Starting phenix.real_space_refine on Sat Aug 8 10:40:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9u6f_63904/08_2026/9u6f_63904.cif Found real_map, /net/cci-nas-00/data/ceres_data/9u6f_63904/08_2026/9u6f_63904.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9u6f_63904/08_2026/9u6f_63904.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9u6f_63904/08_2026/9u6f_63904.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9u6f_63904/08_2026/9u6f_63904.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9u6f_63904/08_2026/9u6f_63904.map" } resolution = 2.2 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= 0.001 sd= 0.037 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 5 5.49 5 Mg 2 5.21 5 S 101 5.16 5 C 17114 2.51 5 N 4643 2.21 5 O 5081 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 72 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 26946 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 4477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4477 Classifications: {'peptide': 578} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 542} Chain: "B" Number of atoms: 4477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4477 Classifications: {'peptide': 578} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 542} Chain: "C" Number of atoms: 4477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4477 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: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 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: 5.90, per 1000 atoms: 0.22 Number of scatterers: 26946 At special positions: 0 Unit cell: (134.706, 138.474, 153.546, 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 101 16.00 P 5 15.00 Mg 2 11.99 O 5081 8.00 N 4643 7.00 C 17114 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: 2.33 Conformation dependent library (CDL) restraints added in 1.1 seconds 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6278 Finding SS restraints... Secondary structure from input PDB file: 135 helices and 27 sheets defined 45.6% alpha, 12.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 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 245 Processing helix chain 'A' and resid 258 through 269 removed outlier: 3.769A pdb=" N MET A 262 " --> pdb=" O ARG A 258 " (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 297 through 316 removed outlier: 4.294A pdb=" N ALA A 301 " --> pdb=" O ALA A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 342 removed outlier: 3.961A pdb=" N TRP A 330 " --> pdb=" O SER A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 350 Processing helix chain 'A' and resid 351 through 352 No H-bonds generated for 'chain 'A' and resid 351 through 352' 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 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: 3.895A pdb=" N GLU A 466 " --> pdb=" O ALA A 462 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ILE A 467 " --> pdb=" O GLY A 463 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU A 470 " --> pdb=" O GLU A 466 " (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 535 through 540 removed outlier: 3.535A pdb=" N ILE A 539 " --> pdb=" O SER A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 551 removed outlier: 4.072A pdb=" N GLU A 546 " --> pdb=" O LEU A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 554 No H-bonds generated for 'chain 'A' and resid 552 through 554' Processing helix chain 'A' and resid 558 through 577 removed outlier: 3.540A pdb=" N PHE A 574 " --> pdb=" O ILE A 570 " (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 Processing helix chain 'B' and resid 258 through 269 Processing helix chain 'B' and resid 270 through 272 No H-bonds generated for 'chain 'B' and resid 270 through 272' Processing helix chain 'B' and resid 280 through 283 Processing helix chain 'B' and resid 295 through 316 removed outlier: 4.932A pdb=" N ILE B 303 " --> pdb=" O ARG B 299 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N TYR B 304 " --> pdb=" O GLU B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 341 removed outlier: 3.504A pdb=" N TRP B 330 " --> pdb=" O SER B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 363 Processing helix chain 'B' and resid 393 through 403 removed outlier: 3.832A pdb=" N ILE B 402 " --> pdb=" O SER B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 416 removed outlier: 3.553A 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 464 Processing helix chain 'B' and resid 464 through 471 Processing helix chain 'B' and resid 472 through 476 Processing helix chain 'B' and resid 477 through 495 Processing helix chain 'B' and resid 508 through 532 Processing helix chain 'B' and resid 535 through 540 removed outlier: 3.935A pdb=" N ILE B 539 " --> pdb=" O SER B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 542 through 550 removed outlier: 4.340A pdb=" N GLU B 546 " --> pdb=" O LEU B 542 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 554 removed outlier: 3.679A pdb=" N VAL B 554 " --> pdb=" O ALA B 551 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 551 through 554' Processing helix chain 'B' and resid 558 through 576 removed outlier: 3.719A pdb=" N PHE B 574 " --> pdb=" O ILE B 570 " (cutoff:3.500A) removed outlier: 3.545A 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 245 Processing helix chain 'C' and resid 258 through 269 removed outlier: 3.722A pdb=" N MET C 262 " --> pdb=" O ARG C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 283 Processing helix chain 'C' and resid 296 through 316 removed outlier: 4.295A pdb=" N GLU C 300 " --> pdb=" O VAL C 296 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ALA C 301 " --> pdb=" O ALA C 297 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR C 304 " --> pdb=" O GLU C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 341 removed outlier: 3.920A 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: 3.553A 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 431 through 443 Proline residue: C 437 - end of helix Processing helix chain 'C' and resid 446 through 472 removed outlier: 4.150A pdb=" N GLU C 466 " --> pdb=" O ALA C 462 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N ILE C 467 " --> pdb=" O GLY C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 473 through 476 removed outlier: 3.689A pdb=" N LEU C 476 " --> pdb=" O PRO C 473 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 473 through 476' 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: 3.679A pdb=" N ILE C 539 " --> pdb=" O SER C 535 " (cutoff:3.500A) Processing helix chain 'C' and resid 543 through 550 Processing helix chain 'C' and resid 551 through 554 Processing helix chain 'C' and resid 558 through 578 removed outlier: 3.515A pdb=" N ALA C 578 " --> pdb=" O PHE C 574 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 89 removed outlier: 3.505A pdb=" N LEU D 89 " --> pdb=" O LYS D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 124 Processing helix chain 'D' and resid 135 through 140 Processing helix chain 'D' and resid 159 through 171 Processing helix chain 'D' and resid 174 through 178 Processing helix chain 'D' and resid 197 through 210 Processing helix chain 'D' and resid 212 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 removed outlier: 3.560A pdb=" N TYR D 263 " --> pdb=" O ASP D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 283 Processing helix chain 'D' and resid 286 through 296 Processing helix chain 'D' and resid 323 through 333 Processing helix chain 'D' and resid 340 through 346 Processing helix chain 'D' and resid 361 through 366 removed outlier: 3.744A pdb=" N GLY D 365 " --> pdb=" O LEU D 361 " (cutoff:3.500A) Processing helix chain 'D' and resid 374 through 400 removed outlier: 3.794A pdb=" N ALA D 397 " --> pdb=" O ARG D 393 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ILE D 398 " --> pdb=" O LYS D 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 422 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 removed outlier: 3.668A pdb=" N LEU E 89 " --> pdb=" O LYS E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 135 through 140 Processing helix chain 'E' and resid 159 through 171 Processing helix chain 'E' and resid 174 through 179 removed outlier: 3.773A pdb=" N GLY E 179 " --> pdb=" O ASP E 176 " (cutoff:3.500A) Processing helix chain 'E' and resid 197 through 211 removed outlier: 3.987A pdb=" N THR E 211 " --> pdb=" O GLU E 207 " (cutoff:3.500A) Processing helix chain 'E' and resid 212 through 215 Processing helix chain 'E' and resid 227 through 250 removed outlier: 3.654A pdb=" N ARG E 231 " --> pdb=" O PRO E 227 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE E 232 " --> pdb=" O THR E 228 " (cutoff:3.500A) Proline residue: E 235 - end of helix Processing helix chain 'E' and resid 259 through 273 removed outlier: 3.577A pdb=" N TYR E 263 " --> pdb=" O ASP E 259 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 