Starting phenix.real_space_refine on Fri Nov 21 01:04:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5i68_8072/11_2025/5i68_8072.cif Found real_map, /net/cci-nas-00/data/ceres_data/5i68_8072/11_2025/5i68_8072.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/5i68_8072/11_2025/5i68_8072.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5i68_8072/11_2025/5i68_8072.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5i68_8072/11_2025/5i68_8072.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5i68_8072/11_2025/5i68_8072.map" } resolution = 3.37 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.023 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 16 5.49 5 Mg 8 5.21 5 S 208 5.16 5 C 26504 2.51 5 N 7272 2.21 5 O 8008 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 64 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 42016 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 662, 5198 Classifications: {'peptide': 662} Link IDs: {'CIS': 1, 'PTRANS': 44, 'TRANS': 616} Chain: "A" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {' MG': 1, 'FAD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: B, C, D, E, F, G, H Time building chain proxies: 6.77, per 1000 atoms: 0.16 Number of scatterers: 42016 At special positions: 0 Unit cell: (140.22, 140.22, 136.8, 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 208 16.00 P 16 15.00 Mg 8 11.99 O 8008 8.00 N 7272 7.00 C 26504 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: 4.03 Conformation dependent library (CDL) restraints added in 1.8 seconds 10560 Ramachandran restraints generated. 5280 Oldfield, 0 Emsley, 5280 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9648 Finding SS restraints... Secondary structure from input PDB file: 200 helices and 56 sheets defined 34.6% alpha, 18.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.02 Creating SS restraints... Processing helix chain 'A' and resid 15 through 30 removed outlier: 4.319A pdb=" N ASP A 29 " --> pdb=" O LEU A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 51 removed outlier: 3.567A pdb=" N LEU A 51 " --> pdb=" O PRO A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 60 Proline residue: A 56 - end of helix Processing helix chain 'A' and resid 74 through 78 Processing helix chain 'A' and resid 91 through 96 Processing helix chain 'A' and resid 105 through 112 removed outlier: 4.139A pdb=" N TYR A 109 " --> pdb=" O SER A 105 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASP A 110 " --> pdb=" O ALA A 106 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE A 112 " --> pdb=" O ASP A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 128 Proline residue: A 124 - end of helix Processing helix chain 'A' and resid 158 through 169 removed outlier: 4.024A pdb=" N ASP A 162 " --> pdb=" O PRO A 158 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N SER A 169 " --> pdb=" O ARG A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 209 removed outlier: 3.547A pdb=" N ALA A 207 " --> pdb=" O ASP A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 216 removed outlier: 3.728A pdb=" N ARG A 214 " --> pdb=" O HIS A 210 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ASN A 215 " --> pdb=" O SER A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 280 removed outlier: 4.141A pdb=" N SER A 272 " --> pdb=" O CYS A 268 " (cutoff:3.500A) Proline residue: A 274 - end of helix Processing helix chain 'A' and resid 284 through 290 removed outlier: 3.858A pdb=" N ALA A 290 " --> pdb=" O ILE A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 328 removed outlier: 4.127A pdb=" N ASP A 327 " --> pdb=" O SER A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 346 removed outlier: 3.576A pdb=" N ARG A 338 " --> pdb=" O GLU A 334 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N TRP A 343 " --> pdb=" O VAL A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.524A pdb=" N THR A 353 " --> pdb=" O PRO A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 373 through 384 removed outlier: 3.659A pdb=" N GLU A 382 " --> pdb=" O GLU A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 408 removed outlier: 3.702A pdb=" N ILE A 408 " --> pdb=" O HIS A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 452 Processing helix chain 'A' and resid 453 through 468 removed outlier: 3.641A pdb=" N GLU A 465 " --> pdb=" O LYS A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 481 Processing helix chain 'A' and resid 496 through 505 Processing helix chain 'A' and resid 547 through 562 removed outlier: 3.771A pdb=" N ALA A 553 " --> pdb=" O GLU A 549 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ILE A 554 " --> pdb=" O ASP A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 609 removed outlier: 3.734A pdb=" N CYS A 609 " --> pdb=" O LEU A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 617 through 636 Processing helix chain 'B' and resid 15 through 30 removed outlier: 4.319A pdb=" N ASP B 29 " --> pdb=" O LEU B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 51 removed outlier: 3.567A pdb=" N LEU B 51 " --> pdb=" O PRO B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 60 Proline residue: B 56 - end of helix Processing helix chain 'B' and resid 74 through 78 Processing helix chain 'B' and resid 91 through 96 Processing helix chain 'B' and resid 105 through 112 removed outlier: 4.139A pdb=" N TYR B 109 " --> pdb=" O SER B 105 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASP B 110 " --> pdb=" O ALA B 106 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE B 112 " --> pdb=" O ASP B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 128 Proline residue: B 124 - end of helix Processing helix chain 'B' and resid 158 through 169 removed outlier: 4.024A pdb=" N ASP B 162 " --> pdb=" O PRO B 158 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N SER B 169 " --> pdb=" O ARG B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 209 removed outlier: 3.547A pdb=" N ALA B 207 " --> pdb=" O ASP B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 216 removed outlier: 3.728A pdb=" N ARG B 214 " --> pdb=" O HIS B 210 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ASN B 215 " --> pdb=" O SER B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 280 removed outlier: 4.141A pdb=" N SER B 272 " --> pdb=" O CYS B 268 " (cutoff:3.500A) Proline residue: B 274 - end of helix Processing helix chain 'B' and resid 284 through 290 removed outlier: 3.858A pdb=" N ALA B 290 " --> pdb=" O ILE B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 328 removed outlier: 4.127A pdb=" N ASP B 327 " --> pdb=" O SER B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 346 removed outlier: 3.576A pdb=" N ARG B 338 " --> pdb=" O GLU B 334 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N TRP B 343 " --> pdb=" O VAL B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.524A pdb=" N THR B 353 " --> pdb=" O PRO B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 373 through 384 removed outlier: 3.659A pdb=" N GLU B 382 " --> pdb=" O GLU B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 408 removed outlier: 3.702A pdb=" N ILE B 408 " --> pdb=" O HIS B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 452 Processing helix chain 'B' and resid 453 through 468 removed outlier: 3.641A pdb=" N GLU B 465 " --> pdb=" O LYS B 461 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 481 Processing helix chain 'B' and resid 496 through 505 Processing helix chain 'B' and resid 547 through 562 removed outlier: 3.771A pdb=" N ALA B 553 " --> pdb=" O GLU B 549 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ILE B 554 " --> pdb=" O ASP B 550 " (cutoff:3.500A) Processing helix chain 'B' and resid 605 through 609 removed outlier: 3.734A pdb=" N CYS B 609 " --> pdb=" O LEU B 606 " (cutoff:3.500A) Processing helix chain 'B' and resid 617 through 636 Processing helix chain 'C' and resid 15 through 30 removed outlier: 4.319A pdb=" N ASP C 29 " --> pdb=" O LEU C 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 51 removed outlier: 3.567A pdb=" N LEU C 51 " --> pdb=" O PRO C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 60 Proline residue: C 56 - end of helix Processing helix chain 'C' and resid 74 through 78 Processing helix chain 'C' and resid 91 through 96 Processing helix chain 'C' and resid 105 through 112 removed outlier: 4.139A pdb=" N TYR C 109 " --> pdb=" O SER C 105 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASP C 110 " --> pdb=" O ALA C 106 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE C 112 " --> pdb=" O ASP C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 128 Proline residue: C 124 - end of helix Processing helix chain 'C' and resid 158 through 169 removed outlier: 4.024A pdb=" N ASP C 162 " --> pdb=" O PRO C 158 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N SER C 169 " --> pdb=" O ARG C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 209 removed outlier: 3.547A pdb=" N ALA C 207 " --> pdb=" O ASP C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 216 removed outlier: 3.728A pdb=" N ARG C 214 " --> pdb=" O HIS C 210 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ASN C 215 " --> pdb=" O SER C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 268 through 280 removed outlier: 4.141A pdb=" N SER C 272 " --> pdb=" O CYS C 268 " (cutoff:3.500A) Proline residue: C 274 - end of helix Processing helix chain 'C' and resid 284 through 290 removed outlier: 3.858A pdb=" N ALA C 290 " --> pdb=" O ILE C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 328 removed outlier: 4.127A pdb=" N ASP C 327 " --> pdb=" O SER C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 346 removed outlier: 3.576A pdb=" N ARG C 338 " --> pdb=" O GLU C 334 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N TRP C 343 " --> pdb=" O VAL C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.524A pdb=" N THR C 353 " --> pdb=" O PRO C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 373 through 384 removed outlier: 3.659A pdb=" N GLU C 382 " --> pdb=" O GLU C 378 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 408 removed outlier: 3.702A pdb=" N ILE C 408 " --> pdb=" O HIS C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 449 through 452 Processing helix chain 'C' and resid 453 through 468 removed outlier: 3.641A pdb=" N GLU C 465 " --> pdb=" O LYS C 461 " (cutoff:3.500A) Processing helix chain 'C' and resid 478 through 481 Processing helix chain 'C' and resid 496 through 505 Processing helix chain 'C' and resid 547 through 562 removed outlier: 3.771A pdb=" N ALA C 553 " --> pdb=" O GLU C 549 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ILE C 554 " --> pdb=" O ASP C 550 " (cutoff:3.500A) Processing helix chain 'C' and resid 605 through 609 removed outlier: 3.734A pdb=" N CYS C 609 " --> pdb=" O LEU C 606 " (cutoff:3.500A) Processing helix chain 'C' and resid 617 through 636 Processing helix chain 'D' and resid 15 through 30 removed outlier: 4.319A pdb=" N ASP D 29 " --> pdb=" O LEU D 25 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 51 removed outlier: 3.567A pdb=" N LEU D 51 " --> pdb=" O PRO D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 60 Proline residue: D 56 - end of helix Processing helix chain 'D' and resid 74 through 78 Processing helix chain 'D' and resid 91 through 96 Processing helix chain 'D' and resid 105 through 112 removed outlier: 4.139A pdb=" N TYR D 109 " --> pdb=" O SER D 105 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASP D 110 " --> pdb=" O ALA D 106 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE D 112 " --> pdb=" O ASP D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 128 Proline residue: D 124 - end of helix Processing helix chain 'D' and resid 158 through 169 removed outlier: 4.024A pdb=" N ASP D 162 " --> pdb=" O PRO D 158 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N SER D 169 " --> pdb=" O ARG D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 209 removed outlier: 3.547A pdb=" N ALA D 207 " --> pdb=" O ASP D 203 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 216 removed outlier: 3.728A pdb=" N ARG D 214 " --> pdb=" O HIS D 210 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ASN D 215 " --> pdb=" O SER D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 268 through 280 removed outlier: 4.141A pdb=" N SER D 272 " --> pdb=" O CYS D 268 " (cutoff:3.500A) Proline residue: D 274 - end of helix Processing helix chain 'D' and resid 284 through 290 removed outlier: 3.858A pdb=" N ALA D 290 " --> pdb=" O ILE D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 328 removed outlier: 4.127A pdb=" N ASP D 327 " --> pdb=" O SER D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 334 through 346 removed outlier: 3.576A pdb=" N ARG D 338 " --> pdb=" O GLU D 334 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N TRP D 343 " --> pdb=" O VAL D 339 " (cutoff:3.500A) Processing helix chain 'D' and resid 349 through 353 removed outlier: 3.524A pdb=" N THR D 353 " --> pdb=" O PRO D 350 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 370 Processing helix chain 'D' and resid 373 through 384 removed outlier: 3.659A pdb=" N GLU D 382 " --> pdb=" O GLU D 378 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 408 removed outlier: 3.702A pdb=" N ILE D 408 " --> pdb=" O HIS D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 449 through 452 Processing helix chain 'D' and resid 453 through 468 removed outlier: 3.641A pdb=" N GLU D 465 " --> pdb=" O LYS D 461 " (cutoff:3.500A) Processing helix chain 'D' and resid 478 through 481 Processing helix chain 'D' and resid 496 through 505 Processing helix chain 'D' and resid 547 through 562 removed outlier: 3.771A pdb=" N ALA D 553 " --> pdb=" O GLU D 549 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ILE D 554 " --> pdb=" O ASP D 550 " (cutoff:3.500A) Processing helix chain 'D' and resid 605 through 609 removed outlier: 3.734A pdb=" N CYS D 609 " --> pdb=" O LEU D 606 " (cutoff:3.500A) Processing helix chain 'D' and resid 617 through 636 Processing helix chain 'E' and resid 15 through 30 removed outlier: 4.319A pdb=" N ASP E 29 " --> pdb=" O LEU E 25 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 51 removed outlier: 3.567A pdb=" N LEU E 51 " --> pdb=" O PRO E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 60 Proline residue: E 56 - end of helix Processing helix chain 'E' and resid 74 through 78 Processing helix chain 'E' and resid 91 through 96 Processing helix chain 'E' and resid 105 through 112 removed outlier: 4.139A pdb=" N TYR E 109 " --> pdb=" O SER E 105 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASP E 110 " --> pdb=" O ALA E 106 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE E 112 " --> pdb=" O ASP E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 128 Proline residue: E 124 - end of helix Processing helix chain 'E' and resid 158 through 169 removed outlier: 4.024A pdb=" N ASP E 162 " --> pdb=" O PRO E 158 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N SER E 169 " --> pdb=" O ARG E 165 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 209 removed outlier: 3.547A pdb=" N ALA E 207 " --> pdb=" O ASP E 203 " (cutoff:3.500A) Processing helix chain 'E' and resid 209 through 216 removed outlier: 3.728A pdb=" N ARG E 214 " --> pdb=" O HIS E 210 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ASN E 215 " --> pdb=" O SER E 211 " (cutoff:3.500A) Processing helix chain 'E' and resid 268 through 280 removed outlier: 4.141A pdb=" N SER E 272 " --> pdb=" O CYS E 268 " (cutoff:3.500A) Proline residue: E 274 - end of helix Processing helix chain 'E' and resid 284 through 290 removed outlier: 3.858A pdb=" N ALA E 290 " --> pdb=" O ILE E 286 " (cutoff:3.500A) Processing helix chain 'E' and resid 324 through 328 removed outlier: 4.127A pdb=" N ASP E 327 " --> pdb=" O SER E 324 " (cutoff:3.500A) Processing helix chain 'E' and resid 334 through 346 removed outlier: 3.576A pdb=" N ARG E 338 " --> pdb=" O GLU E 334 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N TRP E 343 " --> pdb=" O VAL E 339 " (cutoff:3.500A) Processing helix chain 'E' and resid 349 through 353 removed outlier: 3.524A pdb=" N THR E 353 " --> pdb=" O PRO E 350 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 370 Processing helix chain 'E' and resid 373 through 384 removed outlier: 3.659A pdb=" N GLU E 382 " --> pdb=" O GLU E 378 " (cutoff:3.500A) Processing helix chain 'E' and resid 404 through 408 removed outlier: 3.702A pdb=" N ILE E 408 " --> pdb=" O HIS E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 449 through 452 Processing helix chain 'E' and resid 453 through 468 removed outlier: 3.641A pdb=" N GLU E 465 " --> pdb=" O LYS E 461 " (cutoff:3.500A) Processing helix chain 'E' and resid 478 through 481 Processing helix chain 'E' and resid 496 through 505 Processing helix chain 'E' and resid 547 through 562 removed outlier: 3.771A pdb=" N ALA E 553 " --> pdb=" O GLU E 549 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ILE E 554 " --> pdb=" O ASP E 550 " (cutoff:3.500A) Processing helix chain 'E' and resid 605 through 609 removed outlier: 3.734A pdb=" N CYS E 609 " --> pdb=" O LEU E 606 " (cutoff:3.500A) Processing helix chain 'E' and resid 617 through 636 Processing helix chain 'F' and resid 15 through 30 removed outlier: 4.319A pdb=" N ASP F 29 " --> pdb=" O LEU F 25 " (cutoff:3.500A) Processing helix chain 'F' and resid 46 through 51 removed outlier: 3.567A pdb=" N LEU F 51 " --> pdb=" O PRO F 47 " (cutoff:3.500A) Processing helix chain 'F' and resid 52 through 60 Proline residue: F 56 - end of helix Processing helix chain 'F' and resid 74 through 78 Processing helix chain 'F' and resid 91 through 96 Processing helix chain 'F' and resid 105 through 112 removed outlier: 4.139A pdb=" N TYR F 109 " --> pdb=" O SER F 105 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASP F 110 " --> pdb=" O ALA F 106 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE F 112 " --> pdb=" O ASP F 108 " (cutoff:3.500A) Processing helix chain 'F' and resid 118 through 128 Proline residue: F 124 - end of helix Processing helix chain 'F' and resid 158 through 169 removed outlier: 4.024A pdb=" N ASP F 162 " --> pdb=" O PRO F 158 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N SER F 169 " --> pdb=" O ARG F 165 " (cutoff:3.500A) Processing helix chain 'F' and resid 203 through 209 removed outlier: 3.547A pdb=" N ALA F 207 " --> pdb=" O ASP F 203 " (cutoff:3.500A) Processing helix chain 'F' and resid 209 through 216 removed outlier: 3.728A pdb=" N ARG F 214 " --> pdb=" O HIS F 210 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ASN F 215 " --> pdb=" O SER F 211 " (cutoff:3.500A) Processing helix chain 'F' and resid 268 through 280 removed outlier: 4.141A pdb=" N SER F 272 " --> pdb=" O CYS F 268 " (cutoff:3.500A) Proline residue: F 274 - end of helix Processing helix chain 'F' and resid 284 through 290 removed outlier: 3.858A pdb=" N ALA F 290 " --> pdb=" O ILE F 286 " (cutoff:3.500A) Processing helix chain 'F' and resid 324 through 328 removed outlier: 4.127A pdb=" N ASP F 327 " --> pdb=" O SER F 324 " (cutoff:3.500A) Processing helix chain 'F' and resid 334 through 346 removed outlier: 3.576A pdb=" N ARG F 338 " --> pdb=" O GLU F 334 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N TRP F 343 " --> pdb=" O VAL F 339 " (cutoff:3.500A) Processing helix chain 'F' and resid 349 through 353 removed outlier: 3.524A pdb=" N THR F 353 " --> pdb=" O PRO F 350 " (cutoff:3.500A) Processing helix chain 'F' and resid 365 through 370 Processing helix chain 'F' and resid 373 through 384 removed outlier: 3.659A pdb=" N GLU F 382 " --> pdb=" O GLU F 378 " (cutoff:3.500A) Processing helix chain 'F' and resid 404 through 408 removed outlier: 3.702A pdb=" N ILE F 408 " --> pdb=" O HIS F 405 " (cutoff:3.500A) Processing helix chain 'F' and resid 449 through 452 Processing helix chain 'F' and resid 453 through 468 removed outlier: 3.641A pdb=" N GLU F 465 " --> pdb=" O LYS F 461 " (cutoff:3.500A) Processing helix chain 'F' and resid 478 through 481 Processing helix chain 'F' and resid 496 through 505 Processing helix chain 'F' and resid 547 through 562 removed outlier: 3.771A pdb=" N ALA F 553 " --> pdb=" O GLU F 549 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ILE F 554 " --> pdb=" O ASP F 550 " (cutoff:3.500A) Processing helix chain 'F' and resid 605 through 609 removed outlier: 3.734A pdb=" N CYS F 609 " --> pdb=" O LEU F 606 " (cutoff:3.500A) Processing helix chain 'F' and resid 617 through 636 Processing helix chain 'G' and resid 15 through 30 removed outlier: 4.319A pdb=" N ASP G 29 " --> pdb=" O LEU G 25 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 51 removed outlier: 3.567A pdb=" N LEU G 51 " --> pdb=" O PRO G 47 " (cutoff:3.500A) Processing helix chain 'G' and resid 52 through 60 Proline residue: G 56 - end of helix Processing helix chain 'G' and resid 74 through 78 Processing helix chain 'G' and resid 91 through 96 Processing helix chain 'G' and resid 105 through 112 removed outlier: 4.139A pdb=" N TYR G 109 " --> pdb=" O SER G 105 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASP G 110 " --> pdb=" O ALA G 106 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE G 112 " --> pdb=" O ASP G 108 " (cutoff:3.500A) Processing helix chain 'G' and resid 118 through 128 Proline residue: G 124 - end of helix Processing helix chain 'G' and resid 158 through 169 removed outlier: 4.024A pdb=" N ASP G 162 " --> pdb=" O PRO G 158 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N SER G 169 " --> pdb=" O ARG G 165 " (cutoff:3.500A) Processing helix chain 