Starting phenix.real_space_refine on Fri Mar 6 08:01:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vaq_31858/03_2026/7vaq_31858.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vaq_31858/03_2026/7vaq_31858.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7vaq_31858/03_2026/7vaq_31858.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vaq_31858/03_2026/7vaq_31858.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7vaq_31858/03_2026/7vaq_31858.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vaq_31858/03_2026/7vaq_31858.map" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 9 5.49 5 Mg 2 5.21 5 S 103 5.16 5 C 18735 2.51 5 N 5131 2.21 5 O 5578 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29558 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 4475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4475 Classifications: {'peptide': 578} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 542} Chain: "B" Number of atoms: 4475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4475 Classifications: {'peptide': 578} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 542} Chain: "C" Number of atoms: 4475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4475 Classifications: {'peptide': 578} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 542} Chain: "D" Number of atoms: 3682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3682 Classifications: {'peptide': 470} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 442} Chain: "E" Number of atoms: 3668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3668 Classifications: {'peptide': 468} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 441} Chain: "F" Number of atoms: 3694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3694 Classifications: {'peptide': 471} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 444} Chain: "G" Number of atoms: 1619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1619 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 9, 'TRANS': 196} Chain: "H" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 792 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "I" Number of atoms: 313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 313 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "J" Number of atoms: 976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 976 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 7, 'TRANS': 119} Chain: "K" Number of atoms: 313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 313 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "L" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 980 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.31, per 1000 atoms: 0.21 Number of scatterers: 29558 At special positions: 0 Unit cell: (136.4, 147.84, 173.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 103 16.00 P 9 15.00 Mg 2 11.99 O 5578 8.00 N 5131 7.00 C 18735 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: 2.49 Conformation dependent library (CDL) restraints added in 1.6 seconds 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6918 Finding SS restraints... Secondary structure from input PDB file: 131 helices and 27 sheets defined 45.2% alpha, 10.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.00 Creating SS restraints... Processing helix chain 'A' and resid 90 through 99 Processing helix chain 'A' and resid 209 through 215 Processing helix chain 'A' and resid 233 through 244 Processing helix chain 'A' and resid 258 through 269 removed outlier: 3.794A pdb=" N VAL A 265 " --> pdb=" O GLU A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 272 No H-bonds generated for 'chain 'A' and resid 270 through 272' Processing helix chain 'A' and resid 280 through 283 Processing helix chain 'A' and resid 295 through 316 removed outlier: 4.479A pdb=" N ILE A 303 " --> pdb=" O ARG A 299 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N TYR A 304 " --> pdb=" O GLU A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 342 removed outlier: 3.603A pdb=" N ALA A 333 " --> pdb=" O ARG A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 363 Processing helix chain 'A' and resid 386 through 390 Processing helix chain 'A' and resid 393 through 401 removed outlier: 3.613A pdb=" N ARG A 401 " --> pdb=" O GLN A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 416 Processing helix chain 'A' and resid 435 through 443 Processing helix chain 'A' and resid 446 through 472 removed outlier: 4.012A pdb=" N GLU A 466 " --> pdb=" O ALA A 462 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ILE A 467 " --> pdb=" O GLY A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 476 Processing helix chain 'A' and resid 477 through 494 Processing helix chain 'A' and resid 508 through 531 Processing helix chain 'A' and resid 543 through 550 removed outlier: 3.918A pdb=" N ARG A 547 " --> pdb=" O PRO A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 554 Processing helix chain 'A' and resid 558 through 578 removed outlier: 3.809A pdb=" N GLU A 564 " --> pdb=" O PRO A 560 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N PHE A 574 " --> pdb=" O ILE A 570 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS A 575 " --> pdb=" O GLN A 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 99 Processing helix chain 'B' and resid 209 through 215 Processing helix chain 'B' and resid 233 through 245 removed outlier: 3.518A pdb=" N SER B 245 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 272 Proline residue: B 270 - end of helix Processing helix chain 'B' and resid 280 through 283 Processing helix chain 'B' and resid 295 through 316 removed outlier: 4.663A pdb=" N ILE B 303 " --> pdb=" O ARG B 299 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N TYR B 304 " --> pdb=" O GLU B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 341 removed outlier: 3.660A pdb=" N TRP B 330 " --> pdb=" O SER B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 364 removed outlier: 3.851A pdb=" N ARG B 364 " --> pdb=" O ALA B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 401 Processing helix chain 'B' and resid 410 through 416 removed outlier: 4.027A pdb=" N ALA B 414 " --> pdb=" O ASP B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 443 Proline residue: B 437 - end of helix Processing helix chain 'B' and resid 446 through 463 Processing helix chain 'B' and resid 464 through 471 removed outlier: 3.749A pdb=" N VAL B 468 " --> pdb=" O LEU B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 494 Processing helix chain 'B' and resid 508 through 532 removed outlier: 3.591A pdb=" N ALA B 512 " --> pdb=" O SER B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 535 through 541 removed outlier: 4.052A pdb=" N GLN B 541 " --> pdb=" O ASP B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 542 through 550 removed outlier: 4.001A pdb=" N GLU B 546 " --> pdb=" O LEU B 542 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 577 removed outlier: 3.716A pdb=" N PHE B 574 " --> pdb=" O ILE B 570 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N LYS B 575 " --> pdb=" O GLN B 571 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 99 Processing helix chain 'C' and resid 209 through 215 Processing helix chain 'C' and resid 233 through 244 Processing helix chain 'C' and resid 258 through 269 removed outlier: 4.006A pdb=" N MET C 262 " --> pdb=" O ARG C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 272 No H-bonds generated for 'chain 'C' and resid 270 through 272' Processing helix chain 'C' and resid 280 through 283 Processing helix chain 'C' and resid 297 through 316 removed outlier: 4.136A pdb=" N ALA C 301 " --> pdb=" O ALA C 297 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N TYR C 304 " --> pdb=" O GLU C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 341 removed outlier: 4.099A pdb=" N TRP C 330 " --> pdb=" O SER C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 363 Processing helix chain 'C' and resid 386 through 390 Processing helix chain 'C' and resid 393 through 401 removed outlier: 3.798A pdb=" N ARG C 401 " --> pdb=" O GLN C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 410 through 416 Processing helix chain 'C' and resid 432 through 434 No H-bonds generated for 'chain 'C' and resid 432 through 434' Processing helix chain 'C' and resid 435 through 443 Processing helix chain 'C' and resid 446 through 469 removed outlier: 3.764A pdb=" N GLU C 466 " --> pdb=" O ALA C 462 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ILE C 467 " --> pdb=" O GLY C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 477 through 494 Processing helix chain 'C' and resid 508 through 532 Processing helix chain 'C' and resid 535 through 541 removed outlier: 3.656A pdb=" N ILE C 539 " --> pdb=" O SER C 535 " (cutoff:3.500A) Processing helix chain 'C' and resid 543 through 550 removed outlier: 3.715A pdb=" N ARG C 547 " --> pdb=" O PRO C 543 " (cutoff:3.500A) Processing helix chain 'C' and resid 558 through 574 removed outlier: 4.000A pdb=" N PHE C 574 " --> pdb=" O ILE C 570 " (cutoff:3.500A) Processing helix chain 'C' and resid 575 through 578 Processing helix chain 'D' and resid 120 through 124 Processing helix chain 'D' and resid 135 through 142 Processing helix chain 'D' and resid 159 through 171 removed outlier: 3.782A pdb=" N ILE D 163 " --> pdb=" O PRO D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 179 Processing helix chain 'D' and resid 197 through 212 removed outlier: 3.959A pdb=" N THR D 211 " --> pdb=" O GLU D 207 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLY D 212 " --> pdb=" O PHE D 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 213 through 215 No H-bonds generated for 'chain 'D' and resid 213 through 215' Processing helix chain 'D' and resid 227 through 250 Proline residue: D 235 - end of helix Processing helix chain 'D' and resid 259 through 274 Processing helix chain 'D' and resid 279 through 283 Processing helix chain 'D' and resid 284 through 285 No H-bonds generated for 'chain 'D' and resid 284 through 285' Processing helix chain 'D' and resid 286 through 296 removed outlier: 3.565A pdb=" N ILE D 294 " --> pdb=" O ASP D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 