296 removed outlier: 3.605A 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 333 Processing helix chain 'E' and resid 340 through 346 Processing helix chain 'E' and resid 361 through 365 Processing helix chain 'E' and resid 374 through 400 removed outlier: 3.621A pdb=" N ALA E 397 " --> pdb=" O ARG E 393 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ILE E 398 " --> pdb=" O LYS E 394 " (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 445 through 446 No H-bonds generated for 'chain 'E' and resid 445 through 446' Processing helix chain 'E' and resid 447 through 451 Processing helix chain 'E' and resid 455 through 463 Processing helix chain 'F' and resid 85 through 89 removed outlier: 3.613A pdb=" N LEU F 89 " --> pdb=" O LYS F 86 " (cutoff:3.500A) 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 228 through 232 Processing helix chain 'F' and resid 233 through 250 Processing helix chain 'F' and resid 259 through 274 removed outlier: 3.505A pdb=" N TYR F 263 " --> pdb=" O ASP F 259 " (cutoff:3.500A) Processing helix chain 'F' and resid 279 through 283 removed outlier: 4.336A pdb=" N GLY F 282 " --> pdb=" O GLY F 279 " (cutoff:3.500A) Processing helix chain 'F' and resid 284 through 285 No H-bonds generated for 'chain 'F' and resid 284 through 285' 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 Processing helix chain 'F' and resid 361 through 366 removed outlier: 3.782A pdb=" N GLY F 365 " --> pdb=" O LEU F 361 " (cutoff:3.500A) Processing helix chain 'F' and resid 374 through 400 removed outlier: 3.944A pdb=" N ILE F 398 " --> pdb=" O LYS F 394 " (cutoff:3.500A) Processing helix chain 'F' and resid 401 through 404 Processing helix chain 'F' and resid 405 through 422 Processing helix chain 'F' and resid 431 through 444 Processing helix chain 'F' and resid 445 through 446 No H-bonds generated for 'chain 'F' and resid 445 through 446' Processing helix chain 'F' and resid 447 through 451 removed outlier: 3.605A pdb=" N LEU F 451 " --> pdb=" O GLN F 448 " (cutoff:3.500A) Processing helix chain 'F' and resid 455 through 463 Processing helix chain 'F' and resid 466 through 471 removed outlier: 3.956A pdb=" N ILE F 470 " --> pdb=" O LYS F 466 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TRP F 471 " --> pdb=" O LEU F 467 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 466 through 471' Processing helix chain 'G' and resid 7 through 71 removed outlier: 3.615A pdb=" N ARG G 44 " --> pdb=" O PHE G 40 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA G 63 " --> pdb=" O GLU G 59 " (cutoff:3.500A) Processing helix chain 'G' and resid 72 through 82 Processing helix chain 'G' and resid 122 through 167 removed outlier: 3.619A pdb=" N ARG G 146 " --> pdb=" O ASN G 142 " (cutoff:3.500A) Processing helix chain 'G' and resid 167 through 209 Processing helix chain 'H' and resid 6 through 16 removed outlier: 3.560A pdb=" N GLN H 11 " --> pdb=" O PRO H 7 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N GLY H 12 " --> pdb=" O GLU H 8 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N PHE H 13 " --> pdb=" O THR H 9 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ARG H 14 " --> pdb=" O ALA H 10 " (cutoff:3.500A) Processing helix chain 'H' and resid 25 through 38 Processing helix chain 'H' and resid 55 through 58 Processing helix chain 'H' and resid 59 through 64 Processing helix chain 'H' and resid 76 through 83 removed outlier: 3.650A pdb=" N PHE H 81 " --> pdb=" O LEU H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 85 through 98 removed outlier: 3.729A pdb=" N TYR H 89 " --> pdb=" O ASP H 85 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 10 removed outlier: 6.512A pdb=" N ILE A 15 " --> pdb=" O GLN A 7 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N ILE A 9 " --> pdb=" O ALA A 13 " (cutoff:3.500A) removed outlier: 7.130A 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: 5.586A pdb=" N ILE A 39 " --> pdb=" O GLN A 50 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N GLN A 50 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 3.560A 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: 5.762A pdb=" N ILE B 39 " --> pdb=" O GLN B 50 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N GLN B 50 " --> pdb=" O ILE B 39 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ARG B 41 " --> pdb=" O PHE B 48 " (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: 5.659A pdb=" N ILE C 39 " --> pdb=" O GLN C 50 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N GLN C 50 " --> pdb=" O ILE C 39 " (cutoff:3.500A) removed outlier: 3.542A 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: 5.622A pdb=" N VAL D 47 " --> pdb=" O GLN D 58 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N GLN D 58 " --> pdb=" O VAL D 47 " (cutoff:3.500A) removed outlier: 3.891A 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: 5.828A pdb=" N VAL E 47 " --> pdb=" O GLN E 58 " (cutoff:3.500A) removed outlier: 6.540A 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: 5.752A pdb=" N VAL F 47 " --> pdb=" O GLN F 58 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N GLN F 58 " --> pdb=" O VAL F 47 " (cutoff:3.500A) 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 83 through 84 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 83 through 84 current: chain 'A' and resid 285 through 290 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 285 through 290 current: chain 'A' and resid 375 through 384 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 375 through 384 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 143 through 148 removed outlier: 6.559A pdb=" N PHE A 143 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N HIS A 145 " --> pdb=" O THR A 137 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N THR A 137 " --> pdb=" O HIS A 145 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ILE A 147 " --> pdb=" O LEU A 135 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N ALA A 118 " --> pdb=" O PRO A 139 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 128 through 129 removed outlier: 6.914A pdb=" N VAL A 174 " --> pdb=" O LYS A 158 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 72 through 75 Processing sheet with id=AA7, first strand: chain 'B' and resid 83 through 84 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 83 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 384 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 375 through 384 current: chain 'B' and resid 428 through 429 No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 143 through 148 removed outlier: 6.935A pdb=" N PHE B 143 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N HIS B 145 " --> pdb=" O THR B 137 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N THR B 137 " --> pdb=" O HIS B 145 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ILE B 147 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N ALA B 118 " --> pdb=" O PRO B 139 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 128 through 129 removed outlier: 6.867A pdb=" N VAL B 174 " --> pdb=" O LYS B 158 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 204 through 205 removed outlier: 4.770A pdb=" N VAL B 218 " --> pdb=" O PHE B 205 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 72 through 75 Processing sheet with id=AB3, 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=AB3 Processing sheet with id=AB4, first strand: chain 'C' and resid 144 through 148 removed outlier: 6.503A pdb=" N HIS C 145 " --> pdb=" O THR C 137 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N THR C 137 " --> pdb=" O HIS C 145 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ILE C 147 " --> pdb=" O LEU C 135 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N ALA C 118 " --> pdb=" O PRO C 139 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 128 through 129 removed outlier: 6.824A pdb=" N VAL C 174 " --> pdb=" O LYS C 158 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 81 through 84 removed outlier: 3.634A pdb=" N LYS D 110 " --> pdb=" O VAL D 84 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 91 through 93 removed outlier: 6.599A pdb=" N ARG D 91 " --> pdb=" O LEU D 219 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N LEU D 221 " --> pdb=" O ARG D 91 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N PHE D 93 " --> pdb=" O LEU D 221 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N LYS D 223 " --> pdb=" O PHE D 93 " (cutoff:3.500A) removed outlier: 8.691A pdb=" N VAL D 218 " --> pdb=" O PHE D 187 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N VAL D 189 " --> pdb=" O VAL D 218 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N PHE D 220 " --> pdb=" O VAL D 189 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N PHE D 191 " --> pdb=" O PHE D 220 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N ASN D 222 " --> pdb=" O PHE D 191 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N ALA D 