Starting phenix.real_space_refine on Tue Aug 26 05:17:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5ftk_3296/08_2025/5ftk_3296.cif Found real_map, /net/cci-nas-00/data/ceres_data/5ftk_3296/08_2025/5ftk_3296.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/5ftk_3296/08_2025/5ftk_3296.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5ftk_3296/08_2025/5ftk_3296.map" model { file = "/net/cci-nas-00/data/ceres_data/5ftk_3296/08_2025/5ftk_3296.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5ftk_3296/08_2025/5ftk_3296.cif" } resolution = 2.4 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= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 24 5.49 5 S 180 5.16 5 C 21486 2.51 5 N 6036 2.21 5 O 6648 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 34374 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 723, 5659 Classifications: {'peptide': 723} Link IDs: {'CIS': 2, 'PCIS': 3, 'PTRANS': 36, 'TRANS': 681} Chain breaks: 1 Chain: "A" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "B" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "C" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "D" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "E" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "F" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Restraints were copied for chains: B, C, D, E, F Time building chain proxies: 6.40, per 1000 atoms: 0.19 Number of scatterers: 34374 At special positions: 0 Unit cell: (167.531, 176.449, 97.461, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 180 16.00 P 24 15.00 O 6648 8.00 N 6036 7.00 C 21486 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: 3.02 Conformation dependent library (CDL) restraints added in 1.3 seconds Enol-peptide restraints added in 238.4 nanoseconds 8628 Ramachandran restraints generated. 4314 Oldfield, 0 Emsley, 4314 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8100 Finding SS restraints... Secondary structure from input PDB file: 186 helices and 30 sheets defined 46.7% alpha, 11.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.00 Creating SS restraints... Processing helix chain 'A' and resid 85 through 93 removed outlier: 3.843A pdb=" N ASN A 91 " --> pdb=" O VAL A 87 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU A 92 " --> pdb=" O VAL A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 135 removed outlier: 3.512A pdb=" N LEU A 135 " --> pdb=" O PHE A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 140 Processing helix chain 'A' and resid 202 through 206 Processing helix chain 'A' and resid 211 through 226 removed outlier: 3.668A pdb=" N GLN A 215 " --> pdb=" O LYS A 211 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N LEU A 222 " --> pdb=" O GLU A 218 " (cutoff:3.500A) Proline residue: A 223 - end of helix Processing helix chain 'A' and resid 226 through 233 removed outlier: 3.975A pdb=" N PHE A 230 " --> pdb=" O HIS A 226 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LYS A 231 " --> pdb=" O PRO A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 263 Processing helix chain 'A' and resid 270 through 277 removed outlier: 3.677A pdb=" N LYS A 277 " --> pdb=" O GLU A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 294 removed outlier: 3.614A pdb=" N ASN A 285 " --> pdb=" O GLU A 281 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N PHE A 290 " --> pdb=" O LEU A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 310 removed outlier: 3.908A pdb=" N ILE A 309 " --> pdb=" O GLU A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 333 removed outlier: 4.035A pdb=" N ARG A 322 " --> pdb=" O GLY A 318 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLN A 327 " --> pdb=" O ARG A 323 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU A 328 " --> pdb=" O ILE A 324 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N THR A 330 " --> pdb=" O SER A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 354 through 359 Processing helix chain 'A' and resid 373 through 385 removed outlier: 4.175A pdb=" N GLU A 379 " --> pdb=" O THR A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 403 Processing helix chain 'A' and resid 407 through 426 Processing helix chain 'A' and resid 438 through 445 removed outlier: 4.219A pdb=" N MET A 442 " --> pdb=" O ASP A 438 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASN A 443 " --> pdb=" O ALA A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 457 removed outlier: 3.576A pdb=" N PHE A 452 " --> pdb=" O THR A 448 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TRP A 454 " --> pdb=" O ASP A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 479 Processing helix chain 'A' and resid 482 through 506 Proline residue: A 496 - end of helix Proline residue: A 500 - end of helix removed outlier: 3.604A pdb=" N PHE A 503 " --> pdb=" O HIS A 499 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N PHE A 506 " --> pdb=" O