'G' and resid 203 through 209 removed outlier: 3.547A pdb=" N ALA G 207 " --> pdb=" O ASP G 203 " (cutoff:3.500A) Processing helix chain 'G' and resid 209 through 216 removed outlier: 3.728A pdb=" N ARG G 214 " --> pdb=" O HIS G 210 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ASN G 215 " --> pdb=" O SER G 211 " (cutoff:3.500A) Processing helix chain 'G' and resid 268 through 280 removed outlier: 4.141A pdb=" N SER G 272 " --> pdb=" O CYS G 268 " (cutoff:3.500A) Proline residue: G 274 - end of helix Processing helix chain 'G' and resid 284 through 290 removed outlier: 3.858A pdb=" N ALA G 290 " --> pdb=" O ILE G 286 " (cutoff:3.500A) Processing helix chain 'G' and resid 324 through 328 removed outlier: 4.127A pdb=" N ASP G 327 " --> pdb=" O SER G 324 " (cutoff:3.500A) Processing helix chain 'G' and resid 334 through 346 removed outlier: 3.576A pdb=" N ARG G 338 " --> pdb=" O GLU G 334 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N TRP G 343 " --> pdb=" O VAL G 339 " (cutoff:3.500A) Processing helix chain 'G' and resid 349 through 353 removed outlier: 3.524A pdb=" N THR G 353 " --> pdb=" O PRO G 350 " (cutoff:3.500A) Processing helix chain 'G' and resid 365 through 370 Processing helix chain 'G' and resid 373 through 384 removed outlier: 3.659A pdb=" N GLU G 382 " --> pdb=" O GLU G 378 " (cutoff:3.500A) Processing helix chain 'G' and resid 404 through 408 removed outlier: 3.702A pdb=" N ILE G 408 " --> pdb=" O HIS G 405 " (cutoff:3.500A) Processing helix chain 'G' and resid 449 through 452 Processing helix chain 'G' and resid 453 through 468 removed outlier: 3.641A pdb=" N GLU G 465 " --> pdb=" O LYS G 461 " (cutoff:3.500A) Processing helix chain 'G' and resid 478 through 481 Processing helix chain 'G' and resid 496 through 505 Processing helix chain 'G' and resid 547 through 562 removed outlier: 3.771A pdb=" N ALA G 553 " --> pdb=" O GLU G 549 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ILE G 554 " --> pdb=" O ASP G 550 " (cutoff:3.500A) Processing helix chain 'G' and resid 605 through 609 removed outlier: 3.734A pdb=" N CYS G 609 " --> pdb=" O LEU G 606 " (cutoff:3.500A) Processing helix chain 'G' and resid 617 through 636 Processing helix chain 'H' and resid 15 through 30 removed outlier: 4.319A pdb=" N ASP H 29 " --> pdb=" O LEU H 25 " (cutoff:3.500A) Processing helix chain 'H' and resid 46 through 51 removed outlier: 3.567A pdb=" N LEU H 51 " --> pdb=" O PRO H 47 " (cutoff:3.500A) Processing helix chain 'H' and resid 52 through 60 Proline residue: H 56 - end of helix Processing helix chain 'H' and resid 74 through 78 Processing helix chain 'H' and resid 91 through 96 Processing helix chain 'H' and resid 105 through 112 removed outlier: 4.139A pdb=" N TYR H 109 " --> pdb=" O SER H 105 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASP H 110 " --> pdb=" O ALA H 106 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE H 112 " --> pdb=" O ASP H 108 " (cutoff:3.500A) Processing helix chain 'H' and resid 118 through 128 Proline residue: H 124 - end of helix Processing helix chain 'H' and resid 158 through 169 removed outlier: 4.024A pdb=" N ASP H 162 " --> pdb=" O PRO H 158 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N SER H 169 " --> pdb=" O ARG H 165 " (cutoff:3.500A) Processing helix chain 'H' and resid 203 through 209 removed outlier: 3.547A pdb=" N ALA H 207 " --> pdb=" O ASP H 203 " (cutoff:3.500A) Processing helix chain 'H' and resid 209 through 216 removed outlier: 3.728A pdb=" N ARG H 214 " --> pdb=" O HIS H 210 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ASN H 215 " --> pdb=" O SER H 211 " (cutoff:3.500A) Processing helix chain 'H' and resid 268 through 280 removed outlier: 4.141A pdb=" N SER H 272 " --> pdb=" O CYS H 268 " (cutoff:3.500A) Proline residue: H 274 - end of helix Processing helix chain 'H' and resid 284 through 290 removed outlier: 3.858A pdb=" N ALA H 290 " --> pdb=" O ILE H 286 " (cutoff:3.500A) Processing helix chain 'H' and resid 324 through 328 removed outlier: 4.127A pdb=" N ASP H 327 " --> pdb=" O SER H 324 " (cutoff:3.500A) Processing helix chain 'H' and resid 334 through 346 removed outlier: 3.576A pdb=" N ARG H 338 " --> pdb=" O GLU H 334 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N TRP H 343 " --> pdb=" O VAL H 339 " (cutoff:3.500A) Processing helix chain 'H' and resid 349 through 353 removed outlier: 3.524A pdb=" N THR H 353 " --> pdb=" O PRO H 350 " (cutoff:3.500A) Processing helix chain 'H' and resid 365 through 370 Processing helix chain 'H' and resid 373 through 384 removed outlier: 3.659A pdb=" N GLU H 382 " --> pdb=" O GLU H 378 " (cutoff:3.500A) Processing helix chain 'H' and resid 404 through 408 removed outlier: 3.702A pdb=" N ILE H 408 " --> pdb=" O HIS H 405 " (cutoff:3.500A) Processing helix chain 'H' and resid 449 through 452 Processing helix chain 'H' and resid 453 through 468 removed outlier: 3.641A pdb=" N GLU H 465 " --> pdb=" O LYS H 461 " (cutoff:3.500A) Processing helix chain 'H' and resid 478 through 481 Processing helix chain 'H' and resid 496 through 505 Processing helix chain 'H' and resid 547 through 562 removed outlier: 3.771A pdb=" N ALA H 553 " --> pdb=" O GLU H 549 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ILE H 554 " --> pdb=" O ASP H 550 " (cutoff:3.500A) Processing helix chain 'H' and resid 605 through 609 removed outlier: 3.734A pdb=" N CYS H 609 " --> pdb=" O LEU H 606 " (cutoff:3.500A) Processing helix chain 'H' and resid 617 through 636 Processing sheet with id=1, first strand: chain 'A' and resid 219 through 222 removed outlier: 3.718A pdb=" N ILE A 37 " --> pdb=" O VAL A 11 " (cutoff:3.500A) removed outlier: 9.048A pdb=" N PHE A 7 " --> pdb=" O ARG A 261 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N GLN A 263 " --> pdb=" O PHE A 7 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N ILE A 9 " --> pdb=" O GLN A 263 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N VAL A 265 " --> pdb=" O ILE A 9 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N VAL A 11 " --> pdb=" O VAL A 265 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N TYR A 258 " --> pdb=" O VAL A 240 " (cutoff:3.500A) Processing sheet with id=2, first strand: chain 'A' and resid 219 through 222 removed outlier: 3.718A pdb=" N ILE A 37 " --> pdb=" O VAL A 11 " (cutoff:3.500A) removed outlier: 9.048A pdb=" N PHE A 7 " --> pdb=" O ARG A 261 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N GLN A 263 " --> pdb=" O PHE A 7 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N ILE A 9 " --> pdb=" O GLN A 263 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N VAL A 265 " --> pdb=" O ILE A 9 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N VAL A 11 " --> pdb=" O VAL A 265 " (cutoff:3.500A) Processing sheet with id=3, first strand: chain 'A' and resid 69 through 70 Processing sheet with id=4, first strand: chain 'A' and resid 130 through 132 Processing sheet with id=5, first strand: chain 'A' and resid 188 through 189 removed outlier: 4.098A pdb=" N ALA A 358 " --> pdb=" O ILE A 397 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N HIS A 418 " --> pdb=" O PHE A 312 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU A 420 " --> pdb=" O TYR A 310 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N TYR A 310 " --> pdb=" O LEU A 420 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLY A 475 " --> pdb=" O ARG A 317 " (cutoff:3.500A) Processing sheet with id=6, first strand: chain 'A' and resid 188 through 189 removed outlier: 4.098A pdb=" N ALA A 358 " --> pdb=" O ILE A 397 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N HIS A 418 " --> pdb=" O PHE A 312 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU A 420 " --> pdb=" O TYR A 310 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N TYR A 310 " --> pdb=" O LEU A 420 " (cutoff:3.500A) Processing sheet with id=7, first strand: chain 'A' and resid 304 through 306 removed outlier: 4.931A pdb=" N ARG A 304 " --> pdb=" O ILE A 429 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ILE A 429 " --> pdb=" O ARG A 304 " (cutoff:3.500A) Processing sheet with id=8, first strand: chain 'B' and resid 219 through 222 removed outlier: 3.718A pdb=" N ILE B 37 " --> pdb=" O VAL B 11 " (cutoff:3.500A) removed outlier: 9.048A pdb=" N PHE B 7 " --> pdb=" O ARG B 261 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N GLN B 263 " --> pdb=" O PHE B 7 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N ILE B 9 " --> pdb=" O GLN B 263 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N VAL B 265 " --> pdb=" O ILE B 9 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N VAL B 11 " --> pdb=" O VAL B 265 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N TYR B 258 " --> pdb=" O VAL B 240 " (cutoff:3.500A) Processing sheet with id=9, first strand: chain 'B' and resid 219 through 222 removed outlier: 3.718A pdb=" N ILE B 37 " --> pdb=" O VAL B 11 " (cutoff:3.500A) removed outlier: 9.048A pdb=" N PHE B 7 " --> pdb=" O ARG B 261 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N GLN B 263 " --> pdb=" O PHE B 7 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N ILE B 9 " --> pdb=" O GLN B 263 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N VAL B 265 " --> pdb=" O ILE B 9 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N VAL B 11 " --> pdb=" O VAL B 265 " (cutoff:3.500A) Processing sheet with id=10, first strand: chain 'B' and resid 69 through 70 Processing sheet with id=11, first strand: chain 'B' and resid 130 through 132 Processing sheet with id=12, first strand: chain 'B' and resid 188 through 189 removed outlier: 4.098A pdb=" N ALA B 358 " --> pdb=" O ILE B 397 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N HIS B 418 " --> pdb=" O PHE B 312 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU B 420 " --> pdb=" O TYR B 310 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N TYR B 310 " --> pdb=" O LEU B 420 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLY B 475 " --> pdb=" O ARG B 317 " (cutoff:3.500A) Processing sheet with id=13, first strand: chain 'B' and resid 188 through 189 removed outlier: 4.098A pdb=" N ALA B 358 " --> pdb=" O ILE B 397 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N HIS B 418 " --> pdb=" O PHE B 312 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU B 420 " --> pdb=" O TYR B 310 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N TYR B 310 " --> pdb=" O LEU B 420 " (cutoff:3.500A) Processing sheet with id=14, first strand: chain 'B' and resid 304 through 306 removed outlier: 4.931A pdb=" N ARG B 304 " --> pdb=" O ILE B 429 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ILE B 429 " --> pdb=" O ARG B 304 " (cutoff:3.500A) Processing sheet with id=15, first strand: chain 'C' and resid 219 through 222 removed outlier: 3.718A pdb=" N ILE C 37 " --> pdb=" O VAL C 11 " (cutoff:3.500A) removed outlier: 9.048A pdb=" N PHE C 7 " --> pdb=" O ARG C 261 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N GLN C 263 " --> pdb=" O PHE C 7 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N ILE C 9 " --> pdb=" O GLN C 263 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N VAL C 265 " --> pdb=" O ILE C 9 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N VAL C 11 " --> pdb=" O VAL C 265 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N TYR C 258 " --> pdb=" O VAL C 240 " (cutoff:3.500A) Processing sheet with id=16, first strand: chain 'C' and resid 219 through 222 removed outlier: 3.718A pdb=" N ILE C 37 " --> pdb=" O VAL C 11 " (cutoff:3.500A) removed outlier: 9.048A pdb=" N PHE C 7 " --> pdb=" O ARG C 261 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N GLN C 263 " --> pdb=" O PHE C 7 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N ILE C 9 " --> pdb=" O GLN C 263 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N VAL C 265 " --> pdb=" O ILE C 9 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N VAL C 11 " --> pdb=" O VAL C 265 " (cutoff:3.500A) Processing sheet with id=17, first strand: chain 'C' and resid 69 through 70 Processing sheet with id=18, first strand: chain 'C' and resid 130 through 132 Processing sheet with id=19, first strand: chain 'C' and resid 188 through 189 removed outlier: 4.098A pdb=" N ALA C 358 " --> pdb=" O ILE C 397 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N HIS C 418 " --> pdb=" O PHE C 312 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU C 420 " --> pdb=" O TYR C 310 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N TYR C 310 " --> pdb=" O LEU C 420 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLY C 475 " --> pdb=" O ARG C 317 " (cutoff:3.500A) Processing sheet with id=20, first strand: chain 'C' and resid 188 through 189 removed outlier: 4.098A pdb=" N ALA C 358 " --> pdb=" O ILE C 397 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N HIS C 418 " --> pdb=" O PHE C 312 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU C 420 " --> pdb=" O TYR C 310 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N TYR C 310 " --> pdb=" O LEU C 420 " (cutoff:3.500A) Processing sheet with id=21, first strand: chain 'C' and resid 304 through 306 removed outlier: 4.931A pdb=" N ARG C 304 " --> pdb=" O ILE C 429 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ILE C 429 " --> pdb=" O ARG C 304 " (cutoff:3.500A) Processing sheet with id=22, first strand: chain 'D' and resid 219 through 222 removed outlier: 3.718A pdb=" N ILE D 37 " --> pdb=" O VAL D 11 " (cutoff:3.500A) removed outlier: 9.048A pdb=" N PHE D 7 " --> pdb=" O ARG D 261 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N GLN D 263 " --> pdb=" O PHE D 7 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N ILE D 9 " --> pdb=" O GLN D 263 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N VAL D 265 " --> pdb=" O ILE D 9 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N VAL D 11 " --> pdb=" O VAL D 265 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N TYR D 258 " --> pdb=" O VAL D 240 " (cutoff:3.500A) Processing sheet with id=23, first strand: chain 'D' and resid 219 through 222 removed outlier: 3.718A pdb=" N ILE D 37 " --> pdb=" O VAL D 11 " (cutoff:3.500A) removed outlier: 9.048A pdb=" N PHE D 7 " --> pdb=" O ARG D 261 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N GLN D 263 " --> pdb=" O PHE D 7 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N ILE D 9 " --> pdb=" O GLN D 263 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N VAL D 265 " --> pdb=" O ILE D 9 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N VAL D 11 " --> pdb=" O VAL D 265 " (cutoff:3.500A) Processing sheet with id=24, first strand: chain 'D' and resid 69 through 70 Processing sheet with id=25, first strand: chain 'D' and resid 130 through 132 Processing sheet with id=26, first strand: chain 'D' and resid 188 through 189 removed outlier: 4.098A pdb=" N ALA D 358 " --> pdb=" O ILE D 397 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N HIS D 418 " --> pdb=" O PHE D 312 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU D 420 " --> pdb=" O TYR D 310 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N TYR D 310 " --> pdb=" O LEU D 420 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLY D 475 " --> pdb=" O ARG D 317 " (cutoff:3.500A) Processing sheet with id=27, first strand: chain 'D' and resid 188 through 189 removed outlier: 4.098A pdb=" N ALA D 358 " --> pdb=" O ILE D 397 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N HIS D 418 " --> pdb=" O PHE D 312 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU D 420 " --> pdb=" O TYR D 310 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N TYR D 310 " --> pdb=" O LEU D 420 " (cutoff:3.500A) Processing sheet with id=28, first strand: chain 'D' and resid 304 through 306 removed outlier: 4.931A pdb=" N ARG D 304 " --> pdb=" O ILE D 429 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ILE D 429 " --> pdb=" O ARG D 304 " (cutoff:3.500A) Processing sheet with id=29, first strand: chain 'E' and resid 219 through 222 removed outlier: 3.718A pdb=" N ILE E 37 " --> pdb=" O VAL E 11 " (cutoff:3.500A) removed outlier: 9.048A pdb=" N PHE E 7 " --> pdb=" O ARG E 261 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N GLN E 263 " --> pdb=" O PHE E 7 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N ILE E 9 " --> pdb=" O GLN E 263 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N VAL E 265 " --> pdb=" O ILE E 9 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N VAL E 11 " --> pdb=" O VAL E 265 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N TYR E 258 " --> pdb=" O VAL E 240 " (cutoff:3.500A) Processing sheet with id=30, first strand: chain 'E' and resid 219 through 222 removed outlier: 3.718A pdb=" N ILE E 37 " --> pdb=" O VAL E 11 " (cutoff:3.500A) removed outlier: 9.048A pdb=" N PHE E 7 " --> pdb=" O ARG E 261 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N GLN E 263 " --> pdb=" O PHE E 7 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N ILE E 9 " --> pdb=" O GLN E 263 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N VAL E 265 " --> pdb=" O ILE E 9 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N VAL E 11 " --> pdb=" O VAL E 265 " (cutoff:3.500A) Processing sheet with id=31, first strand: chain 'E' and resid 69 through 70 Processing sheet with id=32, first strand: chain 'E' and resid 130 through 132 Processing sheet with id=33, first strand: chain 'E' and resid 188 through 189 removed outlier: 4.098A pdb=" N ALA E 358 " --> pdb=" O ILE E 397 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N HIS E 418 " --> pdb=" O PHE E 312 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU E 420 " --> pdb=" O TYR E 310 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N TYR E 310 " --> pdb=" O LEU E 420 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLY E 475 " --> pdb=" O ARG E 317 " (cutoff:3.500A) Processing sheet with id=34, first strand: chain 'E' and resid 188 through 189 removed outlier: 4.098A pdb=" N ALA E 358 " --> pdb=" O ILE E 397 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N HIS E 418 " --> pdb=" O PHE E 312 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU E 420 " --> pdb=" O TYR E 310 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N TYR E 310 " --> pdb=" O LEU E 420 " (cutoff:3.500A) Processing sheet with id=35, first strand: chain 'E' and resid 304 through 306 removed outlier: 4.931A pdb=" N ARG E 304 " --> pdb=" O ILE E 429 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ILE E 429 " --> pdb=" O ARG E 304 " (cutoff:3.500A) Processing sheet with id=36, first strand: chain 'F' and resid 219 through 222 removed outlier: 3.718A pdb=" N ILE F 37 " --> pdb=" O VAL F 11 " (cutoff:3.500A) removed outlier: 9.048A pdb=" N PHE F 7 " --> pdb=" O ARG F 261 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N GLN F 263 " --> pdb=" O PHE F 7 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N ILE F 9 " --> pdb=" O GLN F 263 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N VAL F 265 " --> pdb=" O ILE F 9 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N VAL F 11 " --> pdb=" O VAL F 265 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N TYR F 258 " --> pdb=" O VAL F 240 " (cutoff:3.500A) Processing sheet with id=37, first strand: chain 'F' and resid 219 through 222 removed outlier: 3.718A pdb=" N ILE F 37 " --> pdb=" O VAL F 11 " (cutoff:3.500A) removed outlier: 9.048A pdb=" N PHE F 7 " --> pdb=" O ARG F 261 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N GLN F 263 " --> pdb=" O PHE F 7 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N ILE F 9 " --> pdb=" O GLN F 263 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N VAL F 265 " --> pdb=" O ILE F 9 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N VAL F 11 " --> pdb=" O VAL F 265 " (cutoff:3.500A) Processing sheet with id=38, first strand: chain 'F' and resid 69 through 70 Processing sheet with id=39, first strand: chain 'F' and resid 130 through 132 Processing sheet with id=40, first strand: chain 'F' and resid 188 through 189 removed outlier: 4.098A pdb=" N ALA F 358 " --> pdb=" O ILE F 397 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N HIS F 418 " --> pdb=" O PHE F 312 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU F 420 " --> pdb=" O TYR F 310 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N TYR F 310 " --> pdb=" O LEU F 420 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLY F 475 " --> pdb=" O ARG F 317 " (cutoff:3.500A) Processing sheet with id=41, first strand: chain 'F' and resid 188 through 189 removed outlier: 4.098A pdb=" N ALA F 358 " --> pdb=" O ILE F 397 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N HIS F 418 " --> pdb=" O PHE F 312 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU F 420 " --> pdb=" O TYR F 310 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N TYR F 310 " --> pdb=" O LEU F 420 " (cutoff:3.500A) Processing sheet with id=42, first strand: chain 'F' and resid 304 through 306 removed outlier: 4.931A pdb=" N ARG F 304 " --> pdb=" O ILE F 429 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ILE F 429 " --> pdb=" O ARG F 304 " (cutoff:3.500A) Processing sheet with id=43, first strand: chain 'G' and resid 219 through 222 removed outlier: 3.718A pdb=" N ILE G 37 " --> pdb=" O VAL G 11 " (cutoff:3.500A) removed outlier: 9.048A pdb=" N PHE G 7 " --> pdb=" O ARG G 261 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N GLN G 263 " --> pdb=" O PHE G 7 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N ILE G 9 " --> pdb=" O GLN G 263 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N VAL G 265 " --> pdb=" O ILE G 9 