193 " --> pdb=" O ASN D 222 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 130 through 131 removed outlier: 4.579A pdb=" N LEU D 144 " --> pdb=" O ILE D 131 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 81 through 84 Processing sheet with id=AC1, first strand: chain 'E' and resid 92 through 93 removed outlier: 6.510A pdb=" N PHE E 93 " --> pdb=" O LEU E 221 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N LYS E 223 " --> pdb=" O PHE E 93 " (cutoff:3.500A) removed outlier: 8.719A pdb=" N VAL E 218 " --> pdb=" O PHE E 187 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N VAL E 189 " --> pdb=" O VAL E 218 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N PHE E 220 " --> pdb=" O VAL E 189 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N PHE E 191 " --> pdb=" O PHE E 220 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N ASN E 222 " --> pdb=" O PHE E 191 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N ALA E 193 " --> pdb=" O ASN E 222 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 124 through 125 removed outlier: 4.707A pdb=" N VAL E 300 " --> pdb=" O ARG E 125 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 130 through 131 removed outlier: 4.484A pdb=" N LEU E 144 " --> pdb=" O ILE E 131 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 81 through 84 Processing sheet with id=AC5, first strand: chain 'F' and resid 92 through 94 removed outlier: 6.511A pdb=" N PHE F 93 " --> pdb=" O LEU F 221 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N LYS F 223 " --> pdb=" O PHE F 93 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N VAL F 189 " --> pdb=" O VAL F 218 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N PHE F 220 " --> pdb=" O VAL F 189 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N PHE F 191 " --> pdb=" O PHE F 220 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N ASN F 222 " --> pdb=" O PHE F 191 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N ALA F 193 " --> pdb=" O ASN F 222 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ALA F 188 " --> pdb=" O LEU F 254 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N ILE F 256 " --> pdb=" O ALA F 188 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N VAL F 190 " --> pdb=" O ILE F 256 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU F 257 " --> pdb=" O ILE F 311 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 124 through 125 removed outlier: 4.714A pdb=" N VAL F 300 " --> pdb=" O ARG F 125 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 144 through 145 removed outlier: 4.649A pdb=" N LEU F 144 " --> pdb=" O ILE F 131 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 89 through 96 Processing sheet with id=AC9, first strand: chain 'H' and resid 19 through 22 removed outlier: 4.249A pdb=" N ASP H 48 " --> pdb=" O ILE H 4 " (cutoff:3.500A) 1150 hydrogen bonds defined for protein. 3249 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: 5.68 Time building geometry restraints manager: 3.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 4936 1.32 - 1.45: 6582 1.45 - 1.57: 15757 1.57 - 1.70: 8 1.70 - 1.82: 190 Bond restraints: 27473 Sorted by residual: bond pdb=" CA SER B 232 " pdb=" CB SER B 232 " ideal model delta sigma weight residual 1.532 1.478 0.054 1.74e-02 3.30e+03 9.66e+00 bond pdb=" CA SER A 232 " pdb=" CB SER A 232 " ideal model delta sigma weight residual 1.532 1.487 0.046 1.79e-02 3.12e+03 6.47e+00 bond pdb=" C THR A 235 " pdb=" O THR A 235 " ideal model delta sigma weight residual 1.237 1.206 0.030 1.19e-02 7.06e+03 6.45e+00 bond pdb=" CA SER C 232 " pdb=" CB SER C 232 " ideal model delta sigma weight residual 1.532 1.491 0.041 1.65e-02 3.67e+03 6.19e+00 bond pdb=" C LYS A 234 " pdb=" O LYS A 234 " ideal model delta sigma weight residual 1.236 1.210 0.027 1.15e-02 7.56e+03 5.51e+00 ... (remaining 27468 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.30: 36756 2.30 - 4.60: 423 4.60 - 6.90: 43 6.90 - 9.20: 10 9.20 - 11.50: 1 Bond angle restraints: 37233 Sorted by residual: angle pdb=" C PHE A 230 " pdb=" CA PHE A 230 " pdb=" CB PHE A 230 " ideal model delta sigma weight residual 109.65 117.15 -7.50 1.71e+00 3.42e-01 1.92e+01 angle pdb=" CA PHE A 230 " pdb=" CB PHE A 230 " pdb=" CG PHE A 230 " ideal model delta sigma weight residual 113.80 118.09 -4.29 1.00e+00 1.00e+00 1.84e+01 angle pdb=" C PHE C 230 " pdb=" CA PHE C 230 " pdb=" CB PHE C 230 " ideal model delta sigma weight residual 109.65 116.78 -7.13 1.71e+00 3.42e-01 1.74e+01 angle pdb=" CA PHE C 230 " pdb=" CB PHE C 230 " pdb=" CG PHE C 230 " ideal model delta sigma weight residual 113.80 117.58 -3.78 1.00e+00 1.00e+00 1.43e+01 angle pdb=" N ILE H 98 " pdb=" CA ILE H 98 " pdb=" C ILE H 98 " ideal model delta sigma weight residual 111.81 108.77 3.04 8.60e-01 1.35e+00 1.25e+01 ... (remaining 37228 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 14884 17.81 - 35.63: 1286 35.63 - 53.44: 383 53.44 - 71.26: 98 71.26 - 89.07: 50 Dihedral angle restraints: 16701 sinusoidal: 6852 harmonic: 9849 Sorted by residual: dihedral pdb=" CA VAL A 368 " pdb=" C VAL A 368 " pdb=" N ILE A 369 " pdb=" CA ILE A 369 " ideal model delta harmonic sigma weight residual 180.00 158.54 21.46 0 5.00e+00 4.00e-02 1.84e+01 dihedral pdb=" C5' ADP A 602 " pdb=" O5' ADP A 602 " pdb=" PA ADP A 602 " pdb=" O2A ADP A 602 " ideal model delta sinusoidal sigma weight residual -60.00 13.71 -73.71 1 2.00e+01 2.50e-03 1.73e+01 dihedral pdb=" CA VAL F 21 " pdb=" C VAL F 21 " pdb=" N GLU F 22 " pdb=" CA GLU F 22 " ideal model delta harmonic sigma weight residual 180.00 -159.69 -20.31 0 5.00e+00 4.00e-02 1.65e+01 ... (remaining 16698 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 3346 0.056 - 0.111: 736 0.111 - 0.167: 70 0.167 - 0.222: 3 0.222 - 0.278: 2 Chirality restraints: 4157 Sorted by residual: chirality pdb=" CA SER C 232 " pdb=" N SER C 232 " pdb=" C SER C 232 " pdb=" CB SER C 232 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.93e+00 chirality pdb=" CA THR A 235 " pdb=" N THR A 235 " pdb=" C THR A 235 " pdb=" CB THR A 235 " both_signs ideal model delta sigma weight residual False 2.53 2.29 0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CA THR B 235 " pdb=" N THR B 235 " pdb=" C THR B 235 " pdb=" CB THR B 235 " both_signs ideal model delta sigma weight residual False 2.53 2.32 0.20 2.00e-01 2.50e+01 1.01e+00 ... (remaining 4154 not shown) Planarity restraints: 4867 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO C 229 " -0.011 2.00e-02 2.50e+03 2.17e-02 4.73e+00 pdb=" C PRO C 229 " 0.038 2.00e-02 2.50e+03 pdb=" O PRO C 229 " -0.014 2.00e-02 2.50e+03 pdb=" N PHE C 230 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU B 565 " 0.011 2.00e-02 2.50e+03 2.17e-02 4.71e+00 pdb=" CD GLU B 565 " -0.038 2.00e-02 2.50e+03 pdb=" OE1 GLU B 565 " 0.014 2.00e-02 2.50e+03 pdb=" OE2 GLU B 565 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP B 446 " -0.010 2.00e-02 2.50e+03 2.03e-02 4.13e+00 pdb=" CG ASP B 446 " 0.035 2.00e-02 2.50e+03 pdb=" OD1 ASP B 446 " -0.013 2.00e-02 2.50e+03 pdb=" OD2 ASP B 446 " -0.012 2.00e-02 2.50e+03 ... (remaining 4864 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 148 2.56 - 3.15: 21342 3.15 - 3.73: 43621 3.73 - 4.32: 62663 4.32 - 4.90: 103723 Nonbonded interactions: 231497 Sorted by model distance: nonbonded pdb=" OG1 THR C 235 " pdb="MG MG C 601 " model vdw 1.976 2.170 nonbonded pdb=" OG1 THR A 235 " pdb="MG MG A 601 " model vdw 2.056 2.170 nonbonded pdb="MG MG C 601 " pdb=" O2G ATP C 602 " model vdw 2.061 2.170 nonbonded pdb=" O MET C 220 " pdb=" OG1 THR C 379 " model vdw 2.105 3.040 nonbonded pdb=" O MET A 220 " pdb=" OG1 THR A 379 " model vdw 2.128 3.040 ... (remaining 231492 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' 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) } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.880 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: 0.510 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 25.850 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.060 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:6.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8812 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 27473 Z= 0.178 Angle : 0.612 11.496 37233 Z= 0.345 Chirality : 0.045 0.278 4157 Planarity : 0.005 0.060 4867 Dihedral : 15.921 89.069 10423 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.52 % Allowed : 13.17 % Favored : 85.