LYS A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 536 Processing helix chain 'A' and resid 543 through 553 Processing helix chain 'A' and resid 557 through 569 removed outlier: 3.830A pdb=" N GLU A 561 " --> pdb=" O ALA A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 586 Processing helix chain 'A' and resid 598 through 610 Processing helix chain 'A' and resid 630 through 634 Processing helix chain 'A' and resid 649 through 662 removed outlier: 3.774A pdb=" N ALA A 655 " --> pdb=" O LYS A 651 " (cutoff:3.500A) Processing helix chain 'A' and resid 674 through 679 removed outlier: 4.105A pdb=" N THR A 679 " --> pdb=" O LEU A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 705 removed outlier: 3.589A pdb=" N GLU A 704 " --> pdb=" O ARG A 700 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 741 removed outlier: 3.731A pdb=" N PHE A 736 " --> pdb=" O ARG A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 748 through 763 removed outlier: 3.797A pdb=" N ILE A 752 " --> pdb=" O SER A 748 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ARG A 753 " --> pdb=" O ASP A 749 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLN A 760 " --> pdb=" O GLU A 756 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLN A 763 " --> pdb=" O ALA A 759 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 93 removed outlier: 3.843A pdb=" N ASN B 91 " --> pdb=" O VAL B 87 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LEU B 92 " --> pdb=" O VAL B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 135 removed outlier: 3.512A pdb=" N LEU B 135 " --> pdb=" O PHE B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 140 Processing helix chain 'B' and resid 202 through 206 Processing helix chain 'B' and resid 211 through 226 removed outlier: 3.668A pdb=" N GLN B 215 " --> pdb=" O LYS B 211 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N LEU B 222 " --> pdb=" O GLU B 218 " (cutoff:3.500A) Proline residue: B 223 - end of helix Processing helix chain 'B' and resid 226 through 233 removed outlier: 3.975A pdb=" N PHE B 230 " --> pdb=" O HIS B 226 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LYS B 231 " --> pdb=" O PRO B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 263 Processing helix chain 'B' and resid 270 through 277 removed outlier: 3.676A pdb=" N LYS B 277 " --> pdb=" O GLU B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 294 removed outlier: 3.614A pdb=" N ASN B 285 " --> pdb=" O GLU B 281 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N PHE B 290 " --> pdb=" O LEU B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 310 removed outlier: 3.907A pdb=" N ILE B 309 " --> pdb=" O GLU B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 333 removed outlier: 4.035A pdb=" N ARG B 322 " --> pdb=" O GLY B 318 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLN B 327 " --> pdb=" O ARG B 323 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU B 328 " --> pdb=" O ILE B 324 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N THR B 330 " --> pdb=" O SER B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 354 through 359 Processing helix chain 'B' and resid 373 through 385 removed outlier: 4.174A pdb=" N GLU B 379 " --> pdb=" O THR B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 403 Processing helix chain 'B' and resid 407 through 426 Processing helix chain 'B' and resid 438 through 445 removed outlier: 4.219A pdb=" N MET B 442 " --> pdb=" O ASP B 438 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASN B 443 " --> pdb=" O ALA B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 457 removed outlier: 3.576A pdb=" N PHE B 452 " --> pdb=" O THR B 448 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TRP B 454 " --> pdb=" O ASP B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 479 Processing helix chain 'B' and resid 482 through 506 Proline residue: B 496 - end of helix Proline residue: B 500 - end of helix removed outlier: 3.604A pdb=" N PHE B 503 " --> pdb=" O HIS B 499 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N PHE B 506 " --> pdb=" O LYS B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 536 Processing helix chain 'B' and resid 543 through 553 Processing helix chain 'B' and resid 557 through 569 removed outlier: 3.831A pdb=" N GLU B 561 " --> pdb=" O ALA B 557 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 586 Processing helix chain 'B' and resid 598 through 610 Processing helix chain 'B' and resid 630 through 634 Processing helix chain 'B' and resid 649 through 662 removed outlier: 3.773A pdb=" N ALA B 655 " --> pdb=" O LYS B 651 " (cutoff:3.500A) Processing helix chain 'B' and resid 674 through 679 removed outlier: 4.105A pdb=" N THR B 679 " --> pdb=" O LEU B 675 " (cutoff:3.500A) Processing helix chain 'B' and resid 683 through 705 removed outlier: 3.589A pdb=" N GLU B 704 " --> pdb=" O ARG B 700 " (cutoff:3.500A) Processing