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N VAL G 11 " --> pdb=" O VAL G 265 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N TYR G 258 " --> pdb=" O VAL G 240 " (cutoff:3.500A) Processing sheet with id=44, first strand: chain 'G' and resid 219 through 222 removed outlier: 3.718A pdb=" N ILE G 37 " --> pdb=" O VAL G 11 " (cutoff:3.500A) removed outlier: 9.048A pdb=" N PHE G 7 " --> pdb=" O ARG G 261 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N GLN G 263 " --> pdb=" O PHE G 7 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N ILE G 9 " --> pdb=" O GLN G 263 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N VAL G 265 " --> pdb=" O ILE G 9 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N VAL G 11 " --> pdb=" O VAL G 265 " (cutoff:3.500A) Processing sheet with id=45, first strand: chain 'G' and resid 69 through 70 Processing sheet with id=46, first strand: chain 'G' and resid 130 through 132 Processing sheet with id=47, first strand: chain 'G' and resid 188 through 189 removed outlier: 4.098A pdb=" N ALA G 358 " --> pdb=" O ILE G 397 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N HIS G 418 " --> pdb=" O PHE G 312 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU G 420 " --> pdb=" O TYR G 310 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N TYR G 310 " --> pdb=" O LEU G 420 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLY G 475 " --> pdb=" O ARG G 317 " (cutoff:3.500A) Processing sheet with id=48, first strand: chain 'G' and resid 188 through 189 removed outlier: 4.098A pdb=" N ALA G 358 " --> pdb=" O ILE G 397 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N HIS G 418 " --> pdb=" O PHE G 312 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU G 420 " --> pdb=" O TYR G 310 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N TYR G 310 " --> pdb=" O LEU G 420 " (cutoff:3.500A) Processing sheet with id=49, first strand: chain 'G' and resid 304 through 306 removed outlier: 4.931A pdb=" N ARG G 304 " --> pdb=" O ILE G 429 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ILE G 429 " --> pdb=" O ARG G 304 " (cutoff:3.500A) Processing sheet with id=50, first strand: chain 'H' and resid 219 through 222 removed outlier: 3.718A pdb=" N ILE H 37 " --> pdb=" O VAL H 11 " (cutoff:3.500A) removed outlier: 9.048A pdb=" N PHE H 7 " --> pdb=" O ARG H 261 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N GLN H 263 " --> pdb=" O PHE H 7 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N ILE H 9 " --> pdb=" O GLN H 263 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N VAL H 265 " --> pdb=" O ILE H 9 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N VAL H 11 " --> pdb=" O VAL H 265 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N TYR H 258 " --> pdb=" O VAL H 240 " (cutoff:3.500A) Processing sheet with id=51, first strand: chain 'H' and resid 219 through 222 removed outlier: 3.718A pdb=" N ILE H 37 " --> pdb=" O VAL H 11 " (cutoff:3.500A) removed outlier: 9.048A pdb=" N PHE H 7 " --> pdb=" O ARG H 261 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N GLN H 263 " --> pdb=" O PHE H 7 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N ILE H 9 " --> pdb=" O GLN H 263 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N VAL H 265 " --> pdb=" O ILE H 9 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N VAL H 11 " --> pdb=" O VAL H 265 " (cutoff:3.500A) Processing sheet with id=52, first strand: chain 'H' and resid 69 through 70 Processing sheet with id=53, first strand: chain 'H' and resid 130 through 132 Processing sheet with id=54, first strand: chain 'H' and resid 188 through 189 removed outlier: 4.098A pdb=" N ALA H 358 " --> pdb=" O ILE H 397 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N HIS H 418 " --> pdb=" O PHE H 312 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU H 420 " --> pdb=" O TYR H 310 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N TYR H 310 " --> pdb=" O LEU H 420 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLY H 475 " --> pdb=" O ARG H 317 " (cutoff:3.500A) Processing sheet with id=55, first strand: chain 'H' and resid 188 through 189 removed outlier: 4.098A pdb=" N ALA H 358 " --> pdb=" O ILE H 397 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N HIS H 418 " --> pdb=" O PHE H 312 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU H 420 " --> pdb=" O TYR H 310 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N TYR H 310 " --> pdb=" O LEU H 420 " (cutoff:3.500A) Processing sheet with id=56, first strand: chain 'H' and resid 304 through 306 removed outlier: 4.931A pdb=" N ARG H 304 " --> pdb=" O ILE H 429 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ILE H 429 " --> pdb=" O ARG H 304 " (cutoff:3.500A) 1384 hydrogen bonds defined for protein. 3600 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: 10.99 Time building geometry restraints manager: 5.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 7016 1.31 - 1.44: 12064 1.44 - 1.56: 23736 1.56 - 1.69: 40 1.69 - 1.81: 328 Bond restraints: 43184 Sorted by residual: bond pdb=" C ILE C 408 " pdb=" N PRO C 409 " ideal model delta sigma weight residual 1.331 1.390 -0.058 8.70e-03 1.32e+04 4.50e+01 bond pdb=" C ILE G 408 " pdb=" N PRO G 409 " ideal model delta sigma weight residual 1.331 1.390 -0.058 8.70e-03 1.32e+04 4.50e+01 bond pdb=" C ILE F 408 " pdb=" N PRO F 409 " ideal model delta sigma weight residual 1.331 1.390 -0.058 8.70e-03 1.32e+04 4.50e+01 bond pdb=" C ILE D 408 " pdb=" N PRO D 409 " ideal model delta sigma weight residual 1.331 1.390 -0.058 8.70e-03 1.32e+04 4.50e+01 bond pdb=" C ILE E 408 " pdb=" N PRO E 409 " ideal model delta sigma weight residual 1.331 1.390 -0.058 8.70e-03 1.32e+04 4.50e+01 ... (remaining 43179 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.73: 55352 2.73 - 5.45: 2752 5.45 - 8.18: 424 8.18 - 10.90: 64 10.90 - 13.63: 80 Bond angle restraints: 58672 Sorted by residual: angle pdb=" C LEU G 51 " pdb=" N PRO G 52 " pdb=" CA PRO G 52 " ideal model delta sigma weight residual 119.28 131.27 -11.99 1.10e+00 8.26e-01 1.19e+02 angle pdb=" C LEU H 51 " pdb=" N PRO H 52 " pdb=" CA PRO H 52 " ideal model delta sigma weight residual 119.28 131.27 -11.99 1.10e+00 8.26e-01 1.19e+02 angle pdb=" C LEU E 51 " pdb=" N PRO E 52 " pdb=" CA PRO E 52 " ideal model delta sigma weight residual 119.28 131.27 -11.99 1.10e+00 8.26e-01 1.19e+02 angle pdb=" C LEU F 51 " pdb=" N PRO F 52 " pdb=" CA PRO F 52 " ideal model delta sigma weight residual 119.28 131.27 -11.99 1.10e+00 8.26e-01 1.19e+02 angle pdb=" C LEU D 51 " pdb=" N PRO D 52 " pdb=" CA PRO D 52 " ideal model delta sigma weight residual 119.28 131.27 -11.99 1.10e+00 8.26e-01 1.19e+02 ... (remaining 58667 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.40: 24368 16.40 - 32.79: 1152 32.79 - 49.19: 224 49.19 - 65.58: 16 65.58 - 81.98: 32 Dihedral angle restraints: 25792 sinusoidal: 10616 harmonic: 15176 Sorted by residual: dihedral pdb=" CA ARG D 662 " pdb=" C ARG D 662 " pdb=" N PHE D 663 " pdb=" CA PHE D 663 " ideal model delta harmonic sigma weight residual 180.00 158.14 21.86 0 5.00e+00 4.00e-02 1.91e+01 dihedral pdb=" CA ARG C 662 " pdb=" C ARG C 662 " pdb=" N PHE C 663 " pdb=" CA PHE C 663 " ideal model delta harmonic sigma weight residual 180.00 158.14 21.86 0 5.00e+00 4.00e-02 1.91e+01 dihedral pdb=" CA ARG G 662 " pdb=" C ARG G 662 " pdb=" N PHE G 663 " pdb=" CA PHE G 663 " ideal model delta harmonic sigma weight residual 180.00 158.14 21.86 0 5.00e+00 4.00e-02 1.91e+01 ... (remaining 25789 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 5352 0.096 - 0.192: 592 0.192 - 0.288: 112 0.288 - 0.383: 48 0.383 - 0.479: 16 Chirality restraints: 6120 Sorted by residual: chirality pdb=" CA TYR A 383 " pdb=" N TYR A 383 " pdb=" C TYR A 383 " pdb=" CB TYR A 383 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.74e+00 chirality pdb=" CA TYR D 383 " pdb=" N TYR D 383 " pdb=" C TYR D 383 " pdb=" CB TYR D 383 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.74e+00 chirality pdb=" CA TYR C 383 " pdb=" N TYR C 383 " pdb=" C TYR C 383 " pdb=" CB TYR C 383 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.74e+00 ... (remaining 6117 not shown) Planarity restraints: 7672 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' FAD C 702 " -0.193 2.00e-02 2.50e+03 1.57e-01 1.17e+03 pdb=" C10 FAD C 702 " -0.112 2.00e-02 2.50e+03 pdb=" C2 FAD C 702 " 0.092 2.00e-02 2.50e+03 pdb=" C4 FAD C 702 " 0.081 2.00e-02 2.50e+03 pdb=" C4X FAD C 702 " -0.088 2.00e-02 2.50e+03 pdb=" C5X FAD C 702 " -0.184 2.00e-02 2.50e+03 pdb=" C6 FAD C 702 " -0.151 2.00e-02 2.50e+03 pdb=" C7 FAD C 702 " 0.023 2.00e-02 2.50e+03 pdb=" C7M FAD C 702 " -0.005 2.00e-02 2.50e+03 pdb=" C8 FAD C 702 " -0.045 2.00e-02 2.50e+03 pdb=" C8M FAD C 702 " 0.473 2.00e-02 2.50e+03 pdb=" C9 FAD C 702 " -0.004 2.00e-02 2.50e+03 pdb=" C9A FAD C 702 " -0.075 2.00e-02 2.50e+03 pdb=" N1 FAD C 702 " -0.108 2.00e-02 2.50e+03 pdb=" N10 FAD C 702 " 0.009 2.00e-02 2.50e+03 pdb=" N3 FAD C 702 " 0.217 2.00e-02 2.50e+03 pdb=" N5 FAD C 702 " -0.138 2.00e-02 2.50e+03 pdb=" O2 FAD C 702 " 0.045 2.00e-02 2.50e+03 pdb=" O4 FAD C 702 " 0.162 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' FAD G 702 " 0.193 2.00e-02 2.50e+03 1.57e-01 1.17e+03 pdb=" C10 FAD G 702 " 0.112 2.00e-02 2.50e+03 pdb=" C2 FAD G 702 " -0.092 2.00e-02 2.50e+03 pdb=" C4 FAD G 702 " -0.081 2.00e-02 2.50e+03 pdb=" C4X FAD G 702 " 0.088 2.00e-02 2.50e+03 pdb=" C5X FAD G 702 " 0.184 2.00e-02 2.50e+03 pdb=" C6 FAD G 702 " 0.151 2.00e-02 2.50e+03 pdb=" C7 FAD G 702 " -0.023 2.00e-02 2.50e+03 pdb=" C7M FAD G 702 " 0.005 2.00e-02 2.50e+03 pdb=" C8 FAD G 702 " 0.045 2.00e-02 2.50e+03 pdb=" C8M FAD G 702 " -0.473 2.00e-02 2.50e+03 pdb=" C9 FAD G 702 " 0.004 2.00e-02 2.50e+03 pdb=" C9A FAD G 702 " 0.075 2.00e-02 2.50e+03 pdb=" N1 FAD G 702 " 0.108 2.00e-02 2.50e+03 pdb=" N10 FAD G 702 " -0.009 2.00e-02 2.50e+03 pdb=" N3 FAD G 702 " -0.217 2.00e-02 2.50e+03 pdb=" N5 FAD G 702 " 0.138 2.00e-02 2.50e+03 pdb=" O2 FAD G 702 " -0.045 2.00e-02 2.50e+03 pdb=" O4 FAD G 702 " -0.162 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' FAD A 702 " 0.193 2.00e-02 2.50e+03 1.57e-01 1.17e+03 pdb=" C10 FAD A 702 " 0.112 2.00e-02 2.50e+03 pdb=" C2 FAD A 702 " -0.092 2.00e-02 2.50e+03 pdb=" C4 FAD A 702 " -0.081 2.00e-02 2.50e+03 pdb=" C4X FAD A 702 " 0.088 2.00e-02 2.50e+03 pdb=" C5X FAD A 702 " 0.184 2.00e-02 2.50e+03 pdb=" C6 FAD A 702 " 0.151 2.00e-02 2.50e+03 pdb=" C7 FAD A 702 " -0.023 2.00e-02 2.50e+03 pdb=" C7M FAD A 702 " 0.005 2.00e-02 2.50e+03 pdb=" C8 FAD A 702 " 0.045 2.00e-02 2.50e+03 pdb=" C8M FAD A 702 " -0.473 2.00e-02 2.50e+03 pdb=" C9 FAD A 702 " 0.004 2.00e-02 2.50e+03 pdb=" C9A FAD A 702 " 0.075 2.00e-02 2.50e+03 pdb=" N1 FAD A 702 " 0.108 2.00e-02 2.50e+03 pdb=" N10 FAD A 702 " -0.009 2.00e-02 2.50e+03 pdb=" N3 FAD A 702 " -0.217 2.00e-02 2.50e+03 pdb=" N5 FAD A 702 " 0.138 2.00e-02 2.50e+03 pdb=" O2 FAD A 702 " -0.045 2.00e-02 2.50e+03 pdb=" O4 FAD A 702 " -0.162 2.00e-02 2.50e+03 ... (remaining 7669 not shown) Histogram of nonbonded interaction distances: 1.42 - 2.12: 40 2.12 - 2.81: 13416 2.81 - 3.51: 56480 3.51 - 4.20: 103064 4.20 - 4.90: 181832 Nonbonded interactions: 354832 Sorted by model distance: nonbonded pdb=" OH TYR A 486 " pdb=" OG SER A 517 " model vdw 1.419 3.040 nonbonded pdb=" OH TYR G 486 " pdb=" OG SER G 517 " model vdw 1.419 3.040 nonbonded pdb=" OH TYR D 486 " pdb=" OG SER D 517 " model vdw 1.419 3.040 nonbonded pdb=" OH TYR H 486 " pdb=" OG SER H 517 " model vdw 1.419 3.040 nonbonded pdb=" OH TYR F 486 " pdb=" OG SER F 517 " model vdw 1.419 3.040 ... (remaining 354827 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: 0.15 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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: 0.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.560 Check model and map are aligned: 0.130 Set scattering table: 0.100 Process input model: 39.070 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 42.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 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 : 0.009 0.098 43184 Z= 0.569 Angle : 1.466 13.629 58672 Z= 0.951 Chirality : 0.075 0.479 6120 Planarity : 0.007 0.157 7672 Dihedral : 10.476 81.980 16144 Min Nonbonded Distance : 1.419 Molprobity Statistics. All-atom Clashscore : 25.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 1.25 % Allowed : 3.04 % Favored : 95.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.11), residues: 5280 helix: -1.75 (0.11), residues: 1264 sheet: -0.63 (0.24), residues: 488 loop : 0.52 (0.11), residues: 3528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 200 TYR 0.033 0.003 TYR A 50 PHE 0.025 0.003 PHE D 325 TRP 0.020 0.002 TRP A 48 HIS 0.010 0.002 HIS D 418 Details of bonding type rmsd covalent geometry : bond 0.00937 (43184) covalent geometry : angle 1.46618 (58672) hydrogen bonds : bond 0.23644 ( 1200) hydrogen bonds : angle 9.59537 ( 3600) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10560 Ramachandran restraints generated. 5280 Oldfield, 0 Emsley, 5280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10560 Ramachandran restraints generated. 5280 Oldfield, 0 Emsley, 5280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1199 residues out of total 4480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 1143 time to evaluate : 1.623 Fit side-chains REVERT: A 38 GLU cc_start: 0.7680 (OUTLIER) cc_final: 0.6783 (tm-30) REVERT: A 128 LYS cc_start: 0.7683 (ttpt) cc_final: 0.7404 (mtpt) REVERT: A 308 ASP cc_start: 0.6640 (m-30) cc_final: 0.6274 (m-30) REVERT: A 348 THR cc_start: 0.8509 (p) cc_final: 0.8276 (p) REVERT: A 515 HIS cc_start: 0.7706 (OUTLIER) cc_final: 0.6344 (m-70) REVERT: A 563 GLU cc_start: 0.7864 (pm20) cc_final: 0.6891 (pm20) REVERT: B 38 GLU cc_start: 0.7687 (OUTLIER) cc_final: 0.6777 (tm-30) REVERT: B 318 ILE cc_start: 0.8418 (tt) cc_final: 0.8211 (tt) REVERT: B 348 THR cc_start: 0.8438 (p) cc_final: 0.8238 (p) REVERT: B 563 GLU cc_start: 0.7838 (pm20) cc_final: 0.7049 (pm20) REVERT: C 38 GLU cc_start: 0.7679 (OUTLIER) cc_final: 0.6672 (tm-30) REVERT: C 128 LYS cc_start: 0.7533 (ttpt) cc_final: 0.7285 (mtpt) REVERT: C 230 ILE cc_start: 0.8855 (mt) cc_final: 0.8649 (mt) REVERT: C 348 THR cc_start: 0.8430 (p) cc_final: 0.8214 (p) REVERT: C 354 ASN cc_start: 0.8581 (OUTLIER) cc_final: 0.8278 (t0) REVERT: C 563 GLU cc_start: 0.7777 (pm20) cc_final: 0.7033 (pm20) REVERT: D 38 GLU cc_start: 0.7731 (OUTLIER) cc_final: 0.6782 (tm-30) REVERT: D 128 LYS cc_start: 0.7650 (ttpt) cc_final: 0.7375 (mtpt) REVERT: D 348 THR cc_start: 0.8504 (p) cc_final: 0.8257 (p) REVERT: D 354 ASN cc_start: 0.8588 (OUTLIER) cc_final: 0.8297 (t0) REVERT: D 515 HIS cc_start: 0.7749 (OUTLIER) cc_final: 0.6364 (m-70) REVERT: D 563 GLU cc_start: 0.7910 (pm20) cc_final: 0.7015 (pm20) REVERT: E 38 GLU cc_start: 0.7540 (OUTLIER) cc_final: 0.6528 (tm-30) REVERT: E 128 LYS cc_start: 0.7546 (ttpt) cc_final: 0.7339 (mtpt) REVERT: E 308 ASP cc_start: 0.6578 (m-30) cc_final: 0.6112 (m-30) REVERT: E 563 GLU cc_start: 0.7894 (pm20) cc_final: 0.7088 (pm20) REVERT: F 38 GLU cc_start: 0.7521 (OUTLIER) cc_final: 0.6494 (tm-30) REVERT: F 286 ILE cc_start: 0.7979 (tp) cc_final: 0.7430 (mp) REVERT: F 354 ASN cc_start: 0.8553 (OUTLIER) cc_final: 0.8268 (t0) REVERT: F 431 ILE cc_start: 0.8181 (OUTLIER) cc_final: 0.7942 (tp) REVERT: F 563 GLU cc_start: 0.7799 (pm20) cc_final: 0.7124 (pm20) REVERT: G 38 GLU cc_start: 0.7614 (OUTLIER) cc_final: 0.6648 (tm-30) REVERT: G 230 ILE cc_start: 0.8872 (mt) cc_final: 0.8658 (mt) REVERT: G 286 ILE cc_start: 0.7889 (tp) cc_final: 0.7368 (mp) REVERT: G 308 ASP cc_start: 0.6598 (m-30) cc_final: 0.6121 (m-30) REVERT: G 348 THR cc_start: 0.8500 (p) cc_final: 0.8284 (p) REVERT: G 354 ASN cc_start: 0.8509 (OUTLIER) cc_final: 0.8199 (t0) REVERT: G 515 HIS cc_start: 0.7694 (OUTLIER) cc_final: 0.6299 (m-70) REVERT: G 563 GLU cc_start: 0.7905 (pm20) cc_final: 0.6908 (pm20) REVERT: H 38 GLU cc_start: 0.7604 (OUTLIER) cc_final: 0.6595 (tm-30) REVERT: H 128 LYS cc_start: 0.7616 (ttpt) cc_final: 0.7381 (mtpt) REVERT: H 308 ASP cc_start: 0.6599 (m-30) cc_final: 0.6187 (m-30) REVERT: H 318 ILE cc_start: 0.8526 (tt) cc_final: 0.8282 (tt) REVERT: H 515 HIS cc_start: 0.7713 (OUTLIER) cc_final: 0.6331 (m-70) REVERT: H 563 GLU cc_start: 0.7974 (pm20) cc_final: 0.6951 (pm20) outliers start: 56 outliers final: 12 residues processed: 1191 average time/residue: 0.2909 time to fit residues: 549.4890 Evaluate side-chains 671 residues out of total 4480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 642 time to evaluate : 1.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 GLU Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 515 HIS Chi-restraints excluded: chain B residue 38 GLU Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 515 HIS Chi-restraints excluded: chain C residue 38 GLU Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 354 ASN Chi-restraints excluded: chain C residue 515 HIS Chi-restraints excluded: chain D residue 38 GLU Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain D residue 354 ASN Chi-restraints excluded: chain D residue 515 HIS Chi-restraints excluded: chain E residue 38 GLU Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 515 HIS Chi-restraints excluded: chain F residue 38 GLU Chi-restraints excluded: chain F residue 191 LEU Chi-restraints excluded: chain F residue 354 ASN Chi-restraints excluded: chain F residue 431 ILE Chi-restraints excluded: chain F residue 515 HIS Chi-restraints excluded: chain G residue 38 GLU Chi-restraints excluded: chain G residue 191 LEU Chi-restraints excluded: chain G residue 354 ASN Chi-restraints excluded: chain G residue 515 HIS Chi-restraints excluded: chain H residue 38 GLU Chi-restraints excluded: chain H residue 191 LEU Chi-restraints excluded: chain H residue 515 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 394 optimal weight: 10.0000 chunk 430 optimal weight: 7.9990 chunk 41 optimal weight: 3.9990 chunk 265 optimal weight: 2.9990 chunk 523 optimal weight: 4.9990 chunk 497 optimal weight: 6.9990 chunk 414 optimal weight: 2.9990 chunk 310 optimal weight: 0.8980 chunk 488 optimal weight: 5.9990 chunk 366 optimal weight: 8.9990 chunk 223 optimal weight: 9.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 HIS ** A 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 218 ASN A 249 ASN ** A 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 508 ASN A 541 HIS ** A 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 ASN B 249 ASN ** B 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 508 ASN B 532 HIS B 541 HIS ** C 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 142 HIS ** C 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 218 ASN C 249 ASN ** C 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 480 HIS C 508 ASN C 541 HIS D 30 HIS D 142 HIS ** D 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 218 ASN D 249 ASN ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 508 ASN D 541 HIS D 561 HIS ** D 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 218 ASN E 249 ASN ** E 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 480 HIS E 508 ASN E 532 HIS E 541 HIS ** F 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 218 ASN F 249 ASN ** F 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 480 HIS F 508 ASN F 532 HIS F 541 HIS ** G 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 218 ASN G 249 ASN ** G 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 480 HIS G 508 ASN G 541 HIS ** H 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 218 ASN ** H 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 480 HIS H 508 ASN H 541 HIS Total number of N/Q/H flips: 44 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.144396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.117847 restraints weight = 48394.885| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 1.86 r_work: 0.3086 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 43184 Z= 0.200 Angle : 0.759 9.620 58672 Z= 0.398 Chirality : 0.050 0.151 6120 Planarity : 0.005 0.046 7672 Dihedral : 7.334 48.398 6234 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.75 % Allowed : 8.35 % Favored : 88.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.12), residues: 5280 helix: -0.39 (0.14), residues: 1280 sheet: -0.83 (0.21), residues: 696 loop : 0.21 (0.11), residues: 3304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 196 TYR 0.028 0.002 TYR F 50 PHE 0.025 0.002 PHE D 325 TRP 0.019 0.002 TRP C 566 HIS 0.010 0.002 HIS B 561 Details of bonding type rmsd covalent geometry : bond 0.00475 (43184) covalent geometry : angle 0.75904 (58672) hydrogen bonds : bond 0.05176 ( 1200) hydrogen bonds : angle 6.04266 ( 3600) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10560 Ramachandran restraints generated. 5280 Oldfield, 0 Emsley, 5280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10560 Ramachandran restraints generated. 5280 Oldfield, 0 Emsley, 5280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 820 residues out of total 4480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 697 time to evaluate : 1.