333 Processing helix chain 'D' and resid 340 through 346 Processing helix chain 'D' and resid 374 through 400 removed outlier: 3.867A pdb=" N ASP D 391 " --> pdb=" O ALA D 387 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ILE D 392 " --> pdb=" O ASN D 388 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ALA D 397 " --> pdb=" O ARG D 393 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ILE D 398 " --> pdb=" O LYS D 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 422 removed outlier: 3.532A pdb=" N ARG D 409 " --> pdb=" O THR D 405 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ARG D 410 " --> pdb=" O GLU D 406 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 444 Processing helix chain 'D' and resid 455 through 463 Processing helix chain 'E' and resid 85 through 89 Processing helix chain 'E' and resid 120 through 124 Processing helix chain 'E' and resid 135 through 140 Processing helix chain 'E' and resid 159 through 171 Processing helix chain 'E' and resid 197 through 212 Processing helix chain 'E' and resid 213 through 215 No H-bonds generated for 'chain 'E' and resid 213 through 215' Processing helix chain 'E' and resid 228 through 231 Processing helix chain 'E' and resid 232 through 250 removed outlier: 4.517A pdb=" N ARG E 236 " --> pdb=" O ILE E 232 " (cutoff:3.500A) Processing helix chain 'E' and resid 259 through 275 removed outlier: 3.745A pdb=" N TYR E 263 " --> pdb=" O ASP E 259 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 296 removed outlier: 3.564A pdb=" N ILE E 294 " --> pdb=" O ASP E 290 " (cutoff:3.500A) Processing helix chain 'E' and resid 317 through 320 Processing helix chain 'E' and resid 323 through 331 Processing helix chain 'E' and resid 340 through 346 Processing helix chain 'E' and resid 374 through 400 removed outlier: 4.348A pdb=" N ILE E 398 " --> pdb=" O LYS E 394 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE E 399 " --> pdb=" O LEU E 395 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 422 Processing helix chain 'E' and resid 431 through 444 Processing helix chain 'E' and resid 455 through 463 Processing helix chain 'E' and resid 466 through 470 removed outlier: 4.135A pdb=" N GLU E 469 " --> pdb=" O LYS E 466 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE E 470 " --> pdb=" O LEU E 467 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 466 through 470' Processing helix chain 'F' and resid 85 through 89 removed outlier: 3.820A pdb=" N MET F 88 " --> pdb=" O SER F 85 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LEU F 89 " --> pdb=" O LYS F 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 85 through 89' Processing helix chain 'F' and resid 135 through 140 Processing helix chain 'F' and resid 159 through 171 Processing helix chain 'F' and resid 174 through 179 Processing helix chain 'F' and resid 197 through 212 Processing helix chain 'F' and resid 213 through 215 No H-bonds generated for 'chain 'F' and resid 213 through 215' Processing helix chain 'F' and resid 229 through 232 Processing helix chain 'F' and resid 233 through 250 Processing helix chain 'F' and resid 259 through 274 removed outlier: 4.122A pdb=" N TYR F 263 " --> pdb=" O ASP F 259 " (cutoff:3.500A) Processing helix chain 'F' and resid 286 through 296 Processing helix chain 'F' and resid 317 through 320 Processing helix chain 'F' and resid 323 through 333 Processing helix chain 'F' and resid 340 through 346 removed outlier: 3.596A pdb=" N LYS F 346 " --> pdb=" O GLU F 342 " (cutoff:3.500A) Processing helix chain 'F' and resid 361 through 366 removed outlier: 4.032A pdb=" N GLY F 365 " --> pdb=" O LEU F 361 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL F 366 " --> pdb=" O MET F 362 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 361 through 366' Processing helix chain 'F' and resid 374 through 400 removed outlier: 3.737A pdb=" N ILE F 398 " --> pdb=" O LYS F 394 " (cutoff:3.500A) Processing helix chain 'F' and resid 405 through 422 Processing helix chain 'F' and resid 431 through 444 Processing helix chain 'F' and resid 455 through 463 Processing helix chain 'G' and resid 7 through 71 removed outlier: 3.699A pdb=" N GLU G 48 " --> pdb=" O ARG G 44 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA G 67 " --> pdb=" O ALA G 63 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLN G 68 " --> pdb=" O LEU G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 125 through 207 removed outlier: 5.060A pdb=" N ILE G 169 " --> pdb=" O GLU G 165 " (cutoff:3.500A) Proline residue: G 170 - end of helix Processing helix chain 'H' and resid 8 through 15 removed outlier: 4.211A pdb=" N GLY H 12 " --> pdb=" O GLU H 8 " (cutoff:3.500A) Processing helix chain 'H' and resid 25 through 38 Processing helix chain 'H' and resid 85 through 99 Processing helix chain 'I' and resid 82 through 104 removed outlier: 3.886A pdb=" N ARG I 100 " --> pdb=" O ALA I 96 " (cutoff:3.500A) Processing helix chain 'I' and resid 106 through 119 removed outlier: 3.562A pdb=" N GLU I 117 " --> pdb=" O LEU I 113 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU I 119 " --> pdb=" O LEU I 115 " (cutoff:3.500A) Processing helix chain 'J' and resid 62 through 93 Processing helix chain 'J' and resid 99 through 115 removed outlier: 3.869A pdb=" N VAL J 103 " --> pdb=" O GLU J 99 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ARG J 105 " --> pdb=" O PRO J 101 " (cutoff:3.500A) Processing helix chain 'J' and resid 124 through 126 No H-bonds generated for 'chain 'J' and resid 124 through 126' Processing helix chain 'J' and resid 127 through 139 removed outlier: 4.813A pdb=" N ALA J 133 " --> pdb=" O PRO J 129 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ARG J 136 " --> pdb=" O GLU J 132 " (cutoff:3.500A) Processing helix chain 'J' and resid 146 through 149 removed outlier: 3.696A pdb=" N ARG J 149 " --> pdb=" O PRO J 146 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 146 through 149' Processing helix chain 'J' and resid 166 through 187 removed outlier: 5.397A pdb=" N ASP J 176 " --> pdb=" O ASP J 172 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N ALA J 177 " --> pdb=" O ARG J 173 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N GLN J 184 " --> pdb=" O SER J 180 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ALA J 185 " --> pdb=" O LYS J 181 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 105 removed outlier: 3.819A pdb=" N ALA K 105 " --> pdb=" O GLU K 101 " (cutoff:3.500A) Processing helix chain 'K' and resid 106 through 119 Processing helix chain 'L' and resid 62 through 94 removed outlier: 3.624A pdb=" N VAL L 68 " --> pdb=" O GLY L 64 " (cutoff:3.500A) Processing helix chain 'L' and resid 99 through 115 removed outlier: 4.062A pdb=" N ARG L 105 " --> pdb=" O PRO L 101 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N LYS L 106 " --> pdb=" O GLU L 102 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU L 115 " --> pdb=" O ALA L 111 " (cutoff:3.500A) Processing helix chain 'L' and resid 127 through 139 removed outlier: 4.782A pdb=" N ALA L 133 " --> pdb=" O PRO L 129 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N LEU L 134 " --> pdb=" O HIS L 130 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLU L 137 " --> pdb=" O ALA L 133 " (cutoff:3.500A) Processing helix chain 'L' and resid 167 through 187 removed outlier: 4.280A pdb=" N ASP L 176 " --> pdb=" O ASP L 172 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N ALA L 177 " --> pdb=" O ARG L 173 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N SER L 180 " --> pdb=" O ASP L 176 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N LYS L 181 " --> pdb=" O ALA L 177 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 10 removed outlier: 6.671A pdb=" N ILE A 15 " --> pdb=" O GLN A 7 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N ILE A 9 " --> pdb=" O ALA A 13 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N ALA A 13 " --> pdb=" O ILE A 9 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 13 through 17 current: chain 'A' and resid 35 through 43 removed outlier: 5.449A pdb=" N ILE A 39 " --> pdb=" O GLN A 50 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N GLN A 50 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG A 41 " --> pdb=" O PHE A 48 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 46 through 51 current: chain 'B' and resid 13 through 17 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 13 through 17 current: chain 'B' and resid 35 through 43 removed outlier: 6.666A pdb=" N PHE B 48 " --> pdb=" O ILE B 40 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N LEU B 42 " --> pdb=" O THR B 46 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N THR B 46 " --> pdb=" O LEU B 42 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 46 through 51 current: chain 'C' and resid 13 through 17 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 13 through 17 current: chain 'C' and resid 35 through 43 removed outlier: 5.652A pdb=" N ILE C 39 " --> pdb=" O GLN C 50 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N GLN C 50 " --> pdb=" O ILE C 39 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ARG C 41 " --> pdb=" O PHE C 48 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 46 through 51 current: chain 'D' and resid 18 through 22 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 18 through 22 current: chain 'D' and resid 42 through 51 removed outlier: 5.703A pdb=" N VAL D 47 " --> pdb=" O GLN D 58 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N GLN D 58 " --> pdb=" O VAL D 47 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N TYR D 54 " --> pdb=" O SER D 51 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 54 through 59 current: chain 'E' and resid 18 through 21 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 18 through 21 current: chain 'E' and resid 42 through 51 removed outlier: 5.513A pdb=" N VAL E 47 " --> pdb=" O GLN E 58 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N GLN E 58 " --> pdb=" O VAL E 47 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 55 through 59 current: chain 'F' and resid 18 through 21 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 