helix chain 'B' and resid 732 through 741 removed outlier: 3.731A pdb=" N PHE B 736 " --> pdb=" O ARG B 732 " (cutoff:3.500A) Processing helix chain 'B' and resid 748 through 763 removed outlier: 3.798A pdb=" N ILE B 752 " --> pdb=" O SER B 748 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARG B 753 " --> pdb=" O ASP B 749 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLN B 760 " --> pdb=" O GLU B 756 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLN B 763 " --> pdb=" O ALA B 759 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 93 removed outlier: 3.843A pdb=" N ASN C 91 " --> pdb=" O VAL C 87 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU C 92 " --> pdb=" O VAL C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 135 removed outlier: 3.511A pdb=" N LEU C 135 " --> pdb=" O PHE C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 140 Processing helix chain 'C' and resid 202 through 206 Processing helix chain 'C' and resid 211 through 226 removed outlier: 3.668A pdb=" N GLN C 215 " --> pdb=" O LYS C 211 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N LEU C 222 " --> pdb=" O GLU C 218 " (cutoff:3.500A) Proline residue: C 223 - end of helix Processing helix chain 'C' and resid 226 through 233 removed outlier: 3.974A pdb=" N PHE C 230 " --> pdb=" O HIS C 226 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LYS C 231 " --> pdb=" O PRO C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 263 Processing helix chain 'C' and resid 270 through 277 removed outlier: 3.676A pdb=" N LYS C 277 " --> pdb=" O GLU C 273 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 294 removed outlier: 3.614A pdb=" N ASN C 285 " --> pdb=" O GLU C 281 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N PHE C 290 " --> pdb=" O LEU C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 310 removed outlier: 3.907A pdb=" N ILE C 309 " --> pdb=" O GLU C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 333 removed outlier: 4.035A pdb=" N ARG C 322 " --> pdb=" O GLY C 318 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLN C 327 " --> pdb=" O ARG C 323 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU C 328 " --> pdb=" O ILE C 324 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N THR C 330 " --> pdb=" O SER C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 Processing helix chain 'C' and resid 354 through 359 Processing helix chain 'C' and resid 373 through 385 removed outlier: 4.175A pdb=" N GLU C 379 " --> pdb=" O THR C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 403 Processing helix chain 'C' and resid 407 through 426 Processing helix chain 'C' and resid 438 through 445 removed outlier: 4.219A pdb=" N MET C 442 " --> pdb=" O ASP C 438 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASN C 443 " --> pdb=" O ALA C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 457 removed outlier: 3.576A pdb=" N PHE C 452 " --> pdb=" O THR C 448 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N TRP C 454 " --> pdb=" O ASP C 450 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 479 Processing helix chain 'C' and resid 482 through 506 Proline residue: C 496 - end of helix Proline residue: C 500 - end of helix removed outlier: 3.604A pdb=" N PHE C 503 " --> pdb=" O HIS C 499 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N PHE C 506 " --> pdb=" O LYS C 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 523 through 536 Processing helix chain 'C' and resid 543 through 553 Processing helix chain 'C' and resid 557 through 569 removed outlier: 3.830A pdb=" N GLU C 561 " --> pdb=" O ALA C 557 " (cutoff:3.500A) Processing helix chain 'C' and resid 580 through 586 Processing helix chain 'C' and resid 598 through 610 Processing helix chain 'C' and resid 630 through 634 Processing helix chain 'C' and resid 649 through 662 removed outlier: 3.774A pdb=" N ALA C 655 " --> pdb=" O LYS C 651 " (cutoff:3.500A) Processing helix chain 'C' and resid 674 through 679 removed outlier: 4.105A pdb=" N THR C 679 " --> pdb=" O LEU C 675 " (cutoff:3.500A) Processing helix chain 'C' and resid 683 through 705 removed outlier: 3.589A pdb=" N GLU C 704 " --> pdb=" O ARG C 700 " (cutoff:3.500A) Processing helix chain 'C' and resid 732 through 741 removed outlier: 3.731A pdb=" N PHE C 736 " --> pdb=" O ARG C 732 " (cutoff:3.500A) Processing helix chain 'C' and resid 748 through 763 removed outlier: 3.797A pdb=" N ILE C 752 " --> pdb=" O SER C 748 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ARG C 753 " --> pdb=" O ASP C 749 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLN C 760 " --> pdb=" O GLU C 756 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLN C 763 " --> pdb=" O ALA C 759 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 93 removed outlier: 3.843A pdb=" N ASN D 91 " --> pdb=" O VAL D 87 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU D 92 " --> pdb=" O