Starting phenix.real_space_refine on Sat Aug 8 07:29:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9uka_64232/08_2026/9uka_64232.cif Found real_map, /net/cci-nas-00/data/ceres_data/9uka_64232/08_2026/9uka_64232.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9uka_64232/08_2026/9uka_64232.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9uka_64232/08_2026/9uka_64232.map" model { file = "/net/cci-nas-00/data/ceres_data/9uka_64232/08_2026/9uka_64232.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9uka_64232/08_2026/9uka_64232.cif" } resolution = 4.24 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= 0.039 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 9 5.49 5 S 101 5.16 5 C 16254 2.51 5 N 4598 2.21 5 O 4863 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 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: 25825 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2421 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 12, 'TRANS': 293} Chain breaks: 1 Chain: "B" Number of atoms: 2449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2449 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 12, 'TRANS': 296} Chain breaks: 1 Chain: "C" Number of atoms: 2397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2397 Classifications: {'peptide': 302} Link IDs: {'PTRANS': 12, 'TRANS': 289} Chain breaks: 1 Chain: "D" Number of atoms: 2503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2503 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 12, 'TRANS': 303} Chain: "E" Number of atoms: 2555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2555 Classifications: {'peptide': 324} Link IDs: {'PTRANS': 12, 'TRANS': 311} Chain: "F" Number of atoms: 2555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2555 Classifications: {'peptide': 324} Link IDs: {'PTRANS': 12, 'TRANS': 311} Chain: "G" Number of atoms: 2474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2474 Classifications: {'peptide': 310} Link IDs: {'PTRANS': 10, 'TRANS': 299} Chain: "a" Number of atoms: 1562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1562 Classifications: {'peptide': 204} Link IDs: {'PTRANS': 10, 'TRANS': 193} Chain: "N" Number of atoms: 6816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 887, 6816 Classifications: {'peptide': 887} Link IDs: {'PTRANS': 58, 'TRANS': 828} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.75, per 1000 atoms: 0.22 Number of scatterers: 25825 At special positions: 0 Unit cell: (120.754, 133.318, 164.728, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 101 16.00 P 9 15.00 O 4863 8.00 N 4598 7.00 C 16254 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: 2.15 Conformation dependent library (CDL) restraints added in 1.2 seconds 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6136 Finding SS restraints... Secondary structure from input PDB file: 148 helices and 28 sheets defined 50.2% alpha, 9.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'A' and resid 18 through 22 Processing helix chain 'A' and resid 50 through 63 Processing helix chain 'A' and resid 78 through 88 Processing helix chain 'A' and resid 102 through 107 removed outlier: 4.208A pdb=" N LEU A 106 " --> pdb=" O SER A 102 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL A 107 " --> pdb=" O ARG A 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 102 through 107' Processing helix chain 'A' and resid 126 through 133 Processing helix chain 'A' and resid 152 through 159 Processing helix chain 'A' and resid 206 through 211 Processing helix chain 'A' and resid 221 through 233 removed outlier: 3.544A pdb=" N VAL A 231 " --> pdb=" O ASN A 227 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LYS A 232 " --> pdb=" O ILE A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 237 Processing helix chain 'A' and resid 238 through 262 removed outlier: 4.296A pdb=" N GLU A 243 " --> pdb=" O ALA A 239 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N ILE A 244 " --> pdb=" O GLU A 240 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL A 249 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ARG A 250 " --> pdb=" O ASN A 246 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG A 256 " --> pdb=" O ALA A 252 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLN A 257 " --> pdb=" O ASP A 253 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N ALA A 258 " --> pdb=" O MET A 254 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE A 259 " --> pdb=" O THR A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 284 removed outlier: 3.634A pdb=" N VAL A 273 " --> pdb=" O SER A 269 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLU A 278 " --> pdb=" O ILE A 274 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA A 281 " --> pdb=" O ALA A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 292 removed outlier: 3.881A pdb=" N ARG A 291 " --> pdb=" O GLY A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 315 removed outlier: 4.002A pdb=" N ALA A 304 " --> pdb=" O GLU A 300 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N THR A 305 " --> pdb=" O LEU A 301 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N PHE A 309 " --> pdb=" O THR A 305 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N TYR A 310 " --> pdb=" O VAL A 306 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ARG A 312 " --> pdb=" O GLU A 308 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA A 313 " --> pdb=" O PHE A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 326 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 87 removed outlier: 3.636A pdb=" N ILE B 81 " --> pdb=" O LYS B 77 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N GLU B 82 " --> pdb=" O SER B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 107 removed outlier: 3.753A pdb=" N VAL B 107 " --> pdb=" O ARG B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 134 Processing helix chain 'B' and resid 147 through 149 No H-bonds generated for 'chain 'B' and resid 147 through 149' Processing helix chain 'B' and resid 150 through 160 removed outlier: 3.917A pdb=" N ILE B 154 " --> pdb=" O VAL B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 211 Processing helix chain 'B' and resid 221 through 231 removed outlier: 4.220A pdb=" N VAL B 226 " --> pdb=" O HIS B 222 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N ASN B 227 " --> pdb=" O ASP B 223 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ILE B 228 " --> pdb=" O ASN B 224 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL B 229 " --> pdb=" O GLU B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 261 removed outlier: 3.918A pdb=" N GLN B 257 " --> pdb=" O ASP B 253 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ALA B 258 " --> pdb=" O MET B 254 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N PHE B 259 " --> pdb=" O THR B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 284 removed outlier: 3.563A pdb=" N ILE B 274 " --> pdb=" O PRO B 270 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE B 282 " --> pdb=" O GLU B 278 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASN B 284 " --> pdb=" O ALA B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 294 removed outlier: 3.654A pdb=" N LEU B 292 " --> pdb=" O PHE B 288 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR B 293 " --> pdb=" O ALA B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 314 removed outlier: 4.489A pdb=" N ALA B 304 " --> pdb=" O GLU B 300 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N THR B 305 " --> pdb=" O LEU B 301 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N PHE B 309 " --> pdb=" O THR B 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 64 removed outlier: 3.731A pdb=" N ASN C 64 " --> pdb=" O GLY C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 89 Processing helix chain 'C' and resid 102 through 107 Processing helix chain 'C' and resid 127 through 134 Processing helix chain 'C' and resid 147 through 157 removed outlier: 4.140A pdb=" N PHE C 152 " --> pdb=" O PRO C 148 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N VAL C 153 " --> pdb=" O ASP C 149 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N VAL C 157 " --> pdb=" O VAL C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 160 No H-bonds generated for 'chain 'C' and resid 158 through 160' Processing helix chain 'C' and resid 206 through 210 Processing helix chain 'C' and resid 221 through 231 removed outlier: 3.954A pdb=" N ASN C 227 " --> pdb=" O ASP C 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 237 removed outlier: 5.406A pdb=" N HIS C 235 " --> pdb=" O LYS C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 261 removed outlier: 3.620A pdb=" N ARG C 250 " --> pdb=" O ASN C 246 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ALA C 252 " --> pdb=" O MET C 248 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA C 258 " --> pdb=" O MET C 254 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N PHE C 259 " --> pdb=" O THR C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 284 removed outlier: 3.733A pdb=" N ALA C 281 " --> pdb=" O ALA C 277 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ILE C 282 " --> pdb=" O GLU C 278 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N PHE C 283 " --> pdb=" O ASN C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 294 removed outlier: 4.317A pdb=" N LEU C 292 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N PHE C 294 " --> pdb=" O PHE C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 299 through 314 removed outlier: 3.706A pdb=" N ALA C 304 " --> pdb=" O GLU C 300 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N THR C 305 " --> pdb=" O LEU C 301 " (cutoff:3.500A) removed outlier: 3.582A 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 removed outlier: 4.092A pdb=" N ALA D 56 " --> pdb=" O GLN D 52 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 88 Processing helix chain 'D' and resid 102 through 107 Processing helix chain 'D' and resid 127 through 134 Processing helix chain 'D' and resid 150 through 155 removed outlier: 3.658A pdb=" N VAL D 153 " --> pdb=" O VAL D 150 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE D 154 " --> pdb=" O MET D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 210 removed outlier: 4.344A pdb=" N ARG D 210 " --> pdb=" O ALA D 206 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 233 Processing helix chain 'D' and resid 238 through 262 removed outlier: 3.528A pdb=" N GLU D 243 " --> pdb=" O ALA D 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 280 Processing helix chain 'D' and resid 286 through 294 Processing helix chain 'D' and resid 300 through 315 removed outlier: 4.166A pdb=" N ALA D 304 " --> pdb=" O GLU D 300 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N THR D 305 " --> pdb=" O LEU D 301 " (cutoff:3.500A) Processing helix chain 'E' and resid 18 through 23 Processing helix chain 'E' and resid 51 through 63 removed outlier: 3.797A pdb=" N LEU E 55 " --> pdb=" O ARG E 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 77 through 88 Processing helix chain 'E' and resid 102 through 107 removed outlier: 3.730A pdb=" N LEU E 106 " --> pdb=" O SER E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 114 through 118 Processing helix chain 'E' and resid 126 through 134 Processing helix chain 'E' and resid 143 through 146 removed outlier: 3.609A pdb=" N GLY E 146 " --> pdb=" O TYR E 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 143 through 146' Processing helix chain 'E' and resid 147 through 152 Processing helix chain 'E' and resid 154 through 160 removed outlier: 4.177A pdb=" N GLU E 159 " --> pdb=" O GLN E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 204 through 211 removed outlier: 3.509A pdb=" N MET E 208 " --> pdb=" O ASN E 204 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N TRP E 211 " --> pdb=" O GLN E 207 " (cutoff:3.500A) Processing helix chain 'E' and resid 221 through 233 removed outlier: 3.570A pdb=" N GLU E 225 " --> pdb=" O PRO E 221 " (cutoff:3.500A) Processing helix chain 'E' and resid 234 through 237 Processing helix chain 'E' and resid 238 through 261 removed outlier: 3.552A pdb=" N ARG E 242 " --> pdb=" O ASN E 238 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLU E 243 " --> pdb=" O ALA E 239 " (cutoff:3.500A) Processing helix chain 'E' and resid 271 through 284 removed outlier: 3.932A pdb=" N ALA E 281 " --> pdb=" O ALA E 277 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE E 282 " --> pdb=" O GLU E 278 " (cutoff:3.500A) Processing helix chain 'E' and resid 285 through 292 Processing helix chain 'E' and resid 302 through 315 removed outlier: 3.831A pdb=" N VAL E 306 " --> pdb=" O GLU E 302 " (cutoff:3.500A) Processing helix chain 'F' and resid 18 through 23 Processing helix chain 'F' and resid 50 through 64 Processing helix chain 'F' and resid 76 through 88 removed outlier: 4.267A pdb=" N ILE F 81 " --> pdb=" O LYS F 77 " (cutoff:3.500A) Processing helix chain 'F' and resid 102 through 107 Processing helix chain 'F' and resid 126 through 134 Processing helix chain 'F' and resid 143 through 146 removed outlier: 3.524A pdb=" N GLY F 146 " --> pdb=" O TYR F 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 143 through 146' Processing helix chain 'F' and resid 147 through 159 removed outlier: 4.602A pdb=" N VAL F 153 " --> pdb=" O ASP F 149 " (cutoff:3.500A) Processing helix chain 'F' and resid 204 through 210 removed outlier: 4.232A pdb=" N MET F 208 " --> pdb=" O ASN F 204 " (cutoff:3.500A) Processing helix chain 'F' and resid 221 through 233 Processing helix chain 'F' and resid 240 through 262 removed outlier: 4.110A pdb=" N ILE F 244 " --> pdb=" O GLU F 240 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ALA F 258 " --> pdb=" O MET F 254 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N PHE F 259 " --> pdb=" O THR F 255 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ILE F 260 " --> pdb=" O ARG F 256 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ASN F 261 " --> pdb=" O GLN F 257 " (cutoff:3.500A) Processing helix chain 'F' and resid 269 through 284 Processing helix chain 'F' and resid 285 through 294 removed outlier: 3.762A pdb=" N ALA F 289 " --> pdb=" O ASP F 285 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N PHE F 290 " --> pdb=" O VAL F 286 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ARG F 291 " --> pdb=" O GLY F 287 " (cutoff:3.500A) Processing helix chain 'F' and resid 299 through 315 removed outlier: 3.753A pdb=" N ALA F 304 " --> pdb=" O GLU F 300 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N THR F 305 " --> pdb=" O LEU F 301 " (cutoff:3.500A) Processing helix chain 'G' and resid 330 through 335 Processing helix chain 'G' and resid 336 through 354 removed outlier: 4.034A pdb=" N ARG G 344 " --> pdb=" O LEU G 340 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N GLY G 345 " --> pdb=" O ASP G 341 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N PHE G 346 " --> pdb=" O ARG G 342 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU G 347 " --> pdb=" O LEU G 343 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLN G 350 " --> pdb=" O PHE G 346 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LEU G 351 " --> pdb=" O LEU G 347 " (cutoff:3.500A) Processing helix chain 'G' and resid 354 through 373 removed outlier: 4.145A pdb=" N ARG G 364 " --> pdb=" O ARG G 360 " (cutoff:3.500A) Processing helix chain 'G' and resid 390 through 397 removed outlier: 3.719A pdb=" N ILE G 394 " --> pdb=" O ARG G 390 " (cutoff:3.500A) Processing helix chain 'G' and resid 429 through 450 Processing helix chain 'G' and resid 468 through 475 removed outlier: 4.052A pdb=" N TRP G 472 " --> pdb=" O SER G 468 " (cutoff:3.500A) Processing helix chain 'G' and resid 498 through 503 Processing helix chain 'G' and resid 504 through 511 removed outlier: 3.526A pdb=" N GLY G 507 " --> pdb=" O ARG G 504 " (cutoff:3.500A) Processing helix chain 'G' and resid 519 through 534 removed outlier: 3.611A pdb=" N ALA G 523 " --> pdb=" O ILE G 519 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N GLN G 529 " --> pdb=" O ILE G 525 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N ARG G 530 " --> pdb=" O TRP G 526 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ARG G 534 " --> pdb=" O ARG G 530 " (cutoff:3.500A) Processing helix chain 'G' and resid 553 through 558 removed outlier: 3.784A pdb=" N VAL G 557 " --> pdb=" O SER G 553 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASN G 558 " --> pdb=" O THR G 554 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 553 through 558' Processing helix chain 'G' and resid 560 through 578 removed outlier: 3.912A pdb=" N GLU G 564 " --> pdb=" O GLY G 560 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG G 565 " --> pdb=" O ASN G 561 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N HIS G 566 " --> pdb=" O TYR G 562 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LEU G 567 " --> pdb=" O LEU G 563 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N SER G 578 " --> pdb=" O ILE G 574 " (cutoff:3.500A) Processing helix chain 'G' and resid 590 through 594 Processing helix chain 'G' and resid 603 through 621 removed outlier: 4.454A pdb=" N GLY G 609 " --> pdb=" O GLU G 605 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N MET G 611 " --> pdb=" O LEU G 607 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N THR G 612 " --> pdb=" O ALA G 608 