18 through 21 current: chain 'F' and resid 42 through 51 removed outlier: 5.586A pdb=" N VAL F 47 " --> pdb=" O GLN F 58 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N GLN F 58 " --> pdb=" O VAL F 47 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 55 through 59 current: chain 'J' and resid 143 through 144 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 143 through 144 current: chain 'J' and resid 161 through 164 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 161 through 164 current: chain 'L' and resid 143 through 144 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 143 through 144 current: chain 'L' and resid 161 through 166 Processing sheet with id=AA2, first strand: chain 'A' and resid 72 through 75 Processing sheet with id=AA3, first strand: chain 'A' and resid 82 through 84 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 82 through 84 current: chain 'A' and resid 285 through 291 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 285 through 291 current: chain 'A' and resid 375 through 382 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 375 through 382 current: chain 'A' and resid 428 through 429 No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 117 through 118 Processing sheet with id=AA5, first strand: chain 'A' and resid 120 through 121 removed outlier: 3.855A pdb=" N GLY A 136 " --> pdb=" O ILE A 147 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 128 through 129 removed outlier: 3.662A pdb=" N GLY A 155 " --> pdb=" O VAL A 129 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N VAL A 174 " --> pdb=" O LYS A 158 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL A 173 " --> pdb=" O LEU A 181 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 72 through 75 Processing sheet with id=AA8, first strand: chain 'B' and resid 82 through 84 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 82 through 84 current: chain 'B' and resid 285 through 288 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 285 through 288 current: chain 'B' and resid 375 through 383 No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 143 through 148 removed outlier: 6.513A pdb=" N PHE B 143 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N HIS B 145 " --> pdb=" O THR B 137 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N THR B 137 " --> pdb=" O HIS B 145 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ILE B 147 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N ALA B 118 " --> pdb=" O PRO B 139 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 128 through 129 Processing sheet with id=AB2, first strand: chain 'B' and resid 405 through 406 Processing sheet with id=AB3, first strand: chain 'C' and resid 72 through 75 Processing sheet with id=AB4, first strand: chain 'C' and resid 82 through 84 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 82 through 84 current: chain 'C' and resid 285 through 290 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 285 through 290 current: chain 'C' and resid 375 through 384 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 375 through 384 current: chain 'C' and resid 428 through 429 No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'C' and resid 143 through 148 removed outlier: 3.897A pdb=" N GLY C 136 " --> pdb=" O ILE C 147 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N ALA C 118 " --> pdb=" O PRO C 139 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 128 through 129 removed outlier: 6.808A pdb=" N VAL C 174 " --> pdb=" O LYS C 158 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 81 through 84 removed outlier: 3.589A pdb=" N LYS D 110 " --> pdb=" O VAL D 84 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 92 through 93 removed outlier: 5.829A pdb=" N PHE D 93 " --> pdb=" O LEU D 221 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N LYS D 223 " --> pdb=" O PHE D 93 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N MET D 194 " --> pdb=" O THR D 258 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU D 257 " --> pdb=" O ILE D 311 " (cutoff:3.500A) removed outlier: 9.869A pdb=" N GLN D 336 " --> pdb=" O LEU D 355 " (cutoff:3.500A) removed outlier: 8.969A pdb=" N LEU D 355 " --> pdb=" O GLN D 336 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N GLN D 338 " --> pdb=" O ASP D 353 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 130 through 131 removed outlier: 4.789A pdb=" N LEU D 144 " --> pdb=" O ILE D 131 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 81 through 84 removed outlier: 3.689A pdb=" N LYS E 110 " --> pdb=" O VAL E 84 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 92 through 93 removed outlier: 3.701A pdb=" N LEU E 257 " --> pdb=" O ILE E 311 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 81 through 84 Processing sheet with id=AC4, first strand: chain 'F' and resid 92 through 93 removed outlier: 6.360A pdb=" N VAL F 189 " --> pdb=" O VAL F 218 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N PHE F 220 " --> pdb=" O VAL F 189 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N PHE F 191 " --> pdb=" O PHE F 220 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 144 through 145 removed outlier: 4.719A pdb=" N LEU F 144 " --> pdb=" O ILE F 131 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 313 through 315 Processing sheet with id=AC7, first strand: chain 'F' and resid 278 through 280 removed outlier: 6.342A pdb=" N TYR F 283 " --> pdb=" O GLY F 279 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 91 through 95 removed outlier: 3.533A pdb=" N ARG G 103 " --> pdb=" O GLU G 92 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 19 through 22 removed outlier: 6.207A pdb=" N VAL H 45 " --> pdb=" O LEU H 72 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N ILE H 74 " --> pdb=" O VAL H 45 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N VAL H 47 " --> pdb=" O ILE H 74 " (cutoff:3.500A) 1276 hydrogen bonds defined for protein. 3678 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: 5.55 Time building geometry restraints manager: 3.27 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: 9938 1.34 - 1.46: 3563 1.46 - 1.57: 16406 1.57 - 1.69: 13 1.69 - 1.81: 194 Bond restraints: 30114 Sorted by residual: bond pdb=" O3 PO4 A 603 " pdb=" P PO4 A 603 " ideal model delta sigma weight residual 1.569 1.500 0.069 2.00e-02 2.50e+03 1.19e+01 bond pdb=" O4 PO4 A 603 " pdb=" P PO4 A 603 " ideal model delta sigma weight residual 1.568 1.500 0.068 2.00e-02 2.50e+03 1.17e+01 bond pdb=" O1 PO4 A 603 " pdb=" P PO4 A 603 " ideal model delta sigma weight residual 1.565 1.498 0.067 2.00e-02 2.50e+03 1.12e+01 bond pdb=" O2 PO4 A 603 " pdb=" P PO4 A 603 " ideal model delta sigma weight residual 1.567 1.508 0.059 2.00e-02 2.50e+03 8.64e+00 bond pdb=" C TRP J 100 " pdb=" N PRO J 101 " ideal model delta sigma weight residual 1.334 1.367 -0.033 2.34e-02 1.83e+03 2.00e+00 ... (remaining 30109 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.12: 40430 2.12 - 4.24: 338 4.24 - 6.36: 42 6.36 - 8.48: 2 8.48 - 10.60: 1 Bond angle restraints: 40813 Sorted by residual: angle pdb=" C VAL B 214 " pdb=" N LEU B 215 " pdb=" CA LEU B 215 " ideal model delta sigma weight residual 122.53 116.24 6.29 1.92e+00 2.71e-01 1.07e+01 angle pdb=" CA LEU L 150 " pdb=" CB LEU L 150 " pdb=" CG LEU L 150 " ideal model delta sigma weight residual 116.30 126.90 -10.60 3.50e+00 8.16e-02 9.17e+00 angle pdb=" C GLN G 166 " pdb=" N VAL G 167 " pdb=" CA VAL G 167 " ideal model delta sigma weight residual 121.85 118.33 3.52 1.19e+00 7.06e-01 8.75e+00 angle pdb=" C ASP C 213 " pdb=" N VAL C 214 " pdb=" CA VAL C 214 " ideal model delta sigma weight residual 122.97 120.18 2.79 9.80e-01 1.04e+00 8.12e+00 angle pdb=" C ILE A 536 " pdb=" N ASP A 537 " pdb=" CA ASP A 537 " ideal model delta sigma weight residual 125.66 130.40 -4.74 1.85e+00 2.92e-01 6.57e+00 ... (remaining 40808 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.65: 17198 21.65 - 43.30: 1016 43.30 - 64.95: 113 64.95 - 86.61: 51 86.61 - 108.26: 5 Dihedral angle restraints: 18383 sinusoidal: 7561 harmonic: 10822 Sorted by residual: dihedral pdb=" C5' ADP A 601 " pdb=" O5' ADP A 601 " pdb=" PA ADP A 601 " pdb=" O2A ADP A 601 " ideal model delta sinusoidal sigma weight residual -60.00 48.26 -108.26 1 2.00e+01 2.50e-03 3.15e+01 dihedral pdb=" O1B ADP A 601 " pdb=" O3A ADP A 601 " pdb=" PB ADP A 601 " pdb=" PA ADP A 601 " ideal model delta sinusoidal sigma weight residual -60.00 -143.31 83.31 1 2.00e+01 2.50e-03 2.12e+01 dihedral pdb=" CA ARG D 372 " pdb=" C ARG D 372 " pdb=" N GLU D 373 " pdb=" CA GLU D 373 " ideal model delta harmonic sigma weight residual -180.00 -160.46 -19.54 0 5.00e+00 4.00e-02 1.53e+01 ... (remaining 18380 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 3820 0.055 - 0.111: 672 0.111 - 0.166: 77 0.166 - 0.222: 1 0.222 - 0.277: 2 Chirality restraints: 4572 Sorted by residual: chirality pdb=" CB ILE A 226 " pdb=" CA ILE A 226 " pdb=" CG1 ILE A 226 " pdb=" CG2 ILE A 226 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" CB ILE B 211 " pdb=" CA ILE B 211 " pdb=" CG1 ILE B 211 " pdb=" CG2 ILE B 211 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.71e+00 chirality pdb=" C2' ADP A 601 " pdb=" C1' ADP A 601 " pdb=" C3' ADP A 601 " pdb=" O2' ADP A 601 " both_signs ideal model delta sigma weight residual False -2.51 -2.69 0.18 2.00e-01 2.50e+01 8.12e-01 ... (remaining 4569 not shown) Planarity restraints: 5333 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS E 323 " 0.029 5.00e-02 4.00e+02 4.42e-02 3.13e+00 pdb=" N PRO E 324 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO E 324 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO E 324 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 228 " -0.028 5.00e-02 4.00e+02 4.27e-02 2.91e+00 pdb=" N PRO B 229 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO B 229 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 229 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS F 323 " -0.026 5.00e-02 4.00e+02 4.01e-02 2.57e+00 pdb=" N PRO F 324 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO F 324 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO F 324 " -0.022 5.00e-02 4.00e+02 ... (remaining 5330 not shown) Histogram of nonbonded interaction distances: 1.07 - 1.83: 1 1.83 - 2.60: 273 2.60 - 3.37: 37914 3.37 - 4.13: 68999 4.13 - 4.90: 130703 Nonbonded interactions: 237890 Sorted by model distance: nonbonded pdb=" OG SER A 235 " pdb="MG MG A 602 " model vdw 1.066 2.170 nonbonded pdb=" OG SER C 235 " pdb="MG MG C 601 " model vdw 1.957 2.170 nonbonded pdb=" OE2 GLU C 261 " pdb="MG MG C 601 " model vdw 2.076 2.170 nonbonded pdb=" O MET A 220 " pdb=" OG1 THR A 379 " model vdw 2.130 3.040 nonbonded pdb=" O MET C 220 " pdb=" OG1 THR C 379 " model vdw 2.182 3.040 ... (remaining 237885 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 1 through 578) selection = (chain 'B' and resid 1 through 578) selection = (chain 'C' and resid 1 through 578) } ncs_group { reference = (chain 'D' and resid 5 through 470) selection = (chain 'E' and resid 5 through 470) selection = (chain 'F' and resid 5 through 470) } ncs_group { reference = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'J' selection = (chain 'L' and resid 61 through 187) } 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: 2.390 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: 0.530 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 26.270 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: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 30114 Z= 0.136 Angle : 0.529 10.599 40813 Z= 0.287 Chirality : 0.042 0.277 4572 Planarity : 0.004 0.044 5333 Dihedral : 13.776 108.257 11465 Min Nonbonded Distance : 1.066 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 0.00 % Allowed : 0.06 % Favored : 99.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.14), residues: 3764 helix: 1.73 (0.14), residues: 1554 sheet: 0.01 (0.22), residues: 596 loop : 0.21 (0.16), residues: 1614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 154 TYR 0.013 0.001 TYR D 331 PHE 0.021 0.001 PHE C 269 TRP 0.010 0.001 TRP A 330 HIS 0.003 0.001 HIS A 185 Details of bonding type rmsd covalent geometry : bond 0.00286 (30114) covalent geometry : angle 0.52884 (40813) hydrogen bonds : bond 0.15837 ( 1276) hydrogen bonds : angle 6.05326 ( 3678) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 649 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 649 time to evaluate : 1.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 ASP cc_start: 0.7709 (m-30) cc_final: 0.7456 (m-30) REVERT: A 158 LYS cc_start: 0.7391 (ttmt) cc_final: 0.7095 (tmtt) REVERT: A 159 GLU cc_start: 0.6364 (pt0) cc_final: 0.6157 (pt0) REVERT: A 166 TYR cc_start: 0.7875 (m-80) cc_final: 0.7486 (m-80) REVERT: A 179 THR cc_start: 0.7312 (m) cc_final: 0.6877 (t) REVERT: A 282 MET cc_start: 0.8303 (mmm) cc_final: 0.8087 (tpp) REVERT: A 304 TYR cc_start: 0.7936 (m-80) cc_final: 0.7596 (m-80) REVERT: A 329 ARG cc_start: 0.6071 (mtm-85) cc_final: 0.5830 (mmp80) REVERT: A 363 GLU cc_start: 0.7533 (mm-30) cc_final: 0.7260 (mt-10) REVERT: A 481 ARG cc_start: 0.7415 (mmm-85) cc_final: 0.6826 (ttm-80) REVERT: A 483 VAL cc_start: 0.8286 (t) cc_final: 0.8077 (t) REVERT: A 498 ASN cc_start: 0.7084 (t0) cc_final: 0.6489 (m-40) REVERT: A 524 LYS cc_start: 0.6077 (ttmt) cc_final: 0.5759 (mtmm) REVERT: B 25 TYR cc_start: 0.7857 (m-80) cc_final: 0.7373 (m-10) REVERT: B 93 ARG cc_start: 0.7908 (mmp80) cc_final: 0.7242 (mmm160) REVERT: B 244 TRP cc_start: 0.7223 (m100) cc_final: 0.6954 (m100) REVERT: B 293 ASN cc_start: 0.7795 (p0) cc_final: 0.6928 (t0) REVERT: B 370 THR cc_start: 0.7036 (p) cc_final: 0.6738 (p) REVERT: B 374 GLU cc_start: 0.6044 (mt-10) cc_final: 0.5821 (pm20) REVERT: B 396 THR cc_start: 0.8467 (m) cc_final: 0.7946 (p) REVERT: B 496 GLN cc_start: 0.4402 (tt0) cc_final: 0.3896 (tp40) REVERT: B 504 ASP cc_start: 0.4258 (t0) cc_final: 0.3769 (t0) REVERT: C 1 MET cc_start: 0.7047 (ptt) cc_final: 0.6826 (mtm) REVERT: C 84 TYR cc_start: 0.8347 (m-80) cc_final: 0.7914 (m-80) REVERT: C 123 VAL cc_start: 0.8198 (m) cc_final: 0.7988 (p) REVERT: C 124 LYS cc_start: 0.7545 (ptpp) cc_final: 0.6787 (ttmm) REVERT: C 191 ARG cc_start: 0.7724 (mmm-85) cc_final: 0.7213 (mtm-85) REVERT: C 202 ASN cc_start: 0.7546 (p0) cc_final: 0.7000 (t0) REVERT: C 220 MET cc_start: 0.6781 (mmt) cc_final: 0.6369 (ttp) REVERT: C 264 ASP cc_start: 0.7821 (m-30) cc_final: 0.7612 (m-30) REVERT: C 343 GLU cc_start: 0.7242 (mt-10) cc_final: 0.7033 (mm-30) REVERT: C 524 LYS cc_start: 0.7872 (ttmt) cc_final: 0.7485 (tmtt) REVERT: D 176 ASP cc_start: 0.8062 (t0) cc_final: 0.7840 (t0) REVERT: D 325 ILE cc_start: 0.7945 (mt) cc_final: 0.7570 (mt) REVERT: D 349 TYR cc_start: 0.8253 (t80) cc_final: 0.7573 (t80) REVERT: D 368 LYS cc_start: 0.7590 (tptp) cc_final: 0.7329 (tptt) REVERT: D 376 LYS cc_start: 0.7022 (tttp) cc_final: 0.6800 (tptt) REVERT: D 410 ARG cc_start: 0.6410 (mmm-85) cc_final: 0.5849 (mmt180) REVERT: D 437 GLN cc_start: 0.7864 (mt0) cc_final: 0.7258 (mt0) REVERT: D 452 LYS cc_start: 0.5023 (mmtp) cc_final: 0.4818 (pttt) REVERT: E 126 LYS cc_start: 0.7805 (ttpt) cc_final: 0.7235 (mtpp) REVERT: E 194 MET cc_start: 0.7102 (mtm) cc_final: 0.6251 (mtm) REVERT: E 210 ARG cc_start: 0.7759 (ttp80) cc_final: 0.7526 (ttp-110) REVERT: E 216 ARG cc_start: 0.6516 (mtm-85) cc_final: 0.5956 (ptt180) REVERT: E 420 ARG cc_start: 0.5984 (tmm-80) cc_final: 0.5769 (mmm-85) REVERT: E 468 GLU cc_start: 0.5839 (pp20) cc_final: 0.5435 (tt0) REVERT: F 54 TYR cc_start: 0.7512 (p90) cc_final: 0.6551 (p90) REVERT: F 61 GLU cc_start: 0.5785 (mt-10) cc_final: 0.5567 (mt-10) REVERT: F 108 PRO cc_start: 0.8268 (Cg_endo) cc_final: 0.7995 (Cg_exo) REVERT: F 260 MET cc_start: 0.7661 (mmm) cc_final: 0.7317 (mmt) REVERT: F 315 SER cc_start: 0.8611 (m) cc_final: 0.8359 (p) REVERT: F 372 ARG cc_start: 0.7872 (ttp-170) cc_final: 0.7643 (mtp180) REVERT: G 23 LYS cc_start: 0.6751 (mttt) cc_final: 0.6320 (tppt) REVERT: G 198 LYS cc_start: 0.7977 (tmmt) cc_final: 0.7512 (tttt) REVERT: H 92 GLU cc_start: 0.6639 (tt0) cc_final: 0.5962 (mm-30) REVERT: H 97 THR cc_start: 0.6741 (p) cc_final: 0.6388 (t) REVERT: J 84 ARG cc_start: 0.4157 (ptm160) cc_final: 0.3611 (ttt-90) REVERT: J 170 ARG cc_start: 0.3290 (mtp85) cc_final: 0.2674 (tpt170) REVERT: L 72 ARG cc_start: 0.4482 (ptm160) cc_final: 0.4129 (ptp90) REVERT: L 89 GLU cc_start: 0.5506 (mm-30) cc_final: 0.5272 (pt0) REVERT: L 94 LEU cc_start: 0.3793 (tt) cc_final: 0.3186 (mm) outliers start: 0 outliers final: 0 residues processed: 649 average time/residue: 0.2264 time to fit residues: 218.4237 Evaluate side-chains 343 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 343 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 9.9990 chunk 298 optimal weight: 7.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 GLN ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 260 ASN B 316 GLN B 442 ASN ** B 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 166 GLN E 170 GLN E 363 ASN F 206 GLN F 428 GLN G 166 GLN ** H 82 GLN ** 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 = 0.3776 r_free = 0.3776 target = 0.143944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.121198 restraints weight = 49698.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.119454 restraints weight = 41179.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.120150 restraints weight = 37758.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.121349 restraints weight = 30363.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.121168 restraints weight = 25662.526| |-----------------------------------------------------------------------------| r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.2236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 30114 Z= 0.225 Angle : 0.657 13.721 40813 Z= 0.339 Chirality : 0.048 0.236 4572 Planarity : 0.006 0.055 5333 Dihedral : 6.408 91.224 4259 Min Nonbonded Distance : 1.720 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.82 % Allowed : 8.27 % Favored : 89.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % 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: 0.49 (0.14), residues: 3764 helix: 1.11 (0.13), residues: 1568 sheet: -0.15 (0.21), residues: 599 loop : -0.15 (0.16), residues: 1597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 66 TYR 0.020 0.002 TYR A 513 PHE 0.022 0.002 PHE E 414 TRP 0.020 0.002 TRP A 119 HIS 0.008 0.002 HIS F 375 Details of bonding type rmsd covalent geometry : bond 0.00542 (30114) covalent geometry : angle 0.65693 (40813) hydrogen bonds : bond 0.05471 ( 1276) hydrogen bonds : angle 4.93216 ( 3678) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 350 time to evaluate : 1.092 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 481 ARG cc_start: 0.7399 (mmm-85) cc_final: 0.6877 (ttm-80) REVERT: A 483 VAL cc_start: 0.8654 (t) cc_final: 0.8384 (t) REVERT: B 25 TYR cc_start: 0.7770 (m-80) cc_final: 0.7527 (m-80) REVERT: B 400 LEU cc_start: 0.7922 (mt) cc_final: 0.7592 (mp) REVERT: C 81 ASN cc_start: 0.7625 (t0) cc_final: 0.7397 (t0) REVERT: C 123 VAL cc_start: 0.8384 (m) cc_final: 0.8043 (p) REVERT: C 294 MET cc_start: 0.8403 (mtp) cc_final: 0.8132 (mtp) REVERT: C 489 ILE cc_start: 0.8363 (OUTLIER) cc_final: 0.8089 (mp) REVERT: D 410 ARG cc_start: 0.6552 (mmm-85) cc_final: 0.6128 (mmt180) REVERT: E 6 LYS cc_start: 0.6254 (ttmt) cc_final: 0.5662 (tptm) REVERT: E 216 ARG cc_start: 0.7017 (mtm-85) cc_final: 0.6552 (ptt180) REVERT: F 54 TYR cc_start: 0.7312 (p90) cc_final: 0.6628 (p90) REVERT: G 17 GLN cc_start: 0.7719 (mm-40) cc_final: 0.7450 (mt0) REVERT: H 1 MET cc_start: 0.4037 (ttm) cc_final: 0.3695 (ttm) REVERT: H 86 VAL cc_start: 0.4170 (t) cc_final: 0.3781 (t) REVERT: H 92 GLU cc_start: 0.6113 (tt0) cc_final: 0.5772 (mm-30) REVERT: J 170 ARG cc_start: 0.4242 (mtp85) cc_final: 0.3117 (tpt170) REVERT: L 72 ARG cc_start: 0.4843 (ptm160) cc_final: 0.4453 (ptp90) REVERT: L 89 GLU cc_start: 0.6313 (mm-30) cc_final: 0.5714 (pt0) REVERT: L 150 LEU cc_start: 0.5467 (pt) cc_final: 0.4578 (mt) outliers start: 56 outliers final: 41 residues processed: 393 average time/residue: 0.2070 time to fit residues: 125.9749 Evaluate side-chains 318 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 276 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 424 TRP Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain C residue 173 VAL Chi-restraints excluded: chain C residue 489 ILE Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain D residue 130 PHE Chi-restraints excluded: chain D residue 156 SER Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 269 GLU Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 456 LYS Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 205 ILE Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 363 ASN Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 223 LYS Chi-restraints excluded: chain F residue 396 VAL Chi-restraints excluded: chain F residue 428 GLN Chi-restraints excluded: chain F residue 444 SER Chi-restraints excluded: chain G residue 35 LEU Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain G residue 201 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 49 optimal weight: 10.0000 chunk 118 optimal weight: 9.9990 chunk 270 optimal weight: 7.9990 chunk 137 optimal weight: 5.9990 chunk 307 optimal weight: 9.9990 chunk 42 optimal weight: 10.0000 chunk 95 optimal weight: 20.0000 chunk 169 optimal weight: 8.9990 chunk 251 optimal weight: 5.9990 chunk 170 optimal weight: 5.9990 chunk 138 optimal weight: 2.