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1.36 (0.15), residues: 3437 helix: 1.64 (0.15), residues: 1334 sheet: 0.28 (0.23), residues: 542 loop : 0.65 (0.16), residues: 1561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG A 154 TYR 0.014 0.001 TYR F 54 PHE 0.019 0.001 PHE C 415 TRP 0.007 0.001 TRP C 119 HIS 0.008 0.001 HIS C 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.18 (27473) covalent geometry : angle 0.61242 / 0.34 (37233) hydrogen bonds : bond 0.15617 / 10.51 ( 1150) hydrogen bonds : angle 6.35390 / 4.51 ( 3249) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 296 time to evaluate : 0.973 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: B 446 ASP cc_start: 0.7422 (t0) cc_final: 0.7080 (OUTLIER) REVERT: C 264 ASP cc_start: 0.8187 (OUTLIER) cc_final: 0.7940 (t70) REVERT: D 402 ASP cc_start: 0.8764 (m-30) cc_final: 0.8519 (m-30) REVERT: E 409 ARG cc_start: 0.8595 (ttm110) cc_final: 0.8374 (ttp-170) REVERT: F 98 LYS cc_start: 0.8973 (mmtt) cc_final: 0.8677 (mmmt) REVERT: G 152 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.7820 (tp30) REVERT: H 87 GLU cc_start: 0.8408 (mp0) cc_final: 0.8191 (mp0) REVERT: H 91 ARG cc_start: 0.8107 (mtp85) cc_final: 0.7811 (mtp85) outliers start: 43 outliers final: 28 residues processed: 327 average time/residue: 0.8119 time to fit residues: 300.7088 Evaluate side-chains 306 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 277 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 234 LYS Chi-restraints excluded: chain B residue 255 CYS Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 537 ASP Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 124 LYS Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 264 ASP Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 156 SER Chi-restraints excluded: chain D residue 467 LEU Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 396 VAL Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 152 GLU Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 94 VAL Chi-restraints excluded: chain H residue 98 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 1.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 541 GLN B 202 ASN B 397 GLN B 459 GLN B 496 GLN D 465 GLN G 181 GLN G 185 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.095626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.067190 restraints weight = 40148.282| |-----------------------------------------------------------------------------| r_work (start): 0.2846 rms_B_bonded: 2.03 r_work: 0.2715 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2593 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8868 moved from start: 0.1019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 27473 Z= 0.224 Angle : 0.590 11.394 37233 Z= 0.306 Chirality : 0.047 0.171 4157 Planarity : 0.005 0.054 4867 Dihedral : 6.690 85.428 3903 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.33 % Allowed : 12.04 % Favored : 85.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1.24 (0.15), residues: 3437 helix: 1.59 (0.15), residues: 1331 sheet: 0.18 (0.22), residues: 548 loop : 0.55 (0.16), residues: 1558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 481 TYR 0.015 0.002 TYR F 54 PHE 0.020 0.002 PHE C 559 TRP 0.016 0.002 TRP B 119 HIS 0.006 0.001 HIS C 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00525 / 0.22 (27473) covalent geometry : angle 0.58982 / 0.31 (37233) hydrogen bonds : bond 0.05529 / 3.74 ( 1150) hydrogen bonds : angle 5.21019 / 3.69 ( 3249) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 295 time to evaluate : 1.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 323 MET cc_start: 0.9247 (OUTLIER) cc_final: 0.8183 (mmt) REVERT: B 294 MET cc_start: 0.8984 (mmm) cc_final: 0.8768 (mtt) REVERT: C 541 GLN cc_start: 0.8545 (mm110) cc_final: 0.8293 (mm110) REVERT: D 275 GLU cc_start: 0.8921 (OUTLIER) cc_final: 0.8676 (mt-10) REVERT: F 98 LYS cc_start: 0.9065 (mmtt) cc_final: 0.8705 (mmmt) REVERT: F 206 GLN cc_start: 0.8866 (mt0) cc_final: 0.8639 (mt0) REVERT: G 152 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.7895 (tp30) REVERT: G 165 GLU cc_start: 0.8651 (mm-30) cc_final: 0.8123 (mt-10) REVERT: H 87 GLU cc_start: 0.8457 (mp0) cc_final: 0.8163 (mp0) REVERT: H 91 ARG cc_start: 0.8235 (mtp85) cc_final: 0.7825 (mtp85) outliers start: 66 outliers final: 32 residues processed: 340 average time/residue: 0.8899 time to fit residues: 340.6555 Evaluate side-chains 318 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 283 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 255 CYS Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 530 ILE Chi-restraints excluded: chain B residue 537 ASP Chi-restraints excluded: chain B residue 568 LYS Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 374 GLU Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 275 GLU Chi-restraints excluded: chain D residue 467 LEU Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 78 ASP Chi-restraints excluded: chain E residue 265 GLU Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 152 GLU Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 49 GLU Chi-restraints excluded: chain H residue 94 VAL Chi-restraints excluded: chain H residue 98 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 199 optimal weight: 2.9990 chunk 197 optimal weight: 4.9990 chunk 246 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 47 optimal weight: 10.0000 chunk 124 optimal weight: 2.9990 chunk 274 optimal weight: 7.9990 chunk 251 optimal weight: 3.9990 chunk 52 optimal weight: 4.9990 chunk 262 optimal weight: 0.9980 chunk 283 optimal weight: 0.3980 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 541 GLN B 202 ASN B 459 GLN D 465 GLN E 129 GLN E 428 GLN G 180 GLN G 181 GLN G 185 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.095702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.067260 restraints weight = 40369.583| |-----------------------------------------------------------------------------| r_work (start): 0.2845 rms_B_bonded: 2.04 r_work: 0.2715 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2593 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8867 moved from start: 0.1283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 27473 Z= 0.200 Angle : 0.562 9.933 37233 Z= 0.290 Chirality : 0.046 0.169 4157 Planarity : 0.005 0.050 4867 Dihedral : 6.658 83.336 3887 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.30 % Allowed : 12.68 % Favored : 85.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1.19 (0.15), residues: 3437 helix: 1.64 (0.15), residues: 1314 sheet: -0.01 (0.22), residues: 559 loop : 0.51 (0.16), residues: 1564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 481 TYR 0.016 0.001 TYR H 21 PHE 0.018 0.002 PHE C 559 TRP 0.013 0.001 TRP A 119 HIS 0.005 0.001 HIS C 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00470 / 0.20 (27473) covalent geometry : angle 0.56169 / 0.29 (37233) hydrogen bonds : bond 0.05030 / 3.39 ( 1150) hydrogen bonds : angle 5.04731 / 3.57 ( 3249) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 305 time to evaluate : 1.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 323 MET cc_start: 0.9231 (OUTLIER) cc_final: 0.8133 (mmt) REVERT: B 269 PHE cc_start: 0.9239 (OUTLIER) cc_final: 0.8687 (t80) REVERT: B 294 MET cc_start: 0.9028 (mmm) cc_final: 0.8810 (mtt) REVERT: B 537 ASP cc_start: 0.8577 (OUTLIER) cc_final: 0.8305 (OUTLIER) REVERT: C 336 GLU cc_start: 0.8065 (tp30) cc_final: 0.7812 (mp0) REVERT: C 481 ARG cc_start: 0.8341 (mmm-85) cc_final: 0.7963 (ttp-110) REVERT: C 541 GLN cc_start: 0.8617 (mm110) cc_final: 0.8318 (mm110) REVERT: D 61 GLU cc_start: 0.7955 (OUTLIER) cc_final: 0.7707 (mp0) REVERT: D 275 GLU cc_start: 0.8907 (OUTLIER) cc_final: 0.8693 (mt-10) REVERT: D 394 LYS cc_start: 0.8952 (ttmm) cc_final: 0.8442 (mppt) REVERT: F 206 GLN cc_start: 0.8840 (mt0) cc_final: 0.8572 (mt0) REVERT: G 152 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.8010 (tp30) REVERT: G 165 GLU cc_start: 0.8655 (mm-30) cc_final: 0.8069 (mt-10) REVERT: H 19 GLU cc_start: 0.5416 (tm-30) cc_final: 0.5115 (tm-30) REVERT: H 87 GLU cc_start: 0.8459 (mp0) cc_final: 0.8144 (mp0) REVERT: H 91 ARG cc_start: 0.8319 (mtp85) cc_final: 0.7985 (mtp85) outliers start: 65 outliers final: 35 residues processed: 349 average time/residue: 0.9329 time to fit residues: 365.6400 Evaluate side-chains 323 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 283 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 255 CYS Chi-restraints excluded: chain B residue 269 PHE Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 537 ASP Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 374 GLU Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain D residue 185 GLU Chi-restraints excluded: chain D residue 206 GLN Chi-restraints excluded: chain D residue 275 GLU Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 467 LEU Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 78 ASP Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 265 GLU Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain F residue 305 LYS Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 152 GLU Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 49 GLU Chi-restraints excluded: chain H residue 98 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 157 optimal weight: 0.7980 chunk 34 optimal weight: 3.9990 chunk 131 optimal weight: 4.9990 chunk 98 optimal weight: 1.9990 chunk 138 optimal weight: 2.9990 chunk 192 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 165 optimal weight: 0.7980 chunk 279 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 70.523 > 50:) chunk 247 optimal weight: 3.9990 chunk 60 optimal weight: 10.0000 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 418 HIS A 496 GLN A 541 GLN B 202 ASN B 238 GLN B 459 GLN D 465 GLN G 180 GLN G 181 GLN G 185 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.095536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.067066 restraints weight = 40228.293| |-----------------------------------------------------------------------------| r_work (start): 0.2842 rms_B_bonded: 2.04 r_work: 0.2711 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2589 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8869 moved from start: 0.1475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 27473 Z= 0.202 Angle : 0.563 10.377 37233 Z= 0.290 Chirality : 0.046 0.163 4157 Planarity : 0.005 0.049 4867 Dihedral : 6.493 83.623 3883 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.82 % Allowed : 12.85 % Favored : 84.