Starting phenix.real_space_refine on Tue Sep 15 15:57:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/5i68_8072/09_2026/5i68_8072.cif Found real_map, /net/cci-nas-00/data/ceres_data/5i68_8072/09_2026/5i68_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/5i68_8072/09_2026/5i68_8072.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/5i68_8072/09_2026/5i68_8072.cif" model { file = "/net/cci-nas-00/data/ceres_data/5i68_8072/09_2026/5i68_8072.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5i68_8072/09_2026/5i68_8072.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5i68_8072/09_2026/5i68_8072.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5i68_8072/09_2026/5i68_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/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: 7.96, per 1000 atoms: 0.19 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: 3.71 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: 1.18 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: 12.59 Time building geometry restraints manager: 4.94 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: 24120 16.40 - 32.79: 1064 32.79 - 49.19: 216 49.19 - 65.58: 16 65.58 - 81.98: 32 Dihedral angle restraints: 25448 sinusoidal: 10272 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 25445 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: 0.11 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: 0.670 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: 0.040 Extract box with map and model: 0.660 Check model and map are aligned: 0.130 Set scattering table: 0.120 Process input model: 40.540 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.180 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: 0.020 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 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 : 10.364 81.980 15800 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/Z covalent geometry : bond 0.00937 / 0.57 (43184) covalent geometry : angle 1.46618 / 0.95 (58672) hydrogen bonds : bond 0.23644 / 15.41 ( 1200) hydrogen bonds : angle 9.59537 / 6.69 ( 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 : 1.513 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: 0.7748 (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: 0.6188 (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: 0.2704 time to fit residues: 514.4969 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 : 1.499 ------------------------------------------------------------------------------- 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... A 30 HIS A 142 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 480 HIS A 508 ASN A 541 HIS ** 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 480 HIS 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 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 480 HIS D 508 ASN D 541 HIS D 561 HIS ** 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 142 HIS ** 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 142 HIS ** 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 532 HIS G 541 HIS ** H 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 142 HIS ** 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: 53 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.144889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.119740 restraints weight = 48328.022| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 1.69 r_work: 0.3044 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2901 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 43184 Z= 0.196 Angle : 0.748 9.030 58672 Z= 0.393 Chirality : 0.050 0.150 6120 Planarity : 0.005 0.047 7672 Dihedral : 6.759 48.042 5890 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.79 % Allowed : 7.99 % Favored : 89.22 % 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: -0.24 (0.12), residues: 5280 helix: -0.39 (0.14), residues: 1280 sheet: -0.84 (0.21), residues: 696 loop : 0.23 (0.11), residues: 3304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 426 TYR 0.029 0.002 TYR F 50 PHE 0.024 0.002 PHE D 325 TRP 0.022 0.002 TRP C 566 HIS 0.009 0.002 HIS E 561 Details of bonding type rmsd/Z covalent geometry : bond 0.00462 / 0.20 (43184) covalent geometry : angle 0.74843 / 0.39 (58672) hydrogen bonds : bond 0.05109 / 3.32 ( 1200) hydrogen bonds : angle 5.92752 / 4.13 ( 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 837 residues out of total 4480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 712 time to evaluate : 1.668 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 108 ASP cc_start: 0.8251 (m-30) cc_final: 0.8004 (m-30) REVERT: A 128 LYS cc_start: 0.8093 (ttpt) cc_final: 0.7437 (ttmt) REVERT: A 180 ASP cc_start: 0.8621 (t0) cc_final: 0.8384 (t0) REVERT: A 326 ASP cc_start: 0.8928 (t0) cc_final: 0.8714 (m-30) REVERT: A 383 TYR cc_start: 0.8720 (t80) cc_final: 0.8440 (t80) REVERT: A 447 MET cc_start: 0.9045 (mmt) cc_final: 0.8840 (mmt) REVERT: A 453 MET cc_start: 0.8548 (OUTLIER) cc_final: 0.8229 (tpt) REVERT: A 594 ASN cc_start: 0.7739 (m-40) cc_final: 0.6757 (p0) REVERT: A 596 TYR cc_start: 0.8284 (m-80) cc_final: 0.7954 (m-80) REVERT: A 660 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.7990 (pp) REVERT: B 262 LYS cc_start: 0.7743 (ptpt) cc_final: 0.7532 (mttt) REVERT: B 453 MET cc_start: 0.8578 (OUTLIER) cc_final: 0.8355 (tpt) REVERT: B 596 TYR cc_start: 0.8250 (m-80) cc_final: 0.7953 (m-80) REVERT: B 626 GLU cc_start: 0.7715 (mm-30) cc_final: 0.7439 (mm-30) REVERT: B 634 GLU cc_start: 0.7907 (tp30) cc_final: 0.7061 (mt-10) REVERT: B 660 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.7982 (pp) REVERT: C 128 LYS cc_start: 0.8038 (ttpt) cc_final: 0.7348 (ttmt) REVERT: C 374 GLU cc_start: 0.7415 (tm-30) cc_final: 0.6874 (mp0) REVERT: C 596 TYR cc_start: 0.8194 (m-80) cc_final: 0.7863 (m-80) REVERT: C 660 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.7853 (pp) REVERT: D 128 LYS cc_start: 0.8033 (ttpt) cc_final: 0.7357 (ttmt) REVERT: D 180 ASP cc_start: 0.8583 (t0) cc_final: 0.8372 (t0) REVERT: D 326 ASP cc_start: 0.8970 (t0) cc_final: 0.8762 (m-30) REVERT: D 594 ASN cc_start: 0.7766 (m-40) cc_final: 0.6823 (p0) REVERT: D 596 TYR cc_start: 0.8260 (m-80) cc_final: 0.7927 (m-80) REVERT: D 660 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.7945 (pp) REVERT: E 128 LYS cc_start: 0.8104 (ttpt) cc_final: 0.7413 (ttmt) REVERT: E 180 ASP cc_start: 0.8503 (t0) cc_final: 0.8272 (t0) REVERT: E 383 TYR cc_start: 0.8744 (t80) cc_final: 0.8491 (t80) REVERT: E 453 MET cc_start: 0.8608 (OUTLIER) cc_final: 0.8370 (tpt) REVERT: E 596 TYR cc_start: 0.8271 (m-80) cc_final: 0.8026 (m-80) REVERT: E 634 GLU cc_start: 0.7966 (tp30) cc_final: 0.7090 (mt-10) REVERT: E 660 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.7995 (pp) REVERT: F 596 TYR cc_start: 0.8260 (m-80) cc_final: 0.8007 (m-80) REVERT: F 660 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.7952 (pp) REVERT: G 326 ASP cc_start: 0.8934 (t0) cc_final: 0.8648 (m-30) REVERT: G 378 GLU cc_start: 0.7344 (tp30) cc_final: 0.7095 (tt0) REVERT: G 383 TYR cc_start: 0.8777 (t80) cc_final: 0.8481 (t80) REVERT: G 565 THR cc_start: 0.8727 (m) cc_final: 0.8526 (m) REVERT: G 594 ASN cc_start: 0.7759 (m-40) cc_final: 0.6848 (p0) REVERT: G 596 TYR cc_start: 0.8290 (m-80) cc_final: 0.8007 (m-80) REVERT: G 660 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.7963 (pp) REVERT: H 128 LYS cc_start: 0.8070 (ttpt) cc_final: 0.7451 (ttmt) REVERT: H 326 ASP cc_start: 0.8933 (t0) cc_final: 0.8625 (m-30) REVERT: H 383 TYR cc_start: 0.8756 (t80) cc_final: 0.8505 (t80) REVERT: H 596 TYR cc_start: 0.8307 (m-80) cc_final: 0.8032 (m-80) REVERT: H 660 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.8026 (pp) outliers start: 125 outliers final: 43 residues processed: 799 average time/residue: 0.2484 time to fit residues: 323.5772 Evaluate side-chains 628 residues out of total 4480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 574 time to evaluate : 1.525 ------------------------------------------------------------------------------- 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 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 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 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 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: 3.9990 chunk 491 optimal weight: 10.0000 chunk 152 optimal weight: 9.9990 chunk 524 optimal weight: 2.9990 chunk 6 optimal weight: 8.9990 chunk 164 optimal weight: 0.9990 chunk 61 optimal weight: 9.9990 chunk 33 optimal weight: 9.9990 chunk 414 optimal weight: 20.0000 chunk 381 optimal weight: 10.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 27 ASN ** A 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 480 HIS 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 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 480 HIS B 508 ASN ** B 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 480 HIS C 508 ASN ** C 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 480 HIS D 508 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 480 HIS E 508 ASN ** E 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 480 HIS 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 480 HIS 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.138988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.112330 restraints weight = 48755.442| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 1.82 r_work: 0.2966 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2819 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.3095 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= 0.235 Angle : 0.721 10.359 58672 Z= 0.378 Chirality : 0.050 0.221 6120 Planarity : 0.006 0.050 7672 Dihedral : 5.678 28.054 5824 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 3.95 % Allowed : 10.04 % Favored : 86.00 % 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: -0.19 (0.12), residues: 5280 helix: 0.07 (0.14), residues: 1296 sheet: -0.63 (0.22), residues: 648 loop : 0.01 (0.11), residues: 3336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 451 TYR 0.023 0.002 TYR F 50 PHE 0.029 0.003 PHE E 442 TRP 0.015 0.002 TRP C 566 HIS 0.008 0.002 HIS E 515 Details of bonding type rmsd/Z covalent geometry : bond 0.00568 / 0.24 (43184) covalent geometry : angle 0.72108 / 0.38 (58672) hydrogen bonds : bond 0.04854 / 3.19 ( 1200) hydrogen bonds : angle 5.60837 / 3.92 ( 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 845 residues out of total 4480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 177 poor density : 668 time to evaluate : 1.569 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 108 ASP cc_start: 0.8282 (m-30) cc_final: 0.8021 (m-30) REVERT: A 128 LYS cc_start: 0.8259 (ttpt) cc_final: 0.7652 (ttmt) REVERT: A 374 GLU cc_start: 0.6649 (mp0) cc_final: 0.6351 (mm-30) REVERT: A 383 TYR cc_start: 0.8729 (t80) cc_final: 0.8487 (t80) REVERT: A 660 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.7899 (pp) REVERT: B 180 ASP cc_start: 0.8696 (t0) cc_final: 0.8433 (t0) REVERT: B 378 GLU cc_start: 0.7208 (tp30) cc_final: 0.6755 (tt0) REVERT: B 383 TYR cc_start: 0.8730 (t80) cc_final: 0.8494 (t80) REVERT: B 626 GLU cc_start: 0.7821 (mm-30) cc_final: 0.7534 (mm-30) REVERT: B 634 GLU cc_start: 0.7741 (tp30) cc_final: 0.7104 (mt-10) REVERT: B 660 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.7915 (pp) REVERT: C 180 ASP cc_start: 0.8625 (t0) cc_final: 0.8311 (t0) REVERT: C 374 GLU cc_start: 0.7408 (tm-30) cc_final: 0.7018 (mp0) REVERT: C 383 TYR cc_start: 0.8727 (t80) cc_final: 0.8466 (t80) REVERT: C 660 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.7850 (pp) REVERT: D 354 ASN cc_start: 0.8319 (OUTLIER) cc_final: 0.7914 (t0) REVERT: D 378 GLU cc_start: 0.7173 (tp30) cc_final: 0.6813 (tt0) REVERT: D 383 TYR cc_start: 0.8678 (t80) cc_final: 0.8433 (t80) REVERT: D 660 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.7941 (pp) REVERT: E 252 LYS cc_start: 0.6882 (ttmt) cc_final: 0.6554 (tttt) REVERT: E 378 GLU cc_start: 0.7098 (tp30) cc_final: 0.6777 (tt0) REVERT: E 383 TYR cc_start: 0.8764 (t80) cc_final: 0.8538 (t80) REVERT: E 634 GLU cc_start: 0.7812 (tp30) cc_final: 0.7119 (mt-10) REVERT: E 660 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.7983 (pp) REVERT: F 128 LYS cc_start: 0.8138 (ttmt) cc_final: 0.7603 (ttpp) REVERT: F 180 ASP cc_start: 0.8638 (t0) cc_final: 0.8332 (t0) REVERT: F 375 SER cc_start: 0.7995 (m) cc_final: 0.7753 (p) REVERT: F 378 GLU cc_start: 0.7047 (tp30) cc_final: 0.6745 (tt0) REVERT: F 383 TYR cc_start: 0.8707 (t80) cc_final: 0.8431 (t80) REVERT: F 456 MET cc_start: 0.8857 (mtp) cc_final: 0.8448 (mtp) REVERT: F 660 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.7970 (pp) REVERT: G 128 LYS cc_start: 0.8170 (ttpt) cc_final: 0.7432 (ttmt) REVERT: G 180 ASP cc_start: 0.8557 (t0) cc_final: 0.8276 (t0) REVERT: G 383 TYR cc_start: 0.8713 (t80) cc_final: 0.8468 (t80) REVERT: G 413 TYR cc_start: 0.9224 (m-80) cc_final: 0.8997 (m-80) REVERT: G 660 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.7984 (pp) REVERT: H 128 LYS cc_start: 0.8140 (ttpt) cc_final: 0.7469 (ttmt) REVERT: H 180 ASP cc_start: 0.8641 (t0) cc_final: 0.8364 (t0) REVERT: H 252 LYS cc_start: 0.7109 (ttmt) cc_final: 0.6713 (tttt) REVERT: H 378 GLU cc_start: 0.7022 (tp30) cc_final: 0.6781 (tt0) REVERT: H 383 TYR cc_start: 0.8713 (t80) cc_final: 0.8501 (t80) REVERT: H 660 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.7981 (pp) outliers start: 177 outliers final: 102 residues processed: 793 average time/residue: 0.2727 time to fit residues: 342.9086 Evaluate side-chains 693 residues out of total 4480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 582 time to evaluate : 1.783 ------------------------------------------------------------------------------- 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 168 GLU Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 318 ILE 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 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 264 ILE Chi-restraints excluded: chain B residue 318 ILE Chi-restraints excluded: chain B residue 327 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 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 425 SER Chi-restraints excluded: chain C residue 477 VAL Chi-restraints excluded: chain C residue 495 MET 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 264 ILE 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 418 HIS Chi-restraints excluded: chain D residue 425 SER 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 32 LEU Chi-restraints excluded: chain E residue 168 GLU Chi-restraints excluded: chain E residue 240 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 425 SER 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 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 565 THR 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 32 LEU Chi-restraints excluded: chain H residue 54 ILE 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 425 SER 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: 4.9990 chunk 438 optimal weight: 9.9990 chunk 5 optimal weight: 0.9990 chunk 106 optimal weight: 0.1980 chunk 222 optimal weight: 9.9990 chunk 112 optimal weight: 0.8980 chunk 483 optimal weight: 10.0000 chunk 271 optimal weight: 7.9990 chunk 161 optimal weight: 8.9990 chunk 69 optimal weight: 5.9990 chunk 315 optimal weight: 9.9990 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** ** B 515 HIS ** 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 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 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** ** 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** ** 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 612 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.140410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.111415 restraints weight = 48496.396| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 1.97 r_work: 0.3021 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2874 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.3403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 43184 Z= 0.154 Angle : 0.632 9.072 58672 Z= 0.328 Chirality : 0.047 0.224 6120 Planarity : 0.005 0.046 7672 Dihedral : 5.335 26.492 5824 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 3.93 % Allowed : 11.83 % Favored : 84.24 % 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: -0.21 (0.12), residues: 5280 helix: 0.38 (0.14), residues: 1296 sheet: -1.17 (0.21), residues: 592 loop : -0.06 (0.11), residues: 3392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 304 TYR 0.024 0.002 TYR C 132 PHE 0.018 0.002 PHE C 325 TRP 0.020 0.001 TRP E 566 HIS 0.008 0.001 HIS G 515 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.15 (43184) covalent geometry : angle 0.63229 / 0.33 (58672) hydrogen bonds : bond 0.03897 / 2.54 ( 1200) hydrogen bonds : angle 5.29998 / 3.71 ( 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 796 residues out of total 4480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 176 poor density : 620 time to evaluate : 1.509 Fit side-chains REVERT: A 38 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.7493 (tm-30) REVERT: A 128 LYS cc_start: 0.8113 (ttpt) cc_final: 0.7587 (ttmt) REVERT: A 179 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.8092 (mp0) REVERT: A 180 ASP cc_start: 0.8684 (t0) cc_final: 0.8417 (t0) REVERT: A 374 GLU cc_start: 0.6764 (mp0) cc_final: 0.6472 (mm-30) REVERT: A 378 GLU cc_start: 0.7170 (tp30) cc_final: 0.6892 (tt0) REVERT: A 389 ASP cc_start: 0.7650 (OUTLIER) cc_final: 0.7344 (t70) REVERT: A 456 MET cc_start: 0.8796 (mtp) cc_final: 0.8367 (mtp) REVERT: A 563 GLU cc_start: 0.8443 (pm20) cc_final: 0.7133 (mt-10) REVERT: A 660 LEU cc_start: 0.8403 (OUTLIER) cc_final: 0.7880 (pp) REVERT: B 38 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7437 (tm-30) REVERT: B 179 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.8083 (mp0) REVERT: B 180 ASP cc_start: 0.8737 (t0) cc_final: 0.8433 (t0) REVERT: B 378 GLU cc_start: 0.7266 (tp30) cc_final: 0.6874 (tt0) REVERT: B 383 TYR cc_start: 0.8682 (t80) cc_final: 0.8473 (t80) REVERT: B 451 ARG cc_start: 0.8237 (mtm-85) cc_final: 0.7886 (mtm-85) REVERT: B 456 MET cc_start: 0.8829 (mtp) cc_final: 0.8465 (mtp) REVERT: B 563 GLU cc_start: 0.8254 (pm20) cc_final: 0.7375 (pm20) REVERT: B 596 TYR cc_start: 0.8232 (m-80) cc_final: 0.7916 (m-80) REVERT: B 598 VAL cc_start: 0.8592 (t) cc_final: 0.8287 (p) REVERT: B 626 GLU cc_start: 0.7836 (mm-30) cc_final: 0.7630 (mm-30) REVERT: B 634 GLU cc_start: 0.7617 (tp30) cc_final: 0.7022 (mt-10) REVERT: B 660 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.7923 (pp) REVERT: C 32 LEU cc_start: 0.8082 (OUTLIER) cc_final: 0.7875 (mp) REVERT: C 38 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7411 (tm-30) REVERT: C 128 LYS cc_start: 0.7703 (ttpp) cc_final: 0.7345 (ttmt) REVERT: C 180 ASP cc_start: 0.8619 (t0) cc_final: 0.8279 (t0) REVERT: C 374 GLU cc_start: 0.7357 (tm-30) cc_final: 0.7068 (mm-30) REVERT: C 378 GLU cc_start: 0.7109 (tp30) cc_final: 0.6719 (tt0) REVERT: C 451 ARG cc_start: 0.8260 (mtm-85) cc_final: 0.7916 (mtm-85) REVERT: C 456 MET cc_start: 0.8806 (mtp) cc_final: 0.8495 (mtp) REVERT: C 563 GLU cc_start: 0.8416 (pm20) cc_final: 0.7477 (pm20) REVERT: C 660 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.7862 (pp) REVERT: D 32 LEU cc_start: 0.8106 (OUTLIER) cc_final: 0.7875 (mp) REVERT: D 38 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7456 (tm-30) REVERT: D 128 LYS cc_start: 0.7629 (ttpp) cc_final: 0.7266 (ttmt) REVERT: D 179 GLU cc_start: 0.8276 (OUTLIER) cc_final: 0.8058 (mp0) REVERT: D 180 ASP cc_start: 0.8612 (t0) cc_final: 0.8324 (t0) REVERT: D 383 TYR cc_start: 0.8660 (t80) cc_final: 0.8439 (t80) REVERT: D 413 TYR cc_start: 0.9289 (m-80) cc_final: 0.9067 (m-80) REVERT: D 456 MET cc_start: 0.8871 (mtp) cc_final: 0.8579 (mtp) REVERT: D 563 GLU cc_start: 0.8368 (pm20) cc_final: 0.7476 (pm20) REVERT: D 660 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.7895 (pp) REVERT: E 38 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.7455 (tm-30) REVERT: E 128 LYS cc_start: 0.7724 (ttpp) cc_final: 0.7361 (ttmt) REVERT: E 180 ASP cc_start: 0.8608 (t0) cc_final: 0.8326 (t0) REVERT: E 252 LYS cc_start: 0.7033 (ttmt) cc_final: 0.6602 (tttt) REVERT: E 389 ASP cc_start: 0.7651 (OUTLIER) cc_final: 0.7369 (t70) REVERT: E 413 TYR cc_start: 0.9306 (m-80) cc_final: 0.9102 (m-80) REVERT: E 456 MET cc_start: 0.8811 (mtp) cc_final: 0.8484 (mtp) REVERT: E 563 GLU cc_start: 0.8422 (pm20) cc_final: 0.7495 (pm20) REVERT: E 634 GLU cc_start: 0.7768 (tp30) cc_final: 0.7133 (mt-10) REVERT: F 38 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7457 (tm-30) REVERT: F 128 LYS cc_start: 0.8194 (ttmt) cc_final: 0.7634 (ttpp) REVERT: F 180 ASP cc_start: 0.8697 (t0) cc_final: 0.8337 (t0) REVERT: F 451 ARG cc_start: 0.8201 (mtm-85) cc_final: 0.7831 (mtm-85) REVERT: F 456 MET cc_start: 0.8828 (mtp) cc_final: 0.8508 (mtp) REVERT: F 563 GLU cc_start: 0.8400 (pm20) cc_final: 0.7461 (pm20) REVERT: F 660 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.7963 (pp) REVERT: G 38 GLU cc_start: 0.8275 (OUTLIER) cc_final: 0.7496 (tm-30) REVERT: G 128 LYS cc_start: 0.8138 (ttpt) cc_final: 0.7350 (ttmt) REVERT: G 180 ASP cc_start: 0.8593 (t0) cc_final: 0.8217 (t0) REVERT: G 374 GLU cc_start: 0.6784 (mp0) cc_final: 0.6540 (mm-30) REVERT: G 378 GLU cc_start: 0.7109 (tp30) cc_final: 0.6887 (tt0) REVERT: G 456 MET cc_start: 0.8830 (mtp) cc_final: 0.8360 (mtp) REVERT: G 563 GLU cc_start: 0.8426 (pm20) cc_final: 0.7500 (pm20) REVERT: G 660 LEU cc_start: 0.8457 (OUTLIER) cc_final: 0.7912 (pp) REVERT: H 38 GLU cc_start: 0.8245 (OUTLIER) cc_final: 0.7497 (tm-30) REVERT: H 128 LYS cc_start: 0.7942 (ttpt) cc_final: 0.7530 (ttmt) REVERT: H 180 ASP cc_start: 0.8732 (t0) cc_final: 0.8412 (t0) REVERT: H 252 LYS cc_start: 0.7148 (ttmt) cc_final: 0.6716 (tttt) REVERT: H 378 GLU cc_start: 0.7230 (tp30) cc_final: 0.6882 (tt0) REVERT: H 389 ASP cc_start: 0.7678 (OUTLIER) cc_final: 0.7358 (t70) REVERT: H 413 TYR cc_start: 0.9252 (m-80) cc_final: 0.8969 (m-80) REVERT: H 563 GLU cc_start: 0.8419 (pm20) cc_final: 0.7489 (pm20) REVERT: H 660 LEU cc_start: 0.8457 (OUTLIER) cc_final: 0.7967 (pp) outliers start: 176 outliers final: 102 residues processed: 742 average time/residue: 0.2590 time to fit residues: 309.1302 Evaluate side-chains 705 residues out of total 4480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 580 time to evaluate : 1.