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N ALA G 616 " --> pdb=" O THR G 612 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N SER G 617 " --> pdb=" O GLU G 613 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLU G 621 " --> pdb=" O SER G 617 " (cutoff:3.500A) Processing helix chain 'a' and resid 22 through 38 Processing helix chain 'a' and resid 68 through 89 removed outlier: 4.423A pdb=" N GLN a 86 " --> pdb=" O MET a 82 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ALA a 87 " --> pdb=" O ALA a 83 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ARG a 88 " --> pdb=" O LEU a 84 " (cutoff:3.500A) Processing helix chain 'a' and resid 90 through 95 Processing helix chain 'a' and resid 101 through 113 removed outlier: 3.517A pdb=" N ASP a 109 " --> pdb=" O ARG a 105 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA a 110 " --> pdb=" O ALA a 106 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLN a 113 " --> pdb=" O ASP a 109 " (cutoff:3.500A) Processing helix chain 'a' and resid 113 through 123 removed outlier: 3.585A pdb=" N GLY a 120 " --> pdb=" O VAL a 116 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ALA a 123 " --> pdb=" O ILE a 119 " (cutoff:3.500A) Processing helix chain 'a' and resid 124 through 143 Processing helix chain 'a' and resid 144 through 147 Processing helix chain 'a' and resid 155 through 168 removed outlier: 4.217A pdb=" N VAL a 159 " --> pdb=" O LEU a 155 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N SER a 160 " --> pdb=" O GLU a 156 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU a 162 " --> pdb=" O ALA a 158 " (cutoff:3.500A) Processing helix chain 'a' and resid 173 through 177 removed outlier: 3.943A pdb=" N ALA a 176 " --> pdb=" O PRO a 173 " (cutoff:3.500A) Processing helix chain 'a' and resid 178 through 192 removed outlier: 3.943A pdb=" N LEU a 182 " --> pdb=" O GLN a 178 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N TRP a 183 " --> pdb=" O VAL a 179 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N ASP a 185 " --> pdb=" O GLU a 181 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N TRP a 186 " --> pdb=" O LEU a 182 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LYS a 190 " --> pdb=" O TRP a 186 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N SER a 192 " --> pdb=" O GLU a 188 " (cutoff:3.500A) Processing helix chain 'a' and resid 193 through 196 Processing helix chain 'a' and resid 197 through 204 removed outlier: 4.099A pdb=" N GLU a 203 " --> pdb=" O GLY a 199 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASP a 204 " --> pdb=" O GLU a 200 " (cutoff:3.500A) Processing helix chain 'a' and resid 204 through 219 removed outlier: 3.897A pdb=" N MET a 219 " --> pdb=" O MET a 215 " (cutoff:3.500A) Processing helix chain 'N' and resid 370 through 374 Processing helix chain 'N' and resid 404 through 418 removed outlier: 4.574A pdb=" N VAL N 410 " --> pdb=" O GLY N 406 " (cutoff:3.500A) Processing helix chain 'N' and resid 427 through 437 removed outlier: 3.873A pdb=" N ALA N 437 " --> pdb=" O ARG N 433 " (cutoff:3.500A) Processing helix chain 'N' and resid 454 through 463 Processing helix chain 'N' and resid 466 through 477 removed outlier: 3.786A pdb=" N GLN N 470 " --> pdb=" O ALA N 466 " (cutoff:3.500A) Processing helix chain 'N' and resid 529 through 541 removed outlier: 4.458A pdb=" N ILE N 533 " --> pdb=" O PRO N 529 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ALA N 534 " --> pdb=" O HIS N 530 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N TYR N 538 " --> pdb=" O ALA N 534 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N LEU N 539 " --> pdb=" O TYR N 535 " (cutoff:3.500A) Processing helix chain 'N' and resid 571 through 576 Processing helix chain 'N' and resid 590 through 596 removed outlier: 3.848A pdb=" N GLY N 594 " --> pdb=" O ASP N 590 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N GLN N 596 " --> pdb=" O GLY N 592 " (cutoff:3.500A) Processing helix chain 'N' and resid 596 through 601 Processing helix chain 'N' and resid 620 through 636 Processing helix chain 'N' and resid 639 through 657 removed outlier: 3.521A pdb=" N ALA N 648 " --> pdb=" O LEU N 644 " (cutoff:3.500A) Processing helix chain 'N' and resid 670 through 688 removed outlier: 4.796A pdb=" N GLN N 676 " --> pdb=" O ASP N 672 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N LYS N 677 " --> pdb=" O MET N 673 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LEU N 678 " --> pdb=" O ALA N 674 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N ASP N 679 " --> pdb=" O LEU N 675 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N MET N 688 " --> pdb=" O ASP N 684 " (cutoff:3.500A) Processing helix chain 'N' and resid 704 through 714 removed outlier: 4.414A pdb=" N ALA N 712 " --> pdb=" O ASP N 708 " (cutoff:3.500A) Processing helix chain 'N' and resid 727 through 731 removed outlier: 3.848A pdb=" N ASP N 730 " --> pdb=" O ALA N 727 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLN N 731 " --> pdb=" O PRO N 728 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 727 through 731' Processing helix chain 'N' and resid 732 through 742 removed outlier: 3.541A pdb=" N GLY N 742 " --> pdb=" O ALA N 738 " (cutoff:3.500A) Processing helix chain 'N' and resid 748 through 752 Processing helix chain 'N' and resid 763 through 770 removed outlier: 3.872A pdb=" N SER N 770 " --> pdb=" O LEU N 766 " (cutoff:3.500A) Processing helix chain 'N' and resid 776 through 791 removed outlier: 3.627A pdb=" N THR N 780 " --> pdb=" O ILE N 776 " (cutoff:3.500A) Processing helix chain 'N' and resid 802 through 804 No H-bonds generated for 'chain 'N' and resid 802 through 804' Processing helix chain 'N' and resid 805 through 815 Processing helix chain 'N' and resid 815 through 837 Proline residue: N 825 - end of helix removed outlier: 5.088A pdb=" N ILE N 828 " --> pdb=" O GLY N 824 " (cutoff:3.500A) Processing helix chain 'N' and resid 872 through 880 removed outlier: 4.539A pdb=" N LYS N 880 " --> pdb=" O TRP N 876 " (cutoff:3.500A) Processing helix chain 'N' and resid 882 through 895 Processing helix chain 'N' and resid 906 through 912 removed outlier: 3.965A pdb=" N ARG N 912 " --> pdb=" O THR N 908 " (cutoff:3.500A) Processing helix chain 'N' and resid 915 through 925 Processing helix chain 'N' and resid 945 through 950 removed outlier: 3.581A pdb=" N LEU N 949 " --> pdb=" O PRO N 945 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA N 950 " --> pdb=" O PRO N 946 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 945 through 950' Processing helix chain 'N' and resid 961 through 968 Processing helix chain 'N' and resid 968 through 985 removed outlier: 4.206A pdb=" N ILE N 972 " --> pdb=" O PHE N 968 " (cutoff:3.500A) Processing helix chain 'N' and resid 992 through 1008 removed outlier: 3.894A pdb=" N ALA N 996 " --> pdb=" O ASN N 992 " (cutoff:3.500A) Processing helix chain 'N' and resid 1011 through 1020 removed outlier: 3.583A pdb=" N GLY N1020 " --> pdb=" O GLU N1016 " (cutoff:3.500A) Processing helix chain 'N' and resid 1034 through 1041 removed outlier: 4.009A pdb=" N LEU N1038 " --> pdb=" O GLY N1034 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE N1039 " --> pdb=" O LEU N1035 " (cutoff:3.500A) Processing helix chain 'N' and resid 1047 through 1058 Processing helix chain 'N' and resid 1071 through 1082 removed outlier: 5.560A pdb=" N GLU N1077 " --> pdb=" O GLY N1073 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ARG N1078 " --> pdb=" O LEU N1074 " (cutoff:3.500A) Processing helix chain 'N' and resid 1109 through 1118 removed outlier: 3.611A pdb=" N GLU N1114 " --> pdb=" O ALA N1110 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N SER N1115 " --> pdb=" O ALA N1111 " (cutoff:3.500A) Processing helix chain 'N' and resid 1139 through 1150 removed outlier: 4.727A pdb=" N SER N1144 " --> pdb=" O GLU N1140 " (cutoff:3.500A) Processing helix chain 'N' and resid 1153 through 1162 removed outlier: 3.782A pdb=" N ILE N1157 " --> pdb=" O ASN N1153 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ARG N1162 " --> pdb=" O ALA N1158 " (cutoff:3.500A) Processing helix chain 'N' and resid 1165 through 1185 removed outlier: 4.874A pdb=" N ILE N1171 " --> pdb=" O GLY N1167 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N VAL N1175 " --> pdb=" O ILE N1171 " (cutoff:3.500A) Processing helix chain 'N' and resid 1193 through 1202 Processing helix chain 'N' and resid 1203 through 1214 Processing helix chain 'N' and resid 1214 through 1231 removed outlier: 3.614A pdb=" N LYS N1224 " --> pdb=" O GLU N1220 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE N1229 " --> pdb=" O LEU N1225 " (cutoff:3.500A) Processing helix chain 'N' and resid 1240 through 1252 removed outlier: 3.546A pdb=" N GLU N1244 " --> pdb=" O SER N1240 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N SER N1249 " --> pdb=" O LEU N1245 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL N1250 " --> pdb=" O GLU N1246 " (cutoff:3.500A) 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: 6.064A pdb=" N VAL A 93 " --> pdb=" O VAL A 139 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N ASP A 141 " --> pdb=" O VAL A 93 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N VAL A 95 " --> pdb=" O ASP A 141 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N PHE A 182 " --> pdb=" O LEU A 138 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N VAL A 67 " --> pdb=" O ALA A 183 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER A 70 " --> pdb=" O THR A 215 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 108 through 115 removed outlier: 4.064A pdb=" N LYS A 109 " --> pdb=" O LYS A 124 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LYS A 124 " --> pdb=" O LYS A 109 " (cutoff:3.500A) 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 96 removed outlier: 6.066A pdb=" N LEU B 138 " --> pdb=" O PHE B 182 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N THR B 184 " --> pdb=" O LEU B 138 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N PHE B 140 " --> pdb=" O THR B 184 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 108 through 114 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: 6.101A pdb=" N VAL C 93 " --> pdb=" O VAL C 139 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N ASP C 141 " --> pdb=" O VAL C 93 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N VAL C 95 " --> pdb=" O ASP C 141 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL C 67 " --> pdb=" O ALA C 183 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N ALA C 185 " --> pdb=" O VAL C 67 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N VAL C 69 " --> pdb=" O ALA C 185 " (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: 6.167A pdb=" N VAL D 93 " --> pdb=" O VAL D 139 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N ASP D 141 " --> pdb=" O VAL D 93 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N VAL D 95 " --> pdb=" O ASP D 141 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N LEU D 138 " --> pdb=" O PHE D 182 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N THR D 184 " --> pdb=" O LEU D 138 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N PHE D 140 " --> pdb=" O THR D 184 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N VAL D 67 " --> pdb=" O ALA D 183 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N MET D 68 " --> pdb=" O THR D 215 " (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 92 through 96 removed outlier: 4.202A pdb=" N VAL E 67 " --> pdb=" O LEU E 181 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N MET E 68 " --> pdb=" O THR E 215 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 108 through 112 Processing sheet with id=AB8, first strand: chain 'F' and resid 16 through 17 Processing sheet with id=AB9, first strand: chain 'F' and resid 92 through 96 removed outlier: 6.401A pdb=" N VAL F 93 " --> pdb=" O VAL F 139 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N ASP F 141 " --> pdb=" O VAL F 93 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N VAL F 95 " --> pdb=" O ASP F 141 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N VAL F 67 " --> pdb=" O ALA F 183 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N ALA F 185 " --> pdb=" O VAL F 67 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N VAL F 69 " --> pdb=" O ALA F 185 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 110 through 115 Processing sheet with id=AC2, first strand: chain 'G' and resid 326 through 329 removed outlier: 6.328A pdb=" N ILE G 455 " --> pdb=" O TYR G 492 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LEU G 456 " --> pdb=" O LEU G 419 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N PHE G 458 " --> pdb=" O LEU G 421 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N VAL G 416 " --> pdb=" O ILE G 540 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N MET G 542 " --> pdb=" O VAL G 416 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N THR G 418 " --> pdb=" O MET G 542 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ILE G 544 " --> pdb=" O THR G 418 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N VAL G 420 " --> pdb=" O ILE G 544 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N LYS G 539 " --> pdb=" O GLU G 581 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N ILE G 583 " --> pdb=" O LYS G 539 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N LEU G 541 " --> pdb=" O ILE G 583 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N ILE G 585 " --> pdb=" O LEU G 541 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N MET G 543 " --> pdb=" O ILE G 585 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 378 through 381 removed outlier: 5.171A pdb=" N PHE G 379 " --> pdb=" O GLN G 406 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N GLN G 406 " --> pdb=" O PHE G 379 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'a' and resid 43 through 46 Processing sheet with id=AC5, first strand: chain 'N' and resid 504 through 507 removed outlier: 4.018A pdb=" N MET N 551 " --> pdb=" O ILE N 384 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N HIS N 582 " --> pdb=" O VAL N 604 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N ILE N 606 " --> pdb=" O HIS N 582 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N TYR N 584 " --> pdb=" O ILE N 606 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'N' and resid 401 through 402 Processing sheet with id=AC7, first strand: chain 'N' and resid 614 through 615 Processing sheet with id=AC8, first strand: chain 'N' and resid 956 through 957 removed outlier: 6.368A pdb=" N PHE N 901 " --> pdb=" O THR N 957 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N ASN N1088 " --> pdb=" O THR N 904 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'N' and resid 927 through 931 removed outlier: 4.303A pdb=" N VAL N 930 " --> pdb=" O GLY N 940 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N GLY N 940 " --> pdb=" O VAL N 930 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'N' and resid 1023 through 1025 removed outlier: 4.448A pdb=" N VAL N1023 " --> pdb=" O TYR N1062 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N GLY N1063 " --> pdb=" O GLU N1067 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N GLU N1067 " --> pdb=" O GLY N1063 " (cutoff:3.500A) 1037 hydrogen bonds defined for protein. 