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1.12 (0.15), residues: 3437 helix: 1.63 (0.15), residues: 1319 sheet: -0.11 (0.22), residues: 553 loop : 0.46 (0.16), residues: 1565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 420 TYR 0.017 0.001 TYR H 21 PHE 0.018 0.002 PHE C 559 TRP 0.013 0.001 TRP A 119 HIS 0.004 0.001 HIS C 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00478 / 0.20 (27473) covalent geometry : angle 0.56337 / 0.29 (37233) hydrogen bonds : bond 0.04860 / 3.28 ( 1150) hydrogen bonds : angle 4.98241 / 3.51 ( 3249) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 302 time to evaluate : 1.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 323 MET cc_start: 0.9222 (OUTLIER) cc_final: 0.8123 (mmt) REVERT: B 269 PHE cc_start: 0.9227 (OUTLIER) cc_final: 0.8614 (t80) REVERT: B 294 MET cc_start: 0.9050 (mmm) cc_final: 0.8814 (mtt) REVERT: C 124 LYS cc_start: 0.9104 (OUTLIER) cc_final: 0.8772 (ptpp) REVERT: C 264 ASP cc_start: 0.8304 (t70) cc_final: 0.7731 (t0) REVERT: C 268 GLU cc_start: 0.8275 (mp0) cc_final: 0.7456 (mt-10) REVERT: C 336 GLU cc_start: 0.8072 (tp30) cc_final: 0.7813 (mp0) REVERT: C 541 GLN cc_start: 0.8652 (mm110) cc_final: 0.8336 (mm110) REVERT: D 61 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.7762 (mp0) REVERT: D 394 LYS cc_start: 0.8913 (ttmm) cc_final: 0.8410 (mppt) REVERT: E 248 GLU cc_start: 0.8561 (OUTLIER) cc_final: 0.8134 (mp0) REVERT: E 305 LYS cc_start: 0.9040 (mtpp) cc_final: 0.8772 (mmmm) REVERT: F 206 GLN cc_start: 0.8835 (mt0) cc_final: 0.8616 (mt0) REVERT: G 152 GLU cc_start: 0.8433 (OUTLIER) cc_final: 0.8003 (tp30) REVERT: G 165 GLU cc_start: 0.8670 (mm-30) cc_final: 0.8093 (mt-10) REVERT: H 21 TYR cc_start: 0.7616 (m-80) cc_final: 0.7060 (m-80) REVERT: H 87 GLU cc_start: 0.8501 (mp0) cc_final: 0.8174 (mp0) REVERT: H 91 ARG cc_start: 0.8338 (mtp85) cc_final: 0.8012 (mtp85) outliers start: 80 outliers final: 43 residues processed: 355 average time/residue: 0.8959 time to fit residues: 358.5852 Evaluate side-chains 336 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 287 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 255 CYS Chi-restraints excluded: chain B residue 269 PHE Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 568 LYS Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 124 LYS Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 374 GLU Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain D residue 185 GLU Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 206 GLN Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 467 LEU Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 78 ASP Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 248 GLU Chi-restraints excluded: chain E residue 265 GLU Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain F residue 305 LYS Chi-restraints excluded: chain F residue 392 ILE Chi-restraints excluded: chain G residue 9 MET Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 152 GLU Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 49 GLU Chi-restraints excluded: chain H residue 72 LEU Chi-restraints excluded: chain H residue 94 VAL Chi-restraints excluded: chain H residue 98 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 80 optimal weight: 0.8980 chunk 314 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 156 optimal weight: 0.9990 chunk 183 optimal weight: 2.9990 chunk 330 optimal weight: 7.9990 chunk 26 optimal weight: 0.2980 chunk 242 optimal weight: 4.9990 chunk 170 optimal weight: 0.9980 chunk 247 optimal weight: 4.9990 chunk 328 optimal weight: 3.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 541 GLN B 202 ASN B 459 GLN D 465 GLN G 180 GLN G 181 GLN G 185 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.097115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.068843 restraints weight = 39932.214| |-----------------------------------------------------------------------------| r_work (start): 0.2876 rms_B_bonded: 2.04 r_work: 0.2748 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2627 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8848 moved from start: 0.1565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 27473 Z= 0.128 Angle : 0.515 10.196 37233 Z= 0.264 Chirality : 0.043 0.157 4157 Planarity : 0.004 0.046 4867 Dihedral : 6.005 77.183 3879 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.37 % Allowed : 14.02 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.15), residues: 3437 helix: 1.69 (0.15), residues: 1339 sheet: -0.10 (0.22), residues: 543 loop : 0.49 (0.16), residues: 1555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 420 TYR 0.014 0.001 TYR H 21 PHE 0.016 0.001 PHE C 559 TRP 0.012 0.001 TRP A 119 HIS 0.005 0.001 HIS C 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (27473) covalent geometry : angle 0.51515 / 0.26 (37233) hydrogen bonds : bond 0.04160 / 2.81 ( 1150) hydrogen bonds : angle 4.79322 / 3.38 ( 3249) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 310 time to evaluate : 1.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 323 MET cc_start: 0.9220 (OUTLIER) cc_final: 0.8105 (mmt) REVERT: B 269 PHE cc_start: 0.9218 (OUTLIER) cc_final: 0.8550 (t80) REVERT: B 294 MET cc_start: 0.9035 (mmm) cc_final: 0.8755 (mtt) REVERT: B 393 GLU cc_start: 0.7744 (tt0) cc_final: 0.7417 (pt0) REVERT: B 478 ASP cc_start: 0.8081 (m-30) cc_final: 0.7862 (m-30) REVERT: C 154 ARG cc_start: 0.8836 (mtp-110) cc_final: 0.8564 (mtp-110) REVERT: C 264 ASP cc_start: 0.8340 (t70) cc_final: 0.7672 (t0) REVERT: C 268 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.7429 (mt-10) REVERT: C 336 GLU cc_start: 0.8030 (tp30) cc_final: 0.7790 (mp0) REVERT: C 393 GLU cc_start: 0.8740 (OUTLIER) cc_final: 0.8507 (pp20) REVERT: C 481 ARG cc_start: 0.8460 (mmm-85) cc_final: 0.8063 (ttp-110) REVERT: C 541 GLN cc_start: 0.8673 (mm110) cc_final: 0.8315 (mm110) REVERT: D 206 GLN cc_start: 0.8415 (OUTLIER) cc_final: 0.7470 (mt0) REVERT: D 394 LYS cc_start: 0.8810 (ttmm) cc_final: 0.8363 (mppt) REVERT: E 248 GLU cc_start: 0.8526 (OUTLIER) cc_final: 0.8098 (mp0) REVERT: E 305 LYS cc_start: 0.9050 (mtpp) cc_final: 0.8781 (mmmm) REVERT: F 206 GLN cc_start: 0.8797 (mt0) cc_final: 0.8518 (mt0) REVERT: F 465 GLN cc_start: 0.8377 (OUTLIER) cc_final: 0.7390 (tm-30) REVERT: G 152 GLU cc_start: 0.8447 (tt0) cc_final: 0.7993 (tp30) REVERT: H 21 TYR cc_start: 0.7616 (m-80) cc_final: 0.7041 (m-80) REVERT: H 87 GLU cc_start: 0.8462 (mp0) cc_final: 0.8143 (mp0) REVERT: H 91 ARG cc_start: 0.8360 (mtp85) cc_final: 0.8036 (mtp85) outliers start: 67 outliers final: 36 residues processed: 357 average time/residue: 0.8637 time to fit residues: 347.8988 Evaluate side-chains 329 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 286 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 255 CYS Chi-restraints excluded: chain B residue 269 PHE Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 268 GLU Chi-restraints excluded: chain C residue 348 GLU Chi-restraints excluded: chain C residue 374 GLU Chi-restraints excluded: chain C residue 393 GLU Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 185 GLU Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 206 GLN Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 467 LEU Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 248 GLU Chi-restraints excluded: chain E residue 265 GLU Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain F residue 305 LYS Chi-restraints excluded: chain F residue 392 ILE Chi-restraints excluded: chain F residue 465 GLN Chi-restraints excluded: chain G residue 9 MET Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain H residue 49 GLU Chi-restraints excluded: chain H residue 94 VAL Chi-restraints excluded: chain H residue 98 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 25 optimal weight: 7.9990 chunk 151 optimal weight: 0.6980 chunk 13 optimal weight: 9.9990 chunk 116 optimal weight: 5.9990 chunk 212 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 192 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 297 optimal weight: 2.9990 chunk 250 optimal weight: 3.9990 chunk 87 optimal weight: 0.