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 GLU Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 179 GLU Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 389 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 646 THR Chi-restraints excluded: chain A residue 654 THR Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain B residue 38 GLU 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 264 ILE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 318 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 654 THR Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 38 GLU Chi-restraints excluded: chain C residue 264 ILE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 327 ASP Chi-restraints excluded: chain C residue 408 ILE 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 646 THR Chi-restraints excluded: chain C residue 654 THR Chi-restraints excluded: chain C residue 660 LEU 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 131 THR Chi-restraints excluded: chain D residue 168 GLU Chi-restraints excluded: chain D residue 179 GLU Chi-restraints excluded: chain D residue 264 ILE Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 288 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 544 ILE Chi-restraints excluded: chain D residue 646 THR Chi-restraints excluded: chain D residue 660 LEU Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 38 GLU Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain E residue 131 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 453 MET 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 F residue 32 LEU Chi-restraints excluded: chain F residue 38 GLU Chi-restraints excluded: chain F residue 131 THR 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 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 654 THR Chi-restraints excluded: chain F residue 660 LEU Chi-restraints excluded: chain G residue 32 LEU Chi-restraints excluded: chain G residue 38 GLU Chi-restraints excluded: chain G residue 99 MET Chi-restraints excluded: chain G residue 168 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 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 565 THR 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 32 LEU Chi-restraints excluded: chain H residue 38 GLU Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 99 MET Chi-restraints excluded: chain H residue 168 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 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 495 MET Chi-restraints excluded: chain H residue 646 THR Chi-restraints excluded: chain H residue 660 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 92 optimal weight: 20.0000 chunk 351 optimal weight: 6.9990 chunk 69 optimal weight: 4.9990 chunk 200 optimal weight: 3.9990 chunk 115 optimal weight: 5.9990 chunk 462 optimal weight: 0.6980 chunk 109 optimal weight: 10.0000 chunk 38 optimal weight: 1.9990 chunk 418 optimal weight: 5.9990 chunk 506 optimal weight: 7.9990 chunk 167 optimal weight: 4.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 210 HIS ** 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 ** 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 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 612 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** C 612 ASN D 210 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 612 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 ** 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 508 ASN ** F 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 210 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** ** H 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 210 HIS ** 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: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.141189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.114284 restraints weight = 48004.904| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 1.89 r_work: 0.3048 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2900 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.3622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 43184 Z= 0.174 Angle : 0.637 8.474 58672 Z= 0.331 Chirality : 0.047 0.225 6120 Planarity : 0.005 0.050 7672 Dihedral : 5.234 24.384 5824 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 4.11 % Allowed : 12.83 % Favored : 83.06 % 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: -0.17 (0.12), residues: 5280 helix: 0.57 (0.15), residues: 1296 sheet: -0.97 (0.20), residues: 624 loop : -0.13 (0.11), residues: 3360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 196 TYR 0.023 0.002 TYR A 132 PHE 0.021 0.002 PHE F 325 TRP 0.013 0.001 TRP E 566 HIS 0.007 0.002 HIS E 394 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.17 (43184) covalent geometry : angle 0.63685 / 0.33 (58672) hydrogen bonds : bond 0.03945 / 2.58 ( 1200) hydrogen bonds : angle 5.23564 / 3.66 ( 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 806 residues out of total 4480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 184 poor density : 622 time to evaluate : 1.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 GLU cc_start: 0.8272 (OUTLIER) cc_final: 0.7502 (tm-30) REVERT: A 41 GLU cc_start: 0.8575 (OUTLIER) cc_final: 0.8307 (pt0) REVERT: A 128 LYS cc_start: 0.8112 (ttpt) cc_final: 0.7612 (ttmt) REVERT: A 179 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.7762 (mm-30) REVERT: A 456 MET cc_start: 0.8849 (mtp) cc_final: 0.8576 (mtp) REVERT: A 563 GLU cc_start: 0.8442 (pm20) cc_final: 0.7492 (pm20) REVERT: A 598 VAL cc_start: 0.8702 (t) cc_final: 0.8406 (p) REVERT: B 38 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.7492 (tm-30) REVERT: B 128 LYS cc_start: 0.8291 (ttmt) cc_final: 0.7748 (ttpp) REVERT: B 179 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.8164 (mp0) REVERT: B 413 TYR cc_start: 0.9269 (m-80) cc_final: 0.9067 (m-80) REVERT: B 456 MET cc_start: 0.8839 (mtp) cc_final: 0.8468 (mtp) REVERT: B 563 GLU cc_start: 0.8410 (pm20) cc_final: 0.7439 (pm20) REVERT: B 598 VAL cc_start: 0.8602 (t) cc_final: 0.8298 (p) REVERT: B 634 GLU cc_start: 0.7587 (tp30) cc_final: 0.6946 (mt-10) REVERT: C 32 LEU cc_start: 0.7959 (OUTLIER) cc_final: 0.7725 (mp) REVERT: C 38 GLU cc_start: 0.8172 (OUTLIER) cc_final: 0.7405 (tm-30) REVERT: C 128 LYS cc_start: 0.7719 (ttpp) cc_final: 0.7356 (ttmt) REVERT: C 354 ASN cc_start: 0.8228 (OUTLIER) cc_final: 0.7860 (t0) REVERT: C 389 ASP cc_start: 0.7603 (OUTLIER) cc_final: 0.7343 (t70) REVERT: C 451 ARG cc_start: 0.8292 (mtm-85) cc_final: 0.7925 (mtm-85) REVERT: C 456 MET cc_start: 0.8807 (mtp) cc_final: 0.8561 (mtp) REVERT: C 470 MET cc_start: 0.9361 (mtm) cc_final: 0.9147 (mtm) REVERT: C 563 GLU cc_start: 0.8519 (pm20) cc_final: 0.7872 (pm20) REVERT: D 38 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7448 (tm-30) REVERT: D 128 LYS cc_start: 0.7707 (ttpp) cc_final: 0.7431 (ttmt) REVERT: D 179 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.7621 (mm-30) REVERT: D 456 MET cc_start: 0.8877 (mtp) cc_final: 0.8601 (mtp) REVERT: D 563 GLU cc_start: 0.8430 (pm20) cc_final: 0.7486 (pm20) REVERT: D 598 VAL cc_start: 0.8652 (t) cc_final: 0.8333 (p) REVERT: E 38 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.7469 (tm-30) REVERT: E 128 LYS cc_start: 0.7784 (ttpp) cc_final: 0.7527 (ttmt) REVERT: E 252 LYS cc_start: 0.7122 (ttmt) cc_final: 0.6672 (tttt) REVERT: E 456 MET cc_start: 0.8809 (mtp) cc_final: 0.8514 (mtp) REVERT: E 563 GLU cc_start: 0.8430 (pm20) cc_final: 0.7449 (pm20) REVERT: E 634 GLU cc_start: 0.7712 (tp30) cc_final: 0.7011 (mt-10) REVERT: E 660 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.7882 (pp) REVERT: F 32 LEU cc_start: 0.8113 (OUTLIER) cc_final: 0.7871 (mp) REVERT: F 38 GLU cc_start: 0.8223 (OUTLIER) cc_final: 0.7471 (tm-30) REVERT: F 180 ASP cc_start: 0.8622 (t0) cc_final: 0.8368 (t0) REVERT: F 354 ASN cc_start: 0.8240 (OUTLIER) cc_final: 0.7846 (t0) REVERT: F 374 GLU cc_start: 0.6889 (mp0) cc_final: 0.6679 (mm-30) REVERT: F 383 TYR cc_start: 0.8648 (t80) cc_final: 0.8325 (t80) REVERT: F 389 ASP cc_start: 0.7650 (OUTLIER) cc_final: 0.7369 (t70) REVERT: F 413 TYR cc_start: 0.9263 (m-80) cc_final: 0.9017 (m-80) REVERT: F 451 ARG cc_start: 0.8265 (mtm-85) cc_final: 0.7901 (mtm-85) REVERT: F 563 GLU cc_start: 0.8482 (pm20) cc_final: 0.7844 (pm20) REVERT: F 599 LYS cc_start: 0.8508 (mppt) cc_final: 0.8295 (mppt) REVERT: G 38 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.7493 (tm-30) REVERT: G 252 LYS cc_start: 0.7089 (ttmt) cc_final: 0.6662 (tttt) REVERT: G 354 ASN cc_start: 0.8209 (OUTLIER) cc_final: 0.7902 (t0) REVERT: G 374 GLU cc_start: 0.6793 (mp0) cc_final: 0.6576 (mm-30) REVERT: G 383 TYR cc_start: 0.8690 (t80) cc_final: 0.8358 (t80) REVERT: G 413 TYR cc_start: 0.9271 (m-80) cc_final: 0.9038 (m-80) REVERT: G 456 MET cc_start: 0.8856 (mtp) cc_final: 0.8423 (mtp) REVERT: G 563 GLU cc_start: 0.8453 (pm20) cc_final: 0.7501 (pm20) REVERT: G 660 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.7947 (pp) REVERT: H 38 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.7540 (tm-30) REVERT: H 128 LYS cc_start: 0.8043 (ttpt) cc_final: 0.7556 (ttmt) REVERT: H 252 LYS cc_start: 0.7205 (ttmt) cc_final: 0.6778 (tttt) REVERT: H 374 GLU cc_start: 0.6925 (mp0) cc_final: 0.6708 (mm-30) REVERT: H 456 MET cc_start: 0.8851 (mtp) cc_final: 0.8613 (mtp) REVERT: H 563 GLU cc_start: 0.8483 (pm20) cc_final: 0.7550 (pm20) REVERT: H 598 VAL cc_start: 0.8633 (t) cc_final: 0.8326 (p) outliers start: 184 outliers final: 122 residues processed: 746 average time/residue: 0.2673 time to fit residues: 317.0255 Evaluate side-chains 731 residues out of total 4480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 588 time to evaluate : 1.