VAL D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 135 removed outlier: 3.511A pdb=" N LEU D 135 " --> pdb=" O PHE D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 140 Processing helix chain 'D' and resid 202 through 206 Processing helix chain 'D' and resid 211 through 226 removed outlier: 3.668A pdb=" N GLN D 215 " --> pdb=" O LYS D 211 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N LEU D 222 " --> pdb=" O GLU D 218 " (cutoff:3.500A) Proline residue: D 223 - end of helix Processing helix chain 'D' and resid 226 through 233 removed outlier: 3.975A pdb=" N PHE D 230 " --> pdb=" O HIS D 226 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LYS D 231 " --> pdb=" O PRO D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 263 Processing helix chain 'D' and resid 270 through 277 removed outlier: 3.677A pdb=" N LYS D 277 " --> pdb=" O GLU D 273 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 294 removed outlier: 3.614A pdb=" N ASN D 285 " --> pdb=" O GLU D 281 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N PHE D 290 " --> pdb=" O LEU D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 310 removed outlier: 3.908A pdb=" N ILE D 309 " --> pdb=" O GLU D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 333 removed outlier: 4.035A pdb=" N ARG D 322 " --> pdb=" O GLY D 318 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLN D 327 " --> pdb=" O ARG D 323 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU D 328 " --> pdb=" O ILE D 324 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N THR D 330 " --> pdb=" O SER D 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 349 through 353 Processing helix chain 'D' and resid 354 through 359 Processing helix chain 'D' and resid 373 through 385 removed outlier: 4.174A pdb=" N GLU D 379 " --> pdb=" O THR D 375 " (cutoff:3.500A) Processing helix chain 'D' and resid 398 through 403 Processing helix chain 'D' and resid 407 through 426 Processing helix chain 'D' and resid 438 through 445 removed outlier: 4.219A pdb=" N MET D 442 " --> pdb=" O ASP D 438 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASN D 443 " --> pdb=" O ALA D 439 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 457 removed outlier: 3.575A pdb=" N PHE D 452 " --> pdb=" O THR D 448 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TRP D 454 " --> pdb=" O ASP D 450 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 479 Processing helix chain 'D' and resid 482 through 506 Proline residue: D 496 - end of helix Proline residue: D 500 - end of helix removed outlier: 3.604A pdb=" N PHE D 503 " --> pdb=" O HIS D 499 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N PHE D 506 " --> pdb=" O LYS D 502 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 536 Processing helix chain 'D' and resid 543 through 553 Processing helix chain 'D' and resid 557 through 569 removed outlier: 3.830A pdb=" N GLU D 561 " --> pdb=" O ALA D 557 " (cutoff:3.500A) Processing helix chain 'D' and resid 580 through 586 Processing helix chain 'D' and resid 598 through 610 Processing helix chain 'D' and resid 630 through 634 Processing helix chain 'D' and resid 649 through 662 removed outlier: 3.773A pdb=" N ALA D 655 " --> pdb=" O LYS D 651 " (cutoff:3.500A) Processing helix chain 'D' and resid 674 through 679 removed outlier: 4.104A pdb=" N THR D 679 " --> pdb=" O LEU D 675 " (cutoff:3.500A) Processing helix chain 'D' and resid 683 through 705 removed outlier: 3.590A pdb=" N GLU D 704 " --> pdb=" O ARG D 700 " (cutoff:3.500A) Processing helix chain 'D' and resid 732 through 741 removed outlier: 3.731A pdb=" N PHE D 736 " --> pdb=" O ARG D 732 " (cutoff:3.500A) Processing helix chain 'D' and resid 748 through 763 removed outlier: 3.797A pdb=" N ILE D 752 " --> pdb=" O SER D 748 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ARG D 753 " --> pdb=" O ASP D 749 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLN D 760 " --> pdb=" O GLU D 756 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLN D 763 " --> pdb=" O ALA D 759 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 93 removed outlier: 3.843A pdb=" N ASN E 91 " --> pdb=" O VAL E 87 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU E 92 " --> pdb=" O VAL E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 130 through 135 removed outlier: 3.512A pdb=" N LEU E 135 " --> pdb=" O PHE E 131 " (cutoff:3.500A) Processing helix chain 'E' and resid 135 through 140 Processing helix chain 'E' and resid 202 through 206 Processing helix chain 'E' and resid 211 through 226 removed outlier: 3.669A pdb=" N GLN E 215 " --> pdb=" O LYS E 211 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N LEU E 222 " --> pdb=" O GLU E 218 " (cutoff:3.500A) Proline residue: E 223 - end of helix Processing helix chain 'E' and resid 226 through 233 removed outlier: 3.975A pdb=" N PHE E 230 " --> pdb=" O HIS E 226 