2988 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.19 Time building geometry restraints manager: 2.82 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: 8670 1.34 - 1.46: 3367 1.46 - 1.57: 14125 1.57 - 1.69: 18 1.69 - 1.81: 181 Bond restraints: 26361 Sorted by residual: bond pdb=" O3A ANP D 401 " pdb=" PB ANP D 401 " ideal model delta sigma weight residual 1.700 1.557 0.143 2.00e-02 2.50e+03 5.15e+01 bond pdb=" O3A ANP E 401 " pdb=" PB ANP E 401 " ideal model delta sigma weight residual 1.700 1.557 0.143 2.00e-02 2.50e+03 5.13e+01 bond pdb=" O3A ANP F 401 " pdb=" PB ANP F 401 " ideal model delta sigma weight residual 1.700 1.557 0.143 2.00e-02 2.50e+03 5.13e+01 bond pdb=" N3B ANP E 401 " pdb=" PG ANP E 401 " ideal model delta sigma weight residual 1.795 1.690 0.105 2.00e-02 2.50e+03 2.76e+01 bond pdb=" N3B ANP F 401 " pdb=" PG ANP F 401 " ideal model delta sigma weight residual 1.795 1.691 0.104 2.00e-02 2.50e+03 2.72e+01 ... (remaining 26356 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.81: 35699 3.81 - 7.62: 129 7.62 - 11.43: 18 11.43 - 15.24: 0 15.24 - 19.05: 3 Bond angle restraints: 35849 Sorted by residual: angle pdb=" PB ANP E 401 " pdb=" N3B ANP E 401 " pdb=" PG ANP E 401 " ideal model delta sigma weight residual 126.95 107.90 19.05 3.00e+00 1.11e-01 4.03e+01 angle pdb=" PB ANP D 401 " pdb=" N3B ANP D 401 " pdb=" PG ANP D 401 " ideal model delta sigma weight residual 126.95 108.54 18.41 3.00e+00 1.11e-01 3.77e+01 angle pdb=" PB ANP F 401 " pdb=" N3B ANP F 401 " pdb=" PG ANP F 401 " ideal model delta sigma weight residual 126.95 108.68 18.27 3.00e+00 1.11e-01 3.71e+01 angle pdb=" CA ASP F 13 " pdb=" CB ASP F 13 " pdb=" CG ASP F 13 " ideal model delta sigma weight residual 112.60 118.04 -5.44 1.00e+00 1.00e+00 2.96e+01 angle pdb=" CA ASP E 209 " pdb=" CB ASP E 209 " pdb=" CG ASP E 209 " ideal model delta sigma weight residual 112.60 117.27 -4.67 1.00e+00 1.00e+00 2.18e+01 ... (remaining 35844 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.54: 14631 21.54 - 43.08: 1076 43.08 - 64.62: 105 64.62 - 86.16: 46 86.16 - 107.70: 4 Dihedral angle restraints: 15862 sinusoidal: 6356 harmonic: 9506 Sorted by residual: dihedral pdb=" CA ASP N 667 " pdb=" C ASP N 667 " pdb=" N HIS N 668 " pdb=" CA HIS N 668 " ideal model delta harmonic sigma weight residual 180.00 159.49 20.51 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" O1B ANP D 401 " pdb=" N3B ANP D 401 " pdb=" PB ANP D 401 " pdb=" PG ANP D 401 " ideal model delta sinusoidal sigma weight residual 35.15 -72.55 107.70 1 3.00e+01 1.11e-03 1.39e+01 dihedral pdb=" C THR F 14 " pdb=" N THR F 14 " pdb=" CA THR F 14 " pdb=" CB THR F 14 " ideal model delta harmonic sigma weight residual -122.00 -131.12 9.12 0 2.50e+00 1.60e-01 1.33e+01 ... (remaining 15859 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 3307 0.055 - 0.111: 619 0.111 - 0.166: 69 0.166 - 0.221: 7 0.221 - 0.276: 6 Chirality restraints: 4008 Sorted by residual: chirality pdb=" CA ASP F 13 " pdb=" N ASP F 13 " pdb=" C ASP F 13 " pdb=" CB ASP F 13 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.91e+00 chirality pdb=" C3' ANP F 401 " pdb=" C2' ANP F 401 " pdb=" C4' ANP F 401 " pdb=" O3' ANP F 401 " both_signs ideal model delta sigma weight residual False -2.36 -2.63 0.27 2.00e-01 2.50e+01 1.83e+00 chirality pdb=" C3' ANP E 401 " pdb=" C2' ANP E 401 " pdb=" C4' ANP E 401 " pdb=" O3' ANP E 401 " both_signs ideal model delta sigma weight residual False -2.36 -2.63 0.27 2.00e-01 2.50e+01 1.83e+00 ... (remaining 4005 not shown) Planarity restraints: 4718 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG F 174 " 0.075 5.00e-02 4.00e+02 1.13e-01 2.04e+01 pdb=" N PRO F 175 " -0.195 5.00e-02 4.00e+02 pdb=" CA PRO F 175 " 0.060 5.00e-02 4.00e+02 pdb=" CD PRO F 175 " 0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG B 174 " 0.070 5.00e-02 4.00e+02 1.04e-01 1.74e+01 pdb=" N PRO B 175 " -0.181 5.00e-02 4.00e+02 pdb=" CA PRO B 175 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO B 175 " 0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP N 876 " 0.020 2.00e-02 2.50e+03 1.92e-02 9.25e+00 pdb=" CG TRP N 876 " -0.050 2.00e-02 2.50e+03 pdb=" CD1 TRP N 876 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP N 876 " -0.006 2.00e-02 2.50e+03 pdb=" NE1 TRP N 876 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP N 876 " -0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP N 876 " 0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP N 876 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP N 876 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP N 876 " 0.006 2.00e-02 2.50e+03 ... (remaining 4715 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2038 2.74 - 3.28: 27823 3.28 - 3.82: 43930 3.82 - 4.36: 50626 4.36 - 4.90: 82375 Nonbonded interactions: 206792 Sorted by model distance: nonbonded pdb=" O ALA E 289 " pdb=" OG1 THR E 293 " model vdw 2.197 3.040 nonbonded pdb=" OG SER N 826 " pdb=" O THR N 858 " model vdw 2.203 3.040 nonbonded pdb=" OG SER G 424 " pdb=" OG SER G 426 " model vdw 2.211 3.040 nonbonded pdb=" O SER A 269 " pdb=" OG1 THR A 272 " model vdw 2.214 3.040 nonbonded pdb=" O ASN D 10 " pdb=" OH TYR D 33 " model vdw 2.215 3.040 ... (remaining 206787 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 8 through 319) selection = (chain 'B' and resid 8 through 319) selection = (chain 'C' and (resid 8 through 188 or resid 203 through 319)) selection = (chain 'D' and (resid 8 through 188 or resid 203 through 319)) selection = (chain 'E' and (resid 8 through 188 or resid 203 through 319)) selection = (chain 'F' and (resid 8 through 188 or resid 203 through 319)) } 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: 6.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.520 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 25.430 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6781 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 : 0.004 0.143 26361 Z= 0.187 Angle : 0.677 19.047 35849 Z= 0.340 Chirality : 0.044 0.276 4008 Planarity : 0.005 0.113 4718 Dihedral : 14.753 107.699 9726 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 16.81 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.84 % Favored : 93.09 % Rotamer: Outliers : 0.15 % Allowed : 0.48 % Favored : 99.37 % 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 (0.15), residues: 3258 helix: 0.05 (0.14), residues: 1349 sheet: -0.42 (0.27), residues: 354 loop : -1.04 (0.17), residues: 1555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG F 250 TYR 0.020 0.001 TYR F 143 PHE 0.031 0.001 PHE a 108 TRP 0.050 0.002 TRP N 876 HIS 0.004 0.001 HIS C 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.19 (26361) covalent geometry : angle 0.67730 / 0.34 (35849) hydrogen bonds : bond 0.16566 / 11.32 ( 1037) hydrogen bonds : angle 6.75122 / 4.79 ( 2988) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 806 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 802 time to evaluate : 0.727 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: A 66 ARG cc_start: 0.7667 (mpp-170) cc_final: 0.7168 (mpp-170) REVERT: A 93 VAL cc_start: 0.8592 (p) cc_final: 0.8315 (m) REVERT: A 138 LEU cc_start: 0.8344 (tp) cc_final: 0.7999 (tp) REVERT: A 244 ILE cc_start: 0.9063 (mp) cc_final: 0.8824 (mp) REVERT: A 248 MET cc_start: 0.7042 (ptp) cc_final: 0.5505 (ptp) REVERT: A 255 THR cc_start: 0.8785 (t) cc_final: 0.8582 (t) REVERT: A 294 PHE cc_start: 0.7311 (t80) cc_final: 0.7086 (t80) REVERT: A 299 ASP cc_start: 0.7434 (m-30) cc_final: 0.7227 (m-30) REVERT: A 309 PHE cc_start: 0.8359 (m-80) cc_final: 0.8004 (m-80) REVERT: B 33 TYR cc_start: 0.4270 (m-80) cc_final: 0.3112 (m-80) REVERT: B 64 ASN cc_start: 0.7735 (t0) cc_final: 0.7236 (t0) REVERT: B 159 GLU cc_start: 0.8385 (mm-30) cc_final: 0.8075 (mm-30) REVERT: B 180 ARG cc_start: 0.7351 (mpt180) cc_final: 0.6910 (mpt180) REVERT: B 288 PHE cc_start: 0.7234 (t80) cc_final: 0.6693 (t80) REVERT: B 295 LEU cc_start: 0.7755 (tp) cc_final: 0.7299 (tp) REVERT: B 298 CYS cc_start: 0.7340 (m) cc_final: 0.6852 (m) REVERT: B 309 PHE cc_start: 0.8692 (m-80) cc_final: 0.8340 (m-80) REVERT: C 80 HIS cc_start: 0.7839 (m90) cc_final: 0.7370 (m90) REVERT: C 105 ASP cc_start: 0.8056 (t0) cc_final: 0.7818 (t0) REVERT: C 116 GLU cc_start: 0.7107 (tp30) cc_final: 0.6305 (tp30) REVERT: C 122 GLU cc_start: 0.7690 (tt0) cc_final: 0.7421 (tt0) REVERT: C 208 MET cc_start: 0.8377 (mtm) cc_final: 0.7951 (mtm) REVERT: C 257 GLN cc_start: 0.8323 (mm-40) cc_final: 0.7888 (mm-40) REVERT: C 295 LEU cc_start: 0.7303 (tp) cc_final: 0.6804 (tp) REVERT: C 311 GLN cc_start: 0.8033 (tm-30) cc_final: 0.7542 (tm-30) REVERT: D 28 MET cc_start: 0.3491 (mtt) cc_final: 0.3232 (mtt) REVERT: D 51 ARG cc_start: 0.6560 (ttm170) cc_final: 0.6273 (ttm170) REVERT: D 68 MET cc_start: 0.7940 (tpp) cc_final: 0.7490 (tpt) REVERT: D 88 LEU cc_start: 0.8919 (mt) cc_final: 0.8715 (mt) REVERT: D 224 ASN cc_start: 0.8329 (m110) cc_final: 0.8122 (m110) REVERT: D 254 MET cc_start: 0.7203 (mtp) cc_final: 0.7003 (mtp) REVERT: D 257 GLN cc_start: 0.7961 (mp10) cc_final: 0.7482 (mp10) REVERT: D 261 ASN cc_start: 0.8856 (m-40) cc_final: 0.8578 (m-40) REVERT: D 278 GLU cc_start: 0.8687 (mt-10) cc_final: 0.8474 (mt-10) REVERT: E 44 ASP cc_start: 0.7666 (t70) cc_final: 0.7459 (t0) REVERT: E 64 ASN cc_start: 0.8165 (t0) cc_final: 0.7910 (t0) REVERT: E 138 LEU cc_start: 0.8362 (tp) cc_final: 0.8014 (tp) REVERT: E 154 ILE cc_start: 0.8479 (pt) cc_final: 0.8265 (pt) REVERT: E 222 HIS cc_start: 0.7997 (t70) cc_final: 0.7776 (t70) REVERT: E 275 THR cc_start: 0.8549 (m) cc_final: 0.8009 (m) REVERT: E 296 ASN cc_start: 0.8572 (m110) cc_final: 0.8122 (m-40) REVERT: E 300 GLU cc_start: 0.8038 (tm-30) cc_final: 0.7424 (tm-30) REVERT: F 68 MET cc_start: 0.7106 (tmm) cc_final: 0.6739 (tmm) REVERT: F 135 ASN cc_start: 0.7932 (p0) cc_final: 0.7245 (p0) REVERT: F 147 ARG cc_start: 0.8061 (ptt-90) cc_final: 0.7734 (ptt-90) REVERT: F 174 ARG cc_start: 0.8165 (mmp-170) cc_final: 0.7881 (mmp-170) REVERT: F 176 HIS cc_start: 0.8551 (t70) cc_final: 0.8232 (t70) REVERT: F 181 LEU cc_start: 0.7838 (tp) cc_final: 0.7487 (tt) REVERT: F 208 MET cc_start: 0.6952 (mpp) cc_final: 0.6679 (mpp) REVERT: F 224 ASN cc_start: 0.8661 (t0) cc_final: 0.8320 (t0) REVERT: F 248 MET cc_start: 0.8278 (mtm) cc_final: 0.7792 (mtm) REVERT: F 254 MET cc_start: 0.7482 (tmm) cc_final: 0.7260 (tmm) REVERT: F 265 SER cc_start: 0.8635 (t) cc_final: 0.8261 (t) REVERT: F 275 THR cc_start: 0.7343 (m) cc_final: 0.6872 (m) REVERT: F 279 ASN cc_start: 0.8535 (m-40) cc_final: 0.8010 (m-40) REVERT: G 369 LEU cc_start: 0.8934 (mt) cc_final: 0.8489 (mt) REVERT: G 399 THR cc_start: 0.8127 (p) cc_final: 0.7884 (p) REVERT: G 430 ARG cc_start: 0.8023 (tmm160) cc_final: 0.7757 (tmm160) REVERT: G 505 ASN cc_start: 0.8247 (t0) cc_final: 0.7759 (t0) REVERT: G 543 MET cc_start: 0.6999 (tpt) cc_final: 0.6785 (tpt) REVERT: G 544 ILE cc_start: 0.8897 (mp) cc_final: 0.8624 (mp) REVERT: a 25 PHE cc_start: 0.8233 (m-10) cc_final: 0.8009 (m-80) REVERT: a 113 GLN cc_start: 0.7684 (mp10) cc_final: 0.6893 (mp10) REVERT: a 131 LEU cc_start: 0.8510 (mt) cc_final: 0.7803 (mt) REVERT: a 134 MET cc_start: 0.7465 (ppp) cc_final: 0.6642 (ppp) REVERT: a 135 LEU cc_start: 0.8235 (mt) cc_final: 0.7646 (mt) REVERT: a 214 ASP cc_start: 0.8625 (m-30) cc_final: 0.8345 (m-30) REVERT: N 432 MET cc_start: 0.8413 (mtm) cc_final: 0.7711 (mtm) REVERT: N 433 ARG cc_start: 0.8462 (mtm180) cc_final: 0.7959 (mtt90) REVERT: N 436 MET cc_start: 0.8459 (ttp) cc_final: 0.8175 (ttp) REVERT: N 536 TYR cc_start: 0.8004 (m-80) cc_final: 0.7744 (m-80) REVERT: N 572 TYR cc_start: 0.7529 (m-80) cc_final: 0.7232 (m-80) REVERT: N 586 PHE cc_start: 0.7591 (t80) cc_final: 0.7040 (t80) REVERT: N 688 MET cc_start: 0.7358 (ttp) cc_final: 0.6658 (ttp) REVERT: N 696 VAL cc_start: 0.6261 (p) cc_final: 0.5952 (p) REVERT: N 829 ASP cc_start: 0.6607 (m-30) cc_final: 0.6357 (m-30) REVERT: N 890 TYR cc_start: 0.7797 (t80) cc_final: 0.7580 (t80) REVERT: N 893 ASP cc_start: 0.8267 (m-30) cc_final: 0.7991 (m-30) REVERT: N 960 ILE cc_start: 0.8818 (pt) cc_final: 0.8382 (pt) REVERT: N 964 PHE cc_start: 0.8501 (t80) cc_final: 0.7927 (t80) REVERT: N 1077 GLU cc_start: 0.8600 (tm-30) cc_final: 0.8298 (tm-30) REVERT: N 1155 LYS cc_start: 0.8429 (mtmm) cc_final: 0.7850 (mtmm) REVERT: N 1209 PHE cc_start: 0.8097 (t80) cc_final: 0.7862 (t80) REVERT: N 1210 MET cc_start: 0.8682 (mtm) cc_final: 0.8296 (mtm) REVERT: N 1227 GLU cc_start: 0.7793 (tm-30) cc_final: 0.7093 (tp30) outliers start: 4 outliers final: 2 residues processed: 806 average time/residue: 0.1865 time to fit residues: 229.9037 Evaluate side-chains 784 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 782 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 0.3980 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 0.0770 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 20.0000 chunk 183 optimal weight: 4.9990 chunk 298 optimal weight: 20.0000 overall best weight: 1.0742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 GLN A 261 ASN A 296 ASN A 311 GLN B 155 GLN ** B 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 119 GLN C 222 HIS C 227 ASN ** D 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 207 GLN E 52 GLN E 279 ASN F 134 HIS G 505 ASN ** N1091 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N1163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N1239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.173832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.138178 restraints weight = 49321.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.143770 restraints weight = 30023.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.147723 restraints weight = 20517.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.150623 restraints weight = 15135.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.152826 restraints weight = 11792.092| |-----------------------------------------------------------------------------| r_work (final): 0.3987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6740 moved from start: 0.0898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 26361 Z= 0.141 Angle : 0.583 12.032 35849 Z= 0.298 Chirality : 0.042 0.159 4008 Planarity : 0.005 0.070 4718 Dihedral : 7.721 121.992 3718 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 0.11 % Allowed : 4.59 % Favored : 95.30 % 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: -0.73 (0.15), residues: 3258 helix: 0.17 (0.14), residues: 1361 sheet: -0.50 (0.27), residues: 351 loop : -1.01 (0.17), residues: 1546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG E 250 TYR 0.022 0.002 TYR D 132 PHE 0.019 0.001 PHE D 309 TRP 0.027 0.001 TRP N 876 HIS 0.016 0.001 HIS E 222 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.14 (26361) covalent geometry : angle 0.58337 / 0.30 (35849) hydrogen bonds : bond 0.04065 / 2.73 ( 1037) hydrogen bonds : angle 5.57235 / 3.91 ( 2988) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 820 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 817 time to evaluate : 0.911 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: A 66 ARG cc_start: 0.7561 (mpp-170) cc_final: 0.7029 (mpp-170) REVERT: A 89 ASN cc_start: 0.7485 (t0) cc_final: 0.7273 (t0) REVERT: A 138 LEU cc_start: 0.8340 (tp) cc_final: 0.8011 (tp) REVERT: A 244 ILE cc_start: 0.8935 (mp) cc_final: 0.8703 (mp) REVERT: A 248 MET cc_start: 0.7023 (ptp) cc_final: 0.6561 (ptp) REVERT: A 282 ILE cc_start: 0.8169 (mt) cc_final: 0.7931 (mt) REVERT: A 294 PHE cc_start: 0.7719 (t80) cc_final: 0.7293 (t80) REVERT: B 159 GLU cc_start: 0.8406 (mm-30) cc_final: 0.8173 (mm-30) REVERT: B 210 ARG cc_start: 0.8320 (tpm170) cc_final: 0.7385 (tpm170) REVERT: B 288 PHE cc_start: 0.7316 (t80) cc_final: 0.6667 (t80) REVERT: B 294 PHE cc_start: 0.7557 (t80) cc_final: 0.7323 (t80) REVERT: B 295 LEU cc_start: 0.7729 (tp) cc_final: 0.7104 (tp) REVERT: B 298 CYS cc_start: 0.7633 (m) cc_final: 0.6938 (m) REVERT: B 303 ARG cc_start: 0.7655 (tpt-90) cc_final: 0.7169 (tpt90) REVERT: B 309 PHE cc_start: 0.8644 (m-80) cc_final: 0.8232 (m-80) REVERT: B 312 ARG cc_start: 0.8122 (mtt90) cc_final: 0.7608 (mtt90) REVERT: C 80 HIS cc_start: 0.7962 (m90) cc_final: 0.7574 (m90) REVERT: C 122 GLU cc_start: 0.7808 (tt0) cc_final: 0.7512 (tt0) REVERT: C 208 MET cc_start: 0.8269 (mtm) cc_final: 0.7886 (mtm) REVERT: C 248 MET cc_start: 0.8288 (mmp) cc_final: 0.7980 (mmm) REVERT: C 257 GLN cc_start: 0.8422 (mm-40) cc_final: 0.8041 (mm-40) REVERT: C 271 ARG cc_start: 0.7919 (mtm110) cc_final: 0.7579 (mtm110) REVERT: C 295 LEU cc_start: 0.7358 (tp) cc_final: 0.6780 (tp) REVERT: C 311 GLN cc_start: 0.8290 (tm-30) cc_final: 0.7846 (tm-30) REVERT: D 68 MET cc_start: 0.8097 (tpp) cc_final: 0.7807 (tpp) REVERT: D 144 ASP cc_start: 0.7530 (p0) cc_final: 0.7158 (p0) REVERT: D 261 ASN cc_start: 0.8849 (m-40) cc_final: 0.8589 (m-40) REVERT: D 271 ARG cc_start: 0.8235 (tpt170) cc_final: 0.7326 (tpp80) REVERT: D 278 GLU cc_start: 0.8705 (mt-10) cc_final: 0.8488 (mt-10) REVERT: E 64 ASN cc_start: 0.8201 (t0) cc_final: 0.7956 (t0) REVERT: E 83 GLN cc_start: 0.7780 (tm-30) cc_final: 0.6913 (tm-30) REVERT: E 138 LEU cc_start: 0.8532 (tp) cc_final: 0.8222 (tp) REVERT: E 155 GLN cc_start: 0.8423 (tp40) cc_final: 0.8057 (tp40) REVERT: E 208 MET cc_start: 0.7742 (tpp) cc_final: 0.7246 (tpp) REVERT: E 244 ILE cc_start: 0.8403 (mt) cc_final: 0.8101 (mt) REVERT: E 248 MET cc_start: 0.7193 (mtm) cc_final: 0.6894 (mtm) REVERT: E 275 THR cc_start: 0.8410 (m) cc_final: 0.8184 (m) REVERT: E 278 GLU cc_start: 0.8332 (tp30) cc_final: 0.8032 (tp30) REVERT: E 292 LEU cc_start: 0.8396 (mp) cc_final: 0.8174 (mp) REVERT: E 296 ASN cc_start: 0.8620 (m110) cc_final: 0.8139 (m-40) REVERT: E 297 LYS cc_start: 0.8188 (mppt) cc_final: 0.7887 (mppt) REVERT: E 300 GLU cc_start: 0.7948 (tm-30) cc_final: 0.7379 (tm-30) REVERT: F 48 LEU cc_start: 0.8326 (mm) cc_final: 0.8049 (mm) REVERT: F 68 MET cc_start: 0.7143 (tmm) cc_final: 0.6845 (tmm) REVERT: F 94 ARG cc_start: 0.7480 (ttp80) cc_final: 0.7277 (ttp80) REVERT: F 103 ARG cc_start: 0.7201 (ptm-80) cc_final: 0.6585 (ptm-80) REVERT: F 135 ASN cc_start: 0.8141 (p0) cc_final: 0.7388 (p0) REVERT: F 143 TYR cc_start: 0.8468 (t80) cc_final: 0.7902 (t80) REVERT: F 151 MET cc_start: 0.7363 (mpp) cc_final: 0.7054 (mpp) REVERT: F 176 HIS cc_start: 0.8684 (t70) cc_final: 0.8468 (t70) REVERT: F 181 LEU cc_start: 0.7862 (tp) cc_final: 0.7616 (tt) REVERT: F 208 MET cc_start: 0.6936 (mpp) cc_final: 0.6679 (mpp) REVERT: F 224 ASN cc_start: 0.8729 (t0) cc_final: 0.8157 (t0) REVERT: F 228 ILE cc_start: 0.8295 (OUTLIER) cc_final: 0.7978 (mp) REVERT: F 248 MET cc_start: 0.8158 (mtm) cc_final: 0.7729 (mtm) REVERT: F 254 MET cc_start: 0.7411 (tmm) cc_final: 0.7175 (tmm) REVERT: F 265 SER cc_start: 0.8772 (t) cc_final: 0.8436 (t) REVERT: F 275 THR cc_start: 0.7423 (m) cc_final: 0.6951 (m) REVERT: F 279 ASN cc_start: 0.8562 (m-40) cc_final: 0.8045 (m-40) REVERT: G 366 GLN cc_start: 0.6898 (tp40) cc_final: 0.6477 (tp40) REVERT: G 369 LEU cc_start: 0.8978 (mt) cc_final: 0.8528 (mt) REVERT: G 370 MET cc_start: 0.7033 (mpp) cc_final: 0.6779 (mpp) REVERT: G 399 THR cc_start: 0.8181 (p) cc_final: 0.7793 (p) REVERT: G 406 GLN cc_start: 0.7324 (tm-30) cc_final: 0.6988 (tm-30) REVERT: G 427 MET cc_start: 0.7823 (pmm) cc_final: 0.7588 (pmm) REVERT: G 430 ARG cc_start: 0.8113 (tmm160) cc_final: 0.7830 (tmm160) REVERT: G 505 ASN cc_start: 0.8321 (t0) cc_final: 0.8038 (t0) REVERT: G 530 ARG cc_start: 0.8054 (ttm110) cc_final: 0.7528 (ptm-80) REVERT: G 544 ILE cc_start: 0.8905 (mp) cc_final: 0.8486 (mp) REVERT: a 25 PHE cc_start: 0.8228 (m-10) cc_final: 0.8009 (m-80) REVERT: a 113 GLN cc_start: 0.7661 (mp10) cc_final: 0.6730 (mp10) REVERT: a 131 LEU cc_start: 0.8498 (mt) cc_final: 0.7775 (mt) REVERT: a 134 MET cc_start: 0.7501 (ppp) cc_final: 0.6595 (ppp) REVERT: a 135 LEU cc_start: 0.8379 (mt) cc_final: 0.7657 (mt) REVERT: a 214 ASP cc_start: 0.8634 (m-30) cc_final: 0.8312 (m-30) REVERT: a 215 MET cc_start: 0.8443 (mtm) cc_final: 0.8173 (mtm) REVERT: N 436 MET cc_start: 0.8430 (ttp) cc_final: 0.8133 (ttp) REVERT: N 470 GLN cc_start: 0.6609 (mp10) cc_final: 0.6371 (mp10) REVERT: N 572 TYR cc_start: 0.7500 (m-80) cc_final: 0.7211 (m-80) REVERT: N 586 PHE cc_start: 0.7388 (t80) cc_final: 0.6865 (t80) REVERT: N 677 LYS cc_start: 0.8528 (pttm) cc_final: 0.8279 (mtmt) REVERT: N 688 MET cc_start: 0.7430 (ttp) cc_final: 0.6765 (ttp) REVERT: N 696 VAL cc_start: 0.6233 (p) cc_final: 0.5910 (p) REVERT: N 829 ASP cc_start: 0.6609 (m-30) cc_final: 0.6355 (m-30) REVERT: N 893 ASP cc_start: 0.8240 (m-30) cc_final: 0.7975 (m-30) REVERT: N 960 ILE cc_start: 0.8809 (pt) cc_final: 0.8355 (pt) REVERT: N 964 PHE cc_start: 0.8166 (t80) cc_final: 0.7685 (t80) REVERT: N 1077 GLU cc_start: 0.8689 (tm-30) cc_final: 0.8389 (tm-30) REVERT: N 1155 LYS cc_start: 0.8564 (mtmm) cc_final: 0.8043 (mtmm) REVERT: N 1210 MET cc_start: 0.8629 (mtm) cc_final: 0.8235 (mtm) REVERT: N 1227 GLU cc_start: 0.7697 (tm-30) cc_final: 0.7075 (tp30) outliers start: 3 outliers final: 0 residues processed: 819 average time/residue: 0.1849 time to fit residues: 231.4282 Evaluate side-chains 797 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 796 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 77 optimal weight: 0.9980 chunk 209 optimal weight: 6.9990 chunk 15 optimal weight: 9.9990 chunk 218 optimal weight: 10.0000 chunk 102 optimal weight: 0.0980 chunk 267 optimal weight: 0.0370 chunk 88 optimal weight: 0.0870 chunk 296 optimal weight: 8.9990 chunk 225 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 253 optimal weight: 8.9990 overall best weight: 0.8438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 52 GLN A 80 HIS ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 100 HIS ** B 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 227 ASN E 235 HIS F 134 HIS N 666 HIS N1091 ASN ** N1163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N1239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.182607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.145567 restraints weight = 48796.