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 442 ASN E 166 GLN F 206 GLN ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 96 GLN L 124 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.142386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.120520 restraints weight = 49933.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.119836 restraints weight = 45786.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.120805 restraints weight = 38558.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.121386 restraints weight = 26785.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.121472 restraints weight = 23087.991| |-----------------------------------------------------------------------------| r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.2789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 30114 Z= 0.217 Angle : 0.623 13.348 40813 Z= 0.322 Chirality : 0.046 0.203 4572 Planarity : 0.005 0.056 5333 Dihedral : 6.374 84.503 4259 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.11 % Allowed : 12.23 % Favored : 85.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % 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: 0.21 (0.14), residues: 3764 helix: 0.98 (0.13), residues: 1570 sheet: -0.40 (0.21), residues: 600 loop : -0.37 (0.15), residues: 1594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 177 TYR 0.018 0.002 TYR A 513 PHE 0.020 0.002 PHE E 414 TRP 0.020 0.002 TRP A 119 HIS 0.008 0.002 HIS F 375 Details of bonding type rmsd covalent geometry : bond 0.00525 (30114) covalent geometry : angle 0.62280 (40813) hydrogen bonds : bond 0.05292 ( 1276) hydrogen bonds : angle 4.82117 ( 3678) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 307 time to evaluate : 1.035 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: A 183 MET cc_start: 0.8391 (mtt) cc_final: 0.8145 (ttm) REVERT: A 481 ARG cc_start: 0.7300 (mmm-85) cc_final: 0.6790 (ttm-80) REVERT: A 483 VAL cc_start: 0.8675 (t) cc_final: 0.8406 (t) REVERT: B 400 LEU cc_start: 0.7868 (mt) cc_final: 0.7511 (mp) REVERT: C 294 MET cc_start: 0.8464 (mtp) cc_final: 0.8233 (mtp) REVERT: C 489 ILE cc_start: 0.8386 (OUTLIER) cc_final: 0.8130 (mp) REVERT: D 410 ARG cc_start: 0.6604 (mmm-85) cc_final: 0.6154 (mmt180) REVERT: E 6 LYS cc_start: 0.6447 (ttmt) cc_final: 0.5875 (tptm) REVERT: H 1 MET cc_start: 0.3981 (ttm) cc_final: 0.3751 (ttm) REVERT: J 164 GLU cc_start: 0.3773 (tm-30) cc_final: 0.3098 (tm-30) REVERT: J 170 ARG cc_start: 0.4496 (mtp85) cc_final: 0.3304 (tpt170) REVERT: L 89 GLU cc_start: 0.6288 (mm-30) cc_final: 0.5785 (pt0) REVERT: L 150 LEU cc_start: 0.5451 (pt) cc_final: 0.4568 (mt) outliers start: 65 outliers final: 43 residues processed: 359 average time/residue: 0.2046 time to fit residues: 114.7683 Evaluate side-chains 310 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 266 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 396 THR Chi-restraints excluded: chain B residue 424 TRP Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 489 ILE Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 130 PHE Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 269 GLU Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 438 ILE Chi-restraints excluded: chain D residue 456 LYS Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 412 LEU Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 396 VAL Chi-restraints excluded: chain F residue 428 GLN Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain G residue 35 LEU Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 201 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 260 optimal weight: 0.0770 chunk 206 optimal weight: 8.9990 chunk 155 optimal weight: 6.9990 chunk 10 optimal weight: 9.9990 chunk 293 optimal weight: 7.9990 chunk 31 optimal weight: 8.9990 chunk 311 optimal weight: 6.9990 chunk 86 optimal weight: 10.0000 chunk 118 optimal weight: 4.9990 chunk 342 optimal weight: 8.9990 chunk 239 optimal weight: 10.0000 overall best weight: 5.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 ASN C 442 ASN F 206 GLN F 428 GLN ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.141644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.119505 restraints weight = 49589.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.117935 restraints weight = 40607.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.118691 restraints weight = 39957.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.119320 restraints weight = 30860.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.119419 restraints weight = 25396.184| |-----------------------------------------------------------------------------| r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.3151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 30114 Z= 0.207 Angle : 0.612 13.049 40813 Z= 0.316 Chirality : 0.046 0.205 4572 Planarity : 0.005 0.058 5333 Dihedral : 6.293 82.190 4259 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.72 % Allowed : 14.11 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % 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: 0.09 (0.14), residues: 3764 helix: 0.92 (0.13), residues: 1567 sheet: -0.49 (0.21), residues: 599 loop : -0.48 (0.15), residues: 1598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 154 TYR 0.020 0.002 TYR D 349 PHE 0.020 0.002 PHE E 414 TRP 0.019 0.002 TRP A 119 HIS 0.007 0.002 HIS F 375 Details of bonding type rmsd covalent geometry : bond 0.00496 (30114) covalent geometry : angle 0.61151 (40813) hydrogen bonds : bond 0.05106 ( 1276) hydrogen bonds : angle 4.73206 ( 3678) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 287 time to evaluate : 1.148 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 MET cc_start: 0.8428 (OUTLIER) cc_final: 0.8183 (ttm) REVERT: A 481 ARG cc_start: 0.7319 (mmm-85) cc_final: 0.6751 (ttm-80) REVERT: A 483 VAL cc_start: 0.8657 (t) cc_final: 0.8389 (t) REVERT: B 400 LEU cc_start: 0.7832 (mt) cc_final: 0.7500 (mp) REVERT: B 464 LEU cc_start: 0.5412 (OUTLIER) cc_final: 0.5022 (pp) REVERT: C 81 ASN cc_start: 0.7677 (t160) cc_final: 0.7404 (t0) REVERT: C 294 MET cc_start: 0.8510 (mtp) cc_final: 0.8266 (mtp) REVERT: C 467 ILE cc_start: 0.6737 (mm) cc_final: 0.6311 (mp) REVERT: C 489 ILE cc_start: 0.8363 (OUTLIER) cc_final: 0.8115 (mp) REVERT: D 401 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7530 (tt0) REVERT: D 410 ARG cc_start: 0.6625 (mmm-85) cc_final: 0.6143 (mmt180) REVERT: J 164 GLU cc_start: 0.4004 (tm-30) cc_final: 0.3251 (tm-30) REVERT: J 170 ARG cc_start: 0.4565 (mtp85) cc_final: 0.3267 (tpt170) REVERT: L 89 GLU cc_start: 0.6343 (mm-30) cc_final: 0.5730 (pt0) REVERT: L 150 LEU cc_start: 0.5480 (pt) cc_final: 0.4521 (mt) outliers start: 84 outliers final: 56 residues processed: 356 average time/residue: 0.1920 time to fit residues: 110.1399 Evaluate side-chains 318 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 258 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 183 MET Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 396 THR Chi-restraints excluded: chain B residue 424 TRP Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 525 GLU Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 489 ILE Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain D residue 78 ASP Chi-restraints excluded: chain D residue 130 PHE Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 269 GLU Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 401 GLU Chi-restraints excluded: chain D residue 438 ILE Chi-restraints excluded: chain D residue 455 SER Chi-restraints excluded: chain D residue 456 LYS Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 290 ASP Chi-restraints excluded: chain F residue 373 GLU Chi-restraints excluded: chain F residue 396 VAL Chi-restraints excluded: chain F residue 428 GLN Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain G residue 35 LEU Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain G residue 201 ILE Chi-restraints excluded: chain H residue 63 MET Chi-restraints excluded: chain I residue 104 MET Chi-restraints excluded: chain K residue 99 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 44 optimal weight: 5.9990 chunk 189 optimal weight: 7.9990 chunk 114 optimal weight: 10.0000 chunk 178 optimal weight: 8.9990 chunk 211 optimal weight: 3.9990 chunk 348 optimal weight: 8.9990 chunk 37 optimal weight: 4.9990 chunk 125 optimal weight: 10.0000 chunk 115 optimal weight: 7.9990 chunk 273 optimal weight: 10.0000 chunk 54 optimal weight: 9.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 ASN ** E 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 206 GLN F 428 GLN ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.139924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.118233 restraints weight = 49951.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.116752 restraints weight = 41497.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.117552 restraints weight = 35602.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.119045 restraints weight = 29427.