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 LYS cc_start: 0.8058 (ttpt) cc_final: 0.7368 (ttmt) REVERT: A 180 ASP cc_start: 0.8626 (t0) cc_final: 0.8379 (t0) REVERT: A 326 ASP cc_start: 0.8997 (t0) cc_final: 0.8712 (m-30) REVERT: A 447 MET cc_start: 0.9086 (mmt) cc_final: 0.8858 (mmt) REVERT: A 453 MET cc_start: 0.8553 (OUTLIER) cc_final: 0.8220 (tpt) REVERT: A 594 ASN cc_start: 0.7684 (m-40) cc_final: 0.6687 (p0) REVERT: A 596 TYR cc_start: 0.8273 (m-80) cc_final: 0.7910 (m-80) REVERT: A 660 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.7991 (pp) REVERT: B 453 MET cc_start: 0.8572 (OUTLIER) cc_final: 0.8341 (tpt) REVERT: B 596 TYR cc_start: 0.8271 (m-80) cc_final: 0.7945 (m-80) REVERT: B 626 GLU cc_start: 0.7626 (mm-30) cc_final: 0.7336 (mm-30) REVERT: B 634 GLU cc_start: 0.7862 (tp30) cc_final: 0.6996 (mt-10) REVERT: B 660 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.7988 (pp) REVERT: C 128 LYS cc_start: 0.8012 (ttpt) cc_final: 0.7307 (ttmt) REVERT: C 180 ASP cc_start: 0.8472 (t0) cc_final: 0.8263 (t0) REVERT: C 374 GLU cc_start: 0.7428 (tm-30) cc_final: 0.6804 (mp0) REVERT: C 596 TYR cc_start: 0.8178 (m-80) cc_final: 0.7806 (m-80) REVERT: C 660 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.7853 (pp) REVERT: D 128 LYS cc_start: 0.8009 (ttpt) cc_final: 0.7304 (ttmt) REVERT: D 180 ASP cc_start: 0.8599 (t0) cc_final: 0.8366 (t0) REVERT: D 326 ASP cc_start: 0.9030 (t0) cc_final: 0.8751 (m-30) REVERT: D 594 ASN cc_start: 0.7711 (m-40) cc_final: 0.6748 (p0) REVERT: D 596 TYR cc_start: 0.8259 (m-80) cc_final: 0.7895 (m-80) REVERT: D 660 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.7932 (pp) REVERT: E 128 LYS cc_start: 0.8082 (ttpt) cc_final: 0.7375 (ttmt) REVERT: E 180 ASP cc_start: 0.8488 (t0) cc_final: 0.8239 (t0) REVERT: E 383 TYR cc_start: 0.8759 (t80) cc_final: 0.8515 (t80) REVERT: E 453 MET cc_start: 0.8582 (OUTLIER) cc_final: 0.8342 (tpt) REVERT: E 596 TYR cc_start: 0.8241 (m-80) cc_final: 0.7975 (m-80) REVERT: E 634 GLU cc_start: 0.7809 (tp30) cc_final: 0.6960 (mt-10) REVERT: E 660 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.7993 (pp) REVERT: F 596 TYR cc_start: 0.8258 (m-80) cc_final: 0.7974 (m-80) REVERT: F 660 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.7994 (pp) REVERT: G 180 ASP cc_start: 0.8571 (t0) cc_final: 0.8316 (t0) REVERT: G 414 MET cc_start: 0.9018 (OUTLIER) cc_final: 0.8734 (ptt) REVERT: G 594 ASN cc_start: 0.7714 (m-40) cc_final: 0.6767 (p0) REVERT: G 596 TYR cc_start: 0.8271 (m-80) cc_final: 0.7996 (m-80) REVERT: G 660 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.7965 (pp) REVERT: H 128 LYS cc_start: 0.8037 (ttpt) cc_final: 0.7344 (ttmt) REVERT: H 180 ASP cc_start: 0.8570 (t0) cc_final: 0.8369 (t0) REVERT: H 383 TYR cc_start: 0.8766 (t80) cc_final: 0.8559 (t80) REVERT: H 453 MET cc_start: 0.8558 (OUTLIER) cc_final: 0.8356 (tpt) REVERT: H 596 TYR cc_start: 0.8329 (m-80) cc_final: 0.8010 (m-80) REVERT: H 660 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.8035 (pp) outliers start: 123 outliers final: 46 residues processed: 782 average time/residue: 0.2741 time to fit residues: 346.8338 Evaluate side-chains 632 residues out of total 4480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 573 time to evaluate : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 99 MET Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 453 MET Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 646 THR Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain B residue 3 ILE Chi-restraints excluded: chain B residue 99 MET Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 453 MET Chi-restraints excluded: chain B residue 477 VAL Chi-restraints excluded: chain B residue 495 MET Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain B residue 646 THR Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 99 MET Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 477 VAL Chi-restraints excluded: chain C residue 495 MET Chi-restraints excluded: chain C residue 646 THR Chi-restraints excluded: chain C residue 660 LEU Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 477 VAL Chi-restraints excluded: chain D residue 495 MET Chi-restraints excluded: chain D residue 646 THR Chi-restraints excluded: chain D residue 660 LEU Chi-restraints excluded: chain E residue 3 ILE Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 182 VAL Chi-restraints excluded: chain E residue 418 HIS Chi-restraints excluded: chain E residue 453 MET Chi-restraints excluded: chain E residue 477 VAL Chi-restraints excluded: chain E residue 565 THR Chi-restraints excluded: chain E residue 646 THR Chi-restraints excluded: chain E residue 660 LEU Chi-restraints excluded: chain F residue 3 ILE Chi-restraints excluded: chain F residue 418 HIS Chi-restraints excluded: chain F residue 477 VAL Chi-restraints excluded: chain F residue 495 MET Chi-restraints excluded: chain F residue 646 THR Chi-restraints excluded: chain F residue 660 LEU Chi-restraints excluded: chain G residue 99 MET Chi-restraints excluded: chain G residue 414 MET Chi-restraints excluded: chain G residue 418 HIS Chi-restraints excluded: chain G residue 477 VAL Chi-restraints excluded: chain G residue 646 THR Chi-restraints excluded: chain G residue 660 LEU Chi-restraints excluded: chain H residue 99 MET Chi-restraints excluded: chain H residue 182 VAL Chi-restraints excluded: chain H residue 288 LEU Chi-restraints excluded: chain H residue 418 HIS Chi-restraints excluded: chain H residue 453 MET Chi-restraints excluded: chain H residue 477 VAL Chi-restraints excluded: chain H residue 646 THR Chi-restraints excluded: chain H residue 660 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 494 optimal weight: 6.9990 chunk 100 optimal weight: 0.7980 chunk 491 optimal weight: 9.9990 chunk 152 optimal weight: 9.9990 chunk 524 optimal weight: 5.9990 chunk 6 optimal weight: 7.9990 chunk 164 optimal weight: 4.9990 chunk 61 optimal weight: 5.9990 chunk 33 optimal weight: 9.9990 chunk 414 optimal weight: 9.9990 chunk 381 optimal weight: 10.0000 overall best weight: 4.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 ASN ** A 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 508 ASN ** A 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 561 HIS ** A 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 27 ASN ** B 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 508 ASN B 561 HIS C 27 ASN ** C 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 480 HIS C 508 ASN C 561 HIS ** C 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 27 ASN ** D 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 508 ASN ** D 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 27 ASN ** E 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 508 ASN E 561 HIS F 27 ASN ** F 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 508 ASN F 561 HIS ** F 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 27 ASN ** G 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 508 ASN G 561 HIS H 27 ASN ** H 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 508 ASN ** H 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 561 HIS ** H 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.139567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.113694 restraints weight = 48743.871| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 1.72 r_work: 0.2979 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2831 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.3015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 43184 Z= 0.242 Angle : 0.731 10.188 58672 Z= 0.382 Chirality : 0.050 0.226 6120 Planarity : 0.006 0.053 7672 Dihedral : 6.641 47.970 6168 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 3.66 % Allowed : 9.80 % Favored : 86.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.12), residues: 5280 helix: 0.06 (0.14), residues: 1296 sheet: -0.66 (0.21), residues: 696 loop : -0.06 (0.11), residues: 3288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 451 TYR 0.024 0.003 TYR B 50 PHE 0.026 0.003 PHE D 325 TRP 0.015 0.002 TRP B 566 HIS 0.009 0.002 HIS A 515 Details of bonding type rmsd covalent geometry : bond 0.00584 (43184) covalent geometry : angle 0.73110 (58672) hydrogen bonds : bond 0.04884 ( 1200) hydrogen bonds : angle 5.65332 ( 3600) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10560 Ramachandran restraints generated. 5280 Oldfield, 0 Emsley, 5280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10560 Ramachandran restraints generated. 5280 Oldfield, 0 Emsley, 5280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 819 residues out of total 4480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 164 poor density : 655 time to evaluate : 1.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 LYS cc_start: 0.8184 (ttpt) cc_final: 0.7560 (ttmt) REVERT: A 383 TYR cc_start: 0.8748 (t80) cc_final: 0.8530 (t80) REVERT: A 660 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.7984 (pp) REVERT: B 180 ASP cc_start: 0.8714 (t0) cc_final: 0.8463 (t0) REVERT: B 378 GLU cc_start: 0.7191 (tp30) cc_final: 0.6735 (tt0) REVERT: B 383 TYR cc_start: 0.8745 (t80) cc_final: 0.8525 (t80) REVERT: B 626 GLU cc_start: 0.7824 (mm-30) cc_final: 0.7523 (mm-30) REVERT: B 634 GLU cc_start: 0.7903 (tp30) cc_final: 0.7216 (mt-10) REVERT: B 660 LEU cc_start: 0.8490 (OUTLIER) cc_final: 0.7995 (pp) REVERT: C 374 GLU cc_start: 0.7447 (tm-30) cc_final: 0.7019 (mp0) REVERT: C 383 TYR cc_start: 0.8732 (t80) cc_final: 0.8494 (t80) REVERT: C 456 MET cc_start: 0.8755 (mtp) cc_final: 0.8381 (mtp) REVERT: C 660 LEU cc_start: 0.8434 (OUTLIER) cc_final: 0.7915 (pp) REVERT: D 378 GLU cc_start: 0.7094 (tp30) cc_final: 0.6843 (tt0) REVERT: D 383 TYR cc_start: 0.8694 (t80) cc_final: 0.8482 (t80) REVERT: D 660 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.7972 (pp) REVERT: E 252 LYS cc_start: 0.6962 (ttmt) cc_final: 0.6587 (tttt) REVERT: E 378 GLU cc_start: 0.7097 (tp30) cc_final: 0.6768 (tt0) REVERT: E 383 TYR cc_start: 0.8791 (t80) cc_final: 0.8578 (t80) REVERT: E 634 GLU cc_start: 0.7962 (tp30) cc_final: 0.7204 (mt-10) REVERT: E 660 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.7992 (pp) REVERT: F 128 LYS cc_start: 0.8130 (ttmt) cc_final: 0.7601 (ttpp) REVERT: F 180 ASP cc_start: 0.8648 (t0) cc_final: 0.8339 (t0) REVERT: F 375 SER cc_start: 0.8012 (m) cc_final: 0.7774 (p) REVERT: F 378 GLU cc_start: 0.7068 (tp30) cc_final: 0.6787 (tt0) REVERT: F 383 TYR cc_start: 0.8711 (t80) cc_final: 0.8470 (t80) REVERT: F 660 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.8033 (pp) REVERT: G 128 LYS cc_start: 0.8173 (ttpt) cc_final: 0.7447 (ttmt) REVERT: G 180 ASP cc_start: 0.8507 (t0) cc_final: 0.8306 (t0) REVERT: G 378 GLU cc_start: 0.7017 (tp30) cc_final: 0.6806 (tt0) REVERT: G 383 TYR cc_start: 0.8732 (t80) cc_final: 0.8505 (t80) REVERT: G 451 ARG cc_start: 0.8265 (mtm-85) cc_final: 0.8026 (mtm-85) REVERT: G 660 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.7983 (pp) REVERT: H 128 LYS cc_start: 0.8158 (ttpt) cc_final: 0.7513 (ttmt) REVERT: H 252 LYS cc_start: 0.7115 (ttmt) cc_final: 0.6755 (tttt) REVERT: H 378 GLU cc_start: 0.7026 (tp30) cc_final: 0.6804 (tt0) REVERT: H 660 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.8018 (pp) outliers start: 164 outliers final: 97 residues processed: 764 average time/residue: 0.2979 time to fit residues: 356.3416 Evaluate side-chains 675 residues out of total 4480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 570 time to evaluate : 1.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 99 MET Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 418 HIS Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 491 ARG Chi-restraints excluded: chain A residue 495 MET Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 646 THR Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 99 MET Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 318 ILE Chi-restraints excluded: chain B residue 327 ASP Chi-restraints excluded: chain B residue 418 HIS Chi-restraints excluded: chain B residue 477 VAL Chi-restraints excluded: chain B residue 491 ARG Chi-restraints excluded: chain B residue 495 MET Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain B residue 628 THR Chi-restraints excluded: chain B residue 646 THR Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 99 MET Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 264 ILE Chi-restraints excluded: chain C residue 327 ASP Chi-restraints excluded: chain C residue 418 HIS Chi-restraints excluded: chain C residue 477 VAL Chi-restraints excluded: chain C residue 495 MET Chi-restraints excluded: chain C residue 544 ILE Chi-restraints excluded: chain C residue 628 THR Chi-restraints excluded: chain C residue 646 THR Chi-restraints excluded: chain C residue 660 LEU Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 99 MET Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 327 ASP Chi-restraints excluded: chain D residue 418 HIS Chi-restraints excluded: chain D residue 477 VAL Chi-restraints excluded: chain D residue 495 MET Chi-restraints excluded: chain D residue 544 ILE Chi-restraints excluded: chain D residue 628 THR Chi-restraints excluded: chain D residue 646 THR Chi-restraints excluded: chain D residue 660 LEU Chi-restraints excluded: chain E residue 168 GLU Chi-restraints excluded: chain E residue 182 VAL Chi-restraints excluded: chain E residue 264 ILE Chi-restraints excluded: chain E residue 327 ASP Chi-restraints excluded: chain E residue 418 HIS Chi-restraints excluded: chain E residue 477 VAL Chi-restraints excluded: chain E residue 491 ARG Chi-restraints excluded: chain E residue 495 MET Chi-restraints excluded: chain E residue 565 THR Chi-restraints excluded: chain E residue 628 THR Chi-restraints excluded: chain E residue 646 THR Chi-restraints excluded: chain E residue 660 LEU Chi-restraints excluded: chain F residue 32 LEU Chi-restraints excluded: chain F residue 168 GLU Chi-restraints excluded: chain F residue 264 ILE Chi-restraints excluded: chain F residue 288 LEU Chi-restraints excluded: chain F residue 327 ASP Chi-restraints excluded: chain F residue 418 HIS Chi-restraints excluded: chain F residue 477 VAL Chi-restraints excluded: chain F residue 495 MET Chi-restraints excluded: chain F residue 534 THR Chi-restraints excluded: chain F residue 628 THR Chi-restraints excluded: chain F residue 646 THR Chi-restraints excluded: chain F residue 660 LEU Chi-restraints excluded: chain G residue 3 ILE Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain G residue 99 MET Chi-restraints excluded: chain G residue 264 ILE Chi-restraints excluded: chain G residue 270 THR Chi-restraints excluded: chain G residue 327 ASP Chi-restraints excluded: chain G residue 418 HIS Chi-restraints excluded: chain G residue 433 SER Chi-restraints excluded: chain G residue 477 VAL Chi-restraints excluded: chain G residue 495 MET Chi-restraints excluded: chain G residue 544 ILE Chi-restraints excluded: chain G residue 628 THR Chi-restraints excluded: chain G residue 646 THR Chi-restraints excluded: chain G residue 660 LEU Chi-restraints excluded: chain H residue 3 ILE Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain H residue 99 MET Chi-restraints excluded: chain H residue 240 VAL Chi-restraints excluded: chain H residue 264 ILE Chi-restraints excluded: chain H residue 288 LEU Chi-restraints excluded: chain H residue 318 ILE Chi-restraints excluded: chain H residue 327 ASP Chi-restraints excluded: chain H residue 418 HIS Chi-restraints excluded: chain H residue 433 SER Chi-restraints excluded: chain H residue 477 VAL Chi-restraints excluded: chain H residue 491 ARG Chi-restraints excluded: chain H residue 495 MET Chi-restraints excluded: chain H residue 544 ILE Chi-restraints excluded: chain H residue 628 THR Chi-restraints excluded: chain H residue 646 THR Chi-restraints excluded: chain H residue 660 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 74 optimal weight: 8.9990 chunk 438 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 106 optimal weight: 0.0370 chunk 222 optimal weight: 4.9990 chunk 112 optimal weight: 0.9980 chunk 483 optimal weight: 2.9990 chunk 271 optimal weight: 8.9990 chunk 161 optimal weight: 0.7980 chunk 69 optimal weight: 2.9990 chunk 315 optimal weight: 9.9990 overall best weight: 0.7260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 508 ASN ** A 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 529 ASN A 612 ASN ** B 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 508 ASN ** B 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 529 ASN B 612 ASN ** C 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 430 HIS C 508 ASN ** C 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 508 ASN ** D 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 612 ASN ** E 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 529 ASN ** F 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 529 ASN ** G 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 508 ASN ** G 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 249 ASN ** H 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 508 ASN ** H 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.146353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.121095 restraints weight = 48008.771| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 1.79 r_work: 0.3100 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.3407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 43184 Z= 0.105 Angle : 0.595 8.542 58672 Z= 0.307 Chirality : 0.045 0.210 6120 Planarity : 0.005 0.044 7672 Dihedral : 6.270 47.688 6168 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 3.24 % Allowed : 12.32 % Favored : 84.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.12), residues: 5280 helix: 0.30 (0.14), residues: 1344 sheet: -1.04 (0.20), residues: 680 loop : -0.16 (0.11), residues: 3256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 451 TYR 0.022 0.001 TYR F 132 PHE 0.015 0.002 PHE F 312 TRP 0.020 0.001 TRP E 566 HIS 0.008 0.001 HIS C 515 Details of bonding type rmsd covalent geometry : bond 0.00225 (43184) covalent geometry : angle 0.59512 (58672) hydrogen bonds : bond 0.03430 ( 1200) hydrogen bonds : angle 5.16627 ( 3600) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10560 Ramachandran restraints generated. 5280 Oldfield, 0 Emsley, 5280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10560 Ramachandran restraints generated. 5280 Oldfield, 0 Emsley, 5280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 809 residues out of total 4480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 664 time to evaluate : 1.782 Fit side-chains REVERT: A 128 LYS cc_start: 0.8188 (ttpt) cc_final: 0.7659 (ttmt) REVERT: A 180 ASP cc_start: 0.8596 (t0) cc_final: 0.8327 (t0) REVERT: A 378 GLU cc_start: 0.7207 (tp30) cc_final: 0.6956 (tt0) REVERT: A 598 VAL cc_start: 0.8647 (t) cc_final: 0.8319 (p) REVERT: B 29 ASP cc_start: 0.7179 (t0) cc_final: 0.6945 (t0) REVERT: B 32 LEU cc_start: 0.8009 (OUTLIER) cc_final: 0.7724 (mp) REVERT: B 180 ASP cc_start: 0.8625 (t0) cc_final: 0.8352 (t0) REVERT: B 378 GLU cc_start: 0.7326 (tp30) cc_final: 0.6931 (tt0) REVERT: B 389 ASP cc_start: 0.7645 (OUTLIER) cc_final: 0.7366 (t70) REVERT: B 563 GLU cc_start: 0.8264 (pm20) cc_final: 0.7419 (pm20) REVERT: B 598 VAL cc_start: 0.8686 (t) cc_final: 0.8365 (p) REVERT: B 634 GLU cc_start: 0.7861 (tp30) cc_final: 0.7101 (mt-10) REVERT: C 29 ASP cc_start: 0.7191 (t0) cc_final: 0.6946 (t0) REVERT: C 32 LEU cc_start: 0.8096 (OUTLIER) cc_final: 0.7799 (mp) REVERT: C 180 ASP cc_start: 0.8496 (t0) cc_final: 0.8213 (t0) REVERT: C 374 GLU cc_start: 0.7360 (tm-30) cc_final: 0.7009 (mm-30) REVERT: C 378 GLU cc_start: 0.7194 (tp30) cc_final: 0.6863 (tt0) REVERT: C 451 ARG cc_start: 0.8145 (mtm-85) cc_final: 0.7830 (mtm-85) REVERT: C 456 MET cc_start: 0.8704 (mtp) cc_final: 0.8365 (mtp) REVERT: C 563 GLU cc_start: 0.8225 (pm20) cc_final: 0.7419 (pm20) REVERT: C 596 TYR cc_start: 0.8167 (m-80) cc_final: 0.7873 (m-80) REVERT: C 598 VAL cc_start: 0.8690 (t) cc_final: 0.8346 (p) REVERT: D 32 LEU cc_start: 0.8135 (OUTLIER) cc_final: 0.7906 (mp) REVERT: D 38 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7362 (tm-30) REVERT: D 128 LYS cc_start: 0.7718 (ttpp) cc_final: 0.7391 (ttmt) REVERT: D 180 ASP cc_start: 0.8483 (t0) cc_final: 0.8238 (t0) REVERT: D 378 GLU cc_start: 0.7112 (tp30) cc_final: 0.6770 (tt0) REVERT: D 451 ARG cc_start: 0.8218 (mtm-85) cc_final: 0.7911 (mtm-85) REVERT: D 456 MET cc_start: 0.8764 (mtp) cc_final: 0.8437 (mtp) REVERT: D 563 GLU cc_start: 0.8365 (pm20) cc_final: 0.7603 (pm20) REVERT: E 99 MET cc_start: 0.9333 (mtm) cc_final: 0.8959 (mtm) REVERT: E 128 LYS cc_start: 0.7690 (ttpp) cc_final: 0.7394 (ttmt) REVERT: E 180 ASP cc_start: 0.8513 (t0) cc_final: 0.8201 (t0) REVERT: E 389 ASP cc_start: 0.7527 (OUTLIER) cc_final: 0.7281 (t70) REVERT: E 563 GLU cc_start: 0.8296 (pm20) cc_final: 0.7497 (pm20) REVERT: E 634 GLU cc_start: 0.7851 (tp30) cc_final: 0.7173 (mt-10) REVERT: F 128 LYS cc_start: 0.8134 (ttmt) cc_final: 0.7689 (ttpp) REVERT: F 180 ASP cc_start: 0.8563 (t0) cc_final: 0.8229 (t0) REVERT: F 378 GLU cc_start: 0.7174 (tp30) cc_final: 0.6911 (tt0) REVERT: F 451 ARG cc_start: 0.8209 (mtm-85) cc_final: 0.7912 (mtm-85) REVERT: F 456 MET cc_start: 0.8779 (mtp) cc_final: 0.8484 (mtp) REVERT: F 563 GLU cc_start: 0.8219 (pm20) cc_final: 0.7420 (pm20) REVERT: G 180 ASP cc_start: 0.8379 (t0) cc_final: 0.8175 (t0) REVERT: G 378 GLU cc_start: 0.7157 (tp30) cc_final: 0.6875 (tt0) REVERT: G 503 TYR cc_start: 0.8557 (m-80) cc_final: 0.7590 (m-80) REVERT: G 563 GLU cc_start: 0.8352 (pm20) cc_final: 0.7576 (pm20) REVERT: H 128 LYS cc_start: 0.8112 (ttpt) cc_final: 0.7614 (ttmt) REVERT: H 180 ASP cc_start: 0.8578 (t0) cc_final: 0.8326 (t0) REVERT: H 252 LYS cc_start: 0.6964 (ttmt) cc_final: 0.6684 (ttpt) REVERT: H 378 GLU cc_start: 0.7155 (tp30) cc_final: 0.6859 (tt0) REVERT: H 389 ASP cc_start: 0.7632 (OUTLIER) cc_final: 0.7361 (t70) REVERT: H 503 TYR cc_start: 0.8553 (m-80) cc_final: 0.7673 (m-80) REVERT: H 563 GLU cc_start: 0.8448 (pm20) cc_final: 0.7639 (pm20) REVERT: H 596 TYR cc_start: 0.8159 (m-80) cc_final: 0.7903 (m-80) outliers start: 145 outliers final: 82 residues processed: 768 average time/residue: 0.2923 time to fit residues: 356.5203 Evaluate side-chains 664 residues out of total 4480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 575 time to evaluate : 1.