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 GLU Chi-restraints excluded: chain A residue 41 GLU 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 408 ILE 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 654 THR Chi-restraints excluded: chain B residue 38 GLU 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 179 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 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 654 THR Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 38 GLU 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 240 VAL Chi-restraints excluded: chain C residue 264 ILE 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 408 ILE 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 646 THR Chi-restraints excluded: chain C residue 654 THR 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 179 GLU Chi-restraints excluded: chain D residue 240 VAL Chi-restraints excluded: chain D residue 264 ILE 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 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 E residue 32 LEU Chi-restraints excluded: chain E residue 38 GLU Chi-restraints excluded: chain E residue 131 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 418 HIS Chi-restraints excluded: chain E residue 453 MET 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 38 GLU Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 168 GLU 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 327 ASP Chi-restraints excluded: chain F residue 354 ASN 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 534 THR 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 G residue 32 LEU Chi-restraints excluded: chain G residue 38 GLU Chi-restraints excluded: chain G residue 131 THR Chi-restraints excluded: chain G residue 168 GLU Chi-restraints excluded: chain G residue 240 VAL 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 327 ASP Chi-restraints excluded: chain G residue 354 ASN 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 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 565 THR 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 38 GLU 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 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 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 544 ILE Chi-restraints excluded: chain H residue 646 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 461 optimal weight: 6.9990 chunk 452 optimal weight: 0.9990 chunk 343 optimal weight: 5.9990 chunk 443 optimal weight: 10.0000 chunk 407 optimal weight: 0.4980 chunk 250 optimal weight: 9.9990 chunk 114 optimal weight: 0.0070 chunk 375 optimal weight: 2.9990 chunk 222 optimal weight: 20.0000 chunk 497 optimal weight: 3.9990 chunk 268 optimal weight: 0.9990 overall best weight: 1.1004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 ** B 515 HIS ** 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 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 529 ASN ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 508 ASN ** D 515 HIS ** 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** E 612 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 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 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 H 529 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.142669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.115803 restraints weight = 47998.614| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 1.72 r_work: 0.3086 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.3828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 43184 Z= 0.108 Angle : 0.580 7.863 58672 Z= 0.299 Chirality : 0.045 0.195 6120 Planarity : 0.005 0.047 7672 Dihedral : 4.904 25.017 5824 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 3.06 % Allowed : 14.53 % Favored : 82.41 % 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: -0.10 (0.12), residues: 5280 helix: 0.81 (0.15), residues: 1296 sheet: -1.29 (0.21), residues: 568 loop : -0.12 (0.11), residues: 3416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 196 TYR 0.024 0.001 TYR H 132 PHE 0.015 0.001 PHE C 312 TRP 0.013 0.001 TRP E 566 HIS 0.006 0.001 HIS E 394 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (43184) covalent geometry : angle 0.58030 / 0.30 (58672) hydrogen bonds : bond 0.03207 / 2.08 ( 1200) hydrogen bonds : angle 4.99528 / 3.50 ( 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 776 residues out of total 4480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 639 time to evaluate : 1.715 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.7531 (tm-30) REVERT: A 41 GLU cc_start: 0.8455 (OUTLIER) cc_final: 0.8137 (pt0) REVERT: A 128 LYS cc_start: 0.8076 (ttpt) cc_final: 0.7715 (ttmt) REVERT: A 456 MET cc_start: 0.8771 (mtp) cc_final: 0.8565 (mtp) REVERT: A 563 GLU cc_start: 0.8264 (pm20) cc_final: 0.7415 (pm20) REVERT: A 598 VAL cc_start: 0.8678 (t) cc_final: 0.8432 (p) REVERT: A 599 LYS cc_start: 0.8434 (mppt) cc_final: 0.8172 (mppt) REVERT: A 660 LEU cc_start: 0.8322 (OUTLIER) cc_final: 0.7789 (pp) REVERT: B 38 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7490 (tm-30) REVERT: B 441 ASP cc_start: 0.8109 (p0) cc_final: 0.7835 (p0) REVERT: B 456 MET cc_start: 0.8756 (mtp) cc_final: 0.8499 (mtp) REVERT: B 598 VAL cc_start: 0.8635 (t) cc_final: 0.8358 (p) REVERT: B 634 GLU cc_start: 0.7540 (tp30) cc_final: 0.6969 (mt-10) REVERT: B 660 LEU cc_start: 0.8282 (OUTLIER) cc_final: 0.7736 (pp) REVERT: C 38 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7436 (tm-30) REVERT: C 128 LYS cc_start: 0.7689 (ttpp) cc_final: 0.7432 (ttmt) REVERT: C 378 GLU cc_start: 0.6911 (tp30) cc_final: 0.6690 (tt0) REVERT: C 413 TYR cc_start: 0.9211 (m-80) cc_final: 0.8939 (m-80) REVERT: C 451 ARG cc_start: 0.8249 (mtm-85) cc_final: 0.7947 (mtm-85) REVERT: C 470 MET cc_start: 0.9270 (mtm) cc_final: 0.9033 (mtm) REVERT: C 563 GLU cc_start: 0.8264 (pm20) cc_final: 0.7351 (pm20) REVERT: C 598 VAL cc_start: 0.8505 (t) cc_final: 0.8122 (m) REVERT: C 660 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.7811 (pp) REVERT: D 38 GLU cc_start: 0.8103 (OUTLIER) cc_final: 0.7483 (tm-30) REVERT: D 41 GLU cc_start: 0.8403 (OUTLIER) cc_final: 0.8136 (pt0) REVERT: D 128 LYS cc_start: 0.7754 (ttpp) cc_final: 0.7489 (ttmt) REVERT: D 413 TYR cc_start: 0.9209 (m-80) cc_final: 0.8995 (m-80) REVERT: D 563 GLU cc_start: 0.8354 (pm20) cc_final: 0.7486 (pm20) REVERT: D 598 VAL cc_start: 0.8641 (t) cc_final: 0.8386 (p) REVERT: D 599 LYS cc_start: 0.8407 (mppt) cc_final: 0.8135 (mtmm) REVERT: D 660 LEU cc_start: 0.8335 (OUTLIER) cc_final: 0.7769 (pp) REVERT: E 32 LEU cc_start: 0.8083 (OUTLIER) cc_final: 0.7851 (mp) REVERT: E 38 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7477 (tm-30) REVERT: E 99 MET cc_start: 0.9379 (mtm) cc_final: 0.9029 (mtm) REVERT: E 128 LYS cc_start: 0.7776 (ttpp) cc_final: 0.7480 (ttmt) REVERT: E 456 MET cc_start: 0.8798 (mtp) cc_final: 0.8483 (mtp) REVERT: E 563 GLU cc_start: 0.8231 (pm20) cc_final: 0.7329 (pm20) REVERT: E 598 VAL cc_start: 0.8526 (t) cc_final: 0.8192 (m) REVERT: E 634 GLU cc_start: 0.7608 (tp30) cc_final: 0.7002 (mt-10) REVERT: E 660 LEU cc_start: 0.8291 (OUTLIER) cc_final: 0.7633 (pp) REVERT: F 38 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7437 (tm-30) REVERT: F 99 MET cc_start: 0.9409 (mtm) cc_final: 0.9045 (mtm) REVERT: F 383 TYR cc_start: 0.8698 (t80) cc_final: 0.8391 (t80) REVERT: F 451 ARG cc_start: 0.8230 (mtm-85) cc_final: 0.7898 (mtm-85) REVERT: F 456 MET cc_start: 0.8834 (mtp) cc_final: 0.8511 (mtp) REVERT: F 563 GLU cc_start: 0.8251 (pm20) cc_final: 0.7336 (pm20) REVERT: F 598 VAL cc_start: 0.8528 (t) cc_final: 0.8161 (m) REVERT: F 660 LEU cc_start: 0.8337 (OUTLIER) cc_final: 0.7799 (pp) REVERT: G 38 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.7486 (tm-30) REVERT: G 383 TYR cc_start: 0.8685 (t80) cc_final: 0.8363 (t80) REVERT: G 413 TYR cc_start: 0.9242 (m-80) cc_final: 0.8989 (m-80) REVERT: G 456 MET cc_start: 0.8784 (mtp) cc_final: 0.8395 (mtp) REVERT: G 563 GLU cc_start: 0.8296 (pm20) cc_final: 0.7411 (pm20) REVERT: H 38 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7513 (tm-30) REVERT: H 128 LYS cc_start: 0.8131 (ttpt) cc_final: 0.7756 (ttmt) REVERT: H 252 LYS cc_start: 0.7188 (ttmt) cc_final: 0.6787 (tttt) REVERT: H 563 GLU cc_start: 0.8290 (pm20) cc_final: 0.7388 (pm20) REVERT: H 598 VAL cc_start: 0.8644 (t) cc_final: 0.8371 (p) REVERT: H 599 LYS cc_start: 0.8425 (mppt) cc_final: 0.8157 (mppt) REVERT: H 660 LEU cc_start: 0.8271 (OUTLIER) cc_final: 0.7628 (pp) outliers start: 137 outliers final: 87 residues processed: 731 average time/residue: 0.2628 time to fit residues: 309.0244 Evaluate side-chains 667 residues out of total 4480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 562 time to evaluate : 1.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 GLU Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 74 SER Chi-restraints excluded: chain A residue 99 MET Chi-restraints excluded: chain A residue 131 THR 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 38 GLU 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 389 ASP 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 654 THR Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain B residue 662 ARG Chi-restraints excluded: chain C residue 38 GLU Chi-restraints excluded: chain C residue 99 MET 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 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 654 THR Chi-restraints excluded: chain C residue 660 LEU Chi-restraints excluded: chain D residue 38 GLU Chi-restraints excluded: chain D residue 41 GLU Chi-restraints excluded: chain D residue 131 THR 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 288 LEU 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 540 LEU Chi-restraints excluded: chain D residue 660 LEU Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 38 GLU 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 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 660 LEU Chi-restraints excluded: chain F residue 38 GLU Chi-restraints excluded: chain F residue 240 VAL Chi-restraints excluded: chain F residue 277 LEU 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 654 THR Chi-restraints excluded: chain F residue 660 LEU Chi-restraints excluded: chain G residue 38 GLU Chi-restraints excluded: chain G residue 99 MET Chi-restraints excluded: chain G residue 168 GLU Chi-restraints excluded: chain G residue 240 VAL Chi-restraints excluded: chain G residue 270 THR Chi-restraints excluded: chain G residue 