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.118833 restraints weight = 23880.938| |-----------------------------------------------------------------------------| r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.3406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 30114 Z= 0.228 Angle : 0.635 13.151 40813 Z= 0.328 Chirality : 0.047 0.191 4572 Planarity : 0.006 0.059 5333 Dihedral : 6.428 79.905 4259 Min Nonbonded Distance : 1.814 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 3.31 % Allowed : 15.05 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % 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: -0.10 (0.14), residues: 3764 helix: 0.79 (0.13), residues: 1570 sheet: -0.49 (0.21), residues: 587 loop : -0.67 (0.15), residues: 1607 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG J 138 TYR 0.020 0.002 TYR D 349 PHE 0.021 0.002 PHE E 414 TRP 0.033 0.002 TRP J 175 HIS 0.007 0.002 HIS A 185 Details of bonding type rmsd covalent geometry : bond 0.00552 (30114) covalent geometry : angle 0.63549 (40813) hydrogen bonds : bond 0.05304 ( 1276) hydrogen bonds : angle 4.77700 ( 3678) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 263 time to evaluate : 1.207 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: A 183 MET cc_start: 0.8448 (OUTLIER) cc_final: 0.8177 (ttm) REVERT: A 481 ARG cc_start: 0.7333 (mmm-85) cc_final: 0.6717 (ttm-80) REVERT: A 483 VAL cc_start: 0.8663 (t) cc_final: 0.8382 (t) REVERT: B 212 LEU cc_start: 0.7408 (OUTLIER) cc_final: 0.7117 (mm) REVERT: B 400 LEU cc_start: 0.7846 (mt) cc_final: 0.7498 (mp) REVERT: B 464 LEU cc_start: 0.5432 (OUTLIER) cc_final: 0.5076 (pp) REVERT: B 546 GLU cc_start: 0.2558 (mm-30) cc_final: 0.1700 (tp30) REVERT: C 81 ASN cc_start: 0.7593 (t0) cc_final: 0.7385 (t0) REVERT: C 294 MET cc_start: 0.8499 (mtp) cc_final: 0.8210 (mtp) REVERT: C 489 ILE cc_start: 0.8343 (OUTLIER) cc_final: 0.8093 (mp) REVERT: D 401 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7401 (tt0) REVERT: D 410 ARG cc_start: 0.6575 (mmm-85) cc_final: 0.6171 (mmt180) REVERT: G 47 MET cc_start: 0.6399 (OUTLIER) cc_final: 0.5800 (mtp) REVERT: J 164 GLU cc_start: 0.4153 (tm-30) cc_final: 0.3330 (tm-30) REVERT: J 170 ARG cc_start: 0.4569 (mtp85) cc_final: 0.3255 (tpt170) REVERT: L 89 GLU cc_start: 0.6020 (mm-30) cc_final: 0.5547 (pt0) outliers start: 102 outliers final: 69 residues processed: 347 average time/residue: 0.1930 time to fit residues: 107.9969 Evaluate side-chains 329 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 254 time to evaluate : 1.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 183 MET Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 539 ILE Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 396 THR Chi-restraints excluded: chain B residue 424 TRP Chi-restraints excluded: chain B residue 458 LEU Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain B residue 490 ILE Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain B residue 525 GLU Chi-restraints excluded: chain C residue 55 THR Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 489 ILE Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain D residue 78 ASP Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 130 PHE Chi-restraints excluded: chain D residue 156 SER Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 234 THR Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 269 GLU Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 401 GLU Chi-restraints excluded: chain D residue 455 SER Chi-restraints excluded: chain D residue 456 LYS Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 290 ASP Chi-restraints excluded: chain F residue 336 GLN Chi-restraints excluded: chain F residue 373 GLU Chi-restraints excluded: chain F residue 396 VAL Chi-restraints excluded: chain F residue 428 GLN Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain G residue 35 LEU Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 47 MET Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 119 THR Chi-restraints excluded: chain G residue 164 LEU Chi-restraints excluded: chain G residue 201 ILE Chi-restraints excluded: chain H residue 63 MET Chi-restraints excluded: chain I residue 104 MET Chi-restraints excluded: chain K residue 99 VAL Chi-restraints excluded: chain L residue 83 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 158 optimal weight: 5.9990 chunk 76 optimal weight: 5.9990 chunk 61 optimal weight: 7.9990 chunk 64 optimal weight: 1.9990 chunk 253 optimal weight: 6.9990 chunk 41 optimal weight: 0.9990 chunk 296 optimal weight: 0.9990 chunk 242 optimal weight: 6.9990 chunk 240 optimal weight: 2.9990 chunk 257 optimal weight: 1.9990 chunk 361 optimal weight: 10.0000 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 290 ASN B 397 GLN E 310 GLN F 206 GLN H 82 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.143531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.121700 restraints weight = 49507.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.120263 restraints weight = 41610.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.121217 restraints weight = 36403.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.121667 restraints weight = 28859.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.121963 restraints weight = 25063.933| |-----------------------------------------------------------------------------| r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.3401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 30114 Z= 0.114 Angle : 0.528 13.768 40813 Z= 0.268 Chirality : 0.043 0.163 4572 Planarity : 0.004 0.053 5333 Dihedral : 5.996 80.652 4259 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.08 % Allowed : 16.25 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.14), residues: 3764 helix: 1.20 (0.14), residues: 1570 sheet: -0.33 (0.21), residues: 587 loop : -0.48 (0.15), residues: 1607 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 76 TYR 0.019 0.001 TYR G 61 PHE 0.016 0.001 PHE E 414 TRP 0.029 0.001 TRP J 175 HIS 0.005 0.001 HIS B 145 Details of bonding type rmsd covalent geometry : bond 0.00256 (30114) covalent geometry : angle 0.52780 (40813) hydrogen bonds : bond 0.04158 ( 1276) hydrogen bonds : angle 4.46690 ( 3678) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 283 time to evaluate : 1.132 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 MET cc_start: 0.8361 (mtt) cc_final: 0.8110 (ttm) REVERT: A 481 ARG cc_start: 0.7333 (mmm-85) cc_final: 0.6838 (tpt90) REVERT: A 483 VAL cc_start: 0.8645 (t) cc_final: 0.8395 (t) REVERT: B 212 LEU cc_start: 0.7346 (OUTLIER) cc_final: 0.7078 (mm) REVERT: B 391 MET cc_start: 0.7570 (mmp) cc_final: 0.6816 (mmp) REVERT: B 400 LEU cc_start: 0.7806 (mt) cc_final: 0.7499 (mp) REVERT: B 435 LEU cc_start: 0.6136 (OUTLIER) cc_final: 0.5501 (mm) REVERT: B 464 LEU cc_start: 0.5285 (OUTLIER) cc_final: 0.4966 (pp) REVERT: C 81 ASN cc_start: 0.7538 (t0) cc_final: 0.7329 (t0) REVERT: C 123 VAL cc_start: 0.8393 (m) cc_final: 0.8036 (p) REVERT: C 294 MET cc_start: 0.8378 (mtp) cc_final: 0.8138 (mtp) REVERT: C 489 ILE cc_start: 0.8387 (OUTLIER) cc_final: 0.8154 (mp) REVERT: D 401 GLU cc_start: 0.7883 (OUTLIER) cc_final: 0.7392 (tt0) REVERT: D 410 ARG cc_start: 0.6563 (mmm-85) cc_final: 0.6209 (mmm160) REVERT: F 108 PRO cc_start: 0.8144 (Cg_endo) cc_final: 0.7888 (Cg_exo) REVERT: J 164 GLU cc_start: 0.3939 (OUTLIER) cc_final: 0.2989 (tt0) REVERT: J 170 ARG cc_start: 0.4645 (mtp85) cc_final: 0.3307 (tpt170) REVERT: L 89 GLU cc_start: 0.5935 (mm-30) cc_final: 0.5447 (pt0) outliers start: 64 outliers final: 34 residues processed: 336 average time/residue: 0.1947 time to fit residues: 104.9120 Evaluate side-chains 300 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 260 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 539 ILE Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 189 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 424 TRP Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain C residue 489 ILE Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 130 PHE Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 331 TYR Chi-restraints excluded: chain D residue 401 GLU Chi-restraints excluded: chain D residue 438 ILE Chi-restraints excluded: chain D residue 456 LYS Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 130 PHE Chi-restraints excluded: chain F residue 223 LYS Chi-restraints excluded: chain F residue 373 GLU Chi-restraints excluded: chain G residue 35 LEU Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain G residue 152 GLU Chi-restraints excluded: chain H residue 63 MET Chi-restraints excluded: chain I residue 104 MET Chi-restraints excluded: chain J residue 164 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 303 optimal weight: 6.9990 chunk 24 optimal weight: 10.0000 chunk 87 optimal weight: 10.0000 chunk 2 optimal weight: 10.0000 chunk 99 optimal weight: 9.9990 chunk 223 optimal weight: 7.9990 chunk 272 optimal weight: 9.9990 chunk 208 optimal weight: 9.9990 chunk 371 optimal weight: 4.9990 chunk 324 optimal weight: 10.0000 chunk 313 optimal weight: 8.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 428 GLN H 30 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.138188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.116490 restraints weight = 50080.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.115364 restraints weight = 40511.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.116279 restraints weight = 37608.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.117137 restraints weight = 27382.