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 327 ASP Chi-restraints excluded: chain A residue 408 ILE Chi-restraints excluded: chain A residue 418 HIS Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 491 ARG Chi-restraints excluded: chain A residue 495 MET Chi-restraints excluded: chain A residue 646 THR Chi-restraints excluded: chain A residue 654 THR Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 99 MET Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain B residue 418 HIS Chi-restraints excluded: chain B residue 453 MET Chi-restraints excluded: chain B residue 477 VAL Chi-restraints excluded: chain B residue 491 ARG Chi-restraints excluded: chain B residue 495 MET Chi-restraints excluded: chain B residue 544 ILE Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain B residue 646 THR Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 264 ILE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 418 HIS Chi-restraints excluded: chain C residue 453 MET Chi-restraints excluded: chain C residue 477 VAL Chi-restraints excluded: chain C residue 646 THR Chi-restraints excluded: chain C residue 654 THR Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 38 GLU Chi-restraints excluded: chain D residue 99 MET Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 408 ILE Chi-restraints excluded: chain D residue 418 HIS Chi-restraints excluded: chain D residue 477 VAL Chi-restraints excluded: chain D residue 495 MET Chi-restraints excluded: chain D residue 646 THR Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 264 ILE Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 389 ASP Chi-restraints excluded: chain E residue 408 ILE Chi-restraints excluded: chain E residue 418 HIS Chi-restraints excluded: chain E residue 477 VAL Chi-restraints excluded: chain E residue 491 ARG Chi-restraints excluded: chain E residue 495 MET Chi-restraints excluded: chain E residue 565 THR Chi-restraints excluded: chain E residue 646 THR Chi-restraints excluded: chain F residue 32 LEU Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 264 ILE Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 408 ILE Chi-restraints excluded: chain F residue 418 HIS Chi-restraints excluded: chain F residue 477 VAL Chi-restraints excluded: chain F residue 495 MET Chi-restraints excluded: chain F residue 646 THR Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain G residue 99 MET Chi-restraints excluded: chain G residue 240 VAL Chi-restraints excluded: chain G residue 264 ILE Chi-restraints excluded: chain G residue 277 LEU Chi-restraints excluded: chain G residue 408 ILE Chi-restraints excluded: chain G residue 418 HIS Chi-restraints excluded: chain G residue 433 SER Chi-restraints excluded: chain G residue 453 MET Chi-restraints excluded: chain G residue 477 VAL Chi-restraints excluded: chain G residue 495 MET Chi-restraints excluded: chain G residue 543 ASP Chi-restraints excluded: chain G residue 646 THR Chi-restraints excluded: chain G residue 654 THR Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain H residue 99 MET Chi-restraints excluded: chain H residue 240 VAL Chi-restraints excluded: chain H residue 264 ILE Chi-restraints excluded: chain H residue 277 LEU Chi-restraints excluded: chain H residue 389 ASP Chi-restraints excluded: chain H residue 408 ILE Chi-restraints excluded: chain H residue 418 HIS Chi-restraints excluded: chain H residue 433 SER Chi-restraints excluded: chain H residue 453 MET Chi-restraints excluded: chain H residue 477 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 92 optimal weight: 5.9990 chunk 351 optimal weight: 9.9990 chunk 69 optimal weight: 10.0000 chunk 200 optimal weight: 3.9990 chunk 115 optimal weight: 6.9990 chunk 462 optimal weight: 1.9990 chunk 109 optimal weight: 7.9990 chunk 38 optimal weight: 20.0000 chunk 418 optimal weight: 8.9990 chunk 506 optimal weight: 4.9990 chunk 167 optimal weight: 10.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 HIS ** A 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 529 ASN ** A 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 142 HIS B 210 HIS ** B 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 529 ASN ** C 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 210 HIS ** C 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 210 HIS ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 508 ASN ** D 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 142 HIS E 210 HIS ** E 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 508 ASN E 529 ASN ** F 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 210 HIS ** F 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 480 HIS F 508 ASN F 529 ASN ** F 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 142 HIS G 210 HIS ** G 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 508 ASN ** G 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 142 HIS H 210 HIS ** H 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 508 ASN ** H 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.138337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.111768 restraints weight = 48843.539| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 1.72 r_work: 0.3022 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2878 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.3562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 43184 Z= 0.229 Angle : 0.675 7.835 58672 Z= 0.353 Chirality : 0.049 0.261 6120 Planarity : 0.005 0.048 7672 Dihedral : 6.384 50.449 6168 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 4.20 % Allowed : 12.97 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.12), residues: 5280 helix: 0.51 (0.15), residues: 1296 sheet: -1.29 (0.18), residues: 784 loop : -0.04 (0.12), residues: 3200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 24 TYR 0.023 0.002 TYR G 132 PHE 0.026 0.002 PHE F 325 TRP 0.025 0.002 TRP E 566 HIS 0.008 0.002 HIS F 418 Details of bonding type rmsd covalent geometry : bond 0.00555 (43184) covalent geometry : angle 0.67513 (58672) hydrogen bonds : bond 0.04248 ( 1200) hydrogen bonds : angle 5.34955 ( 3600) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10560 Ramachandran restraints generated. 5280 Oldfield, 0 Emsley, 5280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10560 Ramachandran restraints generated. 5280 Oldfield, 0 Emsley, 5280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 781 residues out of total 4480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 188 poor density : 593 time to evaluate : 1.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 LYS cc_start: 0.8178 (ttpt) cc_final: 0.7649 (ttmt) REVERT: A 179 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.8143 (mp0) REVERT: A 180 ASP cc_start: 0.8688 (t0) cc_final: 0.8373 (t0) REVERT: A 383 TYR cc_start: 0.8726 (t80) cc_final: 0.8361 (t80) REVERT: A 389 ASP cc_start: 0.7738 (t0) cc_final: 0.7499 (t0) REVERT: A 456 MET cc_start: 0.8839 (mtp) cc_final: 0.8506 (mtp) REVERT: A 563 GLU cc_start: 0.8472 (pm20) cc_final: 0.7537 (pm20) REVERT: A 660 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.7915 (pp) REVERT: B 128 LYS cc_start: 0.8253 (ttmt) cc_final: 0.7723 (ttpp) REVERT: B 179 GLU cc_start: 0.8432 (OUTLIER) cc_final: 0.8196 (mp0) REVERT: B 456 MET cc_start: 0.8833 (mtp) cc_final: 0.8422 (mtp) REVERT: B 563 GLU cc_start: 0.8459 (pm20) cc_final: 0.7486 (pm20) REVERT: B 598 VAL cc_start: 0.8723 (t) cc_final: 0.8459 (p) REVERT: B 634 GLU cc_start: 0.7634 (tp30) cc_final: 0.7066 (mt-10) REVERT: B 660 LEU cc_start: 0.8496 (OUTLIER) cc_final: 0.7935 (pp) REVERT: C 32 LEU cc_start: 0.8089 (OUTLIER) cc_final: 0.7874 (mp) REVERT: C 128 LYS cc_start: 0.7734 (ttpp) cc_final: 0.7393 (ttmt) REVERT: C 179 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.8130 (mp0) REVERT: C 180 ASP cc_start: 0.8689 (t0) cc_final: 0.8362 (t0) REVERT: C 451 ARG cc_start: 0.8297 (mtm-85) cc_final: 0.7916 (mtm-85) REVERT: C 456 MET cc_start: 0.8791 (mtp) cc_final: 0.8573 (mtp) REVERT: C 470 MET cc_start: 0.9442 (mtp) cc_final: 0.9207 (mtm) REVERT: C 563 GLU cc_start: 0.8444 (pm20) cc_final: 0.7504 (pm20) REVERT: C 660 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.7857 (pp) REVERT: D 38 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7427 (tm-30) REVERT: D 128 LYS cc_start: 0.7665 (ttpp) cc_final: 0.7314 (ttmt) REVERT: D 179 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.8145 (mp0) REVERT: D 180 ASP cc_start: 0.8670 (t0) cc_final: 0.8337 (t0) REVERT: D 383 TYR cc_start: 0.8699 (t80) cc_final: 0.8379 (t80) REVERT: D 451 ARG cc_start: 0.8324 (mtm-85) cc_final: 0.8105 (mtm-85) REVERT: D 456 MET cc_start: 0.8884 (mtp) cc_final: 0.8557 (mtp) REVERT: D 563 GLU cc_start: 0.8466 (pm20) cc_final: 0.7532 (pm20) REVERT: D 660 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.7900 (pp) REVERT: E 128 LYS cc_start: 0.7767 (ttpp) cc_final: 0.7429 (ttmt) REVERT: E 180 ASP cc_start: 0.8623 (t0) cc_final: 0.8314 (t0) REVERT: E 252 LYS cc_start: 0.7122 (ttmt) cc_final: 0.6685 (tttt) REVERT: E 456 MET cc_start: 0.8854 (mtp) cc_final: 0.8578 (mtp) REVERT: E 563 GLU cc_start: 0.8447 (pm20) cc_final: 0.7479 (pm20) REVERT: E 634 GLU cc_start: 0.7718 (tp30) cc_final: 0.7081 (mt-10) REVERT: E 660 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.7900 (pp) REVERT: F 128 LYS cc_start: 0.8153 (ttmt) cc_final: 0.7698 (ttpp) REVERT: F 179 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.8099 (mp0) REVERT: F 180 ASP cc_start: 0.8608 (t0) cc_final: 0.8366 (t0) REVERT: F 451 ARG cc_start: 0.8277 (mtm-85) cc_final: 0.7907 (mtm-85) REVERT: F 456 MET cc_start: 0.8793 (mtp) cc_final: 0.8558 (mtp) REVERT: F 563 GLU cc_start: 0.8459 (pm20) cc_final: 0.7487 (pm20) REVERT: F 599 LYS cc_start: 0.8495 (mppt) cc_final: 0.8264 (mppt) REVERT: F 660 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.7919 (pp) REVERT: G 179 GLU cc_start: 0.8386 (OUTLIER) cc_final: 0.7727 (mm-30) REVERT: G 374 GLU cc_start: 0.6819 (mp0) cc_final: 0.6601 (mm-30) REVERT: G 456 MET cc_start: 0.8855 (mtp) cc_final: 0.8477 (mtp) REVERT: G 563 GLU cc_start: 0.8510 (pm20) cc_final: 0.7570 (pm20) REVERT: G 660 LEU cc_start: 0.8509 (OUTLIER) cc_final: 0.7933 (pp) REVERT: H 128 LYS cc_start: 0.8018 (ttpt) cc_final: 0.7552 (ttmt) REVERT: H 179 GLU cc_start: 0.8405 (OUTLIER) cc_final: 0.8190 (mp0) REVERT: H 180 ASP cc_start: 0.8670 (t0) cc_final: 0.8352 (t0) REVERT: H 252 LYS cc_start: 0.7214 (ttmt) cc_final: 0.6780 (tttt) REVERT: H 389 ASP cc_start: 0.7652 (OUTLIER) cc_final: 0.7349 (t70) REVERT: H 456 MET cc_start: 0.8843 (mtp) cc_final: 0.8440 (mtp) REVERT: H 563 GLU cc_start: 0.8516 (pm20) cc_final: 0.7611 (pm20) REVERT: H 660 LEU cc_start: 0.8506 (OUTLIER) cc_final: 0.7937 (pp) outliers start: 188 outliers final: 108 residues processed: 721 average time/residue: 0.3008 time to fit residues: 340.9934 Evaluate side-chains 691 residues out of total 4480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 565 time to evaluate : 1.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 99 MET Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 179 GLU Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 327 ASP Chi-restraints excluded: chain A residue 418 HIS Chi-restraints excluded: chain A residue 453 MET Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 491 ARG Chi-restraints excluded: chain A residue 495 MET Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 646 THR Chi-restraints excluded: chain A residue 654 THR Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 179 GLU Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 318 ILE Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 418 HIS Chi-restraints excluded: chain B residue 477 VAL Chi-restraints excluded: chain B residue 491 ARG Chi-restraints excluded: chain B residue 495 MET Chi-restraints excluded: chain B residue 544 ILE Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain B residue 646 THR Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 99 MET Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 179 GLU Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 264 ILE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 418 HIS Chi-restraints excluded: chain C residue 453 MET Chi-restraints excluded: chain C residue 477 VAL Chi-restraints excluded: chain C residue 646 THR Chi-restraints excluded: chain C residue 654 THR Chi-restraints excluded: chain C residue 660 LEU Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain D residue 38 GLU Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 179 GLU Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 389 ASP Chi-restraints excluded: chain D residue 418 HIS Chi-restraints excluded: chain D residue 477 VAL Chi-restraints excluded: chain D residue 495 MET Chi-restraints excluded: chain D residue 544 ILE Chi-restraints excluded: chain D residue 646 THR Chi-restraints excluded: chain D residue 660 LEU Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 168 GLU Chi-restraints excluded: chain E residue 264 ILE Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 389 ASP Chi-restraints excluded: chain E residue 418 HIS Chi-restraints excluded: chain E residue 477 VAL Chi-restraints excluded: chain E residue 491 ARG Chi-restraints excluded: chain E residue 495 MET Chi-restraints excluded: chain E residue 544 ILE Chi-restraints excluded: chain E residue 565 THR Chi-restraints excluded: chain E residue 646 THR Chi-restraints excluded: chain E residue 660 LEU Chi-restraints excluded: chain F residue 32 LEU Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 168 GLU Chi-restraints excluded: chain F residue 179 GLU Chi-restraints excluded: chain F residue 264 ILE Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 389 ASP Chi-restraints excluded: chain F residue 418 HIS Chi-restraints excluded: chain F residue 453 MET Chi-restraints excluded: chain F residue 477 VAL Chi-restraints excluded: chain F residue 495 MET Chi-restraints excluded: chain F residue 544 ILE Chi-restraints excluded: chain F residue 646 THR Chi-restraints excluded: chain F residue 660 LEU Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain G residue 131 THR Chi-restraints excluded: chain G residue 168 GLU Chi-restraints excluded: chain G residue 179 GLU Chi-restraints excluded: chain G residue 264 ILE Chi-restraints excluded: chain G residue 270 THR Chi-restraints excluded: chain G residue 277 LEU Chi-restraints excluded: chain G residue 389 ASP Chi-restraints excluded: chain G residue 418 HIS Chi-restraints excluded: chain G residue 433 SER Chi-restraints excluded: chain G residue 453 MET Chi-restraints excluded: chain G residue 477 VAL Chi-restraints excluded: chain G residue 495 MET Chi-restraints excluded: chain G residue 544 ILE Chi-restraints excluded: chain G residue 646 THR Chi-restraints excluded: chain G residue 654 THR Chi-restraints excluded: chain G residue 660 LEU Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 99 MET Chi-restraints excluded: chain H residue 131 THR Chi-restraints excluded: chain H residue 168 GLU Chi-restraints excluded: chain H residue 179 GLU Chi-restraints excluded: chain H residue 240 VAL Chi-restraints excluded: chain H residue 264 ILE Chi-restraints excluded: chain H residue 277 LEU Chi-restraints excluded: chain H residue 288 LEU Chi-restraints excluded: chain H residue 318 ILE Chi-restraints excluded: chain H residue 389 ASP Chi-restraints excluded: chain H residue 418 HIS Chi-restraints excluded: chain H residue 433 SER Chi-restraints excluded: chain H residue 477 VAL Chi-restraints excluded: chain H residue 491 ARG Chi-restraints excluded: chain H residue 646 THR Chi-restraints excluded: chain H residue 660 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 461 optimal weight: 4.9990 chunk 452 optimal weight: 10.0000 chunk 343 optimal weight: 5.9990 chunk 443 optimal weight: 10.0000 chunk 407 optimal weight: 9.9990 chunk 250 optimal weight: 9.9990 chunk 114 optimal weight: 0.6980 chunk 375 optimal weight: 0.9990 chunk 222 optimal weight: 20.0000 chunk 497 optimal weight: 7.9990 chunk 268 optimal weight: 6.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 HIS ** A 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 529 ASN ** B 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 529 ASN ** E 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 612 ASN ** G 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 529 ASN ** H 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 529 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.137904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.112044 restraints weight = 48521.462| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 1.71 r_work: 0.3062 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.3763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 43184 Z= 0.191 Angle : 0.640 7.679 58672 Z= 0.334 Chirality : 0.048 0.224 6120 Planarity : 0.005 0.049 7672 Dihedral : 6.383 51.614 6168 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.62 % Allowed : 14.17 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.12), residues: 5280 helix: 0.61 (0.15), residues: 1296 sheet: -1.38 (0.19), residues: 672 loop : -0.20 (0.11), residues: 3312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 201 TYR 0.023 0.002 TYR H 132 PHE 0.022 0.002 PHE B 325 TRP 0.019 0.001 TRP E 566 HIS 0.007 0.001 HIS E 394 Details of bonding type rmsd covalent geometry : bond 0.00459 (43184) covalent geometry : angle 0.64008 (58672) hydrogen bonds : bond 0.03937 ( 1200) hydrogen bonds : angle 5.27903 ( 3600) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10560 Ramachandran restraints generated. 5280 Oldfield, 0 Emsley, 5280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10560 Ramachandran restraints generated. 5280 Oldfield, 0 Emsley, 5280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 773 residues out of total 4480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 162 poor density : 611 time to evaluate : 1.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 LYS cc_start: 0.8146 (ttpt) cc_final: 0.7531 (ttmt) REVERT: A 179 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.8165 (mp0) REVERT: A 383 TYR cc_start: 0.8706 (t80) cc_final: 0.8362 (t80) REVERT: A 389 ASP cc_start: 0.7587 (t0) cc_final: 0.7367 (t0) REVERT: A 456 MET cc_start: 0.8835 (mtp) cc_final: 0.8590 (mtp) REVERT: A 563 GLU cc_start: 0.8358 (pm20) cc_final: 0.7452 (pm20) REVERT: A 598 VAL cc_start: 0.8670 (t) cc_final: 0.8389 (p) REVERT: A 660 LEU cc_start: 0.8377 (OUTLIER) cc_final: 0.7797 (pp) REVERT: B 128 LYS cc_start: 0.8314 (ttmt) cc_final: 0.7776 (ttpp) REVERT: B 563 GLU cc_start: 0.8355 (pm20) cc_final: 0.7669 (pm20) REVERT: B 598 VAL cc_start: 0.8768 (t) cc_final: 0.8494 (p) REVERT: B 634 GLU cc_start: 0.7595 (tp30) cc_final: 0.7016 (mt-10) REVERT: B 660 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.7765 (pp) REVERT: C 128 LYS cc_start: 0.7715 (ttpp) cc_final: 0.7358 (ttmt) REVERT: C 383 TYR cc_start: 0.8689 (t80) cc_final: 0.8436 (t80) REVERT: C 413 TYR cc_start: 0.9229 (m-80) cc_final: 0.9027 (m-80) REVERT: C 451 ARG cc_start: 0.8313 (mtm-85) cc_final: 0.7965 (mtm-85) REVERT: C 456 MET cc_start: 0.8754 (mtp) cc_final: 0.8518 (mtp) REVERT: C 470 MET cc_start: 0.9438 (mtp) cc_final: 0.9221 (mtm) REVERT: C 563 GLU cc_start: 0.8457 (pm20) cc_final: 0.7777 (pm20) REVERT: C 660 LEU cc_start: 0.8384 (OUTLIER) cc_final: 0.7802 (pp) REVERT: D 38 GLU cc_start: 0.8043 (OUTLIER) cc_final: 0.7349 (tm-30) REVERT: D 128 LYS cc_start: 0.7747 (ttpp) cc_final: 0.7509 (ttmt) REVERT: D 179 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.8047 (mp0) REVERT: D 252 LYS cc_start: 0.7133 (ttmt) cc_final: 0.6700 (tttt) REVERT: D 354 ASN cc_start: 0.8169 (OUTLIER) cc_final: 0.7883 (t0) REVERT: D 383 TYR cc_start: 0.8675 (t80) cc_final: 0.8348 (t80) REVERT: D 563 GLU cc_start: 0.8417 (pm20) cc_final: 0.7466 (pm20) REVERT: D 598 VAL cc_start: 0.8679 (t) cc_final: 0.8365 (p) REVERT: D 660 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.7842 (pp) REVERT: E 128 LYS cc_start: 0.7799 (ttpp) cc_final: 0.7422 (ttmt) REVERT: E 252 LYS cc_start: 0.7249 (ttmt) cc_final: 0.6810 (tttt) REVERT: E 413 TYR cc_start: 0.9248 (m-80) cc_final: 0.9041 (m-80) REVERT: E 456 MET cc_start: 0.8780 (mtp) cc_final: 0.8561 (mtp) REVERT: E 598 VAL cc_start: 0.8609 (t) cc_final: 0.8290 (m) REVERT: E 634 GLU cc_start: 0.7697 (tp30) cc_final: 0.7092 (mt-10) REVERT: E 660 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.7846 (pp) REVERT: F 383 TYR cc_start: 0.8714 (t80) cc_final: 0.8355 (t80) REVERT: F 451 ARG cc_start: 0.8342 (mtm-85) cc_final: 0.7988 (mtm-85) REVERT: F 563 GLU cc_start: 0.8509 (pm20) cc_final: 0.7533 (pm20) REVERT: F 598 VAL cc_start: 0.8579 (t) cc_final: 0.8246 (m) REVERT: F 660 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.7808 (pp) REVERT: G 179 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.8034 (mp0) REVERT: G 383 TYR cc_start: 0.8703 (t80) cc_final: 0.8337 (t80) REVERT: G 413 TYR cc_start: 0.9257 (m-80) cc_final: 0.9056 (m-80) REVERT: G 456 MET cc_start: 0.8817 (mtp) cc_final: 0.8442 (mtp) REVERT: G 563 GLU cc_start: 0.8373 (pm20) cc_final: 0.7450 (pm20) REVERT: G 598 VAL cc_start: 0.8676 (t) cc_final: 0.8352 (p) REVERT: G 660 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.7868 (pp) REVERT: H 128 LYS cc_start: 0.8119 (ttpt) cc_final: 0.7614 (ttmt) REVERT: H 179 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.8068 (mp0) REVERT: H 252 LYS cc_start: 0.7215 (ttmt) cc_final: 0.6751 (tttt) REVERT: H 389 ASP cc_start: 0.7633 (OUTLIER) cc_final: 0.7303 (t70) REVERT: H 563 GLU cc_start: 0.8427 (pm20) cc_final: 0.7511 (pm20) REVERT: H 599 LYS cc_start: 0.8523 (mppt) cc_final: 0.8285 (mppt) REVERT: H 660 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.7795 (pp) outliers start: 162 outliers final: 119 residues processed: 709 average time/residue: 0.2979 time to fit residues: 332.3663 Evaluate side-chains 712 residues out of total 4480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 578 time to evaluate : 1.