277 LEU 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 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 565 THR Chi-restraints excluded: chain G residue 654 THR Chi-restraints excluded: chain H residue 38 GLU Chi-restraints excluded: chain H residue 99 MET Chi-restraints excluded: chain H residue 168 GLU Chi-restraints excluded: chain H residue 240 VAL Chi-restraints excluded: chain H residue 277 LEU 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 660 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 58 optimal weight: 8.9990 chunk 377 optimal weight: 4.9990 chunk 258 optimal weight: 6.9990 chunk 520 optimal weight: 6.9990 chunk 9 optimal weight: 0.7980 chunk 454 optimal weight: 6.9990 chunk 210 optimal weight: 20.0000 chunk 337 optimal weight: 10.0000 chunk 14 optimal weight: 10.0000 chunk 394 optimal weight: 6.9990 chunk 62 optimal weight: 2.9990 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** ** B 515 HIS ** 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 ** 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** ** 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** ** 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 480 HIS ** H 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 529 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.134983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.108662 restraints weight = 49280.344| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 1.67 r_work: 0.2989 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2850 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.3848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 43184 Z= 0.218 Angle : 0.662 8.278 58672 Z= 0.345 Chirality : 0.049 0.235 6120 Planarity : 0.005 0.049 7672 Dihedral : 5.147 23.017 5824 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.48 % Allowed : 15.51 % Favored : 81.00 % 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: 0.74 (0.15), residues: 1296 sheet: -1.43 (0.18), residues: 784 loop : -0.13 (0.12), residues: 3200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 196 TYR 0.021 0.002 TYR E 132 PHE 0.027 0.002 PHE G 325 TRP 0.026 0.001 TRP B 566 HIS 0.007 0.002 HIS G 418 Details of bonding type rmsd/Z covalent geometry : bond 0.00530 / 0.22 (43184) covalent geometry : angle 0.66180 / 0.34 (58672) hydrogen bonds : bond 0.04044 / 2.66 ( 1200) hydrogen bonds : angle 5.19959 / 3.64 ( 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 735 residues out of total 4480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 579 time to evaluate : 1.634 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 GLU cc_start: 0.8120 (OUTLIER) cc_final: 0.7461 (tm-30) REVERT: A 41 GLU cc_start: 0.8580 (OUTLIER) cc_final: 0.8320 (pt0) REVERT: A 362 ILE cc_start: 0.8601 (OUTLIER) cc_final: 0.8212 (pt) REVERT: A 383 TYR cc_start: 0.8767 (t80) cc_final: 0.8424 (t80) REVERT: A 413 TYR cc_start: 0.9200 (m-80) cc_final: 0.8998 (m-80) REVERT: A 456 MET cc_start: 0.8785 (mtp) cc_final: 0.8476 (mtp) REVERT: A 563 GLU cc_start: 0.8438 (pm20) cc_final: 0.7521 (pm20) REVERT: A 598 VAL cc_start: 0.8788 (t) cc_final: 0.8539 (p) REVERT: A 660 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.7928 (pp) REVERT: B 38 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.7483 (tm-30) REVERT: B 180 ASP cc_start: 0.8625 (t0) cc_final: 0.8316 (t0) REVERT: B 456 MET cc_start: 0.8729 (mtp) cc_final: 0.8452 (mtp) REVERT: B 563 GLU cc_start: 0.8383 (pm20) cc_final: 0.7575 (pm20) REVERT: B 598 VAL cc_start: 0.8667 (t) cc_final: 0.8440 (p) REVERT: B 634 GLU cc_start: 0.7617 (tp30) cc_final: 0.7056 (mt-10) REVERT: B 660 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.7911 (pp) REVERT: C 38 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7422 (tm-30) REVERT: C 128 LYS cc_start: 0.7862 (ttpp) cc_final: 0.7606 (ttmt) REVERT: C 130 GLU cc_start: 0.9204 (OUTLIER) cc_final: 0.7674 (pm20) REVERT: C 383 TYR cc_start: 0.8699 (t80) cc_final: 0.8375 (t80) REVERT: C 456 MET cc_start: 0.8824 (mtp) cc_final: 0.8576 (mtp) REVERT: C 598 VAL cc_start: 0.8498 (t) cc_final: 0.8232 (p) REVERT: C 660 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.7904 (pp) REVERT: D 38 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.7434 (tm-30) REVERT: D 41 GLU cc_start: 0.8560 (OUTLIER) cc_final: 0.8345 (pt0) REVERT: D 128 LYS cc_start: 0.7879 (ttpp) cc_final: 0.7638 (ttmt) REVERT: D 179 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.7695 (mm-30) REVERT: D 180 ASP cc_start: 0.8537 (t0) cc_final: 0.8315 (t0) REVERT: D 252 LYS cc_start: 0.7180 (ttmt) cc_final: 0.6772 (tttt) REVERT: D 362 ILE cc_start: 0.8635 (OUTLIER) cc_final: 0.8276 (pt) REVERT: D 383 TYR cc_start: 0.8768 (t80) cc_final: 0.8498 (t80) REVERT: D 563 GLU cc_start: 0.8441 (pm20) cc_final: 0.7487 (pm20) REVERT: D 598 VAL cc_start: 0.8698 (t) cc_final: 0.8419 (p) REVERT: D 660 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.7912 (pp) REVERT: E 32 LEU cc_start: 0.7983 (OUTLIER) cc_final: 0.7758 (mp) REVERT: E 38 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7458 (tm-30) REVERT: E 128 LYS cc_start: 0.7915 (ttpp) cc_final: 0.7642 (ttmt) REVERT: E 180 ASP cc_start: 0.8489 (t0) cc_final: 0.8288 (t0) REVERT: E 252 LYS cc_start: 0.7267 (ttmt) cc_final: 0.6865 (tttt) REVERT: E 456 MET cc_start: 0.8734 (mtp) cc_final: 0.8448 (mtp) REVERT: E 563 GLU cc_start: 0.8466 (pm20) cc_final: 0.7529 (pm20) REVERT: E 598 VAL cc_start: 0.8650 (t) cc_final: 0.8258 (m) REVERT: E 634 GLU cc_start: 0.7649 (tp30) cc_final: 0.7087 (mt-10) REVERT: E 660 LEU cc_start: 0.8411 (OUTLIER) cc_final: 0.8020 (pp) REVERT: F 38 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7415 (tm-30) REVERT: F 180 ASP cc_start: 0.8394 (t0) cc_final: 0.8138 (t0) REVERT: F 383 TYR cc_start: 0.8723 (t80) cc_final: 0.8412 (t80) REVERT: F 451 ARG cc_start: 0.8359 (mtm-85) cc_final: 0.8153 (mtm-85) REVERT: F 456 MET cc_start: 0.8857 (mtp) cc_final: 0.8580 (mtp) REVERT: F 660 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.7902 (pp) REVERT: G 38 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7451 (tm-30) REVERT: G 130 GLU cc_start: 0.9202 (OUTLIER) cc_final: 0.7659 (pm20) REVERT: G 180 ASP cc_start: 0.8523 (t0) cc_final: 0.8203 (t0) REVERT: G 252 LYS cc_start: 0.7214 (ttmt) cc_final: 0.6813 (tttt) REVERT: G 383 TYR cc_start: 0.8730 (t80) cc_final: 0.8487 (t80) REVERT: G 563 GLU cc_start: 0.8466 (pm20) cc_final: 0.7541 (pm20) REVERT: H 38 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7471 (tm-30) REVERT: H 128 LYS cc_start: 0.8233 (ttpt) cc_final: 0.7892 (ttmt) REVERT: H 180 ASP cc_start: 0.8520 (t0) cc_final: 0.8214 (t0) REVERT: H 252 LYS cc_start: 0.7311 (ttmt) cc_final: 0.6917 (tttt) REVERT: H 383 TYR cc_start: 0.8702 (t80) cc_final: 0.8377 (t80) REVERT: H 563 GLU cc_start: 0.8484 (pm20) cc_final: 0.7565 (pm20) REVERT: H 598 VAL cc_start: 0.8716 (t) cc_final: 0.8401 (p) REVERT: H 660 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.8024 (pp) outliers start: 156 outliers final: 113 residues processed: 677 average time/residue: 0.2781 time to fit residues: 299.3962 Evaluate side-chains 697 residues out of total 4480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 561 time to evaluate : 1.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 38 GLU Chi-restraints excluded: chain A residue 41 GLU 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 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 362 ILE 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 654 THR Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain B residue 38 GLU 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 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 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 654 THR Chi-restraints excluded: chain B residue 660 LEU Chi-restraints excluded: chain B residue 662 ARG Chi-restraints excluded: chain C residue 38 GLU 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 389 ASP 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 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 41 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 179 GLU 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 362 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 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 32 LEU Chi-restraints excluded: chain E residue 38 GLU 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 288 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 544 ILE Chi-restraints excluded: chain E residue 565 THR Chi-restraints excluded: chain E residue 660 LEU Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain F residue 38 GLU Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 168 GLU 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 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 654 THR Chi-restraints excluded: chain F residue 660 LEU Chi-restraints excluded: chain G residue 38 GLU 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 240 VAL Chi-restraints excluded: chain G residue 277 LEU 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 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 565 THR Chi-restraints excluded: chain G residue 654 THR Chi-restraints excluded: chain H residue 38 GLU 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 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 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 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: 6.9990 chunk 142 optimal weight: 8.9990 chunk 358 optimal weight: 8.9990 chunk 408 optimal weight: 5.9990 chunk 474 optimal weight: 10.0000 chunk 248 optimal weight: 1.9990 chunk 11 optimal weight: 9.9990 chunk 102 optimal weight: 9.9990 chunk 176 optimal weight: 7.9990 chunk 182 optimal weight: 4.9990 chunk 513 optimal weight: 7.