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.117075 restraints weight = 24483.693| |-----------------------------------------------------------------------------| r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.3753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 30114 Z= 0.276 Angle : 0.705 14.105 40813 Z= 0.363 Chirality : 0.049 0.202 4572 Planarity : 0.006 0.064 5333 Dihedral : 6.450 81.121 4259 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.89 % Allowed : 16.77 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % 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: -0.33 (0.13), residues: 3764 helix: 0.65 (0.13), residues: 1561 sheet: -0.59 (0.21), residues: 594 loop : -0.85 (0.15), residues: 1609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG I 87 TYR 0.027 0.002 TYR D 349 PHE 0.021 0.003 PHE E 418 TRP 0.024 0.002 TRP J 100 HIS 0.008 0.002 HIS F 375 Details of bonding type rmsd covalent geometry : bond 0.00671 (30114) covalent geometry : angle 0.70518 (40813) hydrogen bonds : bond 0.05845 ( 1276) hydrogen bonds : angle 4.92841 ( 3678) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 266 time to evaluate : 1.155 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: A 481 ARG cc_start: 0.7278 (mmm-85) cc_final: 0.6695 (ttm-80) REVERT: A 483 VAL cc_start: 0.8660 (t) cc_final: 0.8383 (t) REVERT: B 212 LEU cc_start: 0.7457 (OUTLIER) cc_final: 0.7091 (mm) REVERT: B 391 MET cc_start: 0.7655 (mmp) cc_final: 0.7045 (mmp) REVERT: B 400 LEU cc_start: 0.7834 (mt) cc_final: 0.7518 (mp) REVERT: B 435 LEU cc_start: 0.6087 (OUTLIER) cc_final: 0.5440 (mm) REVERT: B 464 LEU cc_start: 0.5388 (OUTLIER) cc_final: 0.5058 (pp) REVERT: B 567 MET cc_start: 0.3663 (mmm) cc_final: 0.3434 (mmm) REVERT: C 81 ASN cc_start: 0.7666 (t0) cc_final: 0.7400 (t0) REVERT: C 294 MET cc_start: 0.8597 (mtp) cc_final: 0.8283 (mtp) REVERT: C 489 ILE cc_start: 0.8361 (OUTLIER) cc_final: 0.8124 (mp) REVERT: H 102 ILE cc_start: 0.6333 (pt) cc_final: 0.5676 (mt) REVERT: J 65 GLU cc_start: 0.3624 (OUTLIER) cc_final: 0.2564 (mp0) REVERT: J 164 GLU cc_start: 0.4418 (tm-30) cc_final: 0.3337 (tt0) REVERT: J 170 ARG cc_start: 0.4472 (mtp85) cc_final: 0.3159 (tpt170) outliers start: 89 outliers final: 60 residues processed: 349 average time/residue: 0.1879 time to fit residues: 106.0949 Evaluate side-chains 315 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 250 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 539 ILE Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 424 TRP Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain B residue 490 ILE Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 489 ILE Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain D residue 78 ASP Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 130 PHE Chi-restraints excluded: chain D residue 217 SER Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 269 GLU Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 438 ILE Chi-restraints excluded: chain D residue 455 SER Chi-restraints excluded: chain D residue 456 LYS Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 196 ILE Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 396 VAL Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 130 PHE Chi-restraints excluded: chain F residue 290 ASP Chi-restraints excluded: chain F residue 336 GLN Chi-restraints excluded: chain F residue 428 GLN Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain G residue 35 LEU Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 164 LEU Chi-restraints excluded: chain G residue 201 ILE Chi-restraints excluded: chain H residue 42 TYR Chi-restraints excluded: chain H residue 63 MET Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain I residue 104 MET Chi-restraints excluded: chain J residue 65 GLU Chi-restraints excluded: chain K residue 99 VAL Chi-restraints excluded: chain L residue 83 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 316 optimal weight: 10.0000 chunk 44 optimal weight: 2.9990 chunk 327 optimal weight: 10.0000 chunk 310 optimal weight: 6.9990 chunk 140 optimal weight: 6.9990 chunk 176 optimal weight: 7.9990 chunk 330 optimal weight: 9.9990 chunk 36 optimal weight: 0.9980 chunk 199 optimal weight: 0.9990 chunk 224 optimal weight: 10.0000 chunk 347 optimal weight: 3.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 13 GLN H 30 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.140413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.118277 restraints weight = 49994.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.117223 restraints weight = 39810.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.117899 restraints weight = 33024.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.118499 restraints weight = 27172.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.118511 restraints weight = 24661.122| |-----------------------------------------------------------------------------| r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.3764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 30114 Z= 0.145 Angle : 0.571 14.002 40813 Z= 0.291 Chirality : 0.044 0.245 4572 Planarity : 0.005 0.054 5333 Dihedral : 5.970 78.551 4259 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.98 % Allowed : 18.26 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % 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: 0.02 (0.14), residues: 3764 helix: 0.97 (0.13), residues: 1564 sheet: -0.50 (0.21), residues: 572 loop : -0.66 (0.15), residues: 1628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 372 TYR 0.017 0.001 TYR D 349 PHE 0.032 0.002 PHE B 415 TRP 0.018 0.001 TRP J 100 HIS 0.005 0.001 HIS B 185 Details of bonding type rmsd covalent geometry : bond 0.00342 (30114) covalent geometry : angle 0.57127 (40813) hydrogen bonds : bond 0.04617 ( 1276) hydrogen bonds : angle 4.62949 ( 3678) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 272 time to evaluate : 1.197 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: A 329 ARG cc_start: 0.7001 (mtt180) cc_final: 0.6457 (mmp80) REVERT: A 481 ARG cc_start: 0.7351 (mmm-85) cc_final: 0.6660 (ttt180) REVERT: A 483 VAL cc_start: 0.8626 (t) cc_final: 0.8378 (t) REVERT: B 391 MET cc_start: 0.7591 (mmp) cc_final: 0.7004 (mmp) REVERT: B 400 LEU cc_start: 0.7805 (mt) cc_final: 0.7497 (mp) REVERT: B 435 LEU cc_start: 0.6109 (OUTLIER) cc_final: 0.5459 (mm) REVERT: B 464 LEU cc_start: 0.5263 (OUTLIER) cc_final: 0.4920 (pp) REVERT: B 567 MET cc_start: 0.3749 (mmm) cc_final: 0.3512 (mmm) REVERT: C 81 ASN cc_start: 0.7559 (t0) cc_final: 0.7317 (t0) REVERT: C 191 ARG cc_start: 0.7850 (mmm-85) cc_final: 0.7349 (mtm-85) REVERT: C 294 MET cc_start: 0.8486 (mtp) cc_final: 0.8236 (mtp) REVERT: C 489 ILE cc_start: 0.8345 (OUTLIER) cc_final: 0.8088 (mp) REVERT: C 567 MET cc_start: 0.8218 (tpp) cc_final: 0.7478 (ttm) REVERT: D 401 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7432 (tt0) REVERT: D 410 ARG cc_start: 0.6897 (mmm160) cc_final: 0.6244 (mmt180) REVERT: F 180 GLU cc_start: 0.5152 (OUTLIER) cc_final: 0.3334 (pp20) REVERT: H 102 ILE cc_start: 0.6308 (pt) cc_final: 0.5738 (mt) REVERT: J 89 GLU cc_start: 0.3958 (OUTLIER) cc_final: 0.3212 (pt0) REVERT: J 164 GLU cc_start: 0.4102 (OUTLIER) cc_final: 0.3746 (tm-30) REVERT: J 170 ARG cc_start: 0.4605 (mtp85) cc_final: 0.3217 (tpt170) outliers start: 61 outliers final: 45 residues processed: 327 average time/residue: 0.1897 time to fit residues: 100.8187 Evaluate side-chains 311 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 259 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 539 ILE Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 424 TRP Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 489 ILE Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain D residue 78 ASP Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 130 PHE Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 401 GLU Chi-restraints excluded: chain D residue 438 ILE Chi-restraints excluded: chain D residue 456 LYS Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 130 PHE Chi-restraints excluded: chain F residue 180 GLU Chi-restraints excluded: chain F residue 290 ASP Chi-restraints excluded: chain F residue 336 GLN Chi-restraints excluded: chain F residue 428 GLN Chi-restraints excluded: chain G residue 35 LEU Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain H residue 30 GLN Chi-restraints excluded: chain H residue 63 MET Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain I residue 104 MET Chi-restraints excluded: chain J residue 89 GLU Chi-restraints excluded: chain J residue 164 GLU Chi-restraints excluded: chain L residue 83 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 371 optimal weight: 20.0000 chunk 370 optimal weight: 8.9990 chunk 203 optimal weight: 1.9990 chunk 6 optimal weight: 7.9990 chunk 141 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 42 optimal weight: 20.0000 chunk 95 optimal weight: 4.9990 chunk 294 optimal weight: 10.0000 chunk 289 optimal weight: 2.9990 chunk 16 optimal weight: 10.0000 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 428 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.142177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.120605 restraints weight = 49689.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.119313 restraints weight = 40165.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.120008 restraints weight = 39000.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.120821 restraints weight = 29770.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.120905 restraints weight = 23873.363| |-----------------------------------------------------------------------------| r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.3792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 30114 Z= 0.129 Angle : 0.549 14.121 40813 Z= 0.278 Chirality : 0.043 0.213 4572 Planarity : 0.004 0.055 5333 Dihedral : 5.750 78.042 4259 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.82 % Allowed : 18.36 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % 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: 0.21 (0.14), residues: 3764 helix: 1.16 (0.13), residues: 1561 sheet: -0.40 (0.22), residues: 572 loop : -0.57 (0.15), residues: 1631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 177 TYR 0.016 0.001 TYR D 349 PHE 0.020 0.001 PHE B 415 TRP 0.014 0.001 TRP J 100 HIS 0.005 0.001 HIS B 145 Details of bonding type rmsd covalent geometry : bond 0.00301 (30114) covalent geometry : angle 0.54947 (40813) hydrogen bonds : bond 0.04314 ( 1276) hydrogen bonds : angle 4.50689 ( 3678) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 270 time to evaluate : 1.