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 99 MET Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 179 GLU Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 327 ASP Chi-restraints excluded: chain A residue 418 HIS Chi-restraints excluded: chain A residue 453 MET Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 491 ARG Chi-restraints excluded: chain A residue 495 MET Chi-restraints excluded: chain A residue 654 THR Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain B residue 99 MET Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 318 ILE Chi-restraints excluded: chain B residue 327 ASP Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain B residue 418 HIS Chi-restraints excluded: chain B residue 453 MET Chi-restraints excluded: chain B residue 477 VAL Chi-restraints excluded: chain B residue 491 ARG Chi-restraints excluded: chain B residue 495 MET Chi-restraints excluded: chain B residue 544 ILE Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain B residue 646 THR Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain B residue 662 ARG Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 99 MET Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 327 ASP Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 418 HIS Chi-restraints excluded: chain C residue 453 MET Chi-restraints excluded: chain C residue 477 VAL Chi-restraints excluded: chain C residue 495 MET Chi-restraints excluded: chain C residue 544 ILE Chi-restraints excluded: chain C residue 646 THR Chi-restraints excluded: chain C residue 654 THR Chi-restraints excluded: chain C residue 660 LEU Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain D residue 38 GLU Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 179 GLU Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 327 ASP Chi-restraints excluded: chain D residue 354 ASN Chi-restraints excluded: chain D residue 389 ASP Chi-restraints excluded: chain D residue 408 ILE Chi-restraints excluded: chain D residue 477 VAL Chi-restraints excluded: chain D residue 495 MET Chi-restraints excluded: chain D residue 544 ILE Chi-restraints excluded: chain D residue 654 THR Chi-restraints excluded: chain D residue 660 LEU Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 168 GLU Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 389 ASP Chi-restraints excluded: chain E residue 418 HIS Chi-restraints excluded: chain E residue 477 VAL Chi-restraints excluded: chain E residue 491 ARG Chi-restraints excluded: chain E residue 495 MET Chi-restraints excluded: chain E residue 544 ILE Chi-restraints excluded: chain E residue 565 THR Chi-restraints excluded: chain E residue 646 THR Chi-restraints excluded: chain E residue 660 LEU Chi-restraints excluded: chain F residue 32 LEU Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 168 GLU Chi-restraints excluded: chain F residue 191 LEU Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 327 ASP Chi-restraints excluded: chain F residue 389 ASP Chi-restraints excluded: chain F residue 408 ILE Chi-restraints excluded: chain F residue 418 HIS Chi-restraints excluded: chain F residue 453 MET Chi-restraints excluded: chain F residue 477 VAL Chi-restraints excluded: chain F residue 495 MET Chi-restraints excluded: chain F residue 544 ILE Chi-restraints excluded: chain F residue 646 THR Chi-restraints excluded: chain F residue 660 LEU Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain G residue 99 MET Chi-restraints excluded: chain G residue 168 GLU Chi-restraints excluded: chain G residue 179 GLU Chi-restraints excluded: chain G residue 240 VAL Chi-restraints excluded: chain G residue 277 LEU Chi-restraints excluded: chain G residue 327 ASP Chi-restraints excluded: chain G residue 389 ASP Chi-restraints excluded: chain G residue 408 ILE Chi-restraints excluded: chain G residue 418 HIS Chi-restraints excluded: chain G residue 433 SER Chi-restraints excluded: chain G residue 477 VAL Chi-restraints excluded: chain G residue 495 MET Chi-restraints excluded: chain G residue 544 ILE Chi-restraints excluded: chain G residue 646 THR Chi-restraints excluded: chain G residue 654 THR Chi-restraints excluded: chain G residue 660 LEU Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 99 MET Chi-restraints excluded: chain H residue 168 GLU Chi-restraints excluded: chain H residue 179 GLU Chi-restraints excluded: chain H residue 240 VAL Chi-restraints excluded: chain H residue 277 LEU Chi-restraints excluded: chain H residue 288 LEU Chi-restraints excluded: chain H residue 318 ILE Chi-restraints excluded: chain H residue 327 ASP Chi-restraints excluded: chain H residue 389 ASP Chi-restraints excluded: chain H residue 408 ILE Chi-restraints excluded: chain H residue 418 HIS Chi-restraints excluded: chain H residue 433 SER Chi-restraints excluded: chain H residue 477 VAL Chi-restraints excluded: chain H residue 491 ARG Chi-restraints excluded: chain H residue 544 ILE Chi-restraints excluded: chain H residue 660 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 58 optimal weight: 10.0000 chunk 377 optimal weight: 9.9990 chunk 258 optimal weight: 9.9990 chunk 520 optimal weight: 3.9990 chunk 9 optimal weight: 7.9990 chunk 454 optimal weight: 2.9990 chunk 210 optimal weight: 5.9990 chunk 337 optimal weight: 7.9990 chunk 14 optimal weight: 1.9990 chunk 394 optimal weight: 4.9990 chunk 62 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 529 ASN ** B 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 HIS ** B 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 612 ASN D 185 HIS ** D 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 529 ASN ** E 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 480 HIS ** E 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 612 ASN ** F 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 185 HIS ** F 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 185 HIS ** G 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 529 ASN G 612 ASN ** H 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 529 ASN H 612 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.144602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.118412 restraints weight = 48346.714| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 1.72 r_work: 0.2969 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2829 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.3871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 43184 Z= 0.197 Angle : 0.653 7.609 58672 Z= 0.341 Chirality : 0.048 0.229 6120 Planarity : 0.006 0.050 7672 Dihedral : 6.402 51.992 6168 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 4.11 % Allowed : 14.31 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.12), residues: 5280 helix: 0.59 (0.15), residues: 1296 sheet: -1.48 (0.19), residues: 672 loop : -0.27 (0.11), residues: 3312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 451 TYR 0.020 0.002 TYR G 50 PHE 0.023 0.002 PHE F 325 TRP 0.018 0.001 TRP E 566 HIS 0.007 0.001 HIS B 394 Details of bonding type rmsd covalent geometry : bond 0.00476 (43184) covalent geometry : angle 0.65345 (58672) hydrogen bonds : bond 0.03982 ( 1200) hydrogen bonds : angle 5.28956 ( 3600) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10560 Ramachandran restraints generated. 5280 Oldfield, 0 Emsley, 5280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10560 Ramachandran restraints generated. 5280 Oldfield, 0 Emsley, 5280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 785 residues out of total 4480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 184 poor density : 601 time to evaluate : 1.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 LYS cc_start: 0.8226 (ttpt) cc_final: 0.7642 (ttmt) REVERT: A 179 GLU cc_start: 0.8465 (OUTLIER) cc_final: 0.7909 (mm-30) REVERT: A 180 ASP cc_start: 0.8639 (t0) cc_final: 0.8410 (t0) REVERT: A 362 ILE cc_start: 0.8488 (OUTLIER) cc_final: 0.8075 (pt) REVERT: A 383 TYR cc_start: 0.8720 (t80) cc_final: 0.8376 (t80) REVERT: A 389 ASP cc_start: 0.7675 (t0) cc_final: 0.7450 (t0) REVERT: A 456 MET cc_start: 0.8790 (mtp) cc_final: 0.8568 (mtp) REVERT: A 563 GLU cc_start: 0.8452 (pm20) cc_final: 0.7472 (pm20) REVERT: A 598 VAL cc_start: 0.8602 (t) cc_final: 0.8346 (p) REVERT: A 660 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.7862 (pp) REVERT: B 389 ASP cc_start: 0.7704 (OUTLIER) cc_final: 0.7406 (t70) REVERT: B 569 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8203 (pp) REVERT: B 598 VAL cc_start: 0.8665 (t) cc_final: 0.8419 (p) REVERT: B 634 GLU cc_start: 0.7588 (tp30) cc_final: 0.7001 (mt-10) REVERT: B 660 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.7819 (pp) REVERT: C 128 LYS cc_start: 0.7850 (ttpp) cc_final: 0.7590 (ttmt) REVERT: C 130 GLU cc_start: 0.9196 (OUTLIER) cc_final: 0.7651 (pm20) REVERT: C 180 ASP cc_start: 0.8539 (t0) cc_final: 0.8278 (t0) REVERT: C 354 ASN cc_start: 0.8191 (OUTLIER) cc_final: 0.7938 (t0) REVERT: C 413 TYR cc_start: 0.9272 (m-80) cc_final: 0.9064 (m-80) REVERT: C 451 ARG cc_start: 0.8337 (mtm-85) cc_final: 0.8125 (mtm-85) REVERT: C 456 MET cc_start: 0.8741 (mtp) cc_final: 0.8498 (mtp) REVERT: C 470 MET cc_start: 0.9466 (mtp) cc_final: 0.9224 (mtm) REVERT: C 569 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8366 (pp) REVERT: C 598 VAL cc_start: 0.8578 (t) cc_final: 0.8273 (p) REVERT: C 660 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.7809 (pp) REVERT: D 38 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7307 (tm-30) REVERT: D 128 LYS cc_start: 0.7793 (ttpp) cc_final: 0.7498 (ttmt) REVERT: D 130 GLU cc_start: 0.9176 (OUTLIER) cc_final: 0.7562 (pm20) REVERT: D 179 GLU cc_start: 0.8276 (OUTLIER) cc_final: 0.7620 (mm-30) REVERT: D 180 ASP cc_start: 0.8585 (t0) cc_final: 0.8346 (t0) REVERT: D 252 LYS cc_start: 0.7097 (ttmt) cc_final: 0.6673 (tttt) REVERT: D 354 ASN cc_start: 0.8198 (OUTLIER) cc_final: 0.7915 (t0) REVERT: D 362 ILE cc_start: 0.8640 (OUTLIER) cc_final: 0.8254 (pt) REVERT: D 383 TYR cc_start: 0.8681 (t80) cc_final: 0.8349 (t80) REVERT: D 563 GLU cc_start: 0.8471 (pm20) cc_final: 0.7771 (pm20) REVERT: D 569 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8253 (pp) REVERT: D 598 VAL cc_start: 0.8643 (t) cc_final: 0.8324 (p) REVERT: D 660 LEU cc_start: 0.8465 (OUTLIER) cc_final: 0.7850 (pp) REVERT: E 128 LYS cc_start: 0.7928 (ttpp) cc_final: 0.7634 (ttmt) REVERT: E 130 GLU cc_start: 0.9196 (OUTLIER) cc_final: 0.7627 (pm20) REVERT: E 180 ASP cc_start: 0.8581 (t0) cc_final: 0.8351 (t0) REVERT: E 252 LYS cc_start: 0.7208 (ttmt) cc_final: 0.6811 (tttt) REVERT: E 456 MET cc_start: 0.8771 (mtp) cc_final: 0.8557 (mtp) REVERT: E 563 GLU cc_start: 0.8408 (pm20) cc_final: 0.7525 (pm20) REVERT: E 598 VAL cc_start: 0.8678 (t) cc_final: 0.8315 (m) REVERT: E 634 GLU cc_start: 0.7596 (tp30) cc_final: 0.7009 (mt-10) REVERT: E 660 LEU cc_start: 0.8448 (OUTLIER) cc_final: 0.7847 (pp) REVERT: F 32 LEU cc_start: 0.8017 (OUTLIER) cc_final: 0.7782 (mp) REVERT: F 130 GLU cc_start: 0.9172 (OUTLIER) cc_final: 0.7584 (pm20) REVERT: F 180 ASP cc_start: 0.8506 (t0) cc_final: 0.8255 (t0) REVERT: F 354 ASN cc_start: 0.8191 (OUTLIER) cc_final: 0.7803 (t0) REVERT: F 383 TYR cc_start: 0.8666 (t80) cc_final: 0.8315 (t80) REVERT: F 470 MET cc_start: 0.9395 (mtp) cc_final: 0.9124 (mtm) REVERT: F 598 VAL cc_start: 0.8616 (t) cc_final: 0.8207 (m) REVERT: F 660 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.7851 (pp) REVERT: G 32 LEU cc_start: 0.8128 (OUTLIER) cc_final: 0.7876 (mp) REVERT: G 130 GLU cc_start: 0.9182 (OUTLIER) cc_final: 0.7593 (pm20) REVERT: G 179 GLU cc_start: 0.8257 (OUTLIER) cc_final: 0.7586 (mm-30) REVERT: G 180 ASP cc_start: 0.8494 (t0) cc_final: 0.8232 (t0) REVERT: G 354 ASN cc_start: 0.8177 (OUTLIER) cc_final: 0.7873 (t0) REVERT: G 383 TYR cc_start: 0.8727 (t80) cc_final: 0.8378 (t80) REVERT: G 456 MET cc_start: 0.8762 (mtp) cc_final: 0.8457 (mtp) REVERT: G 563 GLU cc_start: 0.8451 (pm20) cc_final: 0.7492 (pm20) REVERT: G 569 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8380 (pp) REVERT: G 598 VAL cc_start: 0.8672 (t) cc_final: 0.8349 (p) REVERT: G 660 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.7904 (pp) REVERT: H 128 LYS cc_start: 0.8127 (ttpt) cc_final: 0.7831 (ttmt) REVERT: H 179 GLU cc_start: 0.8270 (OUTLIER) cc_final: 0.7534 (mm-30) REVERT: H 180 ASP cc_start: 0.8606 (t0) cc_final: 0.8392 (t0) REVERT: H 252 LYS cc_start: 0.7169 (ttmt) cc_final: 0.6820 (tttt) REVERT: H 389 ASP cc_start: 0.7679 (OUTLIER) cc_final: 0.7363 (t70) REVERT: H 413 TYR cc_start: 0.9257 (m-80) cc_final: 0.9050 (m-80) REVERT: H 470 MET cc_start: 0.9381 (mtp) cc_final: 0.9148 (mtm) REVERT: H 563 GLU cc_start: 0.8510 (pm20) cc_final: 0.7499 (pm20) REVERT: H 598 VAL cc_start: 0.8568 (t) cc_final: 0.8263 (p) REVERT: H 599 LYS cc_start: 0.8588 (mppt) cc_final: 0.8337 (mppt) REVERT: H 660 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.7818 (pp) outliers start: 184 outliers final: 136 residues processed: 719 average time/residue: 0.2957 time to fit residues: 336.1768 Evaluate side-chains 751 residues out of total 4480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 168 poor density : 583 time to evaluate : 1.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 99 MET Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 179 GLU Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 327 ASP Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 408 ILE Chi-restraints excluded: chain A residue 418 HIS Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 491 ARG Chi-restraints excluded: chain A residue 495 MET Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 654 THR Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 99 MET Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 318 ILE Chi-restraints excluded: chain B residue 327 ASP Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain B residue 418 HIS Chi-restraints excluded: chain B residue 477 VAL Chi-restraints excluded: chain B residue 491 ARG Chi-restraints excluded: chain B residue 495 MET Chi-restraints excluded: chain B residue 544 ILE Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 646 THR Chi-restraints excluded: chain B residue 654 THR Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain B residue 662 ARG Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 99 MET Chi-restraints excluded: chain C residue 130 GLU Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 327 ASP Chi-restraints excluded: chain C residue 354 ASN Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 418 HIS Chi-restraints excluded: chain C residue 453 MET Chi-restraints excluded: chain C residue 477 VAL Chi-restraints excluded: chain C residue 495 MET Chi-restraints excluded: chain C residue 544 ILE Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain C residue 646 THR Chi-restraints excluded: chain C residue 654 THR Chi-restraints excluded: chain C residue 660 LEU Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain D residue 38 GLU Chi-restraints excluded: chain D residue 130 GLU Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 179 GLU Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 327 ASP Chi-restraints excluded: chain D residue 354 ASN Chi-restraints excluded: chain D residue 362 ILE Chi-restraints excluded: chain D residue 389 ASP Chi-restraints excluded: chain D residue 408 ILE Chi-restraints excluded: chain D residue 477 VAL Chi-restraints excluded: chain D residue 495 MET Chi-restraints excluded: chain D residue 540 LEU Chi-restraints excluded: chain D residue 544 ILE Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 646 THR Chi-restraints excluded: chain D residue 654 THR Chi-restraints excluded: chain D residue 660 LEU Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 130 GLU Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 168 GLU Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 327 ASP Chi-restraints excluded: chain E residue 389 ASP Chi-restraints excluded: chain E residue 418 HIS Chi-restraints excluded: chain E residue 477 VAL Chi-restraints excluded: chain E residue 491 ARG Chi-restraints excluded: chain E residue 495 MET Chi-restraints excluded: chain E residue 544 ILE Chi-restraints excluded: chain E residue 565 THR Chi-restraints excluded: chain E residue 646 THR Chi-restraints excluded: chain E residue 660 LEU Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain F residue 32 LEU Chi-restraints excluded: chain F residue 130 GLU Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 168 GLU Chi-restraints excluded: chain F residue 191 LEU Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 288 LEU Chi-restraints excluded: chain F residue 327 ASP Chi-restraints excluded: chain F residue 354 ASN Chi-restraints excluded: chain F residue 367 GLU Chi-restraints excluded: chain F residue 389 ASP Chi-restraints excluded: chain F residue 408 ILE Chi-restraints excluded: chain F residue 418 HIS Chi-restraints excluded: chain F residue 477 VAL Chi-restraints excluded: chain F residue 495 MET Chi-restraints excluded: chain F residue 544 ILE Chi-restraints excluded: chain F residue 646 THR Chi-restraints excluded: chain F residue 654 THR Chi-restraints excluded: chain F residue 660 LEU Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain G residue 99 MET Chi-restraints excluded: chain G residue 130 GLU Chi-restraints excluded: chain G residue 131 THR Chi-restraints excluded: chain G residue 168 GLU Chi-restraints excluded: chain G residue 179 GLU Chi-restraints excluded: chain G residue 191 LEU Chi-restraints excluded: chain G residue 240 VAL Chi-restraints excluded: chain G residue 277 LEU Chi-restraints excluded: chain G residue 327 ASP Chi-restraints excluded: chain G residue 354 ASN Chi-restraints excluded: chain G residue 389 ASP Chi-restraints excluded: chain G residue 418 HIS Chi-restraints excluded: chain G residue 433 SER Chi-restraints excluded: chain G residue 477 VAL Chi-restraints excluded: chain G residue 495 MET Chi-restraints excluded: chain G residue 544 ILE Chi-restraints excluded: chain G residue 569 LEU Chi-restraints excluded: chain G residue 646 THR Chi-restraints excluded: chain G residue 654 THR Chi-restraints excluded: chain G residue 660 LEU Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain H residue 99 MET Chi-restraints excluded: chain H residue 131 THR Chi-restraints excluded: chain H residue 168 GLU Chi-restraints excluded: chain H residue 179 GLU Chi-restraints excluded: chain H residue 191 LEU Chi-restraints excluded: chain H residue 240 VAL Chi-restraints excluded: chain H residue 277 LEU Chi-restraints excluded: chain H residue 318 ILE Chi-restraints excluded: chain H residue 327 ASP Chi-restraints excluded: chain H residue 389 ASP Chi-restraints excluded: chain H residue 408 ILE Chi-restraints excluded: chain H residue 418 HIS Chi-restraints excluded: chain H residue 433 SER Chi-restraints excluded: chain H residue 453 MET Chi-restraints excluded: chain H residue 477 VAL Chi-restraints excluded: chain H residue 491 ARG Chi-restraints excluded: chain H residue 495 MET Chi-restraints excluded: chain H residue 540 LEU Chi-restraints excluded: chain H residue 544 ILE Chi-restraints excluded: chain H residue 660 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 75 optimal weight: 7.9990 chunk 142 optimal weight: 9.9990 chunk 358 optimal weight: 10.0000 chunk 408 optimal weight: 5.9990 chunk 474 optimal weight: 8.9990 chunk 248 optimal weight: 6.9990 chunk 11 optimal weight: 1.9990 chunk 102 optimal weight: 10.0000 chunk 176 optimal weight: 5.9990 chunk 182 optimal weight: 6.9990 chunk 513 optimal weight: 10.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 HIS ** A 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 189 HIS ** B 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 532 HIS ** C 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 HIS C 189 HIS ** C 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 185 HIS ** E 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 532 HIS ** F 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 532 HIS ** G 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 480 HIS ** G 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 185 HIS ** H 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 480 HIS ** H 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.133132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.106494 restraints weight = 49559.187| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 1.69 r_work: 0.2943 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2804 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.3979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 43184 Z= 0.257 Angle : 0.698 8.382 58672 Z= 0.365 Chirality : 0.050 0.237 6120 Planarity : 0.006 0.052 7672 Dihedral : 6.592 52.331 6168 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 4.69 % Allowed : 14.13 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.12), residues: 5280 helix: 0.51 (0.15), residues: 1296 sheet: -1.29 (0.18), residues: 720 loop : -0.36 (0.11), residues: 3264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 451 TYR 0.020 0.002 TYR E 50 PHE 0.029 0.003 PHE F 325 TRP 0.031 0.002 TRP B 566 HIS 0.009 0.002 HIS D 418 Details of bonding type rmsd covalent geometry : bond 0.00624 (43184) covalent geometry : angle 0.69785 (58672) hydrogen bonds : bond 0.04431 ( 1200) hydrogen bonds : angle 5.42157 ( 3600) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10560 Ramachandran restraints generated. 