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 185 HIS A 189 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** ** 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** 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 185 HIS D 189 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 515 HIS ** 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 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** F 532 HIS ** 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 532 HIS ** H 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 185 HIS H 189 HIS ** 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** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.133125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.107148 restraints weight = 49567.749| |-----------------------------------------------------------------------------| r_work (start): 0.3077 rms_B_bonded: 1.61 r_work: 0.2952 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.3988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 43184 Z= 0.256 Angle : 0.697 8.412 58672 Z= 0.365 Chirality : 0.050 0.232 6120 Planarity : 0.006 0.051 7672 Dihedral : 5.369 24.070 5824 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 4.24 % Allowed : 14.89 % Favored : 80.87 % 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: -0.42 (0.12), residues: 5280 helix: 0.58 (0.15), residues: 1296 sheet: -1.26 (0.18), residues: 704 loop : -0.34 (0.11), residues: 3280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 103 TYR 0.022 0.002 TYR E 132 PHE 0.028 0.003 PHE G 325 TRP 0.021 0.002 TRP B 566 HIS 0.009 0.002 HIS C 418 Details of bonding type rmsd/Z covalent geometry : bond 0.00620 / 0.26 (43184) covalent geometry : angle 0.69653 / 0.36 (58672) hydrogen bonds : bond 0.04366 / 2.88 ( 1200) hydrogen bonds : angle 5.35184 / 3.75 ( 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 776 residues out of total 4480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 190 poor density : 586 time to evaluate : 1.845 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.7397 (tm-30) REVERT: A 41 GLU cc_start: 0.8607 (OUTLIER) cc_final: 0.8396 (pt0) REVERT: A 130 GLU cc_start: 0.9193 (OUTLIER) cc_final: 0.7641 (pm20) REVERT: A 180 ASP cc_start: 0.8601 (t0) cc_final: 0.8339 (t0) REVERT: A 252 LYS cc_start: 0.7226 (ttmt) cc_final: 0.6952 (tttt) REVERT: A 383 TYR cc_start: 0.8796 (t80) cc_final: 0.8477 (t80) REVERT: A 415 THR cc_start: 0.9326 (OUTLIER) cc_final: 0.9109 (p) REVERT: A 456 MET cc_start: 0.8759 (mtp) cc_final: 0.8485 (mtp) REVERT: A 563 GLU cc_start: 0.8469 (pm20) cc_final: 0.7486 (pm20) REVERT: A 598 VAL cc_start: 0.8791 (t) cc_final: 0.8570 (p) REVERT: A 660 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.7836 (pp) REVERT: B 38 GLU cc_start: 0.8126 (OUTLIER) cc_final: 0.7448 (tm-30) REVERT: B 130 GLU cc_start: 0.9214 (OUTLIER) cc_final: 0.7658 (pm20) REVERT: B 180 ASP cc_start: 0.8609 (t0) cc_final: 0.8262 (t0) REVERT: B 362 ILE cc_start: 0.8576 (OUTLIER) cc_final: 0.8183 (pt) REVERT: B 383 TYR cc_start: 0.8729 (t80) cc_final: 0.8505 (t80) REVERT: B 569 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8364 (pp) REVERT: B 598 VAL cc_start: 0.8723 (t) cc_final: 0.8485 (p) REVERT: B 634 GLU cc_start: 0.7636 (tp30) cc_final: 0.7098 (mt-10) REVERT: B 660 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.7832 (pp) REVERT: C 38 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7398 (tm-30) REVERT: C 128 LYS cc_start: 0.7918 (ttpp) cc_final: 0.7614 (ttmt) REVERT: C 130 GLU cc_start: 0.9226 (OUTLIER) cc_final: 0.7654 (pm20) REVERT: C 180 ASP cc_start: 0.8579 (t0) cc_final: 0.8321 (t0) REVERT: C 354 ASN cc_start: 0.8234 (OUTLIER) cc_final: 0.7996 (t0) REVERT: C 362 ILE cc_start: 0.8529 (OUTLIER) cc_final: 0.8138 (pt) REVERT: C 383 TYR cc_start: 0.8773 (t80) cc_final: 0.8397 (t80) REVERT: C 451 ARG cc_start: 0.8437 (mtm-85) cc_final: 0.8170 (mtm-85) REVERT: C 456 MET cc_start: 0.8849 (mtp) cc_final: 0.8557 (mtp) REVERT: C 563 GLU cc_start: 0.8321 (pm20) cc_final: 0.7417 (pm20) REVERT: C 569 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8557 (pp) REVERT: C 598 VAL cc_start: 0.8498 (t) cc_final: 0.8209 (p) REVERT: C 660 LEU cc_start: 0.8551 (OUTLIER) cc_final: 0.7918 (pp) REVERT: D 38 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.7388 (tm-30) REVERT: D 128 LYS cc_start: 0.7890 (ttpp) cc_final: 0.7600 (ttmt) REVERT: D 130 GLU cc_start: 0.9214 (OUTLIER) cc_final: 0.7659 (pm20) REVERT: D 179 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.7761 (mm-30) REVERT: D 180 ASP cc_start: 0.8601 (t0) cc_final: 0.8287 (t0) REVERT: D 252 LYS cc_start: 0.7189 (ttmt) cc_final: 0.6900 (tttt) REVERT: D 362 ILE cc_start: 0.8512 (OUTLIER) cc_final: 0.8120 (pt) REVERT: D 383 TYR cc_start: 0.8788 (t80) cc_final: 0.8476 (t80) REVERT: D 563 GLU cc_start: 0.8453 (pm20) cc_final: 0.7465 (pm20) REVERT: D 569 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8642 (pp) REVERT: D 598 VAL cc_start: 0.8608 (t) cc_final: 0.8344 (p) REVERT: D 660 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.7900 (pp) REVERT: E 32 LEU cc_start: 0.7944 (OUTLIER) cc_final: 0.7736 (mp) REVERT: E 38 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7449 (tm-30) REVERT: E 130 GLU cc_start: 0.9193 (OUTLIER) cc_final: 0.7596 (pm20) REVERT: E 180 ASP cc_start: 0.8541 (t0) cc_final: 0.8272 (t0) REVERT: E 252 LYS cc_start: 0.7285 (ttmt) cc_final: 0.7031 (ttpt) REVERT: E 362 ILE cc_start: 0.8593 (OUTLIER) cc_final: 0.8205 (pt) REVERT: E 456 MET cc_start: 0.8720 (mtp) cc_final: 0.8458 (mtp) REVERT: E 563 GLU cc_start: 0.8482 (pm20) cc_final: 0.7474 (pm20) REVERT: E 598 VAL cc_start: 0.8578 (t) cc_final: 0.8325 (m) REVERT: E 634 GLU cc_start: 0.7653 (tp30) cc_final: 0.7116 (mt-10) REVERT: E 660 LEU cc_start: 0.8441 (OUTLIER) cc_final: 0.8063 (pp) REVERT: F 38 GLU cc_start: 0.8103 (OUTLIER) cc_final: 0.7416 (tm-30) REVERT: F 130 GLU cc_start: 0.9194 (OUTLIER) cc_final: 0.7637 (pm20) REVERT: F 180 ASP cc_start: 0.8512 (t0) cc_final: 0.8185 (t0) REVERT: F 354 ASN cc_start: 0.8182 (OUTLIER) cc_final: 0.7895 (t0) REVERT: F 383 TYR cc_start: 0.8744 (t80) cc_final: 0.8420 (t80) REVERT: F 451 ARG cc_start: 0.8382 (mtm-85) cc_final: 0.8182 (mtm-85) REVERT: F 456 MET cc_start: 0.8859 (mtp) cc_final: 0.8609 (mtp) REVERT: F 563 GLU cc_start: 0.8341 (pm20) cc_final: 0.7474 (pm20) REVERT: F 598 VAL cc_start: 0.8494 (t) cc_final: 0.8153 (m) REVERT: F 660 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.7878 (pp) REVERT: G 38 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7436 (tm-30) REVERT: G 130 GLU cc_start: 0.9207 (OUTLIER) cc_final: 0.7628 (pm20) REVERT: G 180 ASP cc_start: 0.8515 (t0) cc_final: 0.8143 (t0) REVERT: G 252 LYS cc_start: 0.7198 (ttmt) cc_final: 0.6878 (tttt) REVERT: G 354 ASN cc_start: 0.8216 (OUTLIER) cc_final: 0.7979 (t0) REVERT: G 383 TYR cc_start: 0.8751 (t80) cc_final: 0.8422 (t80) REVERT: G 563 GLU cc_start: 0.8511 (pm20) cc_final: 0.7521 (pm20) REVERT: G 569 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8547 (pp) REVERT: G 598 VAL cc_start: 0.8550 (t) cc_final: 0.8193 (m) REVERT: G 660 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.8097 (pp) REVERT: H 38 GLU cc_start: 0.8116 (OUTLIER) cc_final: 0.7438 (tm-30) REVERT: H 128 LYS cc_start: 0.8238 (ttpt) cc_final: 0.7617 (ttmt) REVERT: H 130 GLU cc_start: 0.9179 (OUTLIER) cc_final: 0.7647 (pm20) REVERT: H 180 ASP cc_start: 0.8565 (t0) cc_final: 0.8218 (t0) REVERT: H 252 LYS cc_start: 0.7267 (ttmt) cc_final: 0.6930 (tttt) REVERT: H 362 ILE cc_start: 0.8577 (OUTLIER) cc_final: 0.8188 (pt) REVERT: H 383 TYR cc_start: 0.8717 (t80) cc_final: 0.8381 (t80) REVERT: H 393 MET cc_start: 0.8307 (ttt) cc_final: 0.8007 (ttt) REVERT: H 563 GLU cc_start: 0.8502 (pm20) cc_final: 0.7497 (pm20) REVERT: H 598 VAL cc_start: 0.8599 (t) cc_final: 0.8343 (p) REVERT: H 660 LEU cc_start: 0.8449 (OUTLIER) cc_final: 0.8066 (pp) outliers start: 190 outliers final: 120 residues processed: 719 average time/residue: 0.2737 time to fit residues: 312.0545 Evaluate side-chains 710 residues out of total 4480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 160 poor density : 550 time to evaluate : 1.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 38 GLU Chi-restraints excluded: chain A residue 41 GLU 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 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 415 THR 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 38 GLU 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 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 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 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 38 GLU 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 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 477 VAL Chi-restraints excluded: chain C residue 544 ILE Chi-restraints excluded: chain C residue 569 LEU 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 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 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 362 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 569 LEU 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 32 LEU Chi-restraints excluded: chain E residue 38 GLU 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 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 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 38 GLU 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 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 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 534 THR Chi-restraints excluded: chain F residue 544 ILE Chi-restraints excluded: chain F residue 654 THR Chi-restraints excluded: chain F residue 660 LEU Chi-restraints excluded: chain G residue 38 GLU 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 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 367 GLU 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 565 THR Chi-restraints excluded: chain G residue 569 LEU Chi-restraints excluded: chain G residue 654 THR Chi-restraints excluded: chain G residue 660 LEU Chi-restraints excluded: chain H residue 38 GLU Chi-restraints excluded: chain H residue 54 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 240 VAL Chi-restraints excluded: chain H residue 264 ILE 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 495 MET 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: 5.9990 chunk 421 optimal weight: 5.9990 chunk 498 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 chunk 301 optimal weight: 9.9990 chunk 30 optimal weight: 0.9990 chunk 229 optimal weight: 7.9990 chunk 157 optimal weight: 20.0000 chunk 521 optimal weight: 9.9990 chunk 444 optimal weight: 3.9990 chunk 344 optimal weight: 7.