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.151229 restraints weight = 30088.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.155236 restraints weight = 20719.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.158161 restraints weight = 15418.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.160308 restraints weight = 12149.442| |-----------------------------------------------------------------------------| r_work (final): 0.3986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6731 moved from start: 0.1202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 26361 Z= 0.120 Angle : 0.565 9.963 35849 Z= 0.286 Chirality : 0.042 0.187 4008 Planarity : 0.004 0.055 4718 Dihedral : 6.882 122.249 3718 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.05 % Favored : 93.92 % Rotamer: Outliers : 0.22 % Allowed : 3.89 % Favored : 95.89 % 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: -0.70 (0.15), residues: 3258 helix: 0.23 (0.14), residues: 1376 sheet: -0.52 (0.27), residues: 359 loop : -1.04 (0.17), residues: 1523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 87 TYR 0.017 0.001 TYR N1197 PHE 0.024 0.001 PHE D 309 TRP 0.038 0.002 TRP N 876 HIS 0.005 0.001 HIS A 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 (26361) covalent geometry : angle 0.56530 / 0.29 (35849) hydrogen bonds : bond 0.03503 / 2.36 ( 1037) hydrogen bonds : angle 5.29974 / 3.72 ( 2988) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 823 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 817 time to evaluate : 0.915 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: A 66 ARG cc_start: 0.7555 (mpp-170) cc_final: 0.6917 (mpp-170) REVERT: A 68 MET cc_start: 0.7642 (tpp) cc_final: 0.7433 (mmp) REVERT: A 89 ASN cc_start: 0.7601 (t0) cc_final: 0.7340 (t0) REVERT: A 124 LYS cc_start: 0.7744 (mtpt) cc_final: 0.7502 (mtpt) REVERT: A 138 LEU cc_start: 0.8250 (tp) cc_final: 0.7906 (tp) REVERT: A 186 ASN cc_start: 0.6925 (t0) cc_final: 0.6680 (t0) REVERT: A 242 ARG cc_start: 0.7988 (mtp180) cc_final: 0.7584 (mtp180) REVERT: A 243 GLU cc_start: 0.8653 (pm20) cc_final: 0.8404 (pm20) REVERT: A 244 ILE cc_start: 0.8962 (mp) cc_final: 0.8725 (mp) REVERT: A 248 MET cc_start: 0.6883 (ptp) cc_final: 0.6337 (ptp) REVERT: A 255 THR cc_start: 0.8723 (t) cc_final: 0.8485 (t) REVERT: A 276 TRP cc_start: 0.7764 (t60) cc_final: 0.7529 (t60) REVERT: A 282 ILE cc_start: 0.8131 (mt) cc_final: 0.7909 (mt) REVERT: A 294 PHE cc_start: 0.7717 (t80) cc_final: 0.7309 (t80) REVERT: A 309 PHE cc_start: 0.8512 (m-80) cc_final: 0.8071 (m-80) REVERT: B 64 ASN cc_start: 0.7781 (t0) cc_final: 0.7393 (t0) REVERT: B 159 GLU cc_start: 0.8380 (mm-30) cc_final: 0.8153 (mm-30) REVERT: B 180 ARG cc_start: 0.7545 (mpt180) cc_final: 0.6880 (mpt180) REVERT: B 210 ARG cc_start: 0.8298 (tpm170) cc_final: 0.7564 (tpm170) REVERT: B 248 MET cc_start: 0.8522 (mtm) cc_final: 0.7942 (mtm) REVERT: B 253 ASP cc_start: 0.8191 (m-30) cc_final: 0.7932 (m-30) REVERT: B 261 ASN cc_start: 0.8524 (m-40) cc_final: 0.8021 (p0) REVERT: B 263 ASP cc_start: 0.7494 (m-30) cc_final: 0.6242 (m-30) REVERT: B 271 ARG cc_start: 0.7362 (ptm-80) cc_final: 0.7129 (ttt180) REVERT: B 295 LEU cc_start: 0.7764 (tp) cc_final: 0.6773 (tp) REVERT: B 298 CYS cc_start: 0.7566 (m) cc_final: 0.6513 (m) REVERT: B 299 ASP cc_start: 0.7528 (t70) cc_final: 0.7316 (t70) REVERT: B 303 ARG cc_start: 0.7780 (tpt-90) cc_final: 0.7043 (mtp180) REVERT: B 309 PHE cc_start: 0.8642 (m-80) cc_final: 0.8206 (m-80) REVERT: B 312 ARG cc_start: 0.8099 (mtt90) cc_final: 0.7579 (mtt90) REVERT: C 37 ASP cc_start: 0.8503 (t70) cc_final: 0.8249 (t70) REVERT: C 52 GLN cc_start: 0.8320 (mm-40) cc_final: 0.8037 (mm-40) REVERT: C 80 HIS cc_start: 0.7929 (m90) cc_final: 0.7594 (m90) REVERT: C 88 LEU cc_start: 0.8617 (mt) cc_final: 0.8412 (mt) REVERT: C 105 ASP cc_start: 0.7918 (t0) cc_final: 0.7683 (t0) REVERT: C 122 GLU cc_start: 0.7831 (tt0) cc_final: 0.7530 (tt0) REVERT: C 208 MET cc_start: 0.8219 (mtm) cc_final: 0.7884 (mtm) REVERT: C 248 MET cc_start: 0.8228 (mmp) cc_final: 0.7897 (mmm) REVERT: C 271 ARG cc_start: 0.7859 (mtm110) cc_final: 0.7314 (mtm110) REVERT: C 295 LEU cc_start: 0.7387 (tp) cc_final: 0.6782 (tp) REVERT: C 311 GLN cc_start: 0.8371 (tm-30) cc_final: 0.7935 (tm-30) REVERT: D 29 MET cc_start: 0.6319 (tpt) cc_final: 0.5880 (tpt) REVERT: D 68 MET cc_start: 0.8119 (tpp) cc_final: 0.7652 (tpp) REVERT: D 120 VAL cc_start: 0.8280 (t) cc_final: 0.7870 (m) REVERT: D 144 ASP cc_start: 0.7521 (p0) cc_final: 0.7114 (p0) REVERT: D 218 ASN cc_start: 0.7976 (m110) cc_final: 0.7761 (m110) REVERT: D 261 ASN cc_start: 0.8855 (m-40) cc_final: 0.8569 (m-40) REVERT: D 278 GLU cc_start: 0.8638 (mt-10) cc_final: 0.8432 (mt-10) REVERT: D 310 TYR cc_start: 0.8229 (t80) cc_final: 0.7889 (t80) REVERT: E 83 GLN cc_start: 0.7868 (tm-30) cc_final: 0.6893 (tm-30) REVERT: E 138 LEU cc_start: 0.8580 (tp) cc_final: 0.8288 (tp) REVERT: E 154 ILE cc_start: 0.8418 (pt) cc_final: 0.8218 (pt) REVERT: E 208 MET cc_start: 0.7757 (tpp) cc_final: 0.7230 (tpp) REVERT: E 210 ARG cc_start: 0.7974 (mtt-85) cc_final: 0.7735 (mtt-85) REVERT: E 248 MET cc_start: 0.7230 (mtm) cc_final: 0.6924 (mtm) REVERT: E 275 THR cc_start: 0.8543 (m) cc_final: 0.8107 (m) REVERT: E 278 GLU cc_start: 0.8279 (tp30) cc_final: 0.8069 (tp30) REVERT: E 279 ASN cc_start: 0.8883 (m110) cc_final: 0.8671 (m110) REVERT: E 292 LEU cc_start: 0.8412 (mp) cc_final: 0.8137 (mp) REVERT: E 296 ASN cc_start: 0.8590 (m110) cc_final: 0.8187 (m-40) REVERT: E 297 LYS cc_start: 0.8073 (mppt) cc_final: 0.7846 (mppt) REVERT: E 300 GLU cc_start: 0.7946 (tm-30) cc_final: 0.7347 (tm-30) REVERT: F 68 MET cc_start: 0.7187 (tmm) cc_final: 0.6870 (tmm) REVERT: F 103 ARG cc_start: 0.7118 (ptm-80) cc_final: 0.6516 (ptm-80) REVERT: F 135 ASN cc_start: 0.8190 (p0) cc_final: 0.7427 (p0) REVERT: F 174 ARG cc_start: 0.8192 (mmp-170) cc_final: 0.7987 (mmp-170) REVERT: F 208 MET cc_start: 0.6935 (mpp) cc_final: 0.6690 (mpp) REVERT: F 224 ASN cc_start: 0.8717 (t0) cc_final: 0.8093 (t0) REVERT: F 228 ILE cc_start: 0.8275 (OUTLIER) cc_final: 0.7891 (mp) REVERT: F 247 LYS cc_start: 0.7848 (tttp) cc_final: 0.7279 (tttp) REVERT: F 248 MET cc_start: 0.8193 (mtm) cc_final: 0.7611 (mtm) REVERT: F 250 ARG cc_start: 0.7574 (ptt-90) cc_final: 0.7005 (ptt-90) REVERT: F 254 MET cc_start: 0.7516 (tmm) cc_final: 0.7238 (tmm) REVERT: F 265 SER cc_start: 0.8755 (t) cc_final: 0.8385 (t) REVERT: F 279 ASN cc_start: 0.8539 (m-40) cc_final: 0.7972 (m-40) REVERT: G 366 GLN cc_start: 0.6942 (tp40) cc_final: 0.6652 (tp-100) REVERT: G 368 ARG cc_start: 0.8629 (mpt180) cc_final: 0.8407 (mpt-90) REVERT: G 369 LEU cc_start: 0.8991 (mt) cc_final: 0.8633 (mt) REVERT: G 370 MET cc_start: 0.7101 (mpp) cc_final: 0.6774 (mpp) REVERT: G 397 ASP cc_start: 0.7563 (p0) cc_final: 0.6683 (p0) REVERT: G 399 THR cc_start: 0.8103 (p) cc_final: 0.7644 (p) REVERT: G 400 GLN cc_start: 0.8015 (mm-40) cc_final: 0.7603 (mm110) REVERT: G 430 ARG cc_start: 0.8037 (tmm160) cc_final: 0.7789 (tmm160) REVERT: G 544 ILE cc_start: 0.8867 (mp) cc_final: 0.8430 (mp) REVERT: a 25 PHE cc_start: 0.8288 (m-10) cc_final: 0.8061 (m-80) REVERT: a 113 GLN cc_start: 0.7714 (mp10) cc_final: 0.6773 (mp10) REVERT: a 131 LEU cc_start: 0.8510 (mt) cc_final: 0.7787 (mt) REVERT: a 134 MET cc_start: 0.7517 (ppp) cc_final: 0.6711 (ppp) REVERT: a 135 LEU cc_start: 0.8383 (mt) cc_final: 0.7836 (mt) REVERT: a 214 ASP cc_start: 0.8622 (m-30) cc_final: 0.8321 (m-30) REVERT: a 215 MET cc_start: 0.8431 (mtm) cc_final: 0.8119 (mtm) REVERT: N 432 MET cc_start: 0.8080 (mtp) cc_final: 0.7532 (mtp) REVERT: N 433 ARG cc_start: 0.8611 (mtm180) cc_final: 0.8246 (mtm180) REVERT: N 436 MET cc_start: 0.8400 (ttp) cc_final: 0.8127 (ttp) REVERT: N 572 TYR cc_start: 0.7504 (m-80) cc_final: 0.7219 (m-80) REVERT: N 586 PHE cc_start: 0.7320 (t80) cc_final: 0.6838 (t80) REVERT: N 677 LYS cc_start: 0.8572 (ptpp) cc_final: 0.8204 (mtmm) REVERT: N 829 ASP cc_start: 0.6608 (m-30) cc_final: 0.6354 (m-30) REVERT: N 890 TYR cc_start: 0.7859 (t80) cc_final: 0.7613 (t80) REVERT: N 893 ASP cc_start: 0.8232 (m-30) cc_final: 0.7975 (m-30) REVERT: N 960 ILE cc_start: 0.8805 (pt) cc_final: 0.8353 (pt) REVERT: N 964 PHE cc_start: 0.8077 (t80) cc_final: 0.7588 (t80) REVERT: N 1077 GLU cc_start: 0.8661 (tm-30) cc_final: 0.8375 (tm-30) REVERT: N 1155 LYS cc_start: 0.8532 (mtmm) cc_final: 0.8069 (mtmm) REVERT: N 1210 MET cc_start: 0.8577 (mtm) cc_final: 0.8261 (mtm) REVERT: N 1227 GLU cc_start: 0.7649 (tm-30) cc_final: 0.6971 (tp30) outliers start: 6 outliers final: 0 residues processed: 820 average time/residue: 0.1762 time to fit residues: 220.5443 Evaluate side-chains 795 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 794 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 175 optimal weight: 5.9990 chunk 9 optimal weight: 4.9990 chunk 102 optimal weight: 0.7980 chunk 229 optimal weight: 20.0000 chunk 70 optimal weight: 9.9990 chunk 261 optimal weight: 0.8980 chunk 258 optimal weight: 0.9990 chunk 190 optimal weight: 8.9990 chunk 233 optimal weight: 8.9990 chunk 88 optimal weight: 0.5980 chunk 165 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 52 GLN A 207 GLN ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 GLN B 100 HIS ** B 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 169 GLN ** C 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 155 GLN ** E 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 96 ASN F 134 HIS N1042 ASN ** N1091 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N1163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N1239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.181911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.145631 restraints weight = 48332.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.151172 restraints weight = 29917.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.155144 restraints weight = 20653.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.157975 restraints weight = 15346.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.159927 restraints weight = 12095.038| |-----------------------------------------------------------------------------| r_work (final): 0.3985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6738 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 : 0.003 0.038 26361 Z= 0.133 Angle : 0.569 10.931 35849 Z= 0.288 Chirality : 0.042 0.168 4008 Planarity : 0.004 0.048 4718 Dihedral : 6.486 121.934 3718 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.95 % Favored : 94.01 % Rotamer: Outliers : 0.22 % Allowed : 3.26 % Favored : 96.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.15), residues: 3258 helix: 0.23 (0.14), residues: 1381 sheet: -0.53 (0.27), residues: 357 loop : -0.99 (0.17), residues: 1520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 87 TYR 0.017 0.001 TYR A 39 PHE 0.023 0.001 PHE D 309 TRP 0.033 0.002 TRP N 876 HIS 0.004 0.001 HIS F 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 (26361) covalent geometry : angle 0.56862 / 0.29 (35849) hydrogen bonds : bond 0.03324 / 2.21 ( 1037) hydrogen bonds : angle 5.24477 / 3.69 ( 2988) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 823 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 817 time to evaluate : 0.798 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: A 66 ARG cc_start: 0.7495 (mpp-170) cc_final: 0.6881 (mpp-170) REVERT: A 89 ASN cc_start: 0.7627 (t0) cc_final: 0.7371 (t0) REVERT: A 124 LYS cc_start: 0.7764 (mtpt) cc_final: 0.7518 (mtpt) REVERT: A 138 LEU cc_start: 0.8297 (tp) cc_final: 0.7940 (tp) REVERT: A 186 ASN cc_start: 0.6928 (t0) cc_final: 0.6680 (t0) REVERT: A 242 ARG cc_start: 0.7986 (mtp180) cc_final: 0.7593 (mtp180) REVERT: A 243 GLU cc_start: 0.8652 (pm20) cc_final: 0.8361 (pm20) REVERT: A 244 ILE cc_start: 0.8950 (mp) cc_final: 0.8699 (mp) REVERT: A 248 MET cc_start: 0.6901 (ptp) cc_final: 0.6101 (ptp) REVERT: A 276 TRP cc_start: 0.7811 (t60) cc_final: 0.7398 (t60) REVERT: A 282 ILE cc_start: 0.8133 (mt) cc_final: 0.7885 (mt) REVERT: A 294 PHE cc_start: 0.7787 (t80) cc_final: 0.7391 (t80) REVERT: B 64 ASN cc_start: 0.7741 (t0) cc_final: 0.7303 (t0) REVERT: B 83 GLN cc_start: 0.8305 (pt0) cc_final: 0.7840 (pt0) REVERT: B 114 VAL cc_start: 0.8534 (m) cc_final: 0.8324 (p) REVERT: B 159 GLU cc_start: 0.8380 (mm-30) cc_final: 0.8146 (mm-30) REVERT: B 180 ARG cc_start: 0.7521 (mpt180) cc_final: 0.6953 (mpt180) REVERT: B 210 ARG cc_start: 0.8290 (tpm170) cc_final: 0.7590 (tpm170) REVERT: B 246 ASN cc_start: 0.8137 (m110) cc_final: 0.7935 (m-40) REVERT: B 253 ASP cc_start: 0.8195 (m-30) cc_final: 0.7956 (m-30) REVERT: B 261 ASN cc_start: 0.8567 (m-40) cc_final: 0.8051 (p0) REVERT: B 263 ASP cc_start: 0.7529 (m-30) cc_final: 0.6259 (m-30) REVERT: B 271 ARG cc_start: 0.7394 (ptm-80) cc_final: 0.7189 (ttt180) REVERT: B 295 LEU cc_start: 0.7715 (tp) cc_final: 0.7226 (tp) REVERT: B 298 CYS cc_start: 0.7588 (m) cc_final: 0.6927 (m) REVERT: B 309 PHE cc_start: 0.8634 (m-80) cc_final: 0.8163 (m-80) REVERT: B 312 ARG cc_start: 0.8116 (mtt90) cc_final: 0.7568 (mtt90) REVERT: C 37 ASP cc_start: 0.8511 (t70) cc_final: 0.8260 (t70) REVERT: C 46 ASP cc_start: 0.7461 (m-30) cc_final: 0.7244 (m-30) REVERT: C 52 GLN cc_start: 0.8326 (mm-40) cc_final: 0.8050 (mm-40) REVERT: C 80 HIS cc_start: 0.7942 (m90) cc_final: 0.7620 (m90) REVERT: C 105 ASP cc_start: 0.7853 (t0) cc_final: 0.7640 (t0) REVERT: C 122 GLU cc_start: 0.7811 (tt0) cc_final: 0.7540 (tt0) REVERT: C 208 MET cc_start: 0.8194 (mtm) cc_final: 0.7863 (mtm) REVERT: C 271 ARG cc_start: 0.7879 (mtm110) cc_final: 0.7438 (mtm110) REVERT: C 295 LEU cc_start: 0.7418 (tp) cc_final: 0.6885 (tp) REVERT: C 311 GLN cc_start: 0.8372 (tm-30) cc_final: 0.7946 (tm-30) REVERT: D 29 MET cc_start: 0.6331 (tpt) cc_final: 0.6114 (tpt) REVERT: D 68 MET cc_start: 0.8198 (tpp) cc_final: 0.7732 (tpp) REVERT: D 97 LEU cc_start: 0.8561 (mt) cc_final: 0.8332 (mt) REVERT: D 120 VAL cc_start: 0.8271 (t) cc_final: 0.7818 (m) REVERT: D 144 ASP cc_start: 0.7523 (p0) cc_final: 0.7160 (p0) REVERT: D 151 MET cc_start: 0.7533 (ttt) cc_final: 0.7156 (ttt) REVERT: D 210 ARG cc_start: 0.8196 (ptp90) cc_final: 0.7886 (ptp90) REVERT: D 261 ASN cc_start: 0.8852 (m-40) cc_final: 0.8575 (m-40) REVERT: D 271 ARG cc_start: 0.8173 (tpt170) cc_final: 0.7285 (tpp80) REVERT: D 278 GLU cc_start: 0.8684 (mt-10) cc_final: 0.8452 (mt-10) REVERT: D 310 TYR cc_start: 0.8237 (t80) cc_final: 0.7964 (t80) REVERT: E 64 ASN cc_start: 0.8212 (t0) cc_final: 0.7940 (t0) REVERT: E 83 GLN cc_start: 0.7890 (tm-30) cc_final: 0.6997 (tm-30) REVERT: E 138 LEU cc_start: 0.8574 (tp) cc_final: 0.8305 (tp) REVERT: E 155 GLN cc_start: 0.8523 (tp40) cc_final: 0.8226 (tp40) REVERT: E 248 MET cc_start: 0.7240 (mtm) cc_final: 0.6930 (mtm) REVERT: E 275 THR cc_start: 0.8567 (m) cc_final: 0.8135 (m) REVERT: E 278 GLU cc_start: 0.8303 (tp30) cc_final: 0.8100 (tp30) REVERT: E 292 LEU cc_start: 0.8416 (mp) cc_final: 0.8146 (mp) REVERT: E 296 ASN cc_start: 0.8602 (m110) cc_final: 0.8172 (m-40) REVERT: E 300 GLU cc_start: 0.7959 (tm-30) cc_final: 0.7348 (tm-30) REVERT: F 64 ASN cc_start: 0.8133 (t0) cc_final: 0.7933 (t0) REVERT: F 68 MET cc_start: 0.7248 (tmm) cc_final: 0.6996 (tmm) REVERT: F 88 LEU cc_start: 0.8658 (mt) cc_final: 0.8426 (mt) REVERT: F 135 ASN cc_start: 0.8060 (p0) cc_final: 0.7418 (p0) REVERT: F 167 LEU cc_start: 0.7879 (mp) cc_final: 0.7229 (mp) REVERT: F 168 ASP cc_start: 0.6679 (t0) cc_final: 0.6477 (t0) REVERT: F 174 ARG cc_start: 0.8197 (mmp-170) cc_final: 0.7927 (mmp-170) REVERT: F 176 HIS cc_start: 0.8839 (t70) cc_final: 0.8579 (t70) REVERT: F 208 MET cc_start: 0.6924 (mpp) cc_final: 0.6669 (mpp) REVERT: F 224 ASN cc_start: 0.8761 (t0) cc_final: 0.8220 (t0) REVERT: F 228 ILE cc_start: 0.8235 (OUTLIER) cc_final: 0.7916 (mp) REVERT: F 247 LYS cc_start: 0.7856 (tttp) cc_final: 0.7191 (tttp) REVERT: F 248 MET cc_start: 0.8179 (mtm) cc_final: 0.7829 (mtm) REVERT: F 250 ARG cc_start: 0.7617 (ptt-90) cc_final: 0.7106 (ptt-90) REVERT: F 254 MET cc_start: 0.7430 (tmm) cc_final: 0.7101 (tmm) REVERT: F 265 SER cc_start: 0.8795 (t) cc_final: 0.8490 (t) REVERT: F 279 ASN cc_start: 0.8521 (m-40) cc_final: 0.8000 (m-40) REVERT: F 309 PHE cc_start: 0.7754 (m-80) cc_final: 0.7491 (m-80) REVERT: G 368 ARG cc_start: 0.8631 (mpt180) cc_final: 0.8424 (mpt-90) REVERT: G 369 LEU cc_start: 0.8978 (mt) cc_final: 0.8672 (mt) REVERT: G 397 ASP cc_start: 0.7488 (p0) cc_final: 0.7128 (p0) REVERT: G 399 THR cc_start: 0.8212 (p) cc_final: 0.7559 (p) REVERT: G 400 GLN cc_start: 0.8121 (mm-40) cc_final: 0.7558 (mm110) REVERT: G 430 ARG cc_start: 0.8016 (tmm160) cc_final: 0.7782 (tmm160) REVERT: G 544 ILE cc_start: 0.8859 (mp) cc_final: 0.8417 (mp) REVERT: a 25 PHE cc_start: 0.8260 (m-10) cc_final: 0.8054 (m-80) REVERT: a 113 GLN cc_start: 0.7738 (mp10) cc_final: 0.6803 (mp10) REVERT: a 131 LEU cc_start: 0.8515 (mt) cc_final: 0.7787 (mt) REVERT: a 134 MET cc_start: 0.7517 (ppp) cc_final: 0.6655 (ppp) REVERT: a 135 LEU cc_start: 0.8388 (mt) cc_final: 0.7719 (mt) REVERT: a 214 ASP cc_start: 0.8605 (m-30) cc_final: 0.8315 (m-30) REVERT: a 215 MET cc_start: 0.8419 (mtm) cc_final: 0.8114 (mtm) REVERT: N 432 MET cc_start: 0.8091 (mtp) cc_final: 0.7549 (mtp) REVERT: N 433 ARG cc_start: 0.8599 (mtm180) cc_final: 0.8097 (mtt90) REVERT: N 436 MET cc_start: 0.8411 (ttp) cc_final: 0.8135 (ttp) REVERT: N 470 GLN cc_start: 0.6588 (mp10) cc_final: 0.6365 (mp10) REVERT: N 572 TYR cc_start: 0.7553 (m-80) cc_final: 0.7282 (m-80) REVERT: N 650 ILE cc_start: 0.8040 (mm) cc_final: 0.7786 (mm) REVERT: N 677 LYS cc_start: 0.8565 (ptpp) cc_final: 0.8227 (mtmt) REVERT: N 688 MET cc_start: 0.7445 (ttm) cc_final: 0.7143 (ttm) REVERT: N 829 ASP cc_start: 0.6593 (m-30) cc_final: 0.6338 (m-30) REVERT: N 890 TYR cc_start: 0.7820 (t80) cc_final: 0.7569 (t80) REVERT: N 893 ASP cc_start: 0.8239 (m-30) cc_final: 0.7979 (m-30) REVERT: N 960 ILE cc_start: 0.8801 (pt) cc_final: 0.8344 (pt) REVERT: N 964 PHE cc_start: 0.8089 (t80) cc_final: 0.7595 (t80) REVERT: N 1077 GLU cc_start: 0.8637 (tm-30) cc_final: 0.8375 (tm-30) REVERT: N 1088 ASN cc_start: 0.7355 (t0) cc_final: 0.7154 (t0) REVERT: N 1207 HIS cc_start: 0.7295 (t-90) cc_final: 0.7082 (t-90) REVERT: N 1210 MET cc_start: 0.8574 (mtm) cc_final: 0.8258 (mtm) REVERT: N 1227 GLU cc_start: 0.7500 (tm-30) cc_final: 0.6984 (tp30) outliers start: 6 outliers final: 1 residues processed: 821 average time/residue: 0.1756 time to fit residues: 220.3259 Evaluate side-chains 793 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 791 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 50 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 107 optimal weight: 0.4980 chunk 159 optimal weight: 2.9990 chunk 112 optimal weight: 8.9990 chunk 169 optimal weight: 5.9990 chunk 184 optimal weight: 1.9990 chunk 54 optimal weight: 9.9990 chunk 265 optimal weight: 3.9990 chunk 143 optimal weight: 0.6980 chunk 102 optimal weight: 2.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 52 GLN ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 GLN B 100 HIS ** B 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 246 ASN ** D 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 155 GLN ** E 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 96 ASN F 134 HIS G 366 GLN N 666 HIS N 753 ASN N1042 ASN ** N1091 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N1104 GLN ** N1163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N1214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N1239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.181008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.143492 restraints weight = 48828.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.149081 restraints weight = 30440.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.153032 restraints weight = 21125.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.155934 restraints weight = 15857.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.158087 restraints weight = 12585.807| |-----------------------------------------------------------------------------| r_work (final): 0.3962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6774 moved from start: 0.1557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 26361 Z= 0.159 Angle : 0.587 9.997 35849 Z= 0.298 Chirality : 0.043 0.201 4008 Planarity : 0.005 0.058 4718 Dihedral : 6.308 122.123 3718 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.14 % Favored : 93.83 % Rotamer: Outliers : 0.19 % Allowed : 2.29 % Favored : 97.52 % 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: -0.70 (0.15), residues: 3258 helix: 0.26 (0.14), residues: 1378 sheet: -0.66 (0.27), residues: 360 loop : -1.02 (0.17), residues: 1520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 312 TYR 0.019 0.002 TYR E 143 PHE 0.023 0.002 PHE D 309 TRP 0.047 0.002 TRP N 876 HIS 0.006 0.001 HIS F 100 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.16 (26361) covalent geometry : angle 0.58712 / 0.30 (35849) hydrogen bonds : bond 0.03439 / 2.28 ( 1037) hydrogen bonds : angle 5.30792 / 3.73 ( 2988) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 823 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 818 time to evaluate : 0.868 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: A 52 GLN cc_start: 0.8050 (mm110) cc_final: 0.7585 (tp40) REVERT: A 66 ARG cc_start: 0.7455 (mpp-170) cc_final: 0.6822 (mpp-170) REVERT: A 89 ASN cc_start: 0.7690 (t0) cc_final: 0.7413 (t0) REVERT: A 93 VAL cc_start: 0.8581 (p) cc_final: 0.8297 (m) REVERT: A 124 LYS cc_start: 0.7770 (mtpt) cc_final: 0.7514 (mtpt) REVERT: A 138 LEU cc_start: 0.8311 (tp) cc_final: 0.7934 (tp) REVERT: A 180 ARG cc_start: 0.7807 (mmm160) cc_final: 0.7502 (mmm-85) REVERT: A 186 ASN cc_start: 0.6968 (t0) cc_final: 0.6754 (t0) REVERT: A 242 ARG cc_start: 0.7991 (mtp180) cc_final: 0.7576 (mtp180) REVERT: A 243 GLU cc_start: 0.8632 (pm20) cc_final: 0.8280 (pm20) REVERT: A 244 ILE cc_start: 0.8950 (mp) cc_final: 0.8686 (mp) REVERT: A 282 ILE cc_start: 0.8145 (mt) cc_final: 0.7929 (mt) REVERT: A 294 PHE cc_start: 0.7877 (t80) cc_final: 0.7479 (t80) REVERT: B 65 ARG cc_start: 0.8299 (tpp80) cc_final: 0.8041 (tpp80) REVERT: B 152 PHE cc_start: 0.7565 (t80) cc_final: 0.7331 (t80) REVERT: B 159 GLU cc_start: 0.8393 (mm-30) cc_final: 0.8146 (mm-30) REVERT: B 207 GLN cc_start: 0.8351 (pm20) cc_final: 0.7997 (pm20) REVERT: B 210 ARG cc_start: 0.8306 (tpm170) cc_final: 0.7610 (tpm170) REVERT: B 246 ASN cc_start: 0.8191 (m110) cc_final: 0.7985 (m-40) REVERT: B 253 ASP cc_start: 0.8222 (m-30) cc_final: 0.7981 (m-30) REVERT: B 261 ASN cc_start: 0.8583 (m-40) cc_final: 0.8042 (p0) REVERT: B 263 ASP cc_start: 0.7532 (m-30) cc_final: 0.6240 (m-30) REVERT: B 279 ASN cc_start: 0.8442 (m110) cc_final: 0.8165 (m110) REVERT: B 295 LEU cc_start: 0.8035 (tp) cc_final: 0.7571 (tp) REVERT: B 298 CYS cc_start: 0.7679 (m) cc_final: 0.7178 (m) REVERT: B 299 ASP cc_start: 0.7846 (t70) cc_final: 0.7529 (t70) REVERT: B 309 PHE cc_start: 0.8618 (m-80) cc_final: 0.8148 (m-80) REVERT: B 312 ARG cc_start: 0.8148 (mtt90) cc_final: 0.7588 (mtt90) REVERT: C 37 ASP cc_start: 0.8552 (t70) cc_final: 0.8291 (t70) REVERT: C 52 GLN cc_start: 0.8350 (mm-40) cc_final: 0.8106 (mm-40) REVERT: C 80 HIS cc_start: 0.8017 (m90) cc_final: 0.7660 (m90) REVERT: C 105 ASP cc_start: 0.7890 (t0) cc_final: 0.7630 (t0) REVERT: C 122 GLU cc_start: 0.7831 (tt0) cc_final: 0.7539 (tt0) REVERT: C 208 MET cc_start: 0.8250 (mtm) cc_final: 0.7890 (mtm) REVERT: C 295 LEU cc_start: 0.7466 (tp) cc_final: 0.6936 (tp) REVERT: C 300 GLU cc_start: 0.7756 (mm-30) cc_final: 0.7511 (mm-30) REVERT: C 301 LEU cc_start: 0.8550 (mt) cc_final: 0.8309 (mt) REVERT: C 303 ARG cc_start: 0.7902 (ttm170) cc_final: 0.6975 (ttm170) REVERT: C 311 GLN cc_start: 0.8404 (tm-30) cc_final: 0.7963 (tm-30) REVERT: D 19 ARG cc_start: 0.8161 (mpp-170) cc_final: 0.7736 (mpp-170) REVERT: D 29 MET cc_start: 0.6349 (tpt) cc_final: 0.6146 (tpt) REVERT: D 68 MET cc_start: 0.8068 (tpp) cc_final: 0.7689 (tpp) REVERT: D 97 LEU cc_start: 0.8536 (mt) cc_final: 0.8331 (mt) REVERT: D 120 VAL cc_start: 0.8231 (t) cc_final: 0.7822 (m) REVERT: D 135 ASN cc_start: 0.7553 (p0) cc_final: 0.7334 (p0) REVERT: D 144 ASP cc_start: 0.7561 (p0) cc_final: 0.7205 (p0) REVERT: D 151 MET cc_start: 0.7447 (ttt) cc_final: 0.7113 (ttt) REVERT: D 208 MET cc_start: 0.7513 (tpp) cc_final: 0.6892 (tpp) REVERT: D 217 LEU cc_start: 0.7857 (tp) cc_final: 0.7640 (tt) REVERT: D 261 ASN cc_start: 0.8872 (m-40) cc_final: 0.8588 (m-40) REVERT: D 271 ARG cc_start: 0.8158 (tpt170) cc_final: 0.7299 (tpp80) REVERT: D 310 TYR cc_start: 0.8252 (t80) cc_final: 0.7938 (t80) REVERT: E 64 ASN cc_start: 0.8236 (t0) cc_final: 0.7981 (t0) REVERT: E 83 GLN cc_start: 0.8001 (tm-30) cc_final: 0.7135 (tm-30) REVERT: E 119 GLN cc_start: 0.7994 (mm110) cc_final: 0.7750 (mm110) REVERT: E 138 LEU cc_start: 0.8568 (tp) cc_final: 0.8297 (tp) REVERT: E 151 MET cc_start: 0.7399 (tpt) cc_final: 0.7102 (tpt) REVERT: E 202 GLN cc_start: 0.6585 (pm20) cc_final: 0.6375 (pm20) REVERT: E 275 THR cc_start: 0.8596 (m) cc_final: 0.8186 (m) REVERT: E 278 GLU cc_start: 0.8306 (tp30) cc_final: 0.8085 (tp30) REVERT: E 292 LEU cc_start: 0.8417 (mp) cc_final: 0.8072 (mp) REVERT: E 294 PHE cc_start: 0.7550 (t80) cc_final: 0.6905 (t80) REVERT: E 296 ASN cc_start: 0.8586 (m110) cc_final: 0.8030 (m-40) REVERT: E 297 LYS cc_start: 0.8152 (mppt) cc_final: 0.7717 (mppt) REVERT: E 300 GLU cc_start: 0.7996 (tm-30) cc_final: 0.7376 (tm-30) REVERT: F 68 MET cc_start: 0.7307 (tmm) cc_final: 0.6888 (tmm) REVERT: F 88 LEU cc_start: 0.8687 (mt) cc_final: 0.8481 (mt) REVERT: F 135 ASN cc_start: 0.8049 (p0) cc_final: 0.7419 (p0) REVERT: F 143 TYR cc_start: 0.8411 (t80) cc_final: 0.7763 (t80) REVERT: F 151 MET cc_start: 0.7268 (mpp) cc_final: 0.7014 (mpp) REVERT: F 167 LEU cc_start: 0.7871 (mp) cc_final: 0.7616 (mp) REVERT: F 174 ARG cc_start: 0.8224 (mmp-170) cc_final: 0.7940 (mmp-170) REVERT: F 208 MET cc_start: 0.7003 (mpp) cc_final: 0.6715 (mpp) REVERT: F 224 ASN cc_start: 0.8787 (t0) cc_final: 0.8250 (t0) REVERT: F 225 GLU cc_start: 0.8289 (mt-10) cc_final: 0.7908 (mt-10) REVERT: F 228 ILE cc_start: 0.8260 (OUTLIER) cc_final: 0.7957 (mp) REVERT: F 247 LYS cc_start: 0.7890 (tttp) cc_final: 0.7276 (tttp) REVERT: F 248 MET cc_start: 0.8193 (mtm) cc_final: 0.7859 (mtm) REVERT: F 250 ARG cc_start: 0.7644 (ptt-90) cc_final: 0.7095 (ptt-90) REVERT: F 254 MET cc_start: 0.7386 (tmm) cc_final: 0.7018 (tmm) REVERT: F 265 SER cc_start: 0.8778 (t) cc_final: 0.8444 (t) REVERT: F 275 THR cc_start: 0.7454 (m) cc_final: 0.6993 (m) REVERT: F 279 ASN cc_start: 0.8568 (m-40) cc_final: 0.8057 (m-40) REVERT: F 303 ARG cc_start: 0.8326 (ttm170) cc_final: 0.7871 (ttm170) REVERT: F 309 PHE cc_start: 0.7760 (m-80) cc_final: 0.7538 (m-80) REVERT: G 368 ARG cc_start: 0.8665 (mpt180) cc_final: 0.8446 (mpt-90) REVERT: G 369 LEU cc_start: 0.8971 (mt) cc_final: 0.8661 (mt) REVERT: G 397 ASP cc_start: 0.7591 (p0) cc_final: 0.7120 (p0) REVERT: G 399 THR cc_start: 0.8207 (p) cc_final: 0.7498 (p) REVERT: G 400 GLN cc_start: 0.8148 (mm-40) cc_final: 0.7565 (mm110) REVERT: G 430 ARG cc_start: 0.8063 (tmm160) cc_final: 0.7817 (tmm160) REVERT: G 544 ILE cc_start: 0.8881 (mp) cc_final: 0.8441 (mp) REVERT: a 25 PHE cc_start: 0.8264 (m-10) cc_final: 0.8059 (m-80) REVERT: a 113 GLN cc_start: 0.7806 (mp10) cc_final: 0.6897 (mp10) REVERT: a 131 LEU cc_start: 0.8521 (mt) cc_final: 0.7802 (mt) REVERT: a 134 MET cc_start: 0.7572 (ppp) cc_final: 0.6690 (ppp) REVERT: a 135 LEU cc_start: 0.8431 (mt) cc_final: 0.7774 (mt) REVERT: a 214 ASP cc_start: 0.8616 (m-30) cc_final: 0.8302 (m-30) REVERT: a 215 MET cc_start: 0.8412 (mtm) cc_final: 0.8158 (mtm) REVERT: N 432 MET cc_start: 0.8114 (mtp) cc_final: 0.7581 (mtp) REVERT: N 433 ARG cc_start: 0.8607 (mtm180) cc_final: 0.8109 (mtt90) REVERT: N 436 MET cc_start: 0.8451 (ttp) cc_final: 0.8177 (ttp) REVERT: N 470 GLN cc_start: 0.6711 (mp10) cc_final: 0.6468 (mp10) REVERT: N 572 TYR cc_start: 0.7485 (m-80) cc_final: 0.7220 (m-80) REVERT: N 586 PHE cc_start: 0.7410 (t80) cc_final: 0.6906 (t80) REVERT: N 650 ILE cc_start: 0.8044 (mm) cc_final: 0.7789 (mm) REVERT: N 677 LYS cc_start: 0.8527 (ptpp) cc_final: 0.8285 (mtmt) REVERT: N 688 MET cc_start: 0.7453 (ttm) cc_final: 0.7149 (ttm) REVERT: N 829 ASP cc_start: 0.6598 (m-30) cc_final: 0.6333 (m-30) REVERT: N 890 TYR cc_start: 0.7883 (t80) cc_final: 0.7580 (t80) REVERT: N 893 ASP cc_start: 0.8268 (m-30) cc_final: 0.8023 (m-30) REVERT: N 960 ILE cc_start: 0.8825 (pt) cc_final: 0.8344 (pt) REVERT: N 964 PHE cc_start: 0.8117 (t80) cc_final: 0.7619 (t80) REVERT: N 1077 GLU cc_start: 0.8659 (tm-30) cc_final: 0.8384 (tm-30) REVERT: N 1207 HIS cc_start: 0.7358 (t-90) cc_final: 0.7102 (t-90) REVERT: N 1210 MET cc_start: 0.8570 (mtm) cc_final: 0.8234 (mtm) REVERT: N 1227 GLU cc_start: 0.7615 (tm-30) cc_final: 0.7075 (tp30) outliers start: 5 outliers final: 0 residues processed: 820 average time/residue: 0.1819 time to fit residues: 228.0089 Evaluate side-chains 802 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 801 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 319 optimal weight: 0.7980 chunk 147 optimal weight: 1.9990 chunk 64 optimal weight: 9.9990 chunk 38 optimal weight: 0.0040 chunk 137 optimal weight: 3.9990 chunk 271 optimal weight: 0.0470 chunk 323 optimal weight: 5.9990 chunk 51 optimal weight: 4.9990 chunk 231 optimal weight: 9.9990 chunk 199 optimal weight: 6.9990 chunk 83 optimal weight: 4.9990 overall best weight: 1.3694 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 100 HIS ** B 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 246 ASN ** D 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 155 GLN ** E 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 96 ASN F 134 HIS G 372 GLN N 753 ASN N1042 ASN ** N1091 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N1163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N1214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N1239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.172393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.136501 restraints weight = 49713.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.142080 restraints weight = 30408.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.146074 restraints weight = 20788.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.148991 restraints weight = 15330.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.151219 restraints weight = 11951.130| |-----------------------------------------------------------------------------| r_work (final): 0.3973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6749 moved from start: 0.1648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 26361 Z= 0.155 Angle : 0.591 11.212 35849 Z= 0.302 Chirality : 0.043 0.188 4008 Planarity : 0.005 0.055 4718 Dihedral : 6.137 122.192 3718 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.29 % Favored : 93.68 % Rotamer: Outliers : 0.07 % Allowed : 2.18 % Favored : 97.