5280 Oldfield, 0 Emsley, 5280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10560 Ramachandran restraints generated. 5280 Oldfield, 0 Emsley, 5280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 811 residues out of total 4480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 210 poor density : 601 time to evaluate : 1.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 LYS cc_start: 0.8268 (ttpt) cc_final: 0.7631 (ttmt) REVERT: A 130 GLU cc_start: 0.9204 (OUTLIER) cc_final: 0.7673 (pm20) REVERT: A 179 GLU cc_start: 0.8509 (OUTLIER) cc_final: 0.7946 (mm-30) REVERT: A 180 ASP cc_start: 0.8612 (t0) cc_final: 0.8331 (t0) REVERT: A 252 LYS cc_start: 0.7207 (ttmt) cc_final: 0.6924 (tttt) REVERT: A 383 TYR cc_start: 0.8791 (t80) cc_final: 0.8434 (t80) REVERT: A 389 ASP cc_start: 0.7800 (t0) cc_final: 0.7544 (t0) REVERT: A 456 MET cc_start: 0.8736 (mtp) cc_final: 0.8415 (mtp) REVERT: A 563 GLU cc_start: 0.8491 (pm20) cc_final: 0.7498 (pm20) REVERT: A 569 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8615 (pp) REVERT: A 598 VAL cc_start: 0.8706 (t) cc_final: 0.8474 (p) REVERT: A 660 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.7896 (pp) REVERT: B 130 GLU cc_start: 0.9199 (OUTLIER) cc_final: 0.7621 (pm20) REVERT: B 180 ASP cc_start: 0.8576 (t0) cc_final: 0.8368 (t0) REVERT: B 362 ILE cc_start: 0.8611 (OUTLIER) cc_final: 0.8212 (pt) REVERT: B 413 TYR cc_start: 0.9188 (m-80) cc_final: 0.8981 (m-80) REVERT: B 563 GLU cc_start: 0.8298 (pm20) cc_final: 0.7420 (pm20) REVERT: B 569 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8532 (pp) REVERT: B 598 VAL cc_start: 0.8735 (t) cc_final: 0.8498 (p) REVERT: B 634 GLU cc_start: 0.7634 (tp30) cc_final: 0.7071 (mt-10) REVERT: B 660 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.7837 (pp) REVERT: C 128 LYS cc_start: 0.7921 (ttpp) cc_final: 0.7618 (ttmt) REVERT: C 130 GLU cc_start: 0.9208 (OUTLIER) cc_final: 0.7606 (pm20) REVERT: C 180 ASP cc_start: 0.8537 (t0) cc_final: 0.8271 (t0) REVERT: C 252 LYS cc_start: 0.7163 (ttmt) cc_final: 0.6949 (ttpt) REVERT: C 354 ASN cc_start: 0.8251 (OUTLIER) cc_final: 0.7965 (t0) REVERT: C 362 ILE cc_start: 0.8599 (OUTLIER) cc_final: 0.8187 (pt) REVERT: C 378 GLU cc_start: 0.7156 (tp30) cc_final: 0.6856 (tt0) REVERT: C 383 TYR cc_start: 0.8710 (t80) cc_final: 0.8374 (t80) REVERT: C 470 MET cc_start: 0.9475 (mtp) cc_final: 0.9230 (mtm) REVERT: C 563 GLU cc_start: 0.8394 (pm20) cc_final: 0.7486 (pm20) REVERT: C 569 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8556 (pp) REVERT: C 598 VAL cc_start: 0.8498 (t) cc_final: 0.8257 (p) REVERT: C 660 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.7852 (pp) REVERT: D 38 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7394 (tm-30) REVERT: D 128 LYS cc_start: 0.7902 (ttpp) cc_final: 0.7598 (ttmt) REVERT: D 130 GLU cc_start: 0.9187 (OUTLIER) cc_final: 0.7562 (pm20) REVERT: D 179 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.7725 (mm-30) REVERT: D 180 ASP cc_start: 0.8571 (t0) cc_final: 0.8294 (t0) REVERT: D 252 LYS cc_start: 0.7160 (ttmt) cc_final: 0.6877 (tttt) REVERT: D 354 ASN cc_start: 0.8178 (OUTLIER) cc_final: 0.7833 (t0) REVERT: D 383 TYR cc_start: 0.8727 (t80) cc_final: 0.8362 (t80) REVERT: D 563 GLU cc_start: 0.8481 (pm20) cc_final: 0.7475 (pm20) REVERT: D 569 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8407 (pp) REVERT: D 598 VAL cc_start: 0.8666 (t) cc_final: 0.8420 (p) REVERT: D 660 LEU cc_start: 0.8538 (OUTLIER) cc_final: 0.7880 (pp) REVERT: E 130 GLU cc_start: 0.9195 (OUTLIER) cc_final: 0.7582 (pm20) REVERT: E 180 ASP cc_start: 0.8547 (t0) cc_final: 0.8274 (t0) REVERT: E 252 LYS cc_start: 0.7274 (ttmt) cc_final: 0.7004 (ttpt) REVERT: E 362 ILE cc_start: 0.8620 (OUTLIER) cc_final: 0.8215 (pt) REVERT: E 383 TYR cc_start: 0.8722 (t80) cc_final: 0.8330 (t80) REVERT: E 456 MET cc_start: 0.8699 (mtp) cc_final: 0.8367 (mtp) REVERT: E 563 GLU cc_start: 0.8441 (pm20) cc_final: 0.7577 (pm20) REVERT: E 598 VAL cc_start: 0.8564 (t) cc_final: 0.8331 (m) REVERT: E 634 GLU cc_start: 0.7648 (tp30) cc_final: 0.7047 (mt-10) REVERT: E 660 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.8093 (pp) REVERT: F 32 LEU cc_start: 0.7951 (OUTLIER) cc_final: 0.7723 (mp) REVERT: F 130 GLU cc_start: 0.9205 (OUTLIER) cc_final: 0.7647 (pm20) REVERT: F 180 ASP cc_start: 0.8504 (t0) cc_final: 0.8241 (t0) REVERT: F 252 LYS cc_start: 0.7173 (ttmt) cc_final: 0.6825 (tttt) REVERT: F 354 ASN cc_start: 0.8271 (OUTLIER) cc_final: 0.7939 (t0) REVERT: F 383 TYR cc_start: 0.8725 (t80) cc_final: 0.8327 (t80) REVERT: F 451 ARG cc_start: 0.8460 (mtm-85) cc_final: 0.8179 (mtm-85) REVERT: F 470 MET cc_start: 0.9480 (mtp) cc_final: 0.9224 (mtm) REVERT: F 532 HIS cc_start: 0.8895 (OUTLIER) cc_final: 0.7883 (m90) REVERT: F 563 GLU cc_start: 0.8341 (pm20) cc_final: 0.7471 (pm20) REVERT: F 569 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8504 (pp) REVERT: F 598 VAL cc_start: 0.8507 (t) cc_final: 0.8202 (m) REVERT: F 660 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.7834 (pp) REVERT: G 32 LEU cc_start: 0.8029 (OUTLIER) cc_final: 0.7753 (mp) REVERT: G 130 GLU cc_start: 0.9202 (OUTLIER) cc_final: 0.7577 (pm20) REVERT: G 179 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.7750 (mm-30) REVERT: G 180 ASP cc_start: 0.8530 (t0) cc_final: 0.8269 (t0) REVERT: G 252 LYS cc_start: 0.7161 (ttmt) cc_final: 0.6823 (tttt) REVERT: G 354 ASN cc_start: 0.8258 (OUTLIER) cc_final: 0.7938 (t0) REVERT: G 383 TYR cc_start: 0.8741 (t80) cc_final: 0.8431 (t80) REVERT: G 451 ARG cc_start: 0.8484 (mtm-85) cc_final: 0.8270 (mtm-85) REVERT: G 456 MET cc_start: 0.8764 (mtp) cc_final: 0.8490 (mtp) REVERT: G 563 GLU cc_start: 0.8501 (pm20) cc_final: 0.7501 (pm20) REVERT: G 569 LEU cc_start: 0.8954 (OUTLIER) cc_final: 0.8540 (pp) REVERT: G 598 VAL cc_start: 0.8666 (t) cc_final: 0.8418 (p) REVERT: G 660 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.7874 (pp) REVERT: H 128 LYS cc_start: 0.8224 (ttpt) cc_final: 0.7613 (ttmt) REVERT: H 130 GLU cc_start: 0.9207 (OUTLIER) cc_final: 0.7677 (pm20) REVERT: H 179 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.7724 (mm-30) REVERT: H 180 ASP cc_start: 0.8577 (t0) cc_final: 0.8329 (t0) REVERT: H 252 LYS cc_start: 0.7233 (ttmt) cc_final: 0.6875 (tttt) REVERT: H 362 ILE cc_start: 0.8591 (OUTLIER) cc_final: 0.8185 (pt) REVERT: H 389 ASP cc_start: 0.7653 (OUTLIER) cc_final: 0.7351 (t70) REVERT: H 470 MET cc_start: 0.9471 (mtp) cc_final: 0.9248 (mtm) REVERT: H 563 GLU cc_start: 0.8521 (pm20) cc_final: 0.7503 (pm20) REVERT: H 598 VAL cc_start: 0.8528 (t) cc_final: 0.8289 (p) REVERT: H 660 LEU cc_start: 0.8506 (OUTLIER) cc_final: 0.8088 (pp) outliers start: 210 outliers final: 140 residues processed: 749 average time/residue: 0.3001 time to fit residues: 352.7594 Evaluate side-chains 751 residues out of total 4480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 179 poor density : 572 time to evaluate : 1.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 99 MET Chi-restraints excluded: chain A residue 130 GLU Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 179 GLU Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 327 ASP Chi-restraints excluded: chain A residue 418 HIS Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 491 ARG Chi-restraints excluded: chain A residue 495 MET Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 654 THR Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 59 MET Chi-restraints excluded: chain B residue 99 MET Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 318 ILE Chi-restraints excluded: chain B residue 327 ASP Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 477 VAL Chi-restraints excluded: chain B residue 491 ARG Chi-restraints excluded: chain B residue 495 MET Chi-restraints excluded: chain B residue 544 ILE Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 646 THR Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain B residue 662 ARG Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 99 MET Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 130 GLU Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 327 ASP Chi-restraints excluded: chain C residue 354 ASN Chi-restraints excluded: chain C residue 362 ILE Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 418 HIS Chi-restraints excluded: chain C residue 453 MET Chi-restraints excluded: chain C residue 477 VAL Chi-restraints excluded: chain C residue 544 ILE Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain C residue 646 THR Chi-restraints excluded: chain C residue 654 THR Chi-restraints excluded: chain C residue 660 LEU Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 38 GLU Chi-restraints excluded: chain D residue 59 MET Chi-restraints excluded: chain D residue 99 MET Chi-restraints excluded: chain D residue 130 GLU Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 179 GLU Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 327 ASP Chi-restraints excluded: chain D residue 354 ASN Chi-restraints excluded: chain D residue 389 ASP Chi-restraints excluded: chain D residue 477 VAL Chi-restraints excluded: chain D residue 495 MET Chi-restraints excluded: chain D residue 544 ILE Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 646 THR Chi-restraints excluded: chain D residue 654 THR Chi-restraints excluded: chain D residue 660 LEU Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 130 GLU Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 168 GLU Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 288 LEU Chi-restraints excluded: chain E residue 327 ASP Chi-restraints excluded: chain E residue 362 ILE Chi-restraints excluded: chain E residue 389 ASP Chi-restraints excluded: chain E residue 418 HIS Chi-restraints excluded: chain E residue 477 VAL Chi-restraints excluded: chain E residue 491 ARG Chi-restraints excluded: chain E residue 495 MET Chi-restraints excluded: chain E residue 544 ILE Chi-restraints excluded: chain E residue 565 THR Chi-restraints excluded: chain E residue 646 THR Chi-restraints excluded: chain E residue 654 THR Chi-restraints excluded: chain E residue 660 LEU Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain F residue 32 LEU Chi-restraints excluded: chain F residue 130 GLU Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 168 GLU Chi-restraints excluded: chain F residue 191 LEU Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 288 LEU Chi-restraints excluded: chain F residue 327 ASP Chi-restraints excluded: chain F residue 354 ASN Chi-restraints excluded: chain F residue 367 GLU Chi-restraints excluded: chain F residue 389 ASP Chi-restraints excluded: chain F residue 477 VAL Chi-restraints excluded: chain F residue 495 MET Chi-restraints excluded: chain F residue 532 HIS Chi-restraints excluded: chain F residue 534 THR Chi-restraints excluded: chain F residue 544 ILE Chi-restraints excluded: chain F residue 569 LEU Chi-restraints excluded: chain F residue 646 THR Chi-restraints excluded: chain F residue 654 THR Chi-restraints excluded: chain F residue 660 LEU Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain G residue 59 MET Chi-restraints excluded: chain G residue 99 MET Chi-restraints excluded: chain G residue 130 GLU Chi-restraints excluded: chain G residue 131 THR Chi-restraints excluded: chain G residue 168 GLU Chi-restraints excluded: chain G residue 178 LEU Chi-restraints excluded: chain G residue 179 GLU Chi-restraints excluded: chain G residue 191 LEU Chi-restraints excluded: chain G residue 240 VAL Chi-restraints excluded: chain G residue 277 LEU Chi-restraints excluded: chain G residue 327 ASP Chi-restraints excluded: chain G residue 354 ASN Chi-restraints excluded: chain G residue 389 ASP Chi-restraints excluded: chain G residue 418 HIS Chi-restraints excluded: chain G residue 433 SER Chi-restraints excluded: chain G residue 477 VAL Chi-restraints excluded: chain G residue 495 MET Chi-restraints excluded: chain G residue 544 ILE Chi-restraints excluded: chain G residue 569 LEU Chi-restraints excluded: chain G residue 646 THR Chi-restraints excluded: chain G residue 654 THR Chi-restraints excluded: chain G residue 660 LEU Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain H residue 99 MET Chi-restraints excluded: chain H residue 130 GLU Chi-restraints excluded: chain H residue 131 THR Chi-restraints excluded: chain H residue 168 GLU Chi-restraints excluded: chain H residue 179 GLU Chi-restraints excluded: chain H residue 191 LEU Chi-restraints excluded: chain H residue 240 VAL Chi-restraints excluded: chain H residue 277 LEU Chi-restraints excluded: chain H residue 288 LEU Chi-restraints excluded: chain H residue 318 ILE Chi-restraints excluded: chain H residue 327 ASP Chi-restraints excluded: chain H residue 362 ILE Chi-restraints excluded: chain H residue 389 ASP Chi-restraints excluded: chain H residue 418 HIS Chi-restraints excluded: chain H residue 433 SER Chi-restraints excluded: chain H residue 477 VAL Chi-restraints excluded: chain H residue 491 ARG Chi-restraints excluded: chain H residue 495 MET Chi-restraints excluded: chain H residue 540 LEU Chi-restraints excluded: chain H residue 544 ILE Chi-restraints excluded: chain H residue 660 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 142 optimal weight: 7.9990 chunk 421 optimal weight: 20.0000 chunk 498 optimal weight: 7.9990 chunk 31 optimal weight: 4.9990 chunk 301 optimal weight: 10.0000 chunk 30 optimal weight: 0.9980 chunk 229 optimal weight: 5.9990 chunk 157 optimal weight: 8.9990 chunk 521 optimal weight: 10.0000 chunk 444 optimal weight: 1.9990 chunk 344 optimal weight: 7.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 529 ASN ** A 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 249 ASN ** B 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 532 HIS ** C 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.141981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.115399 restraints weight = 48596.295| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 1.74 r_work: 0.2925 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2783 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.4061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 43184 Z= 0.211 Angle : 0.669 7.890 58672 Z= 0.350 Chirality : 0.049 0.228 6120 Planarity : 0.006 0.051 7672 Dihedral : 6.513 51.253 6168 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 4.44 % Allowed : 14.62 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.12), residues: 5280 helix: 0.57 (0.15), residues: 1296 sheet: -1.23 (0.18), residues: 760 loop : -0.34 (0.11), residues: 3224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 451 TYR 0.019 0.002 TYR F 50 PHE 0.023 0.002 PHE F 325 TRP 0.024 0.002 TRP B 566 HIS 0.007 0.002 HIS F 532 Details of bonding type rmsd covalent geometry : bond 0.00512 (43184) covalent geometry : angle 0.66942 (58672) hydrogen bonds : bond 0.04150 ( 1200) hydrogen bonds : angle 5.36167 ( 3600) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10560 Ramachandran restraints generated. 5280 Oldfield, 0 Emsley, 5280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10560 Ramachandran restraints generated. 5280 Oldfield, 0 Emsley, 5280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 796 residues out of total 4480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 199 poor density : 597 time to evaluate : 1.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 LYS cc_start: 0.8220 (ttpt) cc_final: 0.7574 (ttmt) REVERT: A 130 GLU cc_start: 0.9202 (OUTLIER) cc_final: 0.7636 (pm20) REVERT: A 179 GLU cc_start: 0.8455 (OUTLIER) cc_final: 0.7817 (mm-30) REVERT: A 180 ASP cc_start: 0.8673 (t0) cc_final: 0.8419 (t0) REVERT: A 252 LYS cc_start: 0.7160 (ttmt) cc_final: 0.6920 (ttpt) REVERT: A 383 TYR cc_start: 0.8781 (t80) cc_final: 0.8411 (t80) REVERT: A 389 ASP cc_start: 0.7785 (t0) cc_final: 0.7505 (t0) REVERT: A 456 MET cc_start: 0.8765 (mtp) cc_final: 0.8452 (mtp) REVERT: A 563 GLU cc_start: 0.8501 (pm20) cc_final: 0.7455 (pm20) REVERT: A 596 TYR cc_start: 0.8200 (m-80) cc_final: 0.7978 (m-80) REVERT: A 598 VAL cc_start: 0.8745 (t) cc_final: 0.8528 (p) REVERT: A 660 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.7743 (pp) REVERT: B 130 GLU cc_start: 0.9219 (OUTLIER) cc_final: 0.7612 (pm20) REVERT: B 180 ASP cc_start: 0.8567 (t0) cc_final: 0.8310 (t0) REVERT: B 362 ILE cc_start: 0.8485 (OUTLIER) cc_final: 0.8094 (pt) REVERT: B 389 ASP cc_start: 0.7787 (OUTLIER) cc_final: 0.7448 (t70) REVERT: B 563 GLU cc_start: 0.8407 (pm20) cc_final: 0.7473 (pm20) REVERT: B 569 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8526 (pp) REVERT: B 598 VAL cc_start: 0.8725 (t) cc_final: 0.8488 (p) REVERT: B 634 GLU cc_start: 0.7598 (tp30) cc_final: 0.6997 (mt-10) REVERT: B 660 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.7782 (pp) REVERT: C 130 GLU cc_start: 0.9207 (OUTLIER) cc_final: 0.7570 (pm20) REVERT: C 180 ASP cc_start: 0.8578 (t0) cc_final: 0.8320 (t0) REVERT: C 252 LYS cc_start: 0.7132 (ttmt) cc_final: 0.6812 (tttt) REVERT: C 354 ASN cc_start: 0.8215 (OUTLIER) cc_final: 0.7917 (t0) REVERT: C 362 ILE cc_start: 0.8452 (OUTLIER) cc_final: 0.8061 (pt) REVERT: C 378 GLU cc_start: 0.7075 (tp30) cc_final: 0.6808 (tt0) REVERT: C 383 TYR cc_start: 0.8703 (t80) cc_final: 0.8349 (t80) REVERT: C 451 ARG cc_start: 0.8439 (mtm-85) cc_final: 0.8146 (mtm-85) REVERT: C 563 GLU cc_start: 0.8357 (pm20) cc_final: 0.7445 (pm20) REVERT: C 569 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8457 (pp) REVERT: C 598 VAL cc_start: 0.8462 (t) cc_final: 0.8183 (m) REVERT: C 660 LEU cc_start: 0.8385 (OUTLIER) cc_final: 0.7717 (pp) REVERT: D 38 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7301 (tm-30) REVERT: D 130 GLU cc_start: 0.9195 (OUTLIER) cc_final: 0.7592 (pm20) REVERT: D 179 GLU cc_start: 0.8246 (OUTLIER) cc_final: 0.7563 (mm-30) REVERT: D 180 ASP cc_start: 0.8627 (t0) cc_final: 0.8355 (t0) REVERT: D 252 LYS cc_start: 0.7116 (ttmt) cc_final: 0.6801 (tttt) REVERT: D 354 ASN cc_start: 0.8177 (OUTLIER) cc_final: 0.7873 (t0) REVERT: D 383 TYR cc_start: 0.8756 (t80) cc_final: 0.8349 (t80) REVERT: D 569 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8574 (pp) REVERT: D 598 VAL cc_start: 0.8633 (t) cc_final: 0.8385 (p) REVERT: D 660 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.7766 (pp) REVERT: E 128 LYS cc_start: 0.8074 (ttmt) cc_final: 0.7739 (ttmt) REVERT: E 130 GLU cc_start: 0.9185 (OUTLIER) cc_final: 0.7560 (pm20) REVERT: E 180 ASP cc_start: 0.8523 (t0) cc_final: 0.8239 (t0) REVERT: E 252 LYS cc_start: 0.7196 (ttmt) cc_final: 0.6924 (ttpt) REVERT: E 362 ILE cc_start: 0.8522 (OUTLIER) cc_final: 0.8113 (pt) REVERT: E 383 TYR cc_start: 0.8681 (t80) cc_final: 0.8287 (t80) REVERT: E 389 ASP cc_start: 0.7640 (OUTLIER) cc_final: 0.7336 (t70) REVERT: E 456 MET cc_start: 0.8690 (mtp) cc_final: 0.8365 (mtp) REVERT: E 634 GLU cc_start: 0.7659 (tp30) cc_final: 0.7058 (mt-10) REVERT: E 660 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.8014 (pp) REVERT: F 32 LEU cc_start: 0.7887 (OUTLIER) cc_final: 0.7671 (mp) REVERT: F 130 GLU cc_start: 0.9208 (OUTLIER) cc_final: 0.7638 (pm20) REVERT: F 180 ASP cc_start: 0.8555 (t0) cc_final: 0.8282 (t0) REVERT: F 252 LYS cc_start: 0.7089 (ttmt) cc_final: 0.6714 (tttt) REVERT: F 354 ASN cc_start: 0.8223 (OUTLIER) cc_final: 0.7892 (t0) REVERT: F 362 ILE cc_start: 0.8483 (OUTLIER) cc_final: 0.8076 (pt) REVERT: F 383 TYR cc_start: 0.8688 (t80) cc_final: 0.8279 (t80) REVERT: F 451 ARG cc_start: 0.8458 (mtm-85) cc_final: 0.8161 (mtm-85) REVERT: F 470 MET cc_start: 0.9491 (mtp) cc_final: 0.9230 (mtm) REVERT: F 563 GLU cc_start: 0.8365 (pm20) cc_final: 0.7471 (pm20) REVERT: F 569 LEU cc_start: 0.8935 (OUTLIER) cc_final: 0.8474 (pp) REVERT: F 598 VAL cc_start: 0.8485 (t) cc_final: 0.8203 (m) REVERT: F 660 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.8032 (pp) REVERT: G 32 LEU cc_start: 0.8037 (OUTLIER) cc_final: 0.7742 (mp) REVERT: G 130 GLU cc_start: 0.9206 (OUTLIER) cc_final: 0.7547 (pm20) REVERT: G 179 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.7563 (mm-30) REVERT: G 180 ASP cc_start: 0.8601 (t0) cc_final: 0.8345 (t0) REVERT: G 252 LYS cc_start: 0.7074 (ttmt) cc_final: 0.6769 (tttt) REVERT: G 354 ASN cc_start: 0.8186 (OUTLIER) cc_final: 0.7890 (t0) REVERT: G 362 ILE cc_start: 0.8518 (OUTLIER) cc_final: 0.8107 (pt) REVERT: G 383 TYR cc_start: 0.8767 (t80) cc_final: 0.8413 (t80) REVERT: G 451 ARG cc_start: 0.8456 (mtm-85) cc_final: 0.8244 (mtm-85) REVERT: G 563 GLU cc_start: 0.8478 (pm20) cc_final: 0.7460 (pm20) REVERT: G 598 VAL cc_start: 0.8634 (t) cc_final: 0.8386 (p) REVERT: G 660 LEU cc_start: 0.8481 (OUTLIER) cc_final: 0.7940 (pp) REVERT: H 128 LYS cc_start: 0.8200 (ttpt) cc_final: 0.7581 (ttmt) REVERT: H 130 GLU cc_start: 0.9213 (OUTLIER) cc_final: 0.7646 (pm20) REVERT: H 179 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.7497 (mm-30) REVERT: H 180 ASP cc_start: 0.8625 (t0) cc_final: 0.8382 (t0) REVERT: H 252 LYS cc_start: 0.7189 (ttmt) cc_final: 0.6851 (tttt) REVERT: H 362 ILE cc_start: 0.8520 (OUTLIER) cc_final: 0.8118 (pt) REVERT: H 389 ASP cc_start: 0.7661 (OUTLIER) cc_final: 0.7340 (t70) REVERT: H 470 MET cc_start: 0.9467 (mtp) cc_final: 0.9241 (mtm) REVERT: H 563 GLU cc_start: 0.8520 (pm20) cc_final: 0.7460 (pm20) REVERT: H 569 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8457 (pp) REVERT: H 598 VAL cc_start: 0.8486 (t) cc_final: 0.8198 (m) REVERT: H 660 LEU cc_start: 0.8457 (OUTLIER) cc_final: 0.8031 (pp) outliers start: 199 outliers final: 142 residues processed: 733 average time/residue: 0.2972 time to fit residues: 343.5410 Evaluate side-chains 768 residues out of total 4480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 183 poor density : 585 time to evaluate : 1.