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 329 ARG cc_start: 0.6947 (mtt180) cc_final: 0.6423 (mmp80) REVERT: A 481 ARG cc_start: 0.7326 (mmm-85) cc_final: 0.6689 (ttt180) REVERT: A 483 VAL cc_start: 0.8639 (t) cc_final: 0.8400 (t) REVERT: B 230 PHE cc_start: 0.6431 (t80) cc_final: 0.6070 (t80) REVERT: B 391 MET cc_start: 0.7548 (mmp) cc_final: 0.6998 (mmp) REVERT: B 400 LEU cc_start: 0.7818 (mt) cc_final: 0.7540 (mp) REVERT: B 435 LEU cc_start: 0.6108 (OUTLIER) cc_final: 0.5438 (mm) REVERT: B 464 LEU cc_start: 0.5334 (OUTLIER) cc_final: 0.4969 (pp) REVERT: B 496 GLN cc_start: 0.3770 (tt0) cc_final: 0.3490 (tp40) REVERT: B 518 MET cc_start: 0.7463 (mtm) cc_final: 0.7177 (mtp) REVERT: B 567 MET cc_start: 0.3624 (mmm) cc_final: 0.3403 (mmm) REVERT: C 81 ASN cc_start: 0.7514 (t0) cc_final: 0.7271 (t0) REVERT: C 123 VAL cc_start: 0.8371 (m) cc_final: 0.8012 (p) REVERT: C 191 ARG cc_start: 0.7888 (mmm-85) cc_final: 0.7361 (mtm-85) REVERT: C 294 MET cc_start: 0.8461 (mtp) cc_final: 0.8216 (mtp) REVERT: C 489 ILE cc_start: 0.8369 (OUTLIER) cc_final: 0.8135 (mp) REVERT: C 567 MET cc_start: 0.8203 (tpp) cc_final: 0.7465 (ttm) REVERT: D 410 ARG cc_start: 0.6877 (mmm160) cc_final: 0.6221 (mmt180) REVERT: F 108 PRO cc_start: 0.8094 (Cg_endo) cc_final: 0.7853 (Cg_exo) REVERT: F 180 GLU cc_start: 0.5116 (OUTLIER) cc_final: 0.3279 (pp20) REVERT: H 102 ILE cc_start: 0.6557 (pt) cc_final: 0.5920 (mt) REVERT: J 164 GLU cc_start: 0.4113 (OUTLIER) cc_final: 0.3765 (tm-30) REVERT: J 170 ARG cc_start: 0.4667 (mtp85) cc_final: 0.3267 (tpt170) outliers start: 56 outliers final: 45 residues processed: 321 average time/residue: 0.1949 time to fit residues: 100.9656 Evaluate side-chains 310 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 260 time to evaluate : 1.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 539 ILE Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 424 TRP Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 489 ILE Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain D residue 78 ASP Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 130 PHE Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 438 ILE Chi-restraints excluded: chain D residue 456 LYS Chi-restraints excluded: chain E residue 3 LEU Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 130 PHE Chi-restraints excluded: chain F residue 180 GLU Chi-restraints excluded: chain F residue 428 GLN Chi-restraints excluded: chain G residue 35 LEU Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain H residue 63 MET Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain I residue 104 MET Chi-restraints excluded: chain J residue 164 GLU Chi-restraints excluded: chain L residue 83 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 295 optimal weight: 7.9990 chunk 339 optimal weight: 20.0000 chunk 288 optimal weight: 9.9990 chunk 147 optimal weight: 9.9990 chunk 325 optimal weight: 0.7980 chunk 258 optimal weight: 6.9990 chunk 284 optimal weight: 10.0000 chunk 272 optimal weight: 10.0000 chunk 286 optimal weight: 5.9990 chunk 250 optimal weight: 0.8980 chunk 219 optimal weight: 7.9990 overall best weight: 4.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 428 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.140233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.118597 restraints weight = 49850.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.117432 restraints weight = 44399.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.118341 restraints weight = 37339.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.118722 restraints weight = 30438.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.118874 restraints weight = 26412.616| |-----------------------------------------------------------------------------| r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.3858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 30114 Z= 0.177 Angle : 0.587 14.145 40813 Z= 0.298 Chirality : 0.045 0.217 4572 Planarity : 0.005 0.057 5333 Dihedral : 5.797 76.500 4259 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.01 % Allowed : 18.29 % Favored : 79.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % 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: 0.09 (0.14), residues: 3764 helix: 1.06 (0.13), residues: 1562 sheet: -0.43 (0.22), residues: 582 loop : -0.66 (0.15), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 372 TYR 0.020 0.002 TYR D 349 PHE 0.020 0.002 PHE B 415 TRP 0.017 0.001 TRP J 100 HIS 0.006 0.001 HIS B 185 Details of bonding type rmsd covalent geometry : bond 0.00427 (30114) covalent geometry : angle 0.58723 (40813) hydrogen bonds : bond 0.04670 ( 1276) hydrogen bonds : angle 4.56767 ( 3678) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 262 time to evaluate : 1.057 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 329 ARG cc_start: 0.6978 (mtt90) cc_final: 0.6451 (mmp80) REVERT: A 481 ARG cc_start: 0.7330 (mmm-85) cc_final: 0.6698 (ttt180) REVERT: A 483 VAL cc_start: 0.8642 (t) cc_final: 0.8407 (t) REVERT: A 563 PHE cc_start: 0.6875 (t80) cc_final: 0.6559 (t80) REVERT: B 230 PHE cc_start: 0.6454 (t80) cc_final: 0.6104 (t80) REVERT: B 391 MET cc_start: 0.7576 (mmp) cc_final: 0.7049 (mmp) REVERT: B 400 LEU cc_start: 0.7823 (mt) cc_final: 0.7549 (mp) REVERT: B 435 LEU cc_start: 0.6135 (OUTLIER) cc_final: 0.5463 (mm) REVERT: B 464 LEU cc_start: 0.5486 (OUTLIER) cc_final: 0.5111 (pp) REVERT: B 496 GLN cc_start: 0.3823 (tt0) cc_final: 0.3561 (tp40) REVERT: B 567 MET cc_start: 0.3695 (mmm) cc_final: 0.3476 (mmm) REVERT: C 81 ASN cc_start: 0.7587 (t0) cc_final: 0.7335 (t0) REVERT: C 294 MET cc_start: 0.8481 (mtp) cc_final: 0.8239 (mtp) REVERT: C 489 ILE cc_start: 0.8362 (OUTLIER) cc_final: 0.8112 (mp) REVERT: D 401 GLU cc_start: 0.7933 (OUTLIER) cc_final: 0.7394 (tt0) REVERT: D 410 ARG cc_start: 0.6854 (mmm160) cc_final: 0.6233 (mmt180) REVERT: F 108 PRO cc_start: 0.8095 (Cg_endo) cc_final: 0.7861 (Cg_exo) REVERT: F 180 GLU cc_start: 0.5159 (OUTLIER) cc_final: 0.3330 (pp20) REVERT: H 102 ILE cc_start: 0.6471 (pt) cc_final: 0.5776 (mt) REVERT: J 89 GLU cc_start: 0.4214 (OUTLIER) cc_final: 0.3362 (pt0) REVERT: J 164 GLU cc_start: 0.4321 (OUTLIER) cc_final: 0.3937 (tm-30) REVERT: J 170 ARG cc_start: 0.4648 (mtp85) cc_final: 0.3310 (tpt170) outliers start: 62 outliers final: 51 residues processed: 318 average time/residue: 0.1971 time to fit residues: 101.5884 Evaluate side-chains 313 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 255 time to evaluate : 1.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 539 ILE Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 273 THR Chi-restraints excluded: chain B residue 354 LEU Chi-restraints excluded: chain B residue 424 TRP Chi-restraints excluded: chain B residue 435 LEU Chi-restraints excluded: chain B residue 464 LEU Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 490 ILE Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 203 THR Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 489 ILE Chi-restraints excluded: chain D residue 72 SER Chi-restraints excluded: chain D residue 78 ASP Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 130 PHE Chi-restraints excluded: chain D residue 232 ILE Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 401 GLU Chi-restraints excluded: chain D residue 455 SER Chi-restraints excluded: chain D residue 456 LYS Chi-restraints excluded: chain E residue 3 LEU Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 218 VAL Chi-restraints excluded: chain E residue 308 VAL Chi-restraints excluded: chain E residue 396 VAL Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 130 PHE Chi-restraints excluded: chain F residue 180 GLU Chi-restraints excluded: chain F residue 336 GLN Chi-restraints excluded: chain G residue 25 VAL Chi-restraints excluded: chain G residue 35 LEU Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 96 VAL Chi-restraints excluded: chain G residue 201 ILE Chi-restraints excluded: chain H residue 27 GLU Chi-restraints excluded: chain H residue 63 MET Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain I residue 104 MET Chi-restraints excluded: chain J residue 89 GLU Chi-restraints excluded: chain J residue 164 GLU Chi-restraints excluded: chain K residue 99 VAL Chi-restraints excluded: chain L residue 83 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 31 optimal weight: 3.9990 chunk 361 optimal weight: 5.9990 chunk 57 optimal weight: 10.0000 chunk 93 optimal weight: 6.9990 chunk 367 optimal weight: 8.9990 chunk 210 optimal weight: 20.0000 chunk 254 optimal weight: 10.0000 chunk 181 optimal weight: 9.9990 chunk 226 optimal weight: 8.9990 chunk 22 optimal weight: 5.9990 chunk 127 optimal weight: 7.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 428 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.139659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.119775 restraints weight = 49881.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.118510 restraints weight = 45583.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.118872 restraints weight = 42012.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.119497 restraints weight = 34538.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.119527 restraints weight = 31564.015| |-----------------------------------------------------------------------------| r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.4033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 30114 Z= 0.229 Angle : 0.652 14.071 40813 Z= 0.334 Chirality : 0.047 0.223 4572 Planarity : 0.006 0.061 5333 Dihedral : 6.032 75.971 4259 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.27 % Allowed : 18.36 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.14), residues: 3764 helix: 0.79 (0.13), residues: 1561 sheet: -0.60 (0.22), residues: 573 loop : -0.88 (0.15), residues: 1630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 372 TYR 0.026 0.002 TYR D 349 PHE 0.020 0.002 PHE B 415 TRP 0.019 0.002 TRP A 119 HIS 0.008 0.002 HIS B 185 Details of bonding type rmsd covalent geometry : bond 0.00557 (30114) covalent geometry : angle 0.65224 (40813) hydrogen bonds : bond 0.05345 ( 1276) hydrogen bonds : angle 4.79085 ( 3678) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4374.06 seconds wall clock time: 76 minutes 40.49 seconds (4600.49 seconds total)