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.15), residues: 3258 helix: 0.24 (0.14), residues: 1374 sheet: -0.61 (0.27), residues: 363 loop : -1.06 (0.17), residues: 1521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 210 TYR 0.017 0.001 TYR E 143 PHE 0.025 0.001 PHE a 108 TRP 0.037 0.002 TRP N 876 HIS 0.004 0.001 HIS C 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.16 (26361) covalent geometry : angle 0.59079 / 0.30 (35849) hydrogen bonds : bond 0.03393 / 2.26 ( 1037) hydrogen bonds : angle 5.27886 / 3.71 ( 2988) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 817 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 815 time to evaluate : 0.824 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: A 66 ARG cc_start: 0.7382 (mpp-170) cc_final: 0.6637 (mpp-170) REVERT: A 89 ASN cc_start: 0.7650 (t0) cc_final: 0.7427 (t0) REVERT: A 124 LYS cc_start: 0.7763 (mtpt) cc_final: 0.7516 (mtpt) REVERT: A 138 LEU cc_start: 0.8348 (tp) cc_final: 0.7985 (tp) REVERT: A 180 ARG cc_start: 0.7746 (mmt180) cc_final: 0.7438 (mmm160) REVERT: A 242 ARG cc_start: 0.7977 (mtp180) cc_final: 0.7570 (mtp180) REVERT: A 243 GLU cc_start: 0.8639 (pm20) cc_final: 0.8288 (pm20) REVERT: A 244 ILE cc_start: 0.8955 (mp) cc_final: 0.8714 (mp) REVERT: A 248 MET cc_start: 0.6970 (ptp) cc_final: 0.6373 (ptp) REVERT: A 276 TRP cc_start: 0.7771 (t60) cc_final: 0.7559 (t60) REVERT: A 282 ILE cc_start: 0.8147 (mt) cc_final: 0.7922 (mt) REVERT: A 288 PHE cc_start: 0.8052 (t80) cc_final: 0.7845 (t80) REVERT: A 294 PHE cc_start: 0.7908 (t80) cc_final: 0.7629 (t80) REVERT: A 299 ASP cc_start: 0.7295 (m-30) cc_final: 0.7094 (m-30) REVERT: B 10 ASN cc_start: 0.7544 (t0) cc_final: 0.7270 (t0) REVERT: B 65 ARG cc_start: 0.8324 (tpp80) cc_final: 0.8076 (tpp80) REVERT: B 83 GLN cc_start: 0.8274 (pt0) cc_final: 0.7729 (pt0) REVERT: B 152 PHE cc_start: 0.7595 (t80) cc_final: 0.7366 (t80) REVERT: B 159 GLU cc_start: 0.8388 (mm-30) cc_final: 0.8125 (mm-30) REVERT: B 180 ARG cc_start: 0.7592 (mpt180) cc_final: 0.6941 (mpt180) REVERT: B 207 GLN cc_start: 0.8358 (pm20) cc_final: 0.8081 (pm20) REVERT: B 210 ARG cc_start: 0.8344 (tpm170) cc_final: 0.7628 (tpm170) REVERT: B 253 ASP cc_start: 0.8263 (m-30) cc_final: 0.8012 (m-30) REVERT: B 261 ASN cc_start: 0.8594 (m-40) cc_final: 0.8044 (p0) REVERT: B 263 ASP cc_start: 0.7545 (m-30) cc_final: 0.6236 (m-30) REVERT: B 295 LEU cc_start: 0.8033 (tp) cc_final: 0.7022 (tp) REVERT: B 298 CYS cc_start: 0.7716 (m) cc_final: 0.7062 (m) REVERT: B 299 ASP cc_start: 0.7852 (t70) cc_final: 0.7555 (t70) REVERT: B 303 ARG cc_start: 0.8216 (mtp180) cc_final: 0.7338 (mtp180) REVERT: B 309 PHE cc_start: 0.8569 (m-80) cc_final: 0.8121 (m-80) REVERT: B 310 TYR cc_start: 0.7150 (t80) cc_final: 0.6504 (t80) REVERT: B 312 ARG cc_start: 0.8101 (mtt90) cc_final: 0.7546 (mtt90) REVERT: C 37 ASP cc_start: 0.8526 (t70) cc_final: 0.8324 (t70) REVERT: C 52 GLN cc_start: 0.8311 (mm-40) cc_final: 0.8069 (mm-40) REVERT: C 80 HIS cc_start: 0.8005 (m90) cc_final: 0.7625 (m90) REVERT: C 105 ASP cc_start: 0.7885 (t0) cc_final: 0.7654 (t0) REVERT: C 122 GLU cc_start: 0.7820 (tt0) cc_final: 0.7544 (tt0) REVERT: C 208 MET cc_start: 0.8236 (mtm) cc_final: 0.7834 (mtm) REVERT: C 295 LEU cc_start: 0.7449 (tp) cc_final: 0.6859 (tp) REVERT: C 300 GLU cc_start: 0.7755 (mm-30) cc_final: 0.7473 (mm-30) REVERT: C 301 LEU cc_start: 0.8560 (mt) cc_final: 0.8336 (mt) REVERT: C 303 ARG cc_start: 0.7887 (ttm170) cc_final: 0.6924 (ttm170) REVERT: C 311 GLN cc_start: 0.8379 (tm-30) cc_final: 0.7937 (tm-30) REVERT: D 19 ARG cc_start: 0.8178 (mpp-170) cc_final: 0.7751 (mpp-170) REVERT: D 68 MET cc_start: 0.8083 (tpp) cc_final: 0.7710 (tpp) REVERT: D 77 LYS cc_start: 0.7111 (mtpt) cc_final: 0.6911 (mtpt) REVERT: D 135 ASN cc_start: 0.7514 (p0) cc_final: 0.7245 (p0) REVERT: D 144 ASP cc_start: 0.7556 (p0) cc_final: 0.7202 (p0) REVERT: D 151 MET cc_start: 0.7370 (ttt) cc_final: 0.6995 (ttt) REVERT: D 208 MET cc_start: 0.7526 (tpp) cc_final: 0.6874 (tpp) REVERT: D 217 LEU cc_start: 0.7896 (tp) cc_final: 0.7640 (tt) REVERT: D 224 ASN cc_start: 0.8161 (m110) cc_final: 0.7960 (m110) REVERT: D 261 ASN cc_start: 0.8854 (m-40) cc_final: 0.8573 (m-40) REVERT: D 278 GLU cc_start: 0.8612 (mt-10) cc_final: 0.8376 (mt-10) REVERT: D 310 TYR cc_start: 0.8268 (t80) cc_final: 0.7952 (t80) REVERT: E 64 ASN cc_start: 0.8236 (t0) cc_final: 0.8010 (t0) REVERT: E 83 GLN cc_start: 0.7927 (tm-30) cc_final: 0.7323 (tm-30) REVERT: E 119 GLN cc_start: 0.7992 (mm110) cc_final: 0.7708 (mm110) REVERT: E 138 LEU cc_start: 0.8491 (tp) cc_final: 0.8218 (tp) REVERT: E 151 MET cc_start: 0.7546 (tpt) cc_final: 0.6987 (tpp) REVERT: E 154 ILE cc_start: 0.8412 (pt) cc_final: 0.8202 (pt) REVERT: E 155 GLN cc_start: 0.8497 (tp40) cc_final: 0.8204 (tp40) REVERT: E 248 MET cc_start: 0.6737 (mtp) cc_final: 0.6456 (mtp) REVERT: E 275 THR cc_start: 0.8578 (m) cc_final: 0.8192 (m) REVERT: E 278 GLU cc_start: 0.8349 (tp30) cc_final: 0.8138 (tp30) REVERT: E 292 LEU cc_start: 0.8289 (mp) cc_final: 0.7979 (mp) REVERT: E 296 ASN cc_start: 0.8583 (m110) cc_final: 0.8190 (m-40) REVERT: E 297 LYS cc_start: 0.8106 (mppt) cc_final: 0.7886 (mppt) REVERT: E 300 GLU cc_start: 0.7974 (tm-30) cc_final: 0.7340 (tm-30) REVERT: E 312 ARG cc_start: 0.9237 (ttp80) cc_final: 0.9012 (ttp80) REVERT: F 68 MET cc_start: 0.7286 (tmm) cc_final: 0.6862 (tmm) REVERT: F 88 LEU cc_start: 0.8698 (mt) cc_final: 0.8489 (mt) REVERT: F 135 ASN cc_start: 0.8057 (p0) cc_final: 0.7514 (p0) REVERT: F 143 TYR cc_start: 0.8453 (t80) cc_final: 0.7917 (t80) REVERT: F 151 MET cc_start: 0.7241 (mpp) cc_final: 0.7016 (mpp) REVERT: F 174 ARG cc_start: 0.8215 (mmp-170) cc_final: 0.7940 (mmp-170) REVERT: F 208 MET cc_start: 0.6979 (mpp) cc_final: 0.6688 (mpp) REVERT: F 220 LEU cc_start: 0.7996 (mm) cc_final: 0.7767 (mm) REVERT: F 224 ASN cc_start: 0.8806 (t0) cc_final: 0.8387 (t0) REVERT: F 225 GLU cc_start: 0.8287 (mt-10) cc_final: 0.7754 (mt-10) REVERT: F 247 LYS cc_start: 0.7959 (tttp) cc_final: 0.7233 (tttp) REVERT: F 248 MET cc_start: 0.8197 (mtm) cc_final: 0.7854 (mtm) REVERT: F 250 ARG cc_start: 0.7638 (ptt-90) cc_final: 0.7104 (ptt-90) REVERT: F 254 MET cc_start: 0.7390 (tmm) cc_final: 0.7049 (tmm) REVERT: F 265 SER cc_start: 0.8747 (t) cc_final: 0.8340 (t) REVERT: F 275 THR cc_start: 0.7443 (m) cc_final: 0.6986 (m) REVERT: F 279 ASN cc_start: 0.8565 (m-40) cc_final: 0.8059 (m-40) REVERT: F 303 ARG cc_start: 0.8335 (ttm170) cc_final: 0.7879 (ttm170) REVERT: F 309 PHE cc_start: 0.7771 (m-80) cc_final: 0.7513 (m-80) REVERT: G 366 GLN cc_start: 0.6921 (tp40) cc_final: 0.6640 (tp40) REVERT: G 368 ARG cc_start: 0.8640 (mpt180) cc_final: 0.8427 (mpt-90) REVERT: G 369 LEU cc_start: 0.8942 (mt) cc_final: 0.8480 (mt) REVERT: G 397 ASP cc_start: 0.7541 (p0) cc_final: 0.7131 (p0) REVERT: G 399 THR cc_start: 0.8222 (p) cc_final: 0.7511 (p) REVERT: G 400 GLN cc_start: 0.8148 (mm-40) cc_final: 0.7581 (mm110) REVERT: G 430 ARG cc_start: 0.8083 (tmm160) cc_final: 0.7829 (tmm160) REVERT: G 438 CYS cc_start: 0.9054 (m) cc_final: 0.8600 (m) REVERT: G 544 ILE cc_start: 0.8878 (mp) cc_final: 0.8436 (mp) REVERT: a 25 PHE cc_start: 0.8263 (m-10) cc_final: 0.8050 (m-80) REVERT: a 113 GLN cc_start: 0.7710 (mp10) cc_final: 0.6781 (mp10) REVERT: a 131 LEU cc_start: 0.8532 (mt) cc_final: 0.7788 (mt) REVERT: a 134 MET cc_start: 0.7452 (ppp) cc_final: 0.6677 (ppp) REVERT: a 135 LEU cc_start: 0.8333 (mt) cc_final: 0.7719 (mt) REVERT: a 186 TRP cc_start: 0.7529 (t60) cc_final: 0.7328 (t60) REVERT: a 214 ASP cc_start: 0.8577 (m-30) cc_final: 0.8315 (m-30) REVERT: a 215 MET cc_start: 0.8481 (mtm) cc_final: 0.8218 (mtm) REVERT: N 432 MET cc_start: 0.8167 (mtp) cc_final: 0.7615 (mtp) REVERT: N 433 ARG cc_start: 0.8604 (mtm180) cc_final: 0.8099 (mtt90) REVERT: N 436 MET cc_start: 0.8415 (ttp) cc_final: 0.8139 (ttp) REVERT: N 470 GLN cc_start: 0.6811 (mp10) cc_final: 0.6553 (mp10) REVERT: N 572 TYR cc_start: 0.7437 (m-80) cc_final: 0.7161 (m-80) REVERT: N 586 PHE cc_start: 0.7474 (t80) cc_final: 0.6937 (t80) REVERT: N 650 ILE cc_start: 0.8051 (mm) cc_final: 0.7808 (mm) REVERT: N 677 LYS cc_start: 0.8517 (ptpp) cc_final: 0.8297 (mtmt) REVERT: N 688 MET cc_start: 0.7491 (ttm) cc_final: 0.7201 (ttm) REVERT: N 829 ASP cc_start: 0.6597 (m-30) cc_final: 0.6329 (m-30) REVERT: N 890 TYR cc_start: 0.7898 (t80) cc_final: 0.7564 (t80) REVERT: N 893 ASP cc_start: 0.8247 (m-30) cc_final: 0.8001 (m-30) REVERT: N 960 ILE cc_start: 0.8797 (pt) cc_final: 0.8292 (pt) REVERT: N 964 PHE cc_start: 0.8104 (t80) cc_final: 0.7593 (t80) REVERT: N 1077 GLU cc_start: 0.8654 (tm-30) cc_final: 0.8381 (tm-30) REVERT: N 1207 HIS cc_start: 0.7457 (t-90) cc_final: 0.7178 (t-90) REVERT: N 1210 MET cc_start: 0.8623 (mtm) cc_final: 0.8264 (mtm) REVERT: N 1227 GLU cc_start: 0.7630 (tm-30) cc_final: 0.7102 (tp30) outliers start: 2 outliers final: 0 residues processed: 816 average time/residue: 0.1746 time to fit residues: 219.1576 Evaluate side-chains 795 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 795 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 162 optimal weight: 4.9990 chunk 149 optimal weight: 3.9990 chunk 167 optimal weight: 0.6980 chunk 182 optimal weight: 5.9990 chunk 59 optimal weight: 2.9990 chunk 143 optimal weight: 1.9990 chunk 311 optimal weight: 20.0000 chunk 81 optimal weight: 3.9990 chunk 322 optimal weight: 3.9990 chunk 105 optimal weight: 4.9990 chunk 266 optimal weight: 7.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 52 GLN A 73 HIS A 186 ASN A 261 ASN B 100 HIS ** B 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 246 ASN ** D 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 96 ASN F 133 GLN F 134 HIS ** F 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 753 ASN ** N1042 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N1091 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N1104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N1163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N1214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N1239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.177569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.139214 restraints weight = 49599.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.144657 restraints weight = 30975.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.148566 restraints weight = 21711.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.151411 restraints weight = 16432.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.153478 restraints weight = 13200.933| |-----------------------------------------------------------------------------| r_work (final): 0.3903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6877 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 26361 Z= 0.273 Angle : 0.673 12.273 35849 Z= 0.351 Chirality : 0.046 0.222 4008 Planarity : 0.005 0.079 4718 Dihedral : 6.486 122.558 3718 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 16.62 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.89 % Favored : 92.08 % Rotamer: Outliers : 0.07 % Allowed : 1.92 % Favored : 98.00 % 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: -0.97 (0.15), residues: 3258 helix: 0.06 (0.14), residues: 1356 sheet: -0.94 (0.26), residues: 367 loop : -1.15 (0.17), residues: 1535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 303 TYR 0.027 0.002 TYR E 143 PHE 0.025 0.002 PHE a 108 TRP 0.045 0.003 TRP N 876 HIS 0.008 0.001 HIS C 235 Details of bonding type rmsd/Z covalent geometry : bond 0.00543 / 0.27 (26361) covalent geometry : angle 0.67338 / 0.35 (35849) hydrogen bonds : bond 0.04187 / 2.78 ( 1037) hydrogen bonds : angle 5.70686 / 4.01 ( 2988) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 822 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 820 time to evaluate : 0.683 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: A 52 GLN cc_start: 0.8149 (mm110) cc_final: 0.7711 (tp40) REVERT: A 66 ARG cc_start: 0.7417 (mpp-170) cc_final: 0.6601 (mpp-170) REVERT: A 73 HIS cc_start: 0.8523 (OUTLIER) cc_final: 0.8261 (t-90) REVERT: A 80 HIS cc_start: 0.8155 (m170) cc_final: 0.7927 (m170) REVERT: A 89 ASN cc_start: 0.7770 (t0) cc_final: 0.7482 (t0) REVERT: A 93 VAL cc_start: 0.8566 (p) cc_final: 0.8297 (m) REVERT: A 124 LYS cc_start: 0.7777 (mtpt) cc_final: 0.7523 (mtpt) REVERT: A 138 LEU cc_start: 0.8428 (tp) cc_final: 0.8034 (tp) REVERT: A 242 ARG cc_start: 0.8031 (mtp180) cc_final: 0.7534 (mtp180) REVERT: A 244 ILE cc_start: 0.8983 (mp) cc_final: 0.8733 (mp) REVERT: A 248 MET cc_start: 0.6957 (ptp) cc_final: 0.6393 (ptp) REVERT: A 268 MET cc_start: 0.8981 (ttm) cc_final: 0.8761 (ttp) REVERT: A 282 ILE cc_start: 0.8211 (mt) cc_final: 0.7984 (mt) REVERT: A 294 PHE cc_start: 0.8111 (t80) cc_final: 0.7790 (t80) REVERT: A 299 ASP cc_start: 0.7407 (m-30) cc_final: 0.7133 (m-30) REVERT: B 64 ASN cc_start: 0.7682 (t0) cc_final: 0.7457 (t0) REVERT: B 65 ARG cc_start: 0.8369 (tpp80) cc_final: 0.8036 (tpp80) REVERT: B 83 GLN cc_start: 0.8439 (pt0) cc_final: 0.7973 (pt0) REVERT: B 152 PHE cc_start: 0.7776 (t80) cc_final: 0.7338 (t80) REVERT: B 159 GLU cc_start: 0.8427 (mm-30) cc_final: 0.8175 (mm-30) REVERT: B 176 HIS cc_start: 0.8514 (t-90) cc_final: 0.7924 (t-90) REVERT: B 180 ARG cc_start: 0.7645 (mpt180) cc_final: 0.7240 (mpt180) REVERT: B 207 GLN cc_start: 0.8427 (pm20) cc_final: 0.8090 (pm20) REVERT: B 210 ARG cc_start: 0.8345 (tpm170) cc_final: 0.7649 (tpm170) REVERT: B 248 MET cc_start: 0.8438 (mtm) cc_final: 0.7914 (mtm) REVERT: B 253 ASP cc_start: 0.8339 (m-30) cc_final: 0.8053 (m-30) REVERT: B 261 ASN cc_start: 0.8641 (m-40) cc_final: 0.8428 (m-40) REVERT: B 295 LEU cc_start: 0.8043 (tp) cc_final: 0.7054 (tp) REVERT: B 298 CYS cc_start: 0.7748 (m) cc_final: 0.7093 (m) REVERT: B 303 ARG cc_start: 0.8202 (mtp180) cc_final: 0.7354 (mtp180) REVERT: B 309 PHE cc_start: 0.8705 (m-80) cc_final: 0.8201 (m-80) REVERT: B 312 ARG cc_start: 0.8234 (mtt90) cc_final: 0.7657 (mtt90) REVERT: B 314 PHE cc_start: 0.7791 (m-10) cc_final: 0.7339 (m-80) REVERT: C 46 ASP cc_start: 0.7597 (m-30) cc_final: 0.7367 (m-30) REVERT: C 52 GLN cc_start: 0.8345 (mm-40) cc_final: 0.8142 (mm-40) REVERT: C 77 LYS cc_start: 0.8423 (ptpt) cc_final: 0.8095 (ptpt) REVERT: C 80 HIS cc_start: 0.8194 (m90) cc_final: 0.7806 (m90) REVERT: C 122 GLU cc_start: 0.7809 (tt0) cc_final: 0.7554 (tt0) REVERT: C 208 MET cc_start: 0.8255 (mtm) cc_final: 0.7918 (mtm) REVERT: C 227 ASN cc_start: 0.8830 (m110) cc_final: 0.8624 (m-40) REVERT: C 295 LEU cc_start: 0.7564 (tp) cc_final: 0.6961 (tp) REVERT: C 301 LEU cc_start: 0.8690 (mt) cc_final: 0.7851 (mt) REVERT: C 311 GLN cc_start: 0.8417 (tm-30) cc_final: 0.7946 (tm-30) REVERT: D 29 MET cc_start: 0.6320 (tpt) cc_final: 0.5692 (tpt) REVERT: D 68 MET cc_start: 0.8049 (tpp) cc_final: 0.7516 (tpp) REVERT: D 72 TYR cc_start: 0.8284 (m-10) cc_final: 0.8046 (m-10) REVERT: D 135 ASN cc_start: 0.7672 (p0) cc_final: 0.7422 (p0) REVERT: D 144 ASP cc_start: 0.7678 (p0) cc_final: 0.7361 (p0) REVERT: D 151 MET cc_start: 0.7354 (ttt) cc_final: 0.6976 (ttt) REVERT: D 211 TRP cc_start: 0.8962 (m100) cc_final: 0.8315 (m100) REVERT: D 217 LEU cc_start: 0.7916 (tp) cc_final: 0.7661 (tt) REVERT: D 224 ASN cc_start: 0.8258 (m110) cc_final: 0.8035 (m110) REVERT: D 261 ASN cc_start: 0.8877 (m-40) cc_final: 0.8592 (m-40) REVERT: D 271 ARG cc_start: 0.8227 (tpt170) cc_final: 0.7400 (tpp80) REVERT: D 278 GLU cc_start: 0.8676 (mt-10) cc_final: 0.8464 (mt-10) REVERT: D 310 TYR cc_start: 0.8309 (t80) cc_final: 0.8034 (t80) REVERT: E 64 ASN cc_start: 0.8235 (t0) cc_final: 0.8032 (t0) REVERT: E 83 GLN cc_start: 0.7563 (tm-30) cc_final: 0.6527 (tm-30) REVERT: E 119 GLN cc_start: 0.7999 (mm110) cc_final: 0.7748 (mm110) REVERT: E 138 LEU cc_start: 0.8536 (tp) cc_final: 0.8308 (tp) REVERT: E 248 MET cc_start: 0.6845 (mtp) cc_final: 0.6529 (mtp) REVERT: E 292 LEU cc_start: 0.8322 (mp) cc_final: 0.8065 (mp) REVERT: E 296 ASN cc_start: 0.8574 (m110) cc_final: 0.8018 (m-40) REVERT: E 300 GLU cc_start: 0.8022 (tm-30) cc_final: 0.7413 (tm-30) REVERT: F 42 GLU cc_start: 0.7382 (tm-30) cc_final: 0.7142 (tm-30) REVERT: F 44 ASP cc_start: 0.7453 (m-30) cc_final: 0.7192 (m-30) REVERT: F 68 MET cc_start: 0.7324 (tmm) cc_final: 0.6871 (tmm) REVERT: F 135 ASN cc_start: 0.8139 (p0) cc_final: 0.7601 (p0) REVERT: F 143 TYR cc_start: 0.8411 (t80) cc_final: 0.7597 (t80) REVERT: F 151 MET cc_start: 0.7283 (mpp) cc_final: 0.6967 (mpp) REVERT: F 167 LEU cc_start: 0.8070 (mp) cc_final: 0.7373 (mp) REVERT: F 174 ARG cc_start: 0.8270 (mmp-170) cc_final: 0.8029 (mmp-170) REVERT: F 208 MET cc_start: 0.7142 (mpp) cc_final: 0.6789 (mpp) REVERT: F 219 TYR cc_start: 0.8500 (m-80) cc_final: 0.7924 (m-80) REVERT: F 224 ASN cc_start: 0.8874 (t0) cc_final: 0.8448 (t0) REVERT: F 225 GLU cc_start: 0.8360 (mt-10) cc_final: 0.7829 (mt-10) REVERT: F 247 LYS cc_start: 0.8108 (tttp) cc_final: 0.7285 (tttp) REVERT: F 248 MET cc_start: 0.8327 (mtm) cc_final: 0.7898 (mtm) REVERT: F 250 ARG cc_start: 0.7699 (ptt-90) cc_final: 0.7156 (ptt-90) REVERT: F 254 MET cc_start: 0.7509 (tmm) cc_final: 0.7122 (tmm) REVERT: F 265 SER cc_start: 0.8672 (t) cc_final: 0.8303 (t) REVERT: F 275 THR cc_start: 0.7464 (m) cc_final: 0.7031 (m) REVERT: F 279 ASN cc_start: 0.8623 (m-40) cc_final: 0.8151 (m-40) REVERT: F 303 ARG cc_start: 0.8387 (ttm170) cc_final: 0.7973 (ttm170) REVERT: F 309 PHE cc_start: 0.7842 (m-80) cc_final: 0.7605 (m-80) REVERT: G 365 LEU cc_start: 0.9265 (mp) cc_final: 0.9060 (mp) REVERT: G 366 GLN cc_start: 0.7063 (tp40) cc_final: 0.6785 (tp40) REVERT: G 369 LEU cc_start: 0.8959 (mt) cc_final: 0.8543 (mt) REVERT: G 399 THR cc_start: 0.8259 (p) cc_final: 0.7834 (p) REVERT: G 430 ARG cc_start: 0.8164 (tmm160) cc_final: 0.7908 (tmm160) REVERT: G 544 ILE cc_start: 0.8896 (mp) cc_final: 0.8436 (mp) REVERT: a 113 GLN cc_start: 0.7921 (mp10) cc_final: 0.7032 (mp10) REVERT: a 131 LEU cc_start: 0.8507 (mt) cc_final: 0.7772 (mt) REVERT: a 134 MET cc_start: 0.7619 (ppp) cc_final: 0.6714 (ppp) REVERT: a 135 LEU cc_start: 0.8450 (mt) cc_final: 0.7756 (mt) REVERT: a 214 ASP cc_start: 0.8595 (m-30) cc_final: 0.8295 (m-30) REVERT: N 432 MET cc_start: 0.8174 (mtp) cc_final: 0.7632 (mtp) REVERT: N 433 ARG cc_start: 0.8612 (mtm180) cc_final: 0.8107 (mtt90) REVERT: N 436 MET cc_start: 0.8506 (ttp) cc_final: 0.8236 (ttp) REVERT: N 572 TYR cc_start: 0.7585 (m-80) cc_final: 0.7288 (m-80) REVERT: N 586 PHE cc_start: 0.7616 (t80) cc_final: 0.7003 (t80) REVERT: N 596 GLN cc_start: 0.7112 (pm20) cc_final: 0.6660 (pm20) REVERT: N 650 ILE cc_start: 0.8106 (mm) cc_final: 0.7866 (mm) REVERT: N 677 LYS cc_start: 0.8537 (ptpp) cc_final: 0.8300 (mtmt) REVERT: N 688 MET cc_start: 0.7541 (ttm) cc_final: 0.7246 (ttm) REVERT: N 696 VAL cc_start: 0.6194 (p) cc_final: 0.5840 (p) REVERT: N 816 LEU cc_start: 0.8149 (mt) cc_final: 0.7935 (mt) REVERT: N 829 ASP cc_start: 0.6664 (m-30) cc_final: 0.6411 (m-30) REVERT: N 890 TYR cc_start: 0.8023 (t80) cc_final: 0.7722 (t80) REVERT: N 893 ASP cc_start: 0.8332 (m-30) cc_final: 0.8081 (m-30) REVERT: N 960 ILE cc_start: 0.8854 (pt) cc_final: 0.8357 (pt) REVERT: N 964 PHE cc_start: 0.8232 (t80) cc_final: 0.7701 (t80) REVERT: N 1072 ARG cc_start: 0.7462 (tmt170) cc_final: 0.7228 (tpt90) REVERT: N 1077 GLU cc_start: 0.8651 (tm-30) cc_final: 0.8360 (tm-30) REVERT: N 1207 HIS cc_start: 0.7452 (t-90) cc_final: 0.7153 (t-90) REVERT: N 1209 PHE cc_start: 0.8116 (t80) cc_final: 0.7913 (t80) REVERT: N 1210 MET cc_start: 0.8603 (mtm) cc_final: 0.8325 (mtm) REVERT: N 1227 GLU cc_start: 0.7746 (tm-30) cc_final: 0.7218 (tp30) outliers start: 2 outliers final: 0 residues processed: 821 average time/residue: 0.1820 time to fit residues: 228.8070 Evaluate side-chains 790 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 789 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 165 optimal weight: 0.7980 chunk 72 optimal weight: 0.7980 chunk 195 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 184 optimal weight: 9.9990 chunk 83 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 chunk 315 optimal weight: 0.8980 chunk 131 optimal weight: 0.8980 chunk 146 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 261 ASN B 10 ASN B 52 GLN B 100 HIS ** B 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 296 ASN ** B 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 96 ASN F 134 HIS N 753 ASN N1042 ASN ** N1091 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N1163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N1239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.173702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.136983 restraints weight = 50064.