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 99 MET Chi-restraints excluded: chain A residue 130 GLU Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 179 GLU Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 327 ASP Chi-restraints excluded: chain A residue 418 HIS Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 491 ARG Chi-restraints excluded: chain A residue 495 MET Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 646 THR Chi-restraints excluded: chain A residue 654 THR Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 99 MET Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 318 ILE Chi-restraints excluded: chain B residue 327 ASP Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 477 VAL Chi-restraints excluded: chain B residue 491 ARG Chi-restraints excluded: chain B residue 495 MET Chi-restraints excluded: chain B residue 544 ILE Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 646 THR Chi-restraints excluded: chain B residue 654 THR Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain B residue 662 ARG Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 99 MET Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 130 GLU Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 327 ASP Chi-restraints excluded: chain C residue 354 ASN Chi-restraints excluded: chain C residue 362 ILE Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 418 HIS Chi-restraints excluded: chain C residue 453 MET Chi-restraints excluded: chain C residue 477 VAL Chi-restraints excluded: chain C residue 495 MET Chi-restraints excluded: chain C residue 544 ILE Chi-restraints excluded: chain C residue 569 LEU Chi-restraints excluded: chain C residue 582 ILE Chi-restraints excluded: chain C residue 646 THR Chi-restraints excluded: chain C residue 654 THR Chi-restraints excluded: chain C residue 660 LEU Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 38 GLU Chi-restraints excluded: chain D residue 83 ILE Chi-restraints excluded: chain D residue 130 GLU Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 179 GLU Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 288 LEU Chi-restraints excluded: chain D residue 327 ASP Chi-restraints excluded: chain D residue 354 ASN Chi-restraints excluded: chain D residue 389 ASP Chi-restraints excluded: chain D residue 477 VAL Chi-restraints excluded: chain D residue 495 MET Chi-restraints excluded: chain D residue 544 ILE Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 646 THR Chi-restraints excluded: chain D residue 654 THR Chi-restraints excluded: chain D residue 660 LEU Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 83 ILE Chi-restraints excluded: chain E residue 130 GLU Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 168 GLU Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 327 ASP Chi-restraints excluded: chain E residue 362 ILE Chi-restraints excluded: chain E residue 389 ASP Chi-restraints excluded: chain E residue 418 HIS Chi-restraints excluded: chain E residue 477 VAL Chi-restraints excluded: chain E residue 491 ARG Chi-restraints excluded: chain E residue 495 MET Chi-restraints excluded: chain E residue 544 ILE Chi-restraints excluded: chain E residue 565 THR Chi-restraints excluded: chain E residue 646 THR Chi-restraints excluded: chain E residue 654 THR Chi-restraints excluded: chain E residue 660 LEU Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain F residue 32 LEU Chi-restraints excluded: chain F residue 83 ILE Chi-restraints excluded: chain F residue 130 GLU Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 168 GLU Chi-restraints excluded: chain F residue 191 LEU Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 327 ASP Chi-restraints excluded: chain F residue 354 ASN Chi-restraints excluded: chain F residue 362 ILE Chi-restraints excluded: chain F residue 367 GLU Chi-restraints excluded: chain F residue 389 ASP Chi-restraints excluded: chain F residue 477 VAL Chi-restraints excluded: chain F residue 495 MET Chi-restraints excluded: chain F residue 544 ILE Chi-restraints excluded: chain F residue 569 LEU Chi-restraints excluded: chain F residue 646 THR Chi-restraints excluded: chain F residue 660 LEU Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain G residue 83 ILE Chi-restraints excluded: chain G residue 99 MET Chi-restraints excluded: chain G residue 130 GLU Chi-restraints excluded: chain G residue 131 THR Chi-restraints excluded: chain G residue 168 GLU Chi-restraints excluded: chain G residue 178 LEU Chi-restraints excluded: chain G residue 179 GLU Chi-restraints excluded: chain G residue 191 LEU Chi-restraints excluded: chain G residue 240 VAL Chi-restraints excluded: chain G residue 277 LEU Chi-restraints excluded: chain G residue 327 ASP Chi-restraints excluded: chain G residue 354 ASN Chi-restraints excluded: chain G residue 362 ILE Chi-restraints excluded: chain G residue 389 ASP Chi-restraints excluded: chain G residue 418 HIS Chi-restraints excluded: chain G residue 433 SER Chi-restraints excluded: chain G residue 477 VAL Chi-restraints excluded: chain G residue 495 MET Chi-restraints excluded: chain G residue 544 ILE Chi-restraints excluded: chain G residue 646 THR Chi-restraints excluded: chain G residue 654 THR Chi-restraints excluded: chain G residue 660 LEU Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain H residue 83 ILE Chi-restraints excluded: chain H residue 99 MET Chi-restraints excluded: chain H residue 130 GLU Chi-restraints excluded: chain H residue 131 THR Chi-restraints excluded: chain H residue 168 GLU Chi-restraints excluded: chain H residue 178 LEU Chi-restraints excluded: chain H residue 179 GLU Chi-restraints excluded: chain H residue 191 LEU Chi-restraints excluded: chain H residue 240 VAL Chi-restraints excluded: chain H residue 277 LEU Chi-restraints excluded: chain H residue 318 ILE Chi-restraints excluded: chain H residue 327 ASP Chi-restraints excluded: chain H residue 362 ILE Chi-restraints excluded: chain H residue 389 ASP Chi-restraints excluded: chain H residue 418 HIS Chi-restraints excluded: chain H residue 433 SER Chi-restraints excluded: chain H residue 477 VAL Chi-restraints excluded: chain H residue 491 ARG Chi-restraints excluded: chain H residue 495 MET Chi-restraints excluded: chain H residue 540 LEU Chi-restraints excluded: chain H residue 544 ILE Chi-restraints excluded: chain H residue 569 LEU Chi-restraints excluded: chain H residue 660 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 292 optimal weight: 8.9990 chunk 230 optimal weight: 7.9990 chunk 420 optimal weight: 0.9990 chunk 306 optimal weight: 0.0030 chunk 49 optimal weight: 9.9990 chunk 274 optimal weight: 4.9990 chunk 16 optimal weight: 7.9990 chunk 434 optimal weight: 0.6980 chunk 343 optimal weight: 0.8980 chunk 212 optimal weight: 9.9990 chunk 321 optimal weight: 10.0000 overall best weight: 1.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 508 ASN ** A 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 508 ASN ** C 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 529 ASN ** C 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 508 ASN ** D 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 529 ASN ** D 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 508 ASN ** E 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 508 ASN ** F 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 508 ASN ** G 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 529 ASN ** G 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 508 ASN H 515 HIS H 529 ASN ** H 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.138020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.112201 restraints weight = 48946.755| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 1.63 r_work: 0.3032 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.4199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 43184 Z= 0.119 Angle : 0.601 8.435 58672 Z= 0.313 Chirality : 0.045 0.205 6120 Planarity : 0.005 0.051 7672 Dihedral : 6.076 47.591 6168 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 3.37 % Allowed : 15.96 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.12), residues: 5280 helix: 0.81 (0.15), residues: 1296 sheet: -1.53 (0.18), residues: 696 loop : -0.31 (0.11), residues: 3288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 451 TYR 0.018 0.001 TYR E 132 PHE 0.015 0.001 PHE B 312 TRP 0.034 0.001 TRP E 566 HIS 0.007 0.001 HIS B 394 Details of bonding type rmsd covalent geometry : bond 0.00276 (43184) covalent geometry : angle 0.60098 (58672) hydrogen bonds : bond 0.03259 ( 1200) hydrogen bonds : angle 5.12966 ( 3600) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10560 Ramachandran restraints generated. 5280 Oldfield, 0 Emsley, 5280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10560 Ramachandran restraints generated. 5280 Oldfield, 0 Emsley, 5280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 776 residues out of total 4480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 625 time to evaluate : 1.707 Fit side-chains REVERT: A 128 LYS cc_start: 0.8266 (ttpt) cc_final: 0.7704 (ttmt) REVERT: A 179 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.8060 (mp0) REVERT: A 180 ASP cc_start: 0.8564 (t0) cc_final: 0.8338 (t0) REVERT: A 383 TYR cc_start: 0.8804 (t80) cc_final: 0.8445 (t80) REVERT: A 456 MET cc_start: 0.8719 (mtp) cc_final: 0.8444 (mtp) REVERT: A 563 GLU cc_start: 0.8298 (pm20) cc_final: 0.7325 (pm20) REVERT: A 569 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8576 (pp) REVERT: A 598 VAL cc_start: 0.8715 (t) cc_final: 0.8513 (p) REVERT: A 660 LEU cc_start: 0.8435 (OUTLIER) cc_final: 0.7828 (pp) REVERT: B 130 GLU cc_start: 0.9170 (OUTLIER) cc_final: 0.7650 (pm20) REVERT: B 180 ASP cc_start: 0.8482 (t0) cc_final: 0.8221 (t0) REVERT: B 362 ILE cc_start: 0.8250 (OUTLIER) cc_final: 0.7917 (pt) REVERT: B 389 ASP cc_start: 0.7679 (OUTLIER) cc_final: 0.7407 (t70) REVERT: B 563 GLU cc_start: 0.8296 (pm20) cc_final: 0.7410 (pm20) REVERT: B 569 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8526 (pp) REVERT: B 598 VAL cc_start: 0.8659 (t) cc_final: 0.8450 (m) REVERT: B 634 GLU cc_start: 0.7562 (tp30) cc_final: 0.7044 (mt-10) REVERT: B 660 LEU cc_start: 0.8391 (OUTLIER) cc_final: 0.7815 (pp) REVERT: C 130 GLU cc_start: 0.9140 (OUTLIER) cc_final: 0.7640 (pm20) REVERT: C 180 ASP cc_start: 0.8477 (t0) cc_final: 0.8220 (t0) REVERT: C 362 ILE cc_start: 0.8220 (OUTLIER) cc_final: 0.7901 (pt) REVERT: C 378 GLU cc_start: 0.6992 (tp30) cc_final: 0.6783 (tt0) REVERT: C 383 TYR cc_start: 0.8748 (t80) cc_final: 0.8379 (t80) REVERT: C 389 ASP cc_start: 0.7604 (OUTLIER) cc_final: 0.7356 (t70) REVERT: C 413 TYR cc_start: 0.9276 (m-80) cc_final: 0.9059 (m-80) REVERT: C 598 VAL cc_start: 0.8475 (t) cc_final: 0.8243 (m) REVERT: C 660 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.7787 (pp) REVERT: D 38 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.7304 (tm-30) REVERT: D 180 ASP cc_start: 0.8503 (t0) cc_final: 0.8276 (t0) REVERT: D 312 PHE cc_start: 0.8965 (p90) cc_final: 0.8725 (p90) REVERT: D 383 TYR cc_start: 0.8790 (t80) cc_final: 0.8440 (t80) REVERT: D 563 GLU cc_start: 0.8254 (pm20) cc_final: 0.7363 (pm20) REVERT: D 569 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8503 (pp) REVERT: D 596 TYR cc_start: 0.8148 (m-80) cc_final: 0.7942 (m-80) REVERT: D 598 VAL cc_start: 0.8652 (t) cc_final: 0.8425 (p) REVERT: D 660 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.7829 (pp) REVERT: E 99 MET cc_start: 0.9392 (mtm) cc_final: 0.9018 (mtm) REVERT: E 128 LYS cc_start: 0.8056 (ttmt) cc_final: 0.7712 (ttmt) REVERT: E 180 ASP cc_start: 0.8430 (t0) cc_final: 0.8185 (t0) REVERT: E 252 LYS cc_start: 0.7294 (ttmt) cc_final: 0.6951 (tttt) REVERT: E 383 TYR cc_start: 0.8769 (t80) cc_final: 0.8409 (t80) REVERT: E 389 ASP cc_start: 0.7534 (t0) cc_final: 0.7307 (t0) REVERT: E 413 TYR cc_start: 0.9217 (m-80) cc_final: 0.8986 (m-80) REVERT: E 456 MET cc_start: 0.8703 (mtp) cc_final: 0.8422 (mtp) REVERT: E 470 MET cc_start: 0.9301 (mtm) cc_final: 0.9027 (mtm) REVERT: E 563 GLU cc_start: 0.8114 (pm20) cc_final: 0.7269 (pm20) REVERT: E 569 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8553 (pp) REVERT: E 634 GLU cc_start: 0.7588 (tp30) cc_final: 0.7055 (mt-10) REVERT: E 660 LEU cc_start: 0.8331 (OUTLIER) cc_final: 0.7834 (pp) REVERT: F 99 MET cc_start: 0.9396 (mtm) cc_final: 0.9053 (mtm) REVERT: F 180 ASP cc_start: 0.8448 (t0) cc_final: 0.8168 (t0) REVERT: F 362 ILE cc_start: 0.8258 (OUTLIER) cc_final: 0.7918 (pt) REVERT: F 383 TYR cc_start: 0.8751 (t80) cc_final: 0.8406 (t80) REVERT: F 389 ASP cc_start: 0.7570 (t0) cc_final: 0.7310 (t70) REVERT: F 563 GLU cc_start: 0.8271 (pm20) cc_final: 0.7373 (pm20) REVERT: F 569 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8542 (pp) REVERT: F 598 VAL cc_start: 0.8439 (t) cc_final: 0.8216 (m) REVERT: F 660 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.7917 (pp) REVERT: G 32 LEU cc_start: 0.8103 (OUTLIER) cc_final: 0.7896 (mp) REVERT: G 130 GLU cc_start: 0.9144 (OUTLIER) cc_final: 0.7558 (pm20) REVERT: G 179 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7934 (mp0) REVERT: G 180 ASP cc_start: 0.8522 (t0) cc_final: 0.8256 (t0) REVERT: G 362 ILE cc_start: 0.8222 (OUTLIER) cc_final: 0.7904 (pt) REVERT: G 383 TYR cc_start: 0.8796 (t80) cc_final: 0.8438 (t80) REVERT: G 389 ASP cc_start: 0.7640 (OUTLIER) cc_final: 0.7356 (t70) REVERT: G 563 GLU cc_start: 0.8418 (pm20) cc_final: 0.7401 (pm20) REVERT: G 569 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8543 (pp) REVERT: G 598 VAL cc_start: 0.8662 (t) cc_final: 0.8443 (p) REVERT: G 599 LYS cc_start: 0.8576 (mppt) cc_final: 0.8298 (mtmm) REVERT: G 660 LEU cc_start: 0.8156 (OUTLIER) cc_final: 0.7945 (pp) REVERT: H 179 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7508 (mm-30) REVERT: H 180 ASP cc_start: 0.8546 (t0) cc_final: 0.8336 (t0) REVERT: H 252 LYS cc_start: 0.7231 (ttmt) cc_final: 0.6938 (tttt) REVERT: H 362 ILE cc_start: 0.8200 (OUTLIER) cc_final: 0.7887 (pt) REVERT: H 470 MET cc_start: 0.9397 (mtp) cc_final: 0.9186 (mtm) REVERT: H 569 LEU cc_start: 0.8962 (OUTLIER) cc_final: 0.8538 (pp) REVERT: H 598 VAL cc_start: 0.8510 (t) cc_final: 0.8262 (m) REVERT: H 660 LEU cc_start: 0.8350 (OUTLIER) cc_final: 0.7850 (pp) outliers start: 151 outliers final: 90 residues processed: 734 average time/residue: 0.3010 time to fit residues: 347.5116 Evaluate side-chains 717 residues out of total 4480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 596 time to evaluate : 1.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 99 MET Chi-restraints excluded: chain A residue 179 GLU Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 327 ASP Chi-restraints excluded: chain A residue 418 HIS Chi-restraints excluded: chain A residue 477 VAL Chi-restraints excluded: chain A residue 491 ARG Chi-restraints excluded: chain A residue 495 MET Chi-restraints excluded: chain A residue 569 LEU Chi-restraints excluded: chain A residue 654 THR Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 99 MET Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 168 GLU Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 318 ILE Chi-restraints excluded: chain B residue 327 ASP Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 477 VAL Chi-restraints excluded: chain B residue 491 ARG Chi-restraints excluded: chain B residue 495 MET Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain B residue 569 LEU Chi-restraints excluded: chain B residue 654 THR Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain B residue 662 ARG Chi-restraints excluded: chain C residue 99 MET Chi-restraints excluded: chain C residue 130 GLU Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 327 ASP Chi-restraints excluded: chain C residue 362 ILE Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 418 HIS Chi-restraints excluded: chain C residue 453 MET Chi-restraints excluded: chain C residue 477 VAL Chi-restraints excluded: chain C residue 654 THR Chi-restraints excluded: chain C residue 660 LEU Chi-restraints excluded: chain D residue 38 GLU Chi-restraints excluded: chain D residue 99 MET Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 191 LEU Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 477 VAL Chi-restraints excluded: chain D residue 495 MET Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 654 THR Chi-restraints excluded: chain D residue 660 LEU Chi-restraints excluded: chain E residue 168 GLU Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 240 VAL Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 327 ASP Chi-restraints excluded: chain E residue 418 HIS Chi-restraints excluded: chain E residue 477 VAL Chi-restraints excluded: chain E residue 491 ARG Chi-restraints excluded: chain E residue 495 MET Chi-restraints excluded: chain E residue 540 LEU Chi-restraints excluded: chain E residue 565 THR Chi-restraints excluded: chain E residue 569 LEU Chi-restraints excluded: chain E residue 654 THR Chi-restraints excluded: chain E residue 660 LEU Chi-restraints excluded: chain F residue 128 LYS Chi-restraints excluded: chain F residue 168 GLU Chi-restraints excluded: chain F residue 191 LEU Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 277 LEU Chi-restraints excluded: chain F residue 362 ILE Chi-restraints excluded: chain F residue 433 SER Chi-restraints excluded: chain F residue 477 VAL Chi-restraints excluded: chain F residue 495 MET Chi-restraints excluded: chain F residue 569 LEU Chi-restraints excluded: chain F residue 654 THR Chi-restraints excluded: chain F residue 660 LEU Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain G residue 99 MET Chi-restraints excluded: chain G residue 130 GLU Chi-restraints excluded: chain G residue 131 THR Chi-restraints excluded: chain G residue 168 GLU Chi-restraints excluded: chain G residue 179 GLU Chi-restraints excluded: chain G residue 191 LEU Chi-restraints excluded: chain G residue 240 VAL Chi-restraints excluded: chain G residue 277 LEU Chi-restraints excluded: chain G residue 327 ASP Chi-restraints excluded: chain G residue 362 ILE Chi-restraints excluded: chain G residue 389 ASP Chi-restraints excluded: chain G residue 418 HIS Chi-restraints excluded: chain G residue 433 SER Chi-restraints excluded: chain G residue 477 VAL Chi-restraints excluded: chain G residue 495 MET Chi-restraints excluded: chain G residue 569 LEU Chi-restraints excluded: chain G residue 660 LEU Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 99 MET Chi-restraints excluded: chain H residue 168 GLU Chi-restraints excluded: chain H residue 179 GLU Chi-restraints excluded: chain H residue 191 LEU Chi-restraints excluded: chain H residue 240 VAL Chi-restraints excluded: chain H residue 277 LEU Chi-restraints excluded: chain H residue 318 ILE Chi-restraints excluded: chain H residue 327 ASP Chi-restraints excluded: chain H residue 362 ILE Chi-restraints excluded: chain H residue 418 HIS Chi-restraints excluded: chain H residue 433 SER Chi-restraints excluded: chain H residue 477 VAL Chi-restraints excluded: chain H residue 491 ARG Chi-restraints excluded: chain H residue 540 LEU Chi-restraints excluded: chain H residue 569 LEU Chi-restraints excluded: chain H residue 660 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 184 optimal weight: 0.7980 chunk 63 optimal weight: 6.9990 chunk 47 optimal weight: 10.0000 chunk 220 optimal weight: 9.9990 chunk 221 optimal weight: 7.9990 chunk 385 optimal weight: 0.9980 chunk 267 optimal weight: 9.9990 chunk 218 optimal weight: 9.9990 chunk 189 optimal weight: 8.9990 chunk 333 optimal weight: 2.9990 chunk 214 optimal weight: 6.9990 overall best weight: 3.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 529 ASN ** C 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 529 ASN ** G 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.143627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.117078 restraints weight = 48806.151| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 1.75 r_work: 0.2971 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2830 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.4201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 43184 Z= 0.188 Angle : 0.647 7.088 58672 Z= 0.337 Chirality : 0.048 0.231 6120 Planarity : 0.005 0.047 7672 Dihedral : 6.257 50.028 6168 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 3.37 % Allowed : 15.87 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.12), residues: 5280 helix: 0.66 (0.15), residues: 1344 sheet: -1.25 (0.18), residues: 760 loop : -0.31 (0.12), residues: 3176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 196 TYR 0.019 0.002 TYR E 50 PHE 0.021 0.002 PHE F 325 TRP 0.028 0.001 TRP E 566 HIS 0.007 0.001 HIS B 394 Details of bonding type rmsd covalent geometry : bond 0.00454 (43184) covalent geometry : angle 0.64692 (58672) hydrogen bonds : bond 0.03796 ( 1200) hydrogen bonds : angle 5.18686 ( 3600) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11038.33 seconds wall clock time: 190 minutes 17.87 seconds (11417.87 seconds total)