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYS E 231 " --> pdb=" O PRO E 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 263 Processing helix chain 'E' and resid 270 through 277 removed outlier: 3.677A pdb=" N LYS E 277 " --> pdb=" O GLU E 273 " (cutoff:3.500A) Processing helix chain 'E' and resid 281 through 294 removed outlier: 3.615A pdb=" N ASN E 285 " --> pdb=" O GLU E 281 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N PHE E 290 " --> pdb=" O LEU E 286 " (cutoff:3.500A) Processing helix chain 'E' and resid 305 through 310 removed outlier: 3.907A pdb=" N ILE E 309 " --> pdb=" O GLU E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 318 through 333 removed outlier: 4.035A pdb=" N ARG E 322 " --> pdb=" O GLY E 318 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLN E 327 " --> pdb=" O ARG E 323 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU E 328 " --> pdb=" O ILE E 324 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N THR E 330 " --> pdb=" O SER E 326 " (cutoff:3.500A) Processing helix chain 'E' and resid 349 through 353 Processing helix chain 'E' and resid 354 through 359 Processing helix chain 'E' and resid 373 through 385 removed outlier: 4.174A pdb=" N GLU E 379 " --> pdb=" O THR E 375 " (cutoff:3.500A) Processing helix chain 'E' and resid 398 through 403 Processing helix chain 'E' and resid 407 through 426 Processing helix chain 'E' and resid 438 through 445 removed outlier: 4.219A pdb=" N MET E 442 " --> pdb=" O ASP E 438 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASN E 443 " --> pdb=" O ALA E 439 " (cutoff:3.500A) Processing helix chain 'E' and resid 448 through 457 removed outlier: 3.576A pdb=" N PHE E 452 " --> pdb=" O THR E 448 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N TRP E 454 " --> pdb=" O ASP E 450 " (cutoff:3.500A) Processing helix chain 'E' and resid 475 through 479 Processing helix chain 'E' and resid 482 through 506 Proline residue: E 496 - end of helix Proline residue: E 500 - end of helix removed outlier: 3.603A pdb=" N PHE E 503 " --> pdb=" O HIS E 499 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N PHE E 506 " --> pdb=" O LYS E 502 " (cutoff:3.500A) Processing helix chain 'E' and resid 523 through 536 Processing helix chain 'E' and resid 543 through 553 Processing helix chain 'E' and resid 557 through 569 removed outlier: 3.831A pdb=" N GLU E 561 " --> pdb=" O ALA E 557 " (cutoff:3.500A) Processing helix chain 'E' and resid 580 through 586 Processing helix chain 'E' and resid 598 through 610 Processing helix chain 'E' and resid 630 through 634 Processing helix chain 'E' and resid 649 through 662 removed outlier: 3.773A pdb=" N ALA E 655 " --> pdb=" O LYS E 651 " (cutoff:3.500A) Processing helix chain 'E' and resid 674 through 679 removed outlier: 4.105A pdb=" N THR E 679 " --> pdb=" O LEU E 675 " (cutoff:3.500A) Processing helix chain 'E' and resid 683 through 705 removed outlier: 3.590A pdb=" N GLU E 704 " --> pdb=" O ARG E 700 " (cutoff:3.500A) Processing helix chain 'E' and resid 732 through 741 removed outlier: 3.731A pdb=" N PHE E 736 " --> pdb=" O ARG E 732 " (cutoff:3.500A) Processing helix chain 'E' and resid 748 through 763 removed outlier: 3.797A pdb=" N ILE E 752 " --> pdb=" O SER E 748 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ARG E 753 " --> pdb=" O ASP E 749 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLN E 760 " --> pdb=" O GLU E 756 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLN E 763 " --> pdb=" O ALA E 759 " (cutoff:3.500A) Processing helix chain 'F' and resid 85 through 93 removed outlier: 3.843A pdb=" N ASN F 91 " --> pdb=" O VAL F 87 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU F 92 " --> pdb=" O VAL F 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 130 through 135 removed outlier: 3.511A pdb=" N LEU F 135 " --> pdb=" O PHE F 131 " (cutoff:3.500A) Processing helix chain 'F' and resid 135 through 140 Processing helix chain 'F' and resid 202 through 206 Processing helix chain 'F' and resid 211 through 226 removed outlier: 3.669A pdb=" N GLN F 215 " --> pdb=" O LYS F 211 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N LEU F 222 " --> pdb=" O GLU F 218 " (cutoff:3.500A) Proline residue: F 223 - end of helix Processing helix chain 'F' and resid 226 through 233 removed outlier: 3.974A pdb=" N PHE F 230 " --> pdb=" O HIS F 226 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LYS F 231 " --> pdb=" O PRO F 227 " (cutoff:3.500A) Processing helix chain 'F' and resid 250 through 263 Processing helix chain 'F' and resid 270 through 277 removed outlier: 3.677A pdb=" N LYS F 277 " --> pdb=" O GLU F 273 " (cutoff:3.500A) Processing helix chain 'F' and resid 281 through 294 removed outlier: 3.615A pdb=" N ASN F 285 " --> pdb=" O GLU F 281 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N PHE F 290 " --> pdb=" O LEU F 286 " (cutoff:3.500A) Processing helix chain 'F' and resid 305 through 