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.142687 restraints weight = 30861.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.146668 restraints weight = 21112.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.149581 restraints weight = 15639.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.151793 restraints weight = 12261.351| |-----------------------------------------------------------------------------| r_work (final): 0.3980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6756 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 26361 Z= 0.128 Angle : 0.609 12.226 35849 Z= 0.307 Chirality : 0.044 0.362 4008 Planarity : 0.005 0.056 4718 Dihedral : 6.193 121.911 3718 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.80 % Favored : 94.17 % Rotamer: Outliers : 0.07 % Allowed : 1.37 % Favored : 98.56 % 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: -0.81 (0.15), residues: 3258 helix: 0.22 (0.14), residues: 1363 sheet: -0.77 (0.27), residues: 361 loop : -1.11 (0.17), residues: 1534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 303 TYR 0.020 0.001 TYR N1197 PHE 0.028 0.001 PHE a 108 TRP 0.052 0.002 TRP N 876 HIS 0.008 0.001 HIS N 666 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.13 (26361) covalent geometry : angle 0.60923 / 0.31 (35849) hydrogen bonds : bond 0.03297 / 2.19 ( 1037) hydrogen bonds : angle 5.32104 / 3.73 ( 2988) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 821 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 819 time to evaluate : 0.687 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: A 66 ARG cc_start: 0.7354 (mpp-170) cc_final: 0.6522 (mpp-170) REVERT: A 80 HIS cc_start: 0.8075 (m170) cc_final: 0.7798 (m170) REVERT: A 89 ASN cc_start: 0.7646 (t0) cc_final: 0.7439 (t0) REVERT: A 93 VAL cc_start: 0.8575 (p) cc_final: 0.8302 (m) REVERT: A 124 LYS cc_start: 0.7771 (mtpt) cc_final: 0.7514 (mtpt) REVERT: A 138 LEU cc_start: 0.8357 (tp) cc_final: 0.7980 (tp) REVERT: A 180 ARG cc_start: 0.7929 (mmm160) cc_final: 0.7490 (mmm160) REVERT: A 186 ASN cc_start: 0.6896 (t0) cc_final: 0.6613 (t0) REVERT: A 242 ARG cc_start: 0.7991 (mtp180) cc_final: 0.7592 (mtp180) REVERT: A 244 ILE cc_start: 0.8962 (mp) cc_final: 0.8656 (mp) REVERT: A 248 MET cc_start: 0.6827 (ptp) cc_final: 0.6263 (ptp) REVERT: A 282 ILE cc_start: 0.8107 (mt) cc_final: 0.7859 (mt) REVERT: A 288 PHE cc_start: 0.8028 (t80) cc_final: 0.7631 (t80) REVERT: A 294 PHE cc_start: 0.8038 (t80) cc_final: 0.7777 (t80) REVERT: A 299 ASP cc_start: 0.7317 (m-30) cc_final: 0.7079 (m-30) REVERT: B 10 ASN cc_start: 0.7520 (t0) cc_final: 0.7126 (t0) REVERT: B 64 ASN cc_start: 0.7643 (t0) cc_final: 0.7373 (t0) REVERT: B 159 GLU cc_start: 0.8381 (mm-30) cc_final: 0.8129 (mm-30) REVERT: B 176 HIS cc_start: 0.8451 (t-90) cc_final: 0.7868 (t-90) REVERT: B 180 ARG cc_start: 0.7460 (mpt180) cc_final: 0.7220 (mpt180) REVERT: B 207 GLN cc_start: 0.8328 (pm20) cc_final: 0.8065 (pm20) REVERT: B 210 ARG cc_start: 0.8324 (tpm170) cc_final: 0.7609 (tpm170) REVERT: B 248 MET cc_start: 0.8437 (mtm) cc_final: 0.7959 (mtm) REVERT: B 253 ASP cc_start: 0.8227 (m-30) cc_final: 0.7954 (m-30) REVERT: B 254 MET cc_start: 0.7904 (mpp) cc_final: 0.7444 (mpp) REVERT: B 288 PHE cc_start: 0.7170 (t80) cc_final: 0.6565 (t80) REVERT: B 295 LEU cc_start: 0.7916 (tp) cc_final: 0.6907 (tp) REVERT: B 298 CYS cc_start: 0.7685 (m) cc_final: 0.7069 (m) REVERT: B 299 ASP cc_start: 0.7843 (t70) cc_final: 0.7555 (t70) REVERT: B 303 ARG cc_start: 0.8150 (mtp180) cc_final: 0.7303 (mtp180) REVERT: B 309 PHE cc_start: 0.8524 (m-80) cc_final: 0.8063 (m-80) REVERT: B 310 TYR cc_start: 0.7323 (t80) cc_final: 0.7117 (t80) REVERT: B 312 ARG cc_start: 0.8110 (mtt90) cc_final: 0.7517 (mtt90) REVERT: B 314 PHE cc_start: 0.7782 (m-10) cc_final: 0.7052 (m-80) REVERT: C 46 ASP cc_start: 0.7441 (m-30) cc_final: 0.7239 (m-30) REVERT: C 52 GLN cc_start: 0.8282 (mm-40) cc_final: 0.8077 (mm-40) REVERT: C 80 HIS cc_start: 0.7998 (m90) cc_final: 0.7603 (m90) REVERT: C 122 GLU cc_start: 0.7808 (tt0) cc_final: 0.7528 (tt0) REVERT: C 208 MET cc_start: 0.8185 (mtm) cc_final: 0.7834 (mtm) REVERT: C 295 LEU cc_start: 0.7438 (tp) cc_final: 0.6867 (tp) REVERT: C 300 GLU cc_start: 0.7823 (mm-30) cc_final: 0.7474 (mm-30) REVERT: C 301 LEU cc_start: 0.8411 (mt) cc_final: 0.7777 (mt) REVERT: C 303 ARG cc_start: 0.7843 (ttm170) cc_final: 0.6933 (ttm170) REVERT: C 311 GLN cc_start: 0.8346 (tm-30) cc_final: 0.7882 (tm-30) REVERT: D 29 MET cc_start: 0.6276 (tpt) cc_final: 0.5716 (tpt) REVERT: D 68 MET cc_start: 0.7679 (tpp) cc_final: 0.6920 (tpp) REVERT: D 72 TYR cc_start: 0.8185 (m-10) cc_final: 0.7974 (m-10) REVERT: D 77 LYS cc_start: 0.7059 (mtpt) cc_final: 0.6817 (mtpt) REVERT: D 103 ARG cc_start: 0.8446 (ttt-90) cc_final: 0.8174 (ttt-90) REVERT: D 144 ASP cc_start: 0.7511 (p0) cc_final: 0.7187 (p0) REVERT: D 151 MET cc_start: 0.7319 (ttt) cc_final: 0.6969 (ttt) REVERT: D 217 LEU cc_start: 0.7904 (tp) cc_final: 0.7652 (tt) REVERT: D 224 ASN cc_start: 0.8200 (m110) cc_final: 0.7993 (m110) REVERT: D 261 ASN cc_start: 0.8839 (m-40) cc_final: 0.8562 (m-40) REVERT: D 278 GLU cc_start: 0.8597 (mt-10) cc_final: 0.8363 (mt-10) REVERT: D 310 TYR cc_start: 0.8319 (t80) cc_final: 0.8038 (t80) REVERT: E 83 GLN cc_start: 0.7619 (tm-30) cc_final: 0.7153 (tm-30) REVERT: E 119 GLN cc_start: 0.7968 (mm110) cc_final: 0.7693 (mm110) REVERT: E 138 LEU cc_start: 0.8494 (tp) cc_final: 0.8217 (tp) REVERT: E 151 MET cc_start: 0.7866 (tpt) cc_final: 0.7356 (tpp) REVERT: E 248 MET cc_start: 0.7034 (mtp) cc_final: 0.6610 (mtp) REVERT: E 292 LEU cc_start: 0.8373 (mp) cc_final: 0.8053 (mp) REVERT: E 296 ASN cc_start: 0.8536 (m110) cc_final: 0.8281 (m-40) REVERT: E 300 GLU cc_start: 0.7953 (tm-30) cc_final: 0.7304 (tm-30) REVERT: E 317 GLU cc_start: 0.7752 (tt0) cc_final: 0.7465 (tt0) REVERT: F 64 ASN cc_start: 0.8111 (t0) cc_final: 0.7857 (t0) REVERT: F 68 MET cc_start: 0.7344 (tmm) cc_final: 0.6878 (tmm) REVERT: F 88 LEU cc_start: 0.8725 (mt) cc_final: 0.8497 (mt) REVERT: F 135 ASN cc_start: 0.8165 (p0) cc_final: 0.7601 (p0) REVERT: F 143 TYR cc_start: 0.8455 (t80) cc_final: 0.7710 (t80) REVERT: F 151 MET cc_start: 0.7174 (mpp) cc_final: 0.6931 (mpp) REVERT: F 174 ARG cc_start: 0.8242 (mmp-170) cc_final: 0.8016 (mmp-170) REVERT: F 208 MET cc_start: 0.6966 (mpp) cc_final: 0.6671 (mpp) REVERT: F 219 TYR cc_start: 0.8454 (m-80) cc_final: 0.7783 (m-10) REVERT: F 224 ASN cc_start: 0.8803 (t0) cc_final: 0.8370 (t0) REVERT: F 225 GLU cc_start: 0.8219 (mt-10) cc_final: 0.7677 (mt-10) REVERT: F 247 LYS cc_start: 0.8041 (tttp) cc_final: 0.7245 (tttp) REVERT: F 248 MET cc_start: 0.8185 (mtm) cc_final: 0.7844 (mtm) REVERT: F 250 ARG cc_start: 0.7633 (ptt-90) cc_final: 0.7151 (ptt-90) REVERT: F 253 ASP cc_start: 0.8763 (m-30) cc_final: 0.8484 (m-30) REVERT: F 254 MET cc_start: 0.7386 (tmm) cc_final: 0.7070 (tmm) REVERT: F 265 SER cc_start: 0.8746 (t) cc_final: 0.8255 (t) REVERT: F 275 THR cc_start: 0.7389 (m) cc_final: 0.6927 (m) REVERT: F 279 ASN cc_start: 0.8525 (m-40) cc_final: 0.7985 (m-40) REVERT: F 303 ARG cc_start: 0.8253 (ttm170) cc_final: 0.7805 (ttm170) REVERT: F 309 PHE cc_start: 0.7757 (m-80) cc_final: 0.7533 (m-80) REVERT: G 369 LEU cc_start: 0.8951 (mt) cc_final: 0.8538 (mt) REVERT: G 399 THR cc_start: 0.8181 (p) cc_final: 0.7599 (p) REVERT: G 434 VAL cc_start: 0.8874 (t) cc_final: 0.8668 (t) REVERT: G 438 CYS cc_start: 0.9088 (m) cc_final: 0.8648 (m) REVERT: G 454 GLU cc_start: 0.6934 (tp30) cc_final: 0.6639 (tp30) REVERT: G 544 ILE cc_start: 0.8886 (mp) cc_final: 0.8438 (mp) REVERT: G 618 LEU cc_start: 0.9261 (mt) cc_final: 0.9049 (mt) REVERT: a 25 PHE cc_start: 0.8130 (m-80) cc_final: 0.7507 (m-80) REVERT: a 113 GLN cc_start: 0.7716 (mp10) cc_final: 0.6778 (mp10) REVERT: a 131 LEU cc_start: 0.8504 (mt) cc_final: 0.7758 (mt) REVERT: a 134 MET cc_start: 0.7550 (ppp) cc_final: 0.6677 (ppp) REVERT: a 135 LEU cc_start: 0.8418 (mt) cc_final: 0.7735 (mt) REVERT: a 214 ASP cc_start: 0.8553 (m-30) cc_final: 0.8268 (m-30) REVERT: a 215 MET cc_start: 0.8465 (mtm) cc_final: 0.8116 (mtm) REVERT: N 432 MET cc_start: 0.8208 (mtp) cc_final: 0.7656 (mtp) REVERT: N 433 ARG cc_start: 0.8597 (mtm180) cc_final: 0.8067 (mtt90) REVERT: N 436 MET cc_start: 0.8442 (ttp) cc_final: 0.8161 (ttp) REVERT: N 470 GLN cc_start: 0.6657 (mp10) cc_final: 0.6431 (mp10) REVERT: N 572 TYR cc_start: 0.7486 (m-80) cc_final: 0.7198 (m-80) REVERT: N 586 PHE cc_start: 0.7344 (t80) cc_final: 0.6894 (t80) REVERT: N 596 GLN cc_start: 0.6981 (pm20) cc_final: 0.6501 (pm20) REVERT: N 650 ILE cc_start: 0.8082 (mm) cc_final: 0.7838 (mm) REVERT: N 677 LYS cc_start: 0.8497 (ptpp) cc_final: 0.8263 (mtmt) REVERT: N 688 MET cc_start: 0.7450 (ttm) cc_final: 0.7019 (ttm) REVERT: N 816 LEU cc_start: 0.8133 (mt) cc_final: 0.7932 (mt) REVERT: N 829 ASP cc_start: 0.6616 (m-30) cc_final: 0.6352 (m-30) REVERT: N 890 TYR cc_start: 0.7942 (t80) cc_final: 0.7540 (t80) REVERT: N 893 ASP cc_start: 0.8186 (m-30) cc_final: 0.7935 (m-30) REVERT: N 960 ILE cc_start: 0.8810 (pt) cc_final: 0.8302 (pt) REVERT: N 964 PHE cc_start: 0.8142 (t80) cc_final: 0.7616 (t80) REVERT: N 1072 ARG cc_start: 0.7413 (tmt170) cc_final: 0.7174 (tpt90) REVERT: N 1077 GLU cc_start: 0.8669 (tm-30) cc_final: 0.8424 (tm-30) REVERT: N 1096 LEU cc_start: 0.8815 (mt) cc_final: 0.8169 (tt) REVERT: N 1166 LYS cc_start: 0.8466 (mppt) cc_final: 0.8238 (mppt) REVERT: N 1207 HIS cc_start: 0.7436 (t-90) cc_final: 0.7137 (t-90) REVERT: N 1210 MET cc_start: 0.8631 (mtm) cc_final: 0.8311 (mtm) REVERT: N 1227 GLU cc_start: 0.7608 (tm-30) cc_final: 0.7035 (tp30) outliers start: 2 outliers final: 0 residues processed: 820 average time/residue: 0.1738 time to fit residues: 217.7943 Evaluate side-chains 792 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 792 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 264 optimal weight: 2.9990 chunk 159 optimal weight: 2.9990 chunk 11 optimal weight: 20.0000 chunk 244 optimal weight: 7.9990 chunk 33 optimal weight: 5.9990 chunk 42 optimal weight: 0.7980 chunk 65 optimal weight: 0.7980 chunk 184 optimal weight: 0.4980 chunk 4 optimal weight: 2.9990 chunk 169 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 52 GLN A 73 HIS ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 GLN B 100 HIS ** B 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 64 ASN ** E 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 96 ASN F 134 HIS G 400 GLN ** N 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 753 ASN ** N1042 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N1091 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N1163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N1214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N1239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.180333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.141748 restraints weight = 49812.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.147383 restraints weight = 31158.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.151380 restraints weight = 21755.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.154239 restraints weight = 16432.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.156399 restraints weight = 13169.801| |-----------------------------------------------------------------------------| r_work (final): 0.3942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6824 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 26361 Z= 0.178 Angle : 0.636 13.573 35849 Z= 0.323 Chirality : 0.044 0.238 4008 Planarity : 0.005 0.058 4718 Dihedral : 6.300 121.224 3718 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 14.39 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.24 % Favored : 92.73 % Rotamer: Outliers : 0.11 % Allowed : 0.48 % Favored : 99.41 % 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: -0.89 (0.15), residues: 3258 helix: 0.13 (0.14), residues: 1371 sheet: -0.85 (0.27), residues: 364 loop : -1.12 (0.17), residues: 1523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 312 TYR 0.031 0.002 TYR D 132 PHE 0.028 0.002 PHE a 108 TRP 0.050 0.003 TRP C 276 HIS 0.006 0.001 HIS F 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.18 (26361) covalent geometry : angle 0.63639 / 0.32 (35849) hydrogen bonds : bond 0.03525 / 2.33 ( 1037) hydrogen bonds : angle 5.45622 / 3.83 ( 2988) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 812 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 809 time to evaluate : 0.831 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: A 89 ASN cc_start: 0.7734 (t0) cc_final: 0.7479 (t0) REVERT: A 124 LYS cc_start: 0.7790 (mtpt) cc_final: 0.7509 (mtpt) REVERT: A 138 LEU cc_start: 0.8397 (tp) cc_final: 0.7971 (tp) REVERT: A 180 ARG cc_start: 0.7870 (mmm160) cc_final: 0.7479 (mmm160) REVERT: A 186 ASN cc_start: 0.7091 (t0) cc_final: 0.6621 (t0) REVERT: A 242 ARG cc_start: 0.8030 (mtp180) cc_final: 0.7536 (mtp180) REVERT: A 282 ILE cc_start: 0.8174 (mt) cc_final: 0.7957 (mt) REVERT: A 288 PHE cc_start: 0.8024 (t80) cc_final: 0.7642 (t80) REVERT: A 294 PHE cc_start: 0.7960 (t80) cc_final: 0.7560 (t80) REVERT: A 299 ASP cc_start: 0.7391 (m-30) cc_final: 0.7119 (m-30) REVERT: B 64 ASN cc_start: 0.7601 (t0) cc_final: 0.7376 (t0) REVERT: B 159 GLU cc_start: 0.8401 (mm-30) cc_final: 0.8158 (mm-30) REVERT: B 176 HIS cc_start: 0.8493 (t-90) cc_final: 0.7894 (t-90) REVERT: B 207 GLN cc_start: 0.8382 (pm20) cc_final: 0.8076 (pm20) REVERT: B 210 ARG cc_start: 0.8344 (tpm170) cc_final: 0.7672 (tpm170) REVERT: B 246 ASN cc_start: 0.8271 (m110) cc_final: 0.8069 (m110) REVERT: B 248 MET cc_start: 0.8500 (mtm) cc_final: 0.8027 (mtm) REVERT: B 253 ASP cc_start: 0.8282 (m-30) cc_final: 0.7943 (m-30) REVERT: B 254 MET cc_start: 0.7941 (mpp) cc_final: 0.7418 (mpp) REVERT: B 261 ASN cc_start: 0.8553 (m110) cc_final: 0.7976 (p0) REVERT: B 263 ASP cc_start: 0.7537 (m-30) cc_final: 0.6150 (m-30) REVERT: B 288 PHE cc_start: 0.7262 (t80) cc_final: 0.6649 (t80) REVERT: B 295 LEU cc_start: 0.7955 (tp) cc_final: 0.6909 (tp) REVERT: B 298 CYS cc_start: 0.7671 (m) cc_final: 0.7053 (m) REVERT: B 299 ASP cc_start: 0.7860 (t70) cc_final: 0.7578 (t70) REVERT: B 303 ARG cc_start: 0.8042 (mtp180) cc_final: 0.7212 (mtp180) REVERT: B 309 PHE cc_start: 0.8622 (m-80) cc_final: 0.8091 (m-80) REVERT: B 310 TYR cc_start: 0.7517 (t80) cc_final: 0.7033 (t80) REVERT: B 312 ARG cc_start: 0.8180 (mtt90) cc_final: 0.7561 (mtt90) REVERT: B 314 PHE cc_start: 0.7901 (m-10) cc_final: 0.7337 (m-10) REVERT: C 46 ASP cc_start: 0.7566 (m-30) cc_final: 0.7340 (m-30) REVERT: C 68 MET cc_start: 0.6760 (mtp) cc_final: 0.6415 (mtp) REVERT: C 80 HIS cc_start: 0.8133 (m90) cc_final: 0.7706 (m90) REVERT: C 122 GLU cc_start: 0.7814 (tt0) cc_final: 0.7556 (tt0) REVERT: C 208 MET cc_start: 0.8230 (mtm) cc_final: 0.7906 (mtm) REVERT: C 211 TRP cc_start: 0.8281 (m100) cc_final: 0.7999 (m100) REVERT: C 223 ASP cc_start: 0.7518 (m-30) cc_final: 0.7287 (m-30) REVERT: C 295 LEU cc_start: 0.7484 (tp) cc_final: 0.6938 (tp) REVERT: C 300 GLU cc_start: 0.7974 (mm-30) cc_final: 0.7556 (mm-30) REVERT: C 301 LEU cc_start: 0.8491 (mt) cc_final: 0.7873 (mt) REVERT: C 303 ARG cc_start: 0.7902 (ttm170) cc_final: 0.6972 (ttm170) REVERT: C 311 GLN cc_start: 0.8400 (tm-30) cc_final: 0.7937 (tm-30) REVERT: D 29 MET cc_start: 0.6305 (tpt) cc_final: 0.5768 (tpt) REVERT: D 68 MET cc_start: 0.7782 (tpp) cc_final: 0.7134 (tpp) REVERT: D 72 TYR cc_start: 0.8241 (m-10) cc_final: 0.8017 (m-10) REVERT: D 103 ARG cc_start: 0.8453 (ttt-90) cc_final: 0.8198 (ttt-90) REVERT: D 144 ASP cc_start: 0.7574 (p0) cc_final: 0.7225 (p0) REVERT: D 151 MET cc_start: 0.7379 (ttt) cc_final: 0.6946 (ttt) REVERT: D 158 LEU cc_start: 0.8832 (mt) cc_final: 0.8476 (mt) REVERT: D 211 TRP cc_start: 0.8965 (m100) cc_final: 0.7408 (m100) REVERT: D 217 LEU cc_start: 0.7928 (tp) cc_final: 0.7639 (tt) REVERT: D 224 ASN cc_start: 0.8248 (m110) cc_final: 0.8028 (m110) REVERT: D 261 ASN cc_start: 0.8830 (m-40) cc_final: 0.8523 (m-40) REVERT: D 278 GLU cc_start: 0.8652 (mt-10) cc_final: 0.8423 (mt-10) REVERT: D 310 TYR cc_start: 0.8333 (t80) cc_final: 0.8012 (t80) REVERT: E 83 GLN cc_start: 0.7665 (tm-30) cc_final: 0.6787 (tm-30) REVERT: E 119 GLN cc_start: 0.7981 (mm110) cc_final: 0.7684 (mm110) REVERT: E 151 MET cc_start: 0.7875 (tpt) cc_final: 0.7442 (tpt) REVERT: E 169 GLN cc_start: 0.7949 (pm20) cc_final: 0.7662 (pm20) REVERT: E 275 THR cc_start: 0.8568 (m) cc_final: 0.8204 (m) REVERT: E 278 GLU cc_start: 0.8331 (tp30) cc_final: 0.8102 (tp30) REVERT: E 292 LEU cc_start: 0.8343 (mp) cc_final: 0.8134 (mp) REVERT: E 296 ASN cc_start: 0.8626 (m110) cc_final: 0.8301 (m-40) REVERT: E 300 GLU cc_start: 0.7963 (tm-30) cc_final: 0.7311 (tm-30) REVERT: E 317 GLU cc_start: 0.7769 (tt0) cc_final: 0.7468 (tt0) REVERT: F 29 MET cc_start: 0.7932 (mmp) cc_final: 0.7727 (mmp) REVERT: F 64 ASN cc_start: 0.8127 (t0) cc_final: 0.7894 (t0) REVERT: F 68 MET cc_start: 0.7369 (tmm) cc_final: 0.6911 (tmm) REVERT: F 88 LEU cc_start: 0.8742 (mt) cc_final: 0.8520 (mt) REVERT: F 135 ASN cc_start: 0.8135 (p0) cc_final: 0.7636 (p0) REVERT: F 143 TYR cc_start: 0.8426 (t80) cc_final: 0.7708 (t80) REVERT: F 151 MET cc_start: 0.7241 (mpp) cc_final: 0.6954 (mpp) REVERT: F 174 ARG cc_start: 0.8281 (mmp-170) cc_final: 0.8037 (mmp-170) REVERT: F 176 HIS cc_start: 0.8838 (t70) cc_final: 0.8622 (t70) REVERT: F 208 MET cc_start: 0.7049 (mpp) cc_final: 0.6700 (mpp) REVERT: F 219 TYR cc_start: 0.8476 (m-80) cc_final: 0.7780 (m-80) REVERT: F 220 LEU cc_start: 0.7971 (mm) cc_final: 0.7730 (mm) REVERT: F 224 ASN cc_start: 0.8825 (t0) cc_final: 0.8403 (t0) REVERT: F 225 GLU cc_start: 0.8294 (mt-10) cc_final: 0.7781 (mt-10) REVERT: F 247 LYS cc_start: 0.8082 (tttp) cc_final: 0.7403 (tttp) REVERT: F 248 MET cc_start: 0.8242 (mtm) cc_final: 0.7881 (mtm) REVERT: F 250 ARG cc_start: 0.7683 (ptt-90) cc_final: 0.7153 (ptt-90) REVERT: F 254 MET cc_start: 0.7449 (tmm) cc_final: 0.7153 (tmm) REVERT: F 265 SER cc_start: 0.8772 (t) cc_final: 0.8333 (t) REVERT: F 275 THR cc_start: 0.7420 (m) cc_final: 0.6978 (m) REVERT: F 279 ASN cc_start: 0.8516 (m-40) cc_final: 0.8035 (m-40) REVERT: F 303 ARG cc_start: 0.8333 (ttm170) cc_final: 0.7893 (ttm170) REVERT: F 309 PHE cc_start: 0.7807 (m-80) cc_final: 0.7582 (m-80) REVERT: G 369 LEU cc_start: 0.8947 (mt) cc_final: 0.8645 (mt) REVERT: G 399 THR cc_start: 0.8169 (p) cc_final: 0.7592 (p) REVERT: G 400 GLN cc_start: 0.8155 (mm-40) cc_final: 0.7891 (mm110) REVERT: G 406 GLN cc_start: 0.8086 (tm-30) cc_final: 0.7854 (tm-30) REVERT: G 544 ILE cc_start: 0.8899 (mp) cc_final: 0.8463 (mp) REVERT: G 618 LEU cc_start: 0.9305 (mt) cc_final: 0.9027 (mt) REVERT: a 25 PHE cc_start: 0.8125 (m-80) cc_final: 0.7536 (m-80) REVERT: a 113 GLN cc_start: 0.7845 (mp10) cc_final: 0.6935 (mp10) REVERT: a 131 LEU cc_start: 0.8536 (mt) cc_final: 0.7788 (mt) REVERT: a 134 MET cc_start: 0.7610 (ppp) cc_final: 0.6710 (ppp) REVERT: a 135 LEU cc_start: 0.8424 (mt) cc_final: 0.7748 (mt) REVERT: a 186 TRP cc_start: 0.7509 (t60) cc_final: 0.7240 (t60) REVERT: a 214 ASP cc_start: 0.8582 (m-30) cc_final: 0.8278 (m-30) REVERT: a 215 MET cc_start: 0.8417 (mtm) cc_final: 0.8138 (mtm) REVERT: N 432 MET cc_start: 0.8215 (mtp) cc_final: 0.7654 (mtp) REVERT: N 433 ARG cc_start: 0.8614 (mtm180) cc_final: 0.8099 (mtt90) REVERT: N 436 MET cc_start: 0.8495 (ttp) cc_final: 0.8208 (ttp) REVERT: N 536 TYR cc_start: 0.8005 (m-80) cc_final: 0.7781 (m-80) REVERT: N 572 TYR cc_start: 0.7565 (m-80) cc_final: 0.7266 (m-80) REVERT: N 586 PHE cc_start: 0.7442 (t80) cc_final: 0.6906 (t80) REVERT: N 650 ILE cc_start: 0.8082 (mm) cc_final: 0.7842 (mm) REVERT: N 677 LYS cc_start: 0.8508 (ptpp) cc_final: 0.8282 (mtmt) REVERT: N 688 MET cc_start: 0.7496 (ttm) cc_final: 0.7065 (ttm) REVERT: N 829 ASP cc_start: 0.6633 (m-30) cc_final: 0.6373 (m-30) REVERT: N 890 TYR cc_start: 0.8000 (t80) cc_final: 0.7618 (t80) REVERT: N 893 ASP cc_start: 0.8245 (m-30) cc_final: 0.8001 (m-30) REVERT: N 960 ILE cc_start: 0.8820 (pt) cc_final: 0.8322 (pt) REVERT: N 964 PHE cc_start: 0.8181 (t80) cc_final: 0.7658 (t80) REVERT: N 1072 ARG cc_start: 0.7438 (tmt170) cc_final: 0.7189 (tpt90) REVERT: N 1077 GLU cc_start: 0.8667 (tm-30) cc_final: 0.8401 (tm-30) REVERT: N 1207 HIS cc_start: 0.7406 (t-90) cc_final: 0.7120 (t-90) REVERT: N 1210 MET cc_start: 0.8608 (mtm) cc_final: 0.8316 (mtm) REVERT: N 1227 GLU cc_start: 0.7648 (tm-30) cc_final: 0.7080 (tp30) outliers start: 3 outliers final: 1 residues processed: 810 average time/residue: 0.1757 time to fit residues: 218.9577 Evaluate side-chains 787 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 786 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 259 optimal weight: 5.9990 chunk 296 optimal weight: 8.9990 chunk 129 optimal weight: 1.9990 chunk 318 optimal weight: 4.9990 chunk 56 optimal weight: 0.8980 chunk 62 optimal weight: 6.9990 chunk 10 optimal weight: 0.8980 chunk 256 optimal weight: 0.8980 chunk 99 optimal weight: 0.4980 chunk 249 optimal weight: 10.0000 chunk 250 optimal weight: 8.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 10 ASN B 100 HIS ** B 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 52 GLN ** E 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 96 ASN F 134 HIS F 155 GLN ** N 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 753 ASN N1042 ASN ** N1091 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N1163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N1214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N1239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.173787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.137275 restraints weight = 49934.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.142891 restraints weight = 30690.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.146926 restraints weight = 21124.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.149868 restraints weight = 15608.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.152064 restraints weight = 12220.439| |-----------------------------------------------------------------------------| r_work (final): 0.3978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6759 moved from start: 0.1933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 26361 Z= 0.137 Angle : 0.629 13.575 35849 Z= 0.316 Chirality : 0.044 0.289 4008 Planarity : 0.005 0.062 4718 Dihedral : 6.212 121.789 3718 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 13.90 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.99 % Favored : 93.98 % Rotamer: Outliers : 0.11 % Allowed : 0.33 % 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: -0.86 (0.15), residues: 3258 helix: 0.21 (0.14), residues: 1360 sheet: -0.81 (0.26), residues: 375 loop : -1.16 (0.17), residues: 1523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 210 TYR 0.028 0.001 TYR D 132 PHE 0.036 0.001 PHE E 294 TRP 0.046 0.002 TRP B 130 HIS 0.005 0.001 HIS F 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.14 (26361) covalent geometry : angle 0.62910 / 0.32 (35849) hydrogen bonds : bond 0.03305 / 2.22 ( 1037) hydrogen bonds : angle 5.39859 / 3.79 ( 2988) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6516 Ramachandran restraints generated. 3258 Oldfield, 0 Emsley, 3258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 822 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 819 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: A 138 LEU cc_start: 0.8321 (tp) cc_final: 0.7962 (tp) REVERT: A 186 ASN cc_start: 0.6934 (t0) cc_final: 0.6730 (t0) REVERT: A 242 ARG cc_start: 0.7981 (mtp180) cc_final: 0.7504 (mtp180) REVERT: A 282 ILE cc_start: 0.8155 (mt) cc_final: 0.7945 (mt) REVERT: A 288 PHE cc_start: 0.8030 (t80) cc_final: 0.7631 (t80) REVERT: A 299 ASP cc_start: 0.7335 (m-30) cc_final: 0.7070 (m-30) REVERT: B 65 ARG cc_start: 0.8324 (tpp80) cc_final: 0.7997 (tpp80) REVERT: B 159 GLU cc_start: 0.8377 (mm-30) cc_final: 0.8116 (mm-30) REVERT: B 176 HIS cc_start: 0.8446 (t-90) cc_final: 0.7858 (t-90) REVERT: B 207 GLN cc_start: 0.8356 (pm20) cc_final: 0.8049 (pm20) REVERT: B 210 ARG cc_start: 0.8338 (tpm170) cc_final: 0.7671 (tpm170) REVERT: B 248 MET cc_start: 0.8459 (mtm) cc_final: 0.8011 (mtm) REVERT: B 253 ASP cc_start: 0.8250 (m-30) cc_final: 0.7981 (m-30) REVERT: B 261 ASN cc_start: 0.8492 (m110) cc_final: 0.7928 (p0) REVERT: B 263 ASP cc_start: 0.7535 (m-30) cc_final: 0.6181 (m-30) REVERT: B 288 PHE cc_start: 0.7151 (t80) cc_final: 0.6611 (t80) REVERT: B 290 PHE cc_start: 0.6569 (t80) cc_final: 0.6357 (t80) REVERT: B 295 LEU cc_start: 0.7897 (tp) cc_final: 0.6785 (tp) REVERT: B 298 CYS cc_start: 0.7704 (m) cc_final: 0.7113 (m) REVERT: B 299 ASP cc_start: 0.7852 (t70) cc_final: 0.7583 (t70) REVERT: B 303 ARG cc_start: 0.8036 (mtp180) cc_final: 0.7183 (mtp180) REVERT: B 309 PHE cc_start: 0.8509 (m-80) cc_final: 0.8023 (m-80) REVERT: B 312 ARG cc_start: 0.8141 (mtt90) cc_final: 0.7530 (mtt90) REVERT: B 314 PHE cc_start: 0.7869 (m-10) cc_final: 0.7123 (m-80) REVERT: C 68 MET cc_start: 0.6731 (mtp) cc_final: 0.6402 (mtp) REVERT: C 80 HIS cc_start: 0.8024 (m90) cc_final: 0.7615 (m90) REVERT: C 122 GLU cc_start: 0.7814 (tt0) cc_final: 0.7541 (tt0) REVERT: C 208 MET cc_start: 0.8197 (mtm) cc_final: 0.7912 (mtm) REVERT: C 211 TRP cc_start: 0.8281 (m100) cc_final: 0.8012 (m100) REVERT: C 223 ASP cc_start: 0.7477 (m-30) cc_final: 0.7268 (m-30) REVERT: C 295 LEU cc_start: 0.7446 (tp) cc_final: 0.6842 (tp) REVERT: C 301 LEU cc_start: 0.8453 (mt) cc_final: 0.7824 (mt) REVERT: C 311 GLN cc_start: 0.8333 (tm-30) cc_final: 0.7882 (tm-30) REVERT: D 10 ASN cc_start: 0.7880 (t0) cc_final: 0.7678 (t0) REVERT: D 29 MET cc_start: 0.6250 (tpt) cc_final: 0.5710 (tpt) REVERT: D 68 MET cc_start: 0.7862 (tpp) cc_final: 0.7076 (tpp) REVERT: D 77 LYS cc_start: 0.7111 (mtpt) cc_final: 0.6893 (mtpt) REVERT: D 135 ASN cc_start: 0.7497 (p0) cc_final: 0.7033 (p0) REVERT: D 144 ASP cc_start: 0.7477 (p0) cc_final: 0.7141 (p0) REVERT: D 151 MET cc_start: 0.7394 (ttt) cc_final: 0.6975 (ttt) REVERT: D 211 TRP cc_start: 0.8919 (m100) cc_final: 0.8404 (m100) REVERT: D 217 LEU cc_start: 0.7939 (tp) cc_final: 0.7632 (tt) REVERT: D 254 MET cc_start: 0.7101 (mtp) cc_final: 0.6839 (mtp) REVERT: D 257 GLN cc_start: 0.7944 (mp10) cc_final: 0.7434 (mp10) REVERT: D 261 ASN cc_start: 0.8809 (m-40) cc_final: 0.8495 (m-40) REVERT: D 278 GLU cc_start: 0.8614 (mt-10) cc_final: 0.8375 (mt-10) REVERT: D 310 TYR cc_start: 0.8325 (t80) cc_final: 0.8026 (t80) REVERT: E 64 ASN cc_start: 0.8252 (t0) cc_final: 0.8040 (t0) REVERT: E 83 GLN cc_start: 0.7607 (tm-30) cc_final: 0.7074 (tm-30) REVERT: E 119 GLN cc_start: 0.7967 (mm110) cc_final: 0.7686 (mm110) REVERT: E 138 LEU cc_start: 0.8518 (tp) cc_final: 0.8310 (tp) REVERT: E 151 MET cc_start: 0.7857 (tpt) cc_final: 0.7424 (tpt) REVERT: E 275 THR cc_start: 0.8537 (m) cc_final: 0.8136 (m) REVERT: E 278 GLU cc_start: 0.8305 (tp30) cc_final: 0.8065 (tp30) REVERT: E 296 ASN cc_start: 0.8610 (m110) cc_final: 0.8343 (m-40) REVERT: E 300 GLU cc_start: 0.7911 (tm-30) cc_final: 0.7420 (tm-30) REVERT: E 317 GLU cc_start: 0.7766 (tt0) cc_final: 0.7473 (tt0) REVERT: F 64 ASN cc_start: 0.8125 (t0) cc_final: 0.7873 (t0) REVERT: F 68 MET cc_start: 0.7357 (tmm) cc_final: 0.6909 (tmm) REVERT: F 88 LEU cc_start: 0.8724 (mt) cc_final: 0.8508 (mt) REVERT: F 135 ASN cc_start: 0.8117 (p0) cc_final: 0.7625 (p0) REVERT: F 143 TYR cc_start: 0.8475 (t80) cc_final: 0.7843 (t80) REVERT: F 151 MET cc_start: 0.7215 (mpp) cc_final: 0.7000 (mpp) REVERT: F 174 ARG cc_start: 0.8272 (mmp-170) cc_final: 0.8045 (mmp-170) REVERT: F 208 MET cc_start: 0.6943 (mpp) cc_final: 0.6629 (mpp) REVERT: F 219 TYR cc_start: 0.8467 (m-80) cc_final: 0.7814 (m-80) REVERT: F 220 LEU cc_start: 0.7864 (mm) cc_final: 0.7564 (mm) REVERT: F 224 ASN cc_start: 0.8784 (t0) cc_final: 0.8380 (t0) REVERT: F 225 GLU cc_start: 0.8225 (mt-10) cc_final: 0.7712 (mt-10) REVERT: F 247 LYS cc_start: 0.8072 (tttp) cc_final: 0.7346 (tttp) REVERT: F 248 MET cc_start: 0.8182 (mtm) cc_final: 0.7836 (mtm) REVERT: F 250 ARG cc_start: 0.7641 (ptt-90) cc_final: 0.7157 (ptt-90) REVERT: F 253 ASP cc_start: 0.8745 (m-30) cc_final: 0.8461 (m-30) REVERT: F 254 MET cc_start: 0.7399 (tmm) cc_final: 0.7141 (tmm) REVERT: F 265 SER cc_start: 0.8761 (t) cc_final: 0.8304 (t) REVERT: F 275 THR cc_start: 0.7401 (m) cc_final: 0.6940 (m) REVERT: F 279 ASN cc_start: 0.8530 (m-40) cc_final: 0.7999 (m-40) REVERT: F 303 ARG cc_start: 0.8281 (ttm170) cc_final: 0.7789 (ttm170) REVERT: F 309 PHE cc_start: 0.7780 (m-80) cc_final: 0.7565 (m-80) REVERT: G 369 LEU cc_start: 0.8910 (mt) cc_final: 0.8632 (mt) REVERT: G 399 THR cc_start: 0.8172 (p) cc_final: 0.7618 (p) REVERT: G 400 GLN cc_start: 0.8110 (mm-40) cc_final: 0.7862 (mm110) REVERT: G 434 VAL cc_start: 0.8872 (t) cc_final: 0.8654 (t) REVERT: G 438 CYS cc_start: 0.9091 (m) cc_final: 0.8643 (m) REVERT: G 454 GLU cc_start: 0.6934 (tp30) cc_final: 0.6704 (tp30) REVERT: G 544 ILE cc_start: 0.8896 (mp) cc_final: 0.8441 (mp) REVERT: a 25 PHE cc_start: 0.8080 (m-80) cc_final: 0.7509 (m-80) REVERT: a 113 GLN cc_start: 0.7744 (mp10) cc_final: 0.6830 (mp10) REVERT: a 131 LEU cc_start: 0.8516 (mt) cc_final: 0.7765 (mt) REVERT: a 134 MET cc_start: 0.7582 (ppp) cc_final: 0.6696 (ppp) REVERT: a 135 LEU cc_start: 0.8419 (mt) cc_final: 0.7730 (mt) REVERT: a 186 TRP cc_start: 0.7422 (t60) cc_final: 0.7214 (t60) REVERT: a 214 ASP cc_start: 0.8562 (m-30) cc_final: 0.8272 (m-30) REVERT: a 215 MET cc_start: 0.8468 (mtm) cc_final: 0.8094 (mtm) REVERT: N 432 MET cc_start: 0.8214 (mtp) cc_final: 0.7653 (mtp) REVERT: N 433 ARG cc_start: 0.8609 (mtm180) cc_final: 0.8059 (mtt90) REVERT: N 436 MET cc_start: 0.8449 (ttp) cc_final: 0.8167 (ttp) REVERT: N 536 TYR cc_start: 0.7949 (m-80) cc_final: 0.7723 (m-80) REVERT: N 572 TYR cc_start: 0.7479 (m-80) cc_final: 0.7188 (m-80) REVERT: N 586 PHE cc_start: 0.7360 (t80) cc_final: 0.6870 (t80) REVERT: N 650 ILE cc_start: 0.8078 (mm) cc_final: 0.7833 (mm) REVERT: N 677 LYS cc_start: 0.8502 (ptpp) cc_final: 0.8110 (mtmm) REVERT: N 688 MET cc_start: 0.7441 (ttm) cc_final: 0.7003 (ttm) REVERT: N 816 LEU cc_start: 0.8120 (mt) cc_final: 0.7914 (mt) REVERT: N 829 ASP cc_start: 0.6595 (m-30) cc_final: 0.6332 (m-30) REVERT: N 890 TYR cc_start: 0.7957 (t80) cc_final: 0.7579 (t80) REVERT: N 893 ASP cc_start: 0.8209 (m-30) cc_final: 0.7965 (m-30) REVERT: N 960 ILE cc_start: 0.8784 (pt) cc_final: 0.8273 (pt) REVERT: N 964 PHE cc_start: 0.8118 (t80) cc_final: 0.7628 (t80) REVERT: N 992 ASN cc_start: 0.7534 (t0) cc_final: 0.7330 (t0) REVERT: N 1072 ARG cc_start: 0.7397 (tmt170) cc_final: 0.7150 (tpt90) REVERT: N 1077 GLU cc_start: 0.8678 (tm-30) cc_final: 0.8400 (tm-30) REVERT: N 1207 HIS cc_start: 0.7428 (t-90) cc_final: 0.7129 (t-90) REVERT: N 1210 MET cc_start: 0.8649 (mtm) cc_final: 0.8313 (mtm) REVERT: N 1227 GLU cc_start: 0.7617 (tm-30) cc_final: 0.7071 (tp30) REVERT: N 1234 TRP cc_start: 0.7976 (t-100) cc_final: 0.7716 (t-100) outliers start: 3 outliers final: 1 residues processed: 820 average time/residue: 0.1766 time to fit residues: 222.3323 Evaluate side-chains 796 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 795 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 167 optimal weight: 0.7980 chunk 223 optimal weight: 0.1980 chunk 143 optimal weight: 0.5980 chunk 48 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 118 optimal weight: 0.8980 chunk 155 optimal weight: 4.9990 chunk 262 optimal weight: 3.9990 chunk 43 optimal weight: 0.5980 chunk 74 optimal weight: 4.9990 chunk 255 optimal weight: 4.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 52 GLN A 73 HIS ** A 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 GLN B 100 HIS ** B 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 96 ASN ** E 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 279 ASN F 96 ASN F 134 HIS ** N 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N1042 ASN ** N1091 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N1163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N1226 ASN ** N1239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.179358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.144516 restraints weight = 50026.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.150157 restraints weight = 30327.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.154242 restraints weight = 20535.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.157200 restraints weight = 14931.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.159473 restraints weight = 11533.465| |-----------------------------------------------------------------------------| r_work (final): 0.4021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6700 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 26361 Z= 0.118 Angle : 0.604 13.496 35849 Z= 0.304 Chirality : 0.043 0.298 4008 Planarity : 0.005 0.106 4718 Dihedral : 6.034 119.464 3718 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.68 % Favored : 94.29 % Rotamer: Outliers : 0.15 % Allowed : 0.56 % 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: -0.73 (0.15), residues: 3258 helix: 0.30 (0.14), residues: 1350 sheet: -0.70 (0.26), residues: 372 loop : -1.08 (0.17), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 303 TYR 0.026 0.001 TYR D 132 PHE 0.028 0.001 PHE a 108 TRP 0.039 0.002 TRP B 130 HIS 0.007 0.001 HIS F 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (26361) covalent geometry : angle 0.60420 / 0.30 (35849) hydrogen bonds : bond 0.03062 / 2.05 ( 1037) hydrogen bonds : angle 5.23497 / 3.67 ( 2988) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5657.74 seconds wall clock time: 97 minutes 53.41 seconds (5873.41 seconds total)