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 541 GLN B 202 ASN B 459 GLN B 571 GLN ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 465 GLN G 180 GLN G 181 GLN G 185 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.095269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.066830 restraints weight = 40204.696| |-----------------------------------------------------------------------------| r_work (start): 0.2840 rms_B_bonded: 2.04 r_work: 0.2708 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2585 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8873 moved from start: 0.1648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 27473 Z= 0.218 Angle : 0.572 9.856 37233 Z= 0.293 Chirality : 0.046 0.165 4157 Planarity : 0.005 0.054 4867 Dihedral : 6.185 81.220 3872 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.61 % Allowed : 13.84 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1.18 (0.15), residues: 3437 helix: 1.70 (0.15), residues: 1323 sheet: -0.08 (0.22), residues: 541 loop : 0.45 (0.16), residues: 1573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 420 TYR 0.017 0.002 TYR F 54 PHE 0.018 0.002 PHE C 559 TRP 0.010 0.001 TRP B 119 HIS 0.003 0.001 HIS F 252 Details of bonding type rmsd/Z covalent geometry : bond 0.00518 / 0.22 (27473) covalent geometry : angle 0.57223 / 0.29 (37233) hydrogen bonds : bond 0.04837 / 3.26 ( 1150) hydrogen bonds : angle 4.89104 / 3.44 ( 3249) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 298 time to evaluate : 1.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 ARG cc_start: 0.8621 (mtm-85) cc_final: 0.8380 (mtm-85) REVERT: A 323 MET cc_start: 0.9226 (OUTLIER) cc_final: 0.8127 (mmt) REVERT: B 269 PHE cc_start: 0.9225 (OUTLIER) cc_final: 0.8628 (t80) REVERT: B 294 MET cc_start: 0.9059 (mmm) cc_final: 0.8807 (mtt) REVERT: B 393 GLU cc_start: 0.7753 (tt0) cc_final: 0.7406 (pt0) REVERT: B 446 ASP cc_start: 0.7618 (t0) cc_final: 0.7100 (t0) REVERT: B 478 ASP cc_start: 0.8099 (m-30) cc_final: 0.7867 (m-30) REVERT: C 124 LYS cc_start: 0.9106 (OUTLIER) cc_final: 0.8787 (ptpp) REVERT: C 264 ASP cc_start: 0.8362 (t70) cc_final: 0.7683 (t0) REVERT: C 268 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.7413 (mt-10) REVERT: C 336 GLU cc_start: 0.8077 (tp30) cc_final: 0.7809 (mp0) REVERT: C 481 ARG cc_start: 0.8488 (mmm-85) cc_final: 0.8090 (ttp-110) REVERT: C 537 ASP cc_start: 0.8081 (m-30) cc_final: 0.7856 (m-30) REVERT: C 541 GLN cc_start: 0.8678 (mm110) cc_final: 0.8342 (mm110) REVERT: D 61 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.7644 (pm20) REVERT: D 394 LYS cc_start: 0.8852 (ttmm) cc_final: 0.8390 (mppt) REVERT: E 248 GLU cc_start: 0.8562 (OUTLIER) cc_final: 0.8157 (mp0) REVERT: E 305 LYS cc_start: 0.9057 (mtpp) cc_final: 0.8780 (mmmm) REVERT: F 206 GLN cc_start: 0.8836 (mt0) cc_final: 0.8602 (mt0) REVERT: G 152 GLU cc_start: 0.8470 (tt0) cc_final: 0.7979 (tp30) REVERT: G 155 LYS cc_start: 0.8816 (OUTLIER) cc_final: 0.8432 (mmtm) REVERT: H 21 TYR cc_start: 0.7600 (m-80) cc_final: 0.7044 (m-80) REVERT: H 87 GLU cc_start: 0.8501 (mp0) cc_final: 0.8181 (mp0) outliers start: 74 outliers final: 43 residues processed: 350 average time/residue: 0.8194 time to fit residues: 322.9409 Evaluate side-chains 339 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 289 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 104 ARG Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 255 CYS Chi-restraints excluded: chain B residue 269 PHE Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 124 LYS Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 268 GLU Chi-restraints excluded: chain C residue 374 GLU Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain D residue 185 GLU Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 206 GLN Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 467 LEU Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 78 ASP Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 248 GLU Chi-restraints excluded: chain E residue 265 GLU Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain F residue 3 LEU Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain F residue 392 ILE Chi-restraints excluded: chain G residue 9 MET Chi-restraints excluded: chain G residue 20 LEU Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 155 LYS Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 94 VAL Chi-restraints excluded: chain H residue 98 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 34 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 98 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 49 optimal weight: 0.8980 chunk 130 optimal weight: 4.9990 chunk 128 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 257 optimal weight: 3.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 541 GLN B 202 ASN B 459 GLN D 465 GLN G 166 GLN G 180 GLN G 181 GLN G 185 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.096589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.068578 restraints weight = 39827.305| |-----------------------------------------------------------------------------| r_work (start): 0.2871 rms_B_bonded: 2.01 r_work: 0.2742 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2621 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8851 moved from start: 0.1699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 27473 Z= 0.134 Angle : 0.526 10.230 37233 Z= 0.269 Chirality : 0.044 0.155 4157 Planarity : 0.004 0.045 4867 Dihedral : 5.942 77.956 3872 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.33 % Allowed : 14.16 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1.18 (0.15), residues: 3437 helix: 1.65 (0.15), residues: 1354 sheet: -0.11 (0.22), residues: 538 loop : 0.48 (0.16), residues: 1545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 154 TYR 0.013 0.001 TYR H 21 PHE 0.016 0.001 PHE C 559 TRP 0.012 0.001 TRP A 119 HIS 0.005 0.001 HIS E 458 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.13 (27473) covalent geometry : angle 0.52609 / 0.27 (37233) hydrogen bonds : bond 0.04181 / 2.82 ( 1150) hydrogen bonds : angle 4.76027 / 3.35 ( 3249) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 304 time to evaluate : 0.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 ARG cc_start: 0.8596 (mtm-85) cc_final: 0.8383 (mtm-85) REVERT: A 323 MET cc_start: 0.9220 (OUTLIER) cc_final: 0.8108 (mmt) REVERT: B 269 PHE cc_start: 0.9208 (OUTLIER) cc_final: 0.8537 (t80) REVERT: B 294 MET cc_start: 0.9012 (mmm) cc_final: 0.8712 (mtt) REVERT: B 393 GLU cc_start: 0.7718 (tt0) cc_final: 0.7360 (pt0) REVERT: B 478 ASP cc_start: 0.8090 (m-30) cc_final: 0.7848 (m-30) REVERT: B 565 GLU cc_start: 0.7921 (tm-30) cc_final: 0.7721 (tm-30) REVERT: C 124 LYS cc_start: 0.9099 (OUTLIER) cc_final: 0.8794 (ptpp) REVERT: C 264 ASP cc_start: 0.8368 (t70) cc_final: 0.7710 (t0) REVERT: C 268 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.7416 (mt-10) REVERT: C 336 GLU cc_start: 0.8040 (tp30) cc_final: 0.7793 (mp0) REVERT: C 481 ARG cc_start: 0.8450 (mmm-85) cc_final: 0.8037 (ttp-110) REVERT: C 537 ASP cc_start: 0.8095 (m-30) cc_final: 0.7795 (m-30) REVERT: C 541 GLN cc_start: 0.8722 (mm110) cc_final: 0.8314 (mm110) REVERT: E 7 GLU cc_start: 0.5474 (pm20) cc_final: 0.4805 (pm20) REVERT: E 248 GLU cc_start: 0.8505 (OUTLIER) cc_final: 0.8092 (mp0) REVERT: E 305 LYS cc_start: 0.9037 (mtpp) cc_final: 0.8772 (mmmm) REVERT: F 206 GLN cc_start: 0.8824 (mt0) cc_final: 0.8567 (mt0) REVERT: G 152 GLU cc_start: 0.8494 (tt0) cc_final: 0.7955 (tp30) REVERT: G 155 LYS cc_start: 0.8769 (OUTLIER) cc_final: 0.8388 (mmtm) REVERT: H 21 TYR cc_start: 0.7513 (m-80) cc_final: 0.6995 (m-80) REVERT: H 49 GLU cc_start: 0.6833 (pm20) cc_final: 0.6289 (mp0) REVERT: H 87 GLU cc_start: 0.8444 (mp0) cc_final: 0.8122 (mp0) REVERT: H 91 ARG cc_start: 0.8292 (mtp85) cc_final: 0.8055 (mtt90) outliers start: 66 outliers final: 41 residues processed: 352 average time/residue: 0.8333 time to fit residues: 330.3676 Evaluate side-chains 337 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 290 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 340 ARG Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 255 CYS Chi-restraints excluded: chain B residue 269 PHE Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 124 LYS Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 268 GLU Chi-restraints excluded: chain C residue 374 GLU Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 130 PHE Chi-restraints excluded: chain D residue 185 GLU Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 206 GLN Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 467 LEU Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 185 GLU Chi-restraints