310 removed outlier: 3.907A pdb=" N ILE F 309 " --> pdb=" O GLU F 305 " (cutoff:3.500A) Processing helix chain 'F' and resid 318 through 333 removed outlier: 4.036A pdb=" N ARG F 322 " --> pdb=" O GLY F 318 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLN F 327 " --> pdb=" O ARG F 323 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU F 328 " --> pdb=" O ILE F 324 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N THR F 330 " --> pdb=" O SER F 326 " (cutoff:3.500A) Processing helix chain 'F' and resid 349 through 353 Processing helix chain 'F' and resid 354 through 359 Processing helix chain 'F' and resid 373 through 385 removed outlier: 4.175A pdb=" N GLU F 379 " --> pdb=" O THR F 375 " (cutoff:3.500A) Processing helix chain 'F' and resid 398 through 403 Processing helix chain 'F' and resid 407 through 426 Processing helix chain 'F' and resid 438 through 445 removed outlier: 4.218A pdb=" N MET F 442 " --> pdb=" O ASP F 438 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASN F 443 " --> pdb=" O ALA F 439 " (cutoff:3.500A) Processing helix chain 'F' and resid 448 through 457 removed outlier: 3.576A pdb=" N PHE F 452 " --> pdb=" O THR F 448 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N TRP F 454 " --> pdb=" O ASP F 450 " (cutoff:3.500A) Processing helix chain 'F' and resid 475 through 479 Processing helix chain 'F' and resid 482 through 506 Proline residue: F 496 - end of helix Proline residue: F 500 - end of helix removed outlier: 3.604A pdb=" N PHE F 503 " --> pdb=" O HIS F 499 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N PHE F 506 " --> pdb=" O LYS F 502 " (cutoff:3.500A) Processing helix chain 'F' and resid 523 through 536 Processing helix chain 'F' and resid 543 through 553 Processing helix chain 'F' and resid 557 through 569 removed outlier: 3.831A pdb=" N GLU F 561 " --> pdb=" O ALA F 557 " (cutoff:3.500A) Processing helix chain 'F' and resid 580 through 586 Processing helix chain 'F' and resid 598 through 610 Processing helix chain 'F' and resid 630 through 634 Processing helix chain 'F' and resid 649 through 662 removed outlier: 3.773A pdb=" N ALA F 655 " --> pdb=" O LYS F 651 " (cutoff:3.500A) Processing helix chain 'F' and resid 674 through 679 removed outlier: 4.105A pdb=" N THR F 679 " --> pdb=" O LEU F 675 " (cutoff:3.500A) Processing helix chain 'F' and resid 683 through 705 removed outlier: 3.589A pdb=" N GLU F 704 " --> pdb=" O ARG F 700 " (cutoff:3.500A) Processing helix chain 'F' and resid 732 through 741 removed outlier: 3.731A pdb=" N PHE F 736 " --> pdb=" O ARG F 732 " (cutoff:3.500A) Processing helix chain 'F' and resid 748 through 763 removed outlier: 3.797A pdb=" N ILE F 752 " --> pdb=" O SER F 748 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARG F 753 " --> pdb=" O ASP F 749 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLN F 760 " --> pdb=" O GLU F 756 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLN F 763 " --> pdb=" O ALA F 759 " (cutoff:3.500A) Processing sheet with id=AA, first strand: chain 'A' and resid 38 through 42 removed outlier: 3.752A pdb=" N ASP A 74 " --> pdb=" O LEU A 41 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N SER A 101 " --> pdb=" O LYS A 60 " (cutoff:3.500A) Processing sheet with id=AB, first strand: chain 'A' and resid 115 through 118 removed outlier: 6.666A pdb=" N HIS A 115 " --> pdb=" O VAL A 166 " (cutoff:3.500A) Processing sheet with id=AC, first strand: chain 'A' and resid 146 through 147 Processing sheet with id=AD, first strand: chain 'A' and resid 265 through 268 removed outlier: 3.547A pdb=" N ARG A 365 " --> pdb=" O GLY A 240 " (cutoff:3.500A) Processing sheet with id=AE, first strand: chain 'A' and resid 538 through 542 Processing sheet with id=BA, first strand: chain 'B' and resid 38 through 42 removed outlier: 3.752A pdb=" N ASP B 74 " --> pdb=" O LEU B 41 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N SER B 101 " --> pdb=" O LYS B 60 " (cutoff:3.500A) Processing sheet with id=BB, first strand: chain 'B' and resid 115 through 118 removed outlier: 6.665A pdb=" N HIS B 115 " --> pdb=" O VAL B 166 " (cutoff:3.500A) Processing sheet with id=BC, first strand: chain 'B' and resid 146 through 147 Processing sheet with id=BD, first strand: chain 'B' and resid 265 through 268 removed outlier: 3.547A pdb=" N ARG B 365 " --> pdb=" O GLY B 240 " (cutoff:3.500A) Processing sheet with id=BE, first strand: chain 'B' and resid 538 through 542 Processing sheet with id=CA, first strand: chain 'C' and resid 38 through 42 removed outlier: 3.752A pdb=" N ASP C 74 " --> pdb=" O LEU C 41 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N SER C 101 " --> pdb=" O LYS C 60 " (cutoff:3.500A) Processing sheet with id=CB, first strand: chain 'C' and resid 115 through 118 removed outlier: 6.666A pdb=" N HIS C 115 " --> pdb=" O VAL C 166 " (cutoff:3.500A) Processing sheet with id=CC, first strand: chain 'C' and