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 249 ASN ** B 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 515 HIS ** 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 249 ASN ** C 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 529 ASN ** 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 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 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 508 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 532 HIS ** 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 529 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.133725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.107758 restraints weight = 49492.118| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 1.62 r_work: 0.2940 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2801 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.4089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 43184 Z= 0.218 Angle : 0.669 7.968 58672 Z= 0.349 Chirality : 0.048 0.230 6120 Planarity : 0.006 0.052 7672 Dihedral : 5.290 24.227 5824 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 4.13 % Allowed : 15.69 % Favored : 80.18 % 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: -0.41 (0.12), residues: 5280 helix: 0.59 (0.15), residues: 1296 sheet: -1.20 (0.18), residues: 760 loop : -0.33 (0.11), residues: 3224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 196 TYR 0.020 0.002 TYR E 132 PHE 0.024 0.002 PHE G 325 TRP 0.021 0.002 TRP B 566 HIS 0.007 0.002 HIS H 418 Details of bonding type rmsd/Z covalent geometry : bond 0.00530 / 0.22 (43184) covalent geometry : angle 0.66937 / 0.35 (58672) hydrogen bonds : bond 0.04098 / 2.69 ( 1200) hydrogen bonds : angle 5.30679 / 3.73 ( 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 765 residues out of total 4480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 185 poor density : 580 time to evaluate : 1.633 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.7338 (tm-30) REVERT: A 41 GLU cc_start: 0.8558 (OUTLIER) cc_final: 0.8339 (pt0) REVERT: A 130 GLU cc_start: 0.9220 (OUTLIER) cc_final: 0.7661 (pm20) REVERT: A 180 ASP cc_start: 0.8564 (t0) cc_final: 0.8285 (t0) REVERT: A 252 LYS cc_start: 0.7184 (ttmt) cc_final: 0.6962 (ttpt) REVERT: A 383 TYR cc_start: 0.8804 (t80) cc_final: 0.8480 (t80) REVERT: A 415 THR cc_start: 0.9313 (OUTLIER) cc_final: 0.9103 (p) REVERT: A 456 MET cc_start: 0.8743 (mtp) cc_final: 0.8470 (mtp) REVERT: A 563 GLU cc_start: 0.8448 (pm20) cc_final: 0.7438 (pm20) REVERT: A 598 VAL cc_start: 0.8802 (t) cc_final: 0.8596 (p) REVERT: A 660 LEU cc_start: 0.8434 (OUTLIER) cc_final: 0.7783 (pp) REVERT: B 38 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.7358 (tm-30) REVERT: B 130 GLU cc_start: 0.9199 (OUTLIER) cc_final: 0.7616 (pm20) REVERT: B 180 ASP cc_start: 0.8532 (t0) cc_final: 0.8227 (t0) REVERT: B 362 ILE cc_start: 0.8468 (OUTLIER) cc_final: 0.8082 (pt) REVERT: B 383 TYR cc_start: 0.8709 (t80) cc_final: 0.8494 (t80) REVERT: B 393 MET cc_start: 0.8236 (ttt) cc_final: 0.8033 (ttt) REVERT: B 563 GLU cc_start: 0.8195 (pm20) cc_final: 0.7286 (pm20) REVERT: B 569 LEU cc_start: 0.8935 (OUTLIER) cc_final: 0.8549 (pp) REVERT: B 598 VAL cc_start: 0.8748 (t) cc_final: 0.8519 (p) REVERT: B 634 GLU cc_start: 0.7656 (tp30) cc_final: 0.7112 (mt-10) REVERT: B 660 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.7778 (pp) REVERT: C 38 GLU cc_start: 0.8010 (OUTLIER) cc_final: 0.7315 (tm-30) REVERT: C 130 GLU cc_start: 0.9232 (OUTLIER) cc_final: 0.7682 (pm20) REVERT: C 180 ASP cc_start: 0.8585 (t0) cc_final: 0.8298 (t0) REVERT: C 383 TYR cc_start: 0.8759 (t80) cc_final: 0.8394 (t80) REVERT: C 451 ARG cc_start: 0.8425 (mtm-85) cc_final: 0.8117 (mtm-85) REVERT: C 456 MET cc_start: 0.8826 (mtp) cc_final: 0.8550 (mtp) REVERT: C 563 GLU cc_start: 0.8340 (pm20) cc_final: 0.7507 (pm20) REVERT: C 598 VAL cc_start: 0.8467 (t) cc_final: 0.8175 (m) REVERT: C 660 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.7791 (pp) REVERT: D 38 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.7350 (tm-30) REVERT: D 130 GLU cc_start: 0.9197 (OUTLIER) cc_final: 0.7602 (pm20) REVERT: D 179 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.7570 (mm-30) REVERT: D 180 ASP cc_start: 0.8610 (t0) cc_final: 0.8306 (t0) REVERT: D 252 LYS cc_start: 0.7144 (ttmt) cc_final: 0.6911 (ttpt) REVERT: D 383 TYR cc_start: 0.8785 (t80) cc_final: 0.8411 (t80) REVERT: D 563 GLU cc_start: 0.8433 (pm20) cc_final: 0.7397 (pm20) REVERT: D 569 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8579 (pp) REVERT: D 598 VAL cc_start: 0.8679 (t) cc_final: 0.8444 (p) REVERT: D 660 LEU cc_start: 0.8454 (OUTLIER) cc_final: 0.7817 (pp) REVERT: E 38 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.7352 (tm-30) REVERT: E 130 GLU cc_start: 0.9184 (OUTLIER) cc_final: 0.7589 (pm20) REVERT: E 180 ASP cc_start: 0.8564 (t0) cc_final: 0.8262 (t0) REVERT: E 252 LYS cc_start: 0.7222 (ttmt) cc_final: 0.6980 (ttpt) REVERT: E 362 ILE cc_start: 0.8531 (OUTLIER) cc_final: 0.8147 (pt) REVERT: E 456 MET cc_start: 0.8650 (mtp) cc_final: 0.8392 (mtp) REVERT: E 563 GLU cc_start: 0.8486 (pm20) cc_final: 0.7424 (pm20) REVERT: E 634 GLU cc_start: 0.7640 (tp30) cc_final: 0.7107 (mt-10) REVERT: E 660 LEU cc_start: 0.8332 (OUTLIER) cc_final: 0.7977 (pp) REVERT: F 38 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.7325 (tm-30) REVERT: F 130 GLU cc_start: 0.9189 (OUTLIER) cc_final: 0.7594 (pm20) REVERT: F 180 ASP cc_start: 0.8520 (t0) cc_final: 0.8184 (t0) REVERT: F 354 ASN cc_start: 0.8132 (OUTLIER) cc_final: 0.7855 (t0) REVERT: F 383 TYR cc_start: 0.8773 (t80) cc_final: 0.8419 (t80) REVERT: F 413 TYR cc_start: 0.9216 (m-80) cc_final: 0.9009 (m-80) REVERT: F 451 ARG cc_start: 0.8331 (mtm-85) cc_final: 0.8115 (mtm-85) REVERT: F 456 MET cc_start: 0.8838 (mtp) cc_final: 0.8598 (mtp) REVERT: F 563 GLU cc_start: 0.8353 (pm20) cc_final: 0.7499 (pm20) REVERT: F 569 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8462 (pp) REVERT: F 598 VAL cc_start: 0.8467 (t) cc_final: 0.8139 (m) REVERT: F 660 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.7758 (pp) REVERT: G 38 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.7346 (tm-30) REVERT: G 130 GLU cc_start: 0.9206 (OUTLIER) cc_final: 0.7594 (pm20) REVERT: G 180 ASP cc_start: 0.8495 (t0) cc_final: 0.8171 (t0) REVERT: G 252 LYS cc_start: 0.7143 (ttmt) cc_final: 0.6843 (tttt) REVERT: G 354 ASN cc_start: 0.8185 (OUTLIER) cc_final: 0.7942 (t0) REVERT: G 383 TYR cc_start: 0.8756 (t80) cc_final: 0.8409 (t80) REVERT: G 563 GLU cc_start: 0.8490 (pm20) cc_final: 0.7460 (pm20) REVERT: G 569 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8457 (pp) REVERT: G 598 VAL cc_start: 0.8494 (t) cc_final: 0.8156 (m) REVERT: G 660 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.8034 (pp) REVERT: H 38 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7375 (tm-30) REVERT: H 128 LYS cc_start: 0.8222 (ttpt) cc_final: 0.7595 (ttmt) REVERT: H 130 GLU cc_start: 0.9196 (OUTLIER) cc_final: 0.7597 (pm20) REVERT: H 180 ASP cc_start: 0.8503 (t0) cc_final: 0.8191 (t0) REVERT: H 252 LYS cc_start: 0.7277 (ttmt) cc_final: 0.7042 (ttpt) REVERT: H 362 ILE cc_start: 0.8472 (OUTLIER) cc_final: 0.8087 (pt) REVERT: H 383 TYR cc_start: 0.8707 (t80) cc_final: 0.8386 (t80) REVERT: H 413 TYR cc_start: 0.9191 (m-80) cc_final: 0.8985 (m-80) REVERT: H 563 GLU cc_start: 0.8503 (pm20) cc_final: 0.7462 (pm20) REVERT: H 598 VAL cc_start: 0.8664 (t) cc_final: 0.8432 (p) REVERT: H 660 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.7980 (pp) outliers start: 185 outliers final: 128 residues processed: 710 average time/residue: 0.2832 time to fit residues: 316.8910 Evaluate side-chains 727 residues out of total 4480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 164 poor density : 563 time to evaluate : 1.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 38 GLU Chi-restraints excluded: chain A residue 41 GLU 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 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 415 THR 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 38 GLU Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 99 MET 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 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 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 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 38 GLU Chi-restraints excluded: chain C residue 83 ILE 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 389 ASP Chi-restraints excluded: chain C residue 477 VAL 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 32 LEU Chi-restraints excluded: chain D residue 38 GLU Chi-restraints excluded: chain D residue 83 ILE 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 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 654 THR Chi-restraints excluded: chain D residue 660 LEU Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 38 GLU 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 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 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 654 THR Chi-restraints excluded: chain E residue 660 LEU Chi-restraints excluded: chain F residue 32 LEU Chi-restraints excluded: chain F residue 38 GLU 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 418 HIS Chi-restraints excluded: chain F residue 441 ASP 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 534 THR Chi-restraints excluded: chain F residue 544 ILE 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 38 GLU 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 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 367 GLU 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 565 THR Chi-restraints excluded: chain G residue 569 LEU Chi-restraints excluded: chain G residue 654 THR Chi-restraints excluded: chain G residue 660 LEU Chi-restraints excluded: chain H residue 38 GLU Chi-restraints excluded: chain H residue 54 ILE 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 240 VAL Chi-restraints excluded: chain H residue 264 ILE 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 495 MET Chi-restraints excluded: chain H residue 544 ILE 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: 6.9990 chunk 230 optimal weight: 7.9990 chunk 420 optimal weight: 7.9990 chunk 306 optimal weight: 6.9990 chunk 49 optimal weight: 5.9990 chunk 274 optimal weight: 5.9990 chunk 16 optimal weight: 6.9990 chunk 434 optimal weight: 9.9990 chunk 343 optimal weight: 4.9990 chunk 212 optimal weight: 8.9990 chunk 321 optimal weight: 5.