excluded: chain E residue 248 GLU Chi-restraints excluded: chain E residue 265 GLU Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain F residue 3 LEU Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain F residue 305 LYS Chi-restraints excluded: chain F residue 392 ILE Chi-restraints excluded: chain G residue 9 MET Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 155 LYS Chi-restraints excluded: chain H residue 38 GLU Chi-restraints excluded: chain H residue 94 VAL Chi-restraints excluded: chain H residue 98 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 110 optimal weight: 0.5980 chunk 227 optimal weight: 2.9990 chunk 147 optimal weight: 5.9990 chunk 234 optimal weight: 0.8980 chunk 131 optimal weight: 0.5980 chunk 10 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 37 optimal weight: 8.9990 chunk 105 optimal weight: 0.3980 chunk 284 optimal weight: 0.6980 chunk 292 optimal weight: 0.0030 overall best weight: 0.4590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 541 GLN B 202 ASN B 397 GLN B 459 GLN D 465 GLN G 180 GLN G 181 GLN G 185 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.098687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.070829 restraints weight = 40296.633| |-----------------------------------------------------------------------------| r_work (start): 0.2912 rms_B_bonded: 2.03 r_work: 0.2785 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2666 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8822 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 27473 Z= 0.102 Angle : 0.506 10.821 37233 Z= 0.256 Chirality : 0.043 0.169 4157 Planarity : 0.004 0.045 4867 Dihedral : 5.605 76.360 3872 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.66 % Favored : 98.31 % Rotamer: Outliers : 2.01 % Allowed : 14.80 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1.26 (0.15), residues: 3437 helix: 1.76 (0.15), residues: 1362 sheet: -0.20 (0.22), residues: 544 loop : 0.54 (0.16), residues: 1531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D 420 TYR 0.010 0.001 TYR H 21 PHE 0.014 0.001 PHE C 559 TRP 0.015 0.001 TRP A 119 HIS 0.005 0.000 HIS C 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.10 (27473) covalent geometry : angle 0.50569 / 0.26 (37233) hydrogen bonds : bond 0.03610 / 2.45 ( 1150) hydrogen bonds : angle 4.58235 / 3.23 ( 3249) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 312 time to evaluate : 0.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 ARG cc_start: 0.8602 (mtm-85) cc_final: 0.8393 (mtm-85) REVERT: A 323 MET cc_start: 0.9232 (OUTLIER) cc_final: 0.8142 (mmt) REVERT: B 269 PHE cc_start: 0.9173 (OUTLIER) cc_final: 0.8427 (t80) REVERT: B 393 GLU cc_start: 0.7708 (tt0) cc_final: 0.7350 (pt0) REVERT: B 478 ASP cc_start: 0.8036 (m-30) cc_final: 0.7768 (m-30) REVERT: B 531 LYS cc_start: 0.8170 (mppt) cc_final: 0.7966 (mppt) REVERT: C 124 LYS cc_start: 0.9094 (OUTLIER) cc_final: 0.8795 (ptpp) REVERT: C 268 GLU cc_start: 0.8352 (OUTLIER) cc_final: 0.8044 (mt-10) REVERT: C 336 GLU cc_start: 0.8020 (tp30) cc_final: 0.7755 (mp0) REVERT: C 416 ARG cc_start: 0.8585 (mtm-85) cc_final: 0.8369 (mtm110) REVERT: C 456 GLU cc_start: 0.8654 (tt0) cc_final: 0.8317 (tm-30) REVERT: C 481 ARG cc_start: 0.8444 (mmm-85) cc_final: 0.8039 (ttp-110) REVERT: C 537 ASP cc_start: 0.8116 (m-30) cc_final: 0.7766 (m-30) REVERT: C 541 GLN cc_start: 0.8764 (mm110) cc_final: 0.8329 (mm110) REVERT: D 109 GLU cc_start: 0.8005 (mm-30) cc_final: 0.7787 (mm-30) REVERT: D 402 ASP cc_start: 0.8857 (m-30) cc_final: 0.8618 (m-30) REVERT: E 7 GLU cc_start: 0.5449 (pm20) cc_final: 0.4815 (pm20) REVERT: E 248 GLU cc_start: 0.8442 (OUTLIER) cc_final: 0.8050 (mp0) REVERT: E 305 LYS cc_start: 0.9073 (mtpp) cc_final: 0.8811 (mmmm) REVERT: E 420 ARG cc_start: 0.8496 (mtp-110) cc_final: 0.8149 (mtp180) REVERT: F 206 GLN cc_start: 0.8774 (mt0) cc_final: 0.8558 (mt0) REVERT: F 305 LYS cc_start: 0.9048 (OUTLIER) cc_final: 0.8701 (mppt) REVERT: F 342 GLU cc_start: 0.8304 (mp0) cc_final: 0.8090 (mp0) REVERT: G 152 GLU cc_start: 0.8477 (tt0) cc_final: 0.7943 (tp30) REVERT: G 155 LYS cc_start: 0.8793 (OUTLIER) cc_final: 0.8413 (mmtm) REVERT: G 175 GLN cc_start: 0.8815 (mt0) cc_final: 0.8531 (mt0) REVERT: H 21 TYR cc_start: 0.7541 (m-80) cc_final: 0.7041 (m-80) REVERT: H 91 ARG cc_start: 0.8346 (mtp85) cc_final: 0.8086 (mtt90) outliers start: 57 outliers final: 38 residues processed: 352 average time/residue: 0.7553 time to fit residues: 300.3100 Evaluate side-chains 340 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 295 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 340 ARG Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 255 CYS Chi-restraints excluded: chain B residue 269 PHE Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 124 LYS Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 268 GLU Chi-restraints excluded: chain C residue 374 GLU Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 130 PHE Chi-restraints excluded: chain D residue 185 GLU Chi-restraints excluded: chain D residue 206 GLN Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 248 GLU Chi-restraints excluded: chain E residue 265 GLU Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain F residue 3 LEU Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain F residue 305 LYS Chi-restraints excluded: chain F residue 392 ILE Chi-restraints excluded: chain G residue 47 MET Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 155 LYS Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 38 GLU Chi-restraints excluded: chain H residue 94 VAL Chi-restraints excluded: chain H residue 98 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 59 optimal weight: 4.9990 chunk 199 optimal weight: 4.9990 chunk 328 optimal weight: 0.9980 chunk 30 optimal weight: 5.9990 chunk 42 optimal weight: 4.9990 chunk 69 optimal weight: 4.9990 chunk 246 optimal weight: 0.9990 chunk 109 optimal weight: 7.9990 chunk 304 optimal weight: 2.9990 chunk 161 optimal weight: 9.9990 chunk 227 optimal weight: 0.0070 overall best weight: 2.0004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 316 GLN A 541 GLN B 202 ASN B 459 GLN ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 338 GLN D 465 GLN G 166 GLN G 180 GLN G 181 GLN G 185 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.095913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.067604 restraints weight = 40221.059| |-----------------------------------------------------------------------------| r_work (start): 0.2853 rms_B_bonded: 2.03 r_work: 0.2723 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2601 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8864 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 27473 Z= 0.192 Angle : 0.565 10.766 37233 Z= 0.288 Chirality : 0.045 0.166 4157 Planarity : 0.005 0.055 4867 Dihedral : 5.871 80.531 3868 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.86 % Favored : 98.11 % Rotamer: Outliers : 1.94 % Allowed : 15.29 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1.23 (0.15), residues: 3437 helix: 1.73 (0.15), residues: 1344 sheet: -0.13 (0.22), residues: 547 loop : 0.50 (0.16), residues: 1546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D 420 TYR 0.017 0.001 TYR F 54 PHE 0.018 0.002 PHE C 559 TRP 0.009 0.001 TRP B 119 HIS 0.003 0.001 HIS C 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.19 (27473) covalent geometry : angle 0.56499 / 0.29 (37233) hydrogen bonds : bond 0.04512 / 3.04 ( 1150) hydrogen bonds : angle 4.76103 / 3.35 ( 3249) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 299 time to evaluate : 0.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 323 MET cc_start: 0.9226 (OUTLIER) cc_final: 0.8100 (mmt) REVERT: B 269 PHE cc_start: 0.9224 (OUTLIER) cc_final: 0.8566 (t80) REVERT: B 294 MET cc_start: 0.9020 (mmm) cc_final: 0.8718 (mtt) REVERT: B 478 ASP cc_start: 0.8043 (m-30) cc_final: 0.7791 (m-30) REVERT: C 124 LYS cc_start: 0.9102 (OUTLIER) cc_final: 0.8792 (ptpp) REVERT: C 268 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.8065 (mt-10) REVERT: C 336 GLU cc_start: 0.8053 (tp30) cc_final: 0.7796 (mp0) REVERT: C 456 GLU cc_start: 0.8679 (tt0) cc_final: 0.8355 (tm-30) REVERT: C 481 ARG cc_start: 0.8431 (mmm-85) cc_final: 0.8116 (ttp-110) REVERT: C 537 ASP cc_start: 0.8157 (m-30) cc_final: 0.7829 (m-30) REVERT: C 541 GLN cc_start: 0.8757 (mm110) cc_final: 0.8299 (mm110) REVERT: C 557 GLU cc_start: 0.8372 (mp0) cc_final: 0.8144 (mp0) REVERT: D 402 ASP cc_start: 0.8886 (m-30) cc_final: 0.8648 (m-30) REVERT: E 7 GLU cc_start: 0.5352 (pm20) cc_final: 0.4867 (pm20) REVERT: E 248 GLU cc_start: 0.8518 (OUTLIER) cc_final: 0.8120 (mp0) REVERT: E 305 LYS cc_start: 0.9029 (mtpp) cc_final: 0.8765 (mmmm) REVERT: E 368 LYS cc_start: 0.7934 (OUTLIER) cc_final: 0.7625 (mtmm) REVERT: F 206 GLN cc_start: 0.8805 (mt0) cc_final: 0.8549 (mt0) REVERT: G 152 GLU cc_start: 0.8487 (tt0) cc_final: 0.7942 (tp30) REVERT: G 155 LYS cc_start: 0.8784 (OUTLIER) cc_final: 0.8388 (mmtm) REVERT: H 21 TYR cc_start: 0.7503 (m-80) cc_final: 0.7043 (m-80) REVERT: H 91 ARG cc_start: 0.8366 (mtp85) cc_final: 0.8126 (mtt90) outliers start: 55 outliers final: 38 residues processed: 339 average time/residue: 0.7861 time to fit residues: 301.7158 Evaluate side-chains 337 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 292 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 255 CYS Chi-restraints excluded: chain B residue 269 PHE Chi-restraints excluded: chain B residue 285 THR Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 124 LYS Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 154 ARG Chi-restraints excluded: chain C residue 268 GLU Chi-restraints excluded: chain C residue 374 GLU Chi-restraints excluded: chain C residue 536 ILE Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 130 PHE Chi-restraints excluded: chain D residue 185 GLU Chi-restraints excluded: chain D residue 206 GLN Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 185 GLU Chi-restraints excluded: chain E residue 248 GLU Chi-restraints excluded: chain E residue 265 GLU Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain E residue 368 LYS Chi-restraints excluded: chain E residue 395 LEU Chi-restraints excluded: chain F residue 3 LEU Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain F residue 305 LYS Chi-restraints excluded: chain F residue 392 ILE Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 155 LYS Chi-restraints excluded: chain H residue 38 GLU Chi-restraints excluded: chain H residue 94 VAL Chi-restraints excluded: chain H residue 98 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 165 optimal weight: 1.9990 chunk 320 optimal weight: 4.9990 chunk 104 optimal weight: 7.9990 chunk 17 optimal weight: 0.9980 chunk 334 optimal weight: 6.9990 chunk 307 optimal weight: 0.8980 chunk 14 optimal weight: 4.9990 chunk 240 optimal weight: 0.9980 chunk 169 optimal weight: 4.9990 chunk 313 optimal weight: 4.9990 chunk 285 optimal weight: 0.8980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 541 GLN B 202 ASN ** B 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 459 GLN D 465 GLN G 180 GLN G 181 GLN G 185 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.096989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.068896 restraints weight = 40051.654| |-----------------------------------------------------------------------------| r_work (start): 0.2876 rms_B_bonded: 2.03 r_work: 0.2748 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2627 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8849 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 27473 Z= 0.136 Angle : 0.537 11.175 37233 Z= 0.273 Chirality : 0.043 0.155 4157 Planarity : 0.004 0.056 4867 Dihedral : 5.723 77.567 3868 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.83 % Favored : 98.14 % Rotamer: Outliers : 1.69 % Allowed : 15.64 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1.23 (0.15), residues: 3437 helix: 1.71 (0.15), residues: 1358 sheet: -0.08 (0.22), residues: 534 loop : 0.50 (0.16), residues: 1545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG D 420 TYR 0.012 0.001 TYR H 21 PHE 0.017 0.001 PHE C 559 TRP 0.010 0.001 TRP A 119 HIS 0.004 0.001 HIS C 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 (27473) covalent geometry : angle 0.53658 / 0.27 (37233) hydrogen bonds : bond 0.04061 / 2.74 ( 1150) hydrogen bonds : angle 4.68413 / 3.30 ( 3249) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6874 Ramachandran restraints generated. 3437 Oldfield, 0 Emsley, 3437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 296 time to evaluate : 1.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 323 MET cc_start: 0.9222 (OUTLIER) cc_final: 0.8091 (mmt) REVERT: B 269 PHE cc_start: 0.9206 (OUTLIER) cc_final: 0.8547 (t80) REVERT: B 393 GLU cc_start: 0.7703 (tt0) cc_final: 0.7415 (pt0) REVERT: B 478 ASP cc_start: 0.8007 (m-30) cc_final: 0.7733 (m-30) REVERT: C 124 LYS cc_start: 0.9104 (OUTLIER) cc_final: 0.8805 (ptpp) REVERT: C 268 GLU cc_start: 0.8368 (OUTLIER) cc_final: 0.8072 (mt-10) REVERT: C 336 GLU cc_start: 0.8034 (tp30) cc_final: 0.7787 (mp0) REVERT: C 416 ARG cc_start: 0.8563 (mtm-85) cc_final: 0.8357 (mtm110) REVERT: C 456 GLU cc_start: 0.8668 (tt0) cc_final: 0.8342 (tm-30) REVERT: C 481 ARG cc_start: 0.8369 (mmm-85) cc_final: 0.8089 (ttp-110) REVERT: C 537 ASP cc_start: 0.8135 (m-30) cc_final: 0.7812 (m-30) REVERT: C 541 GLN cc_start: 0.8766 (mm110) cc_final: 0.8324 (mm110) REVERT: C 557 GLU cc_start: 0.8376 (mp0) cc_final: 0.8147 (mp0) REVERT: D 109 GLU cc_start: 0.8050 (mm-30) cc_final: 0.7806 (mm-30) REVERT: D 402 ASP cc_start: 0.8863 (m-30) cc_final: 0.8624 (m-30) REVERT: D 467 LEU cc_start: 0.8259 (mt) cc_final: 0.7941 (tm) REVERT: E 7 GLU cc_start: 0.5496 (pm20) cc_final: 0.5130 (pm20) REVERT: E 248 GLU cc_start: 0.8504 (OUTLIER) cc_final: 0.8109 (mp0) REVERT: E 305 LYS cc_start: 0.9070 (mtpp) cc_final: 0.8808 (mmmm) REVERT: E 345 ARG cc_start: 0.8739 (ttm-80) cc_final: 0.8310 (mtm-85) REVERT: E 420 ARG cc_start: 0.8465 (mtp-110) cc_final: 0.8100 (mtp180) REVERT: F 206 GLN cc_start: 0.8799 (mt0) cc_final: 0.8577 (mt0) REVERT: F 305 LYS cc_start: 0.9069 (OUTLIER) cc_final: 0.8704 (mppt) REVERT: G 152 GLU cc_start: 0.8506 (tt0) cc_final: 0.7945 (tp30) REVERT: G 155 LYS cc_start: 0.8771 (OUTLIER) cc_final: 0.8380 (mmtm) REVERT: H 21 TYR cc_start: 0.7527 (m-80) cc_final: 0.7127 (m-80) REVERT: H 38 GLU cc_start: 0.8584 (OUTLIER) cc_final: 0.8180 (OUTLIER) REVERT: H 91 ARG cc_start: 0.8364 (mtp85) cc_final: 0.8103 (mtt90) outliers start: 48 outliers final: 35 residues processed: 333 average time/residue: 0.8704 time to fit residues: 326.9576 Evaluate side-chains 336 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 294 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 LEU Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 255 CYS Chi-restraints excluded: chain B residue 269 PHE Chi-restraints excluded: chain B residue 341 LEU Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 124 LYS Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 268 GLU Chi-restraints excluded: chain C residue 374 GLU Chi-restraints excluded: chain C residue 536 ILE Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 130 PHE Chi-restraints excluded: chain D residue 185 GLU Chi-restraints excluded: chain D residue 206 GLN Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 185 GLU Chi-restraints excluded: chain E residue 248 GLU Chi-restraints excluded: chain E residue 265 GLU Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain F residue 3 LEU Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain F residue 305 LYS Chi-restraints excluded: chain F residue 392 ILE Chi-restraints excluded: chain F residue 467 LEU Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 155 LYS Chi-restraints excluded: chain H residue 38 GLU Chi-restraints excluded: chain H residue 94 VAL Chi-restraints excluded: chain H residue 98 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 257 optimal weight: 6.9990 chunk 1 optimal weight: 8.9990 chunk 304 optimal weight: 0.9990 chunk 291 optimal weight: 0.7980 chunk 115 optimal weight: 2.9990 chunk 16 optimal weight: 6.9990 chunk 43 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 330 optimal weight: 0.9990 chunk 271 optimal weight: 2.9990 chunk 320 optimal weight: 6.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 541 GLN B 202 ASN B 459 GLN D 465 GLN ** F 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 180 GLN G 181 GLN G 185 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.097230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.069163 restraints weight = 39895.008| |-----------------------------------------------------------------------------| r_work (start): 0.2881 rms_B_bonded: 2.03 r_work: 0.2752 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2632 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8847 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 27473 Z= 0.133 Angle : 0.540 11.276 37233 Z= 0.274 Chirality : 0.043 0.153 4157 Planarity : 0.004 0.058 4867 Dihedral : 5.654 78.114 3867 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.83 % Favored : 98.14 % Rotamer: Outliers : 1.73 % Allowed : 15.64 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1.26 (0.15), residues: 3437 helix: 1.75 (0.15), residues: 1358 sheet: -0.11 (0.22), residues: 537 loop : 0.52 (0.16), residues: 1542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG A 154 TYR 0.012 0.001 TYR F 54 PHE 0.017 0.001 PHE C 559 TRP 0.011 0.001 TRP A 119 HIS 0.004 0.001 HIS C 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.13 (27473) covalent geometry : angle 0.53983 / 0.27 (37233) hydrogen bonds : bond 0.04014 / 2.71 ( 1150) hydrogen bonds : angle 4.66106 / 3.28 ( 3249) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13722.52 seconds wall clock time: 233 minutes 13.16 seconds (13993.16 seconds total)