVERT: d 95 VAL cc_start: 0.9077 (t) cc_final: 0.8751 (p) REVERT: d 106 LEU cc_start: 0.8581 (mp) cc_final: 0.8357 (mp) REVERT: d 124 LYS cc_start: 0.8832 (tmmt) cc_final: 0.8461 (tmmt) REVERT: d 128 LEU cc_start: 0.9294 (mt) cc_final: 0.9082 (mt) REVERT: d 130 TRP cc_start: 0.8471 (t60) cc_final: 0.7918 (t60) REVERT: d 138 LEU cc_start: 0.8207 (tp) cc_final: 0.7868 (tp) REVERT: d 156 ARG cc_start: 0.8428 (mmm-85) cc_final: 0.7912 (mmm-85) REVERT: d 166 LEU cc_start: 0.8372 (tp) cc_final: 0.8098 (tp) REVERT: d 208 MET cc_start: 0.7416 (pmm) cc_final: 0.7092 (pmm) REVERT: d 211 TRP cc_start: 0.8357 (m100) cc_final: 0.7439 (m100) REVERT: d 221 PRO cc_start: 0.6991 (Cg_exo) cc_final: 0.6783 (Cg_endo) REVERT: d 242 ARG cc_start: 0.8004 (mmm-85) cc_final: 0.7707 (mmm-85) REVERT: d 248 MET cc_start: 0.7950 (ptt) cc_final: 0.7594 (ptt) REVERT: d 312 ARG cc_start: 0.8743 (ttm170) cc_final: 0.8380 (ttm170) REVERT: e 16 VAL cc_start: 0.8234 (t) cc_final: 0.7970 (t) REVERT: e 67 VAL cc_start: 0.7401 (t) cc_final: 0.7070 (p) REVERT: e 68 MET cc_start: 0.7508 (mtt) cc_final: 0.7144 (mtt) REVERT: e 87 ARG cc_start: 0.8433 (mmp-170) cc_final: 0.8148 (mmp-170) REVERT: e 93 VAL cc_start: 0.8731 (t) cc_final: 0.8429 (p) REVERT: e 103 ARG cc_start: 0.8621 (tmt170) cc_final: 0.8182 (tmt-80) REVERT: e 155 GLN cc_start: 0.8432 (tp40) cc_final: 0.7964 (tp40) REVERT: e 158 LEU cc_start: 0.9210 (tp) cc_final: 0.8923 (tp) REVERT: e 227 ASN cc_start: 0.8703 (m110) cc_final: 0.8437 (m110) REVERT: e 244 ILE cc_start: 0.9381 (mp) cc_final: 0.9164 (mp) REVERT: e 274 ILE cc_start: 0.8120 (mm) cc_final: 0.7886 (mm) REVERT: e 276 TRP cc_start: 0.7119 (t60) cc_final: 0.6783 (t60) REVERT: e 296 ASN cc_start: 0.7787 (t0) cc_final: 0.7578 (t0) REVERT: f 42 GLU cc_start: 0.8036 (pp20) cc_final: 0.7631 (pp20) REVERT: f 68 MET cc_start: 0.7033 (tpt) cc_final: 0.6614 (tpt) REVERT: f 176 HIS cc_start: 0.7933 (t-90) cc_final: 0.7580 (t-90) REVERT: f 248 MET cc_start: 0.8731 (ptp) cc_final: 0.8476 (ptp) REVERT: f 278 GLU cc_start: 0.8264 (mt-10) cc_final: 0.7779 (mt-10) REVERT: f 309 PHE cc_start: 0.9114 (m-80) cc_final: 0.8776 (m-80) outliers start: 1 outliers final: 0 residues processed: 938 average time/residue: 0.2183 time to fit residues: 308.7815 Evaluate side-chains 916 residues out of total 2985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 916 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 342 random chunks: chunk 206 optimal weight: 4.9990 chunk 315 optimal weight: 0.8980 chunk 10 optimal weight: 0.6980 chunk 134 optimal weight: 0.9980 chunk 289 optimal weight: 0.5980 chunk 70 optimal weight: 0.9990 chunk 270 optimal weight: 5.9990 chunk 207 optimal weight: 2.9990 chunk 209 optimal weight: 1.9990 chunk 153 optimal weight: 0.6980 chunk 26 optimal weight: 6.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 296 ASN ** F 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 235 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 83 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.162007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.128991 restraints weight = 59577.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.134156 restraints weight = 37788.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.137938 restraints weight = 26953.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.140523 restraints weight = 20740.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.142259 restraints weight = 16897.562| |-----------------------------------------------------------------------------| r_work (final): 0.3969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6872 moved from start: 0.2589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 28330 Z= 0.113 Angle : 0.593 10.570 38522 Z= 0.307 Chirality : 0.043 0.223 4383 Planarity : 0.005 0.064 5016 Dihedral : 4.308 23.777 3838 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.86 % Favored : 95.06 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.15), residues: 3439 helix: 0.33 (0.13), residues: 1530 sheet: -0.44 (0.24), residues: 487 loop : -0.93 (0.17), residues: 1422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 94 TYR 0.012 0.001 TYR c 143 PHE 0.031 0.002 PHE f 152 TRP 0.038 0.002 TRP e 276 HIS 0.006 0.001 HIS f 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.11 (28330) covalent geometry : angle 0.59337 / 0.31 (38522) hydrogen bonds : bond 0.03067 / 2.06 ( 1188) hydrogen bonds : angle 5.11014 / 3.66 ( 3471) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6380.90 seconds wall clock time: 110 minutes 23.05 seconds (6623.05 seconds total)