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 ** A 616 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** ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 515 HIS ** 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** ** 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** ** 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 529 ASN ** H 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.143451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.117472 restraints weight = 48294.727| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 1.67 r_work: 0.2911 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2770 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.4145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 43184 Z= 0.271 Angle : 0.724 10.162 58672 Z= 0.377 Chirality : 0.051 0.243 6120 Planarity : 0.006 0.054 7672 Dihedral : 5.453 27.380 5824 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 4.00 % Allowed : 16.07 % Favored : 79.93 % 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: -0.50 (0.12), residues: 5280 helix: 0.56 (0.15), residues: 1288 sheet: -1.26 (0.18), residues: 760 loop : -0.41 (0.11), residues: 3232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG G 201 TYR 0.021 0.002 TYR H 50 PHE 0.029 0.003 PHE G 325 TRP 0.019 0.002 TRP B 566 HIS 0.010 0.002 HIS D 418 Details of bonding type rmsd/Z covalent geometry : bond 0.00660 / 0.27 (43184) covalent geometry : angle 0.72420 / 0.38 (58672) hydrogen bonds : bond 0.04486 / 2.95 ( 1200) hydrogen bonds : angle 5.43309 / 3.82 ( 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 747 residues out of total 4480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 179 poor density : 568 time to evaluate : 1.543 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.7334 (tm-30) REVERT: A 130 GLU cc_start: 0.9234 (OUTLIER) cc_final: 0.7687 (pm20) REVERT: A 180 ASP cc_start: 0.8606 (t0) cc_final: 0.8281 (t0) REVERT: A 252 LYS cc_start: 0.7204 (ttmt) cc_final: 0.6957 (ttpt) REVERT: A 383 TYR cc_start: 0.8794 (t80) cc_final: 0.8426 (t80) REVERT: A 456 MET cc_start: 0.8737 (mtp) cc_final: 0.8453 (mtp) REVERT: A 563 GLU cc_start: 0.8533 (pm20) cc_final: 0.7503 (pm20) REVERT: A 598 VAL cc_start: 0.8826 (t) cc_final: 0.8626 (p) REVERT: A 660 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.7801 (pp) REVERT: B 38 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.7395 (tm-30) REVERT: B 130 GLU cc_start: 0.9238 (OUTLIER) cc_final: 0.7691 (pm20) REVERT: B 180 ASP cc_start: 0.8573 (t0) cc_final: 0.8299 (t0) REVERT: B 383 TYR cc_start: 0.8739 (t80) cc_final: 0.8536 (t80) REVERT: B 563 GLU cc_start: 0.8246 (pm20) cc_final: 0.7250 (pm20) REVERT: B 569 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8460 (pp) REVERT: B 598 VAL cc_start: 0.8784 (t) cc_final: 0.8572 (p) REVERT: B 634 GLU cc_start: 0.7665 (tp30) cc_final: 0.7123 (mt-10) REVERT: B 660 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.7795 (pp) REVERT: C 38 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7345 (tm-30) REVERT: C 130 GLU cc_start: 0.9223 (OUTLIER) cc_final: 0.7626 (pm20) REVERT: C 180 ASP cc_start: 0.8631 (t0) cc_final: 0.8303 (t0) REVERT: C 354 ASN cc_start: 0.8303 (OUTLIER) cc_final: 0.8066 (t0) REVERT: C 383 TYR cc_start: 0.8754 (t80) cc_final: 0.8397 (t80) REVERT: C 451 ARG cc_start: 0.8430 (mtm-85) cc_final: 0.8117 (mtm-85) REVERT: C 456 MET cc_start: 0.8795 (mtp) cc_final: 0.8508 (mtp) REVERT: C 569 LEU cc_start: 0.8962 (OUTLIER) cc_final: 0.8478 (pp) REVERT: C 598 VAL cc_start: 0.8509 (t) cc_final: 0.8238 (m) REVERT: C 660 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.7874 (pp) REVERT: D 38 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7369 (tm-30) REVERT: D 130 GLU cc_start: 0.9205 (OUTLIER) cc_final: 0.7609 (pm20) REVERT: D 179 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.7667 (mm-30) REVERT: D 180 ASP cc_start: 0.8565 (t0) cc_final: 0.8304 (t0) REVERT: D 252 LYS cc_start: 0.7150 (ttmt) cc_final: 0.6819 (tttt) REVERT: D 383 TYR cc_start: 0.8753 (t80) cc_final: 0.8380 (t80) REVERT: D 563 GLU cc_start: 0.8413 (pm20) cc_final: 0.7411 (pm20) REVERT: D 569 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8433 (pp) REVERT: D 598 VAL cc_start: 0.8681 (t) cc_final: 0.8439 (p) REVERT: D 660 LEU cc_start: 0.8551 (OUTLIER) cc_final: 0.7891 (pp) REVERT: E 38 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7365 (tm-30) REVERT: E 130 GLU cc_start: 0.9233 (OUTLIER) cc_final: 0.7629 (pm20) REVERT: E 180 ASP cc_start: 0.8555 (t0) cc_final: 0.8217 (t0) REVERT: E 252 LYS cc_start: 0.7295 (ttmt) cc_final: 0.7075 (ttpt) REVERT: E 383 TYR cc_start: 0.8721 (t80) cc_final: 0.8333 (t80) REVERT: E 456 MET cc_start: 0.8662 (mtp) cc_final: 0.8398 (mtp) REVERT: E 563 GLU cc_start: 0.8542 (pm20) cc_final: 0.7475 (pm20) REVERT: E 634 GLU cc_start: 0.7671 (tp30) cc_final: 0.7117 (mt-10) REVERT: E 660 LEU cc_start: 0.8398 (OUTLIER) cc_final: 0.8040 (pp) REVERT: F 38 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.7367 (tm-30) REVERT: F 130 GLU cc_start: 0.9217 (OUTLIER) cc_final: 0.7635 (pm20) REVERT: F 180 ASP cc_start: 0.8571 (t0) cc_final: 0.8263 (t0) REVERT: F 252 LYS cc_start: 0.7156 (ttmt) cc_final: 0.6830 (tttt) REVERT: F 354 ASN cc_start: 0.8243 (OUTLIER) cc_final: 0.7954 (t0) REVERT: F 383 TYR cc_start: 0.8752 (t80) cc_final: 0.8400 (t80) REVERT: F 451 ARG cc_start: 0.8348 (mtm-85) cc_final: 0.8116 (mtm-85) REVERT: F 456 MET cc_start: 0.8794 (mtp) cc_final: 0.8554 (mtp) REVERT: F 569 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8600 (pp) REVERT: F 598 VAL cc_start: 0.8507 (t) cc_final: 0.8207 (m) REVERT: F 660 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.7862 (pp) REVERT: G 38 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7363 (tm-30) REVERT: G 130 GLU cc_start: 0.9230 (OUTLIER) cc_final: 0.7639 (pm20) REVERT: G 180 ASP cc_start: 0.8527 (t0) cc_final: 0.8252 (t0) REVERT: G 252 LYS cc_start: 0.7180 (ttmt) cc_final: 0.6864 (tttt) REVERT: G 354 ASN cc_start: 0.8184 (OUTLIER) cc_final: 0.7902 (t0) REVERT: G 383 TYR cc_start: 0.8744 (t80) cc_final: 0.8402 (t80) REVERT: G 563 GLU cc_start: 0.8530 (pm20) cc_final: 0.7477 (pm20) REVERT: G 569 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8488 (pp) REVERT: G 598 VAL cc_start: 0.8545 (t) cc_final: 0.8274 (m) REVERT: G 660 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.8100 (pp) REVERT: H 38 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7374 (tm-30) REVERT: H 128 LYS cc_start: 0.8217 (ttpt) cc_final: 0.7575 (ttmt) REVERT: H 130 GLU cc_start: 0.9213 (OUTLIER) cc_final: 0.7684 (pm20) REVERT: H 180 ASP cc_start: 0.8539 (t0) cc_final: 0.8267 (t0) REVERT: H 252 LYS cc_start: 0.7336 (ttmt) cc_final: 0.7039 (tttt) REVERT: H 383 TYR cc_start: 0.8740 (t80) cc_final: 0.8389 (t80) REVERT: H 563 GLU cc_start: 0.8482 (pm20) cc_final: 0.7450 (pm20) REVERT: H 598 VAL cc_start: 0.8650 (t) cc_final: 0.8420 (p) REVERT: H 660 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.8070 (pp) outliers start: 179 outliers final: 127 residues processed: 692 average time/residue: 0.2817 time to fit residues: 307.5709 Evaluate side-chains 710 residues out of total 4480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 160 poor density : 550 time to evaluate : 1.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 38 GLU 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 191 LEU Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 264 ILE 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 654 THR Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 38 GLU Chi-restraints excluded: chain B residue 83 ILE Chi-restraints excluded: chain B residue 99 MET 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 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 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 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 38 GLU Chi-restraints excluded: chain C residue 83 ILE 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 288 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 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 32 LEU Chi-restraints excluded: chain D residue 38 GLU Chi-restraints excluded: chain D residue 83 ILE 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 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 660 LEU Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 38 GLU 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 277 LEU Chi-restraints excluded: chain E residue 327 ASP 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 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 38 GLU 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 288 LEU Chi-restraints excluded: chain F residue 327 ASP Chi-restraints excluded: chain F residue 354 ASN Chi-restraints excluded: chain F residue 441 ASP 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 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 38 GLU 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 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 367 GLU 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 565 THR Chi-restraints excluded: chain G residue 569 LEU Chi-restraints excluded: chain G residue 654 THR Chi-restraints excluded: chain G residue 660 LEU Chi-restraints excluded: chain H residue 38 GLU Chi-restraints excluded: chain H residue 54 ILE 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 191 LEU Chi-restraints excluded: chain H residue 264 ILE 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 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 660 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 184 optimal weight: 5.9990 chunk 63 optimal weight: 0.3980 chunk 47 optimal weight: 7.9990 chunk 220 optimal weight: 6.9990 chunk 221 optimal weight: 10.0000 chunk 385 optimal weight: 3.9990 chunk 267 optimal weight: 6.9990 chunk 218 optimal weight: 2.9990 chunk 189 optimal weight: 8.9990 chunk 333 optimal weight: 5.9990 chunk 214 optimal weight: 4.9990 overall best weight: 3.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 ** 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** ** B 515 HIS ** 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 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 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 ** 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 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** ** 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 529 ASN ** H 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.134237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.107907 restraints weight = 49710.782| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 1.66 r_work: 0.2940 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2799 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.4204 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= 0.189 Angle : 0.671 9.333 58672 Z= 0.349 Chirality : 0.048 0.225 6120 Planarity : 0.006 0.054 7672 Dihedral : 5.272 26.830 5824 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 3.88 % Allowed : 16.03 % Favored : 80.09 % 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: -0.42 (0.12), residues: 5280 helix: 0.67 (0.15), residues: 1296 sheet: -1.26 (0.18), residues: 760 loop : -0.36 (0.11), residues: 3224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 196 TYR 0.025 0.002 TYR G 132 PHE 0.021 0.002 PHE G 325 TRP 0.019 0.001 TRP B 566 HIS 0.007 0.001 HIS D 418 Details of bonding type rmsd/Z covalent geometry : bond 0.00457 / 0.19 (43184) covalent geometry : angle 0.67085 / 0.35 (58672) hydrogen bonds : bond 0.03936 / 2.58 ( 1200) hydrogen bonds : angle 5.29880 / 3.73 ( 3600) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10553.89 seconds wall clock time: 182 minutes 9.66 seconds (10929.66 seconds total)