resid 146 through 147 Processing sheet with id=CD, first strand: chain 'C' and resid 265 through 268 removed outlier: 3.546A pdb=" N ARG C 365 " --> pdb=" O GLY C 240 " (cutoff:3.500A) Processing sheet with id=CE, first strand: chain 'C' and resid 538 through 542 Processing sheet with id=DA, first strand: chain 'D' and resid 38 through 42 removed outlier: 3.752A pdb=" N ASP D 74 " --> pdb=" O LEU D 41 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N SER D 101 " --> pdb=" O LYS D 60 " (cutoff:3.500A) Processing sheet with id=DB, first strand: chain 'D' and resid 115 through 118 removed outlier: 6.666A pdb=" N HIS D 115 " --> pdb=" O VAL D 166 " (cutoff:3.500A) Processing sheet with id=DC, first strand: chain 'D' and resid 146 through 147 Processing sheet with id=DD, first strand: chain 'D' and resid 265 through 268 removed outlier: 3.547A pdb=" N ARG D 365 " --> pdb=" O GLY D 240 " (cutoff:3.500A) Processing sheet with id=DE, first strand: chain 'D' and resid 538 through 542 Processing sheet with id=EA, first strand: chain 'E' and resid 38 through 42 removed outlier: 3.752A pdb=" N ASP E 74 " --> pdb=" O LEU E 41 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N SER E 101 " --> pdb=" O LYS E 60 " (cutoff:3.500A) Processing sheet with id=EB, first strand: chain 'E' and resid 115 through 118 removed outlier: 6.665A pdb=" N HIS E 115 " --> pdb=" O VAL E 166 " (cutoff:3.500A) Processing sheet with id=EC, first strand: chain 'E' and resid 146 through 147 Processing sheet with id=ED, first strand: chain 'E' and resid 265 through 268 removed outlier: 3.546A pdb=" N ARG E 365 " --> pdb=" O GLY E 240 " (cutoff:3.500A) Processing sheet with id=EE, first strand: chain 'E' and resid 538 through 542 Processing sheet with id=FA, first strand: chain 'F' and resid 38 through 42 removed outlier: 3.752A pdb=" N ASP F 74 " --> pdb=" O LEU F 41 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N SER F 101 " --> pdb=" O LYS F 60 " (cutoff:3.500A) Processing sheet with id=FB, first strand: chain 'F' and resid 115 through 118 removed outlier: 6.666A pdb=" N HIS F 115 " --> pdb=" O VAL F 166 " (cutoff:3.500A) Processing sheet with id=FC, first strand: chain 'F' and resid 146 through 147 Processing sheet with id=FD, first strand: chain 'F' and resid 265 through 268 removed outlier: 3.547A pdb=" N ARG F 365 " --> pdb=" O GLY F 240 " (cutoff:3.500A) Processing sheet with id=FE, first strand: chain 'F' and resid 538 through 542 1392 hydrogen bonds defined for protein. 3906 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: 7.06 Time building geometry restraints manager: 3.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 10389 1.33 - 1.45: 5517 1.45 - 1.58: 18618 1.58 - 1.70: 42 1.70 - 1.82: 288 Bond restraints: 34854 Sorted by residual: bond pdb=" CB VAL A 367 " pdb=" CG1 VAL A 367 " ideal model delta sigma weight residual 1.521 1.429 0.092 3.30e-02 9.18e+02 7.69e+00 bond pdb=" CB VAL F 367 " pdb=" CG1 VAL F 367 " ideal model delta sigma weight residual 1.521 1.430 0.091 3.30e-02 9.18e+02 7.69e+00 bond pdb=" CB VAL C 367 " pdb=" CG1 VAL C 367 " ideal model delta sigma weight residual 1.521 1.430 0.091 3.30e-02 9.18e+02 7.69e+00 bond pdb=" CB VAL E 367 " pdb=" CG1 VAL E 367 " ideal model delta sigma weight residual 1.521 1.430 0.091 3.30e-02 9.18e+02 7.67e+00 bond pdb=" CB VAL D 367 " pdb=" CG1 VAL D 367 " ideal model delta sigma weight residual 1.521 1.430 0.091 3.30e-02 9.18e+02 7.67e+00 ... (remaining 34849 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.86: 44717 2.86 - 5.72: 2157 5.72 - 8.58: 214 8.58 - 11.44: 42 11.44 - 14.30: 12 Bond angle restraints: 47142 Sorted by residual: angle pdb=" N THR C 122 " pdb=" CA THR C 122 " pdb=" C THR C 122 " ideal model delta sigma weight residual 112.92 127.22 -14.30 1.23e+00 6.61e-01 1.35e+02 angle pdb=" N THR F 122 " pdb=" CA THR F 122 " pdb=" C THR F 122 " ideal model delta sigma weight residual 112.92 127.20 -14.28 1.23e+00 6.61e-01 1.35e+02 angle pdb=" N THR D 122 " pdb=" CA THR D 122 " pdb=" C THR D 122 " ideal model delta sigma weight residual 112.92 127.19 -14.27 1.23e+00 6.61e-01 1.35e+02 angle pdb=" N THR A 122 " pdb=" CA THR A 122 " pdb=" C THR A 122 " ideal model delta sigma weight residual 112.92 127.18 -14.26 1.23e+00 6.61e-01 1.34e+02 angle pdb=" N THR E 122 " pdb=" CA THR E 122 " pdb=" C THR E 122 " ideal model delta sigma weight residual 112.92 127.17 -14.25 1.23e+00 6.61e-01 1.34e+02 ... (remaining 47137 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.99: 20985 24.99 - 49.98: 519 49.98 - 74.98: 36 74.98 - 99.97: 36 99.97 - 124.96: 6 Dihedral angle restraints: 21582 sinusoidal: 9090 harmonic: 12492 Sorted by residual: dihedral pdb=" CA ARG E 210 " pdb=" C ARG E 210 " pdb=" N LYS E 211 " pdb=" CA LYS E 211 " ideal model delta harmonic sigma weight residual 180.00 140.91 39.09 0 5.00e+00 4.00e-02 6.11e+01 dihedral pdb=" CA ARG A 210 " pdb=" C ARG A 210 " pdb=" N LYS A 211 " pdb=" CA LYS A 211 " ideal model delta harmonic sigma weight residual 180.00 140.95 39.05 0 5.00e+00 4.00e-02 6.10e+01 dihedral pdb=" CA ARG D 210 " pdb=" C ARG D 210 " pdb=" N LYS D 211 " pdb=" CA LYS D 211 " ideal model delta harmonic sigma weight residual 180.00 140.95 39.05 0 5.00e+00 4.00e-02 6.10e+01 ... (remaining 21579 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 3294 0.057 - 0.113: 1488 0.113 - 0.170: 427 0.170 - 0.226: 76 0.226 - 0.283: 31 Chirality restraints: 5316 Sorted by residual: chirality pdb=" CA THR E 122 " pdb=" N THR E 122 " pdb=" C THR E 122 " pdb=" CB THR E 122 " both_signs ideal model delta sigma weight residual False 2.53 2.24 0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" CA THR C 122 " pdb=" N THR C 122 " pdb=" C THR C 122 " pdb=" CB THR C 122 " both_signs ideal model delta sigma weight residual False 2.53 2.24 0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" CA THR A 122 " pdb=" N THR A 122 " pdb=" C THR A 122 " pdb=" CB THR A 122 " both_signs ideal model delta sigma weight residual False 2.53 2.25 0.28 2.00e-01 2.50e+01 1.97e+00 ... (remaining 5313 not shown) Planarity restraints: 6186 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG E 225 " -0.494 9.50e-02 1.11e+02 2.21e-01 2.98e+01 pdb=" NE ARG E 225 " 0.028 2.00e-02 2.50e+03 pdb=" CZ ARG E 225 " 0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG E 225 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG E 225 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 225 " -0.493 9.50e-02 1.11e+02 2.21e-01 2.97e+01 pdb=" NE ARG C 225 " 0.028 2.00e-02 2.50e+03 pdb=" CZ ARG C 225 " 0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG C 225 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG C 225 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 225 " -0.492 9.50e-02 1.11e+02 2.21e-01 2.97e+01 pdb=" NE ARG A 225 " 0.028 2.00e-02 2.50e+03 pdb=" CZ ARG A 225 " 0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG A 225 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 225 " -0.017 2.00e-02 2.50e+03 ... (remaining 6183 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 6089 2.75 - 3.29: 35725 3.29 - 3.83: 56764 3.83 - 4.36: 71199 4.36 - 4.90: 111792 Nonbonded interactions: 281569 Sorted by model distance: nonbonded pdb=" NH2 ARG A 53 " pdb=" OG SER A 73 " model vdw 2.216 3.120 nonbonded pdb=" NH2 ARG D 53 " pdb=" OG SER D 73 " model vdw 2.217 3.120 nonbonded pdb=" NH2 ARG F 53 " pdb=" OG SER F 73 " model vdw 2.217 3.120 nonbonded pdb=" NH2 ARG E 53 " pdb=" OG SER E 73 " model vdw 2.217 3.120 nonbonded pdb=" NH2 ARG B 53 " pdb=" OG SER B 73 " model vdw 2.217 3.120 ... (remaining 281564 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: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 2.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.560 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 29.010 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:5.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6473 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 : 0.011 0.092 34854 Z= 0.496 Angle : 1.387 14.301 47142 Z= 0.797 Chirality : 0.070 0.283 5316 Planarity : 0.011 0.221 6186 Dihedral : 12.311 124.961 13482 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 25.01 Ramachandran Plot: Outliers : 0.42 % Allowed : 6.12 % Favored : 93.46 % Rotamer: Outliers : 0.65 % Allowed : 2.47 % Favored : 96.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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 aren not related in a simple way. whole: -4.37 (0.09), residues: 4314 helix: -3.50 (0.08), residues: 1560 sheet: -2.10 (0.15), residues: 678 loop : -2.60 (0.11), residues: 2076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.002 ARG F 155 TYR 0.039 0.006 TYR D 755 PHE 0.067 0.007 PHE B 563 TRP 0.033 0.005 TRP F 551 HIS 0.015 0.003 HIS D 406 Details of bonding type rmsd covalent geometry : bond 0.01133 (34854) covalent geometry : angle 1.38730 (47142) hydrogen bonds : bond 0.26556 ( 1392) hydrogen bonds : angle 9.05779 ( 3906) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8628 Ramachandran restraints generated. 4314 Oldfield, 0 Emsley, 4314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8628 Ramachandran restraints generated. 4314 Oldfield, 0 Emsley, 4314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 929 residues out of total 3690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 905 time to evaluate : 1.113 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 36 ASN cc_start: 0.5270 (m-40) cc_final: 0.4852 (m110) REVERT: A 46 MET cc_start: 0.2692 (mmt) cc_final: 0.2409 (mmm) REVERT: A 56 THR cc_start: 0.5790 (p) cc_final: 0.4999 (m) REVERT: A 57 VAL cc_start: 0.5716 (t) cc_final: 0.5502 (p) REVERT: A 60 LYS cc_start: 0.4751 (mmtm) cc_final: 0.4248 (mppt) REVERT: A 110 TYR cc_start: 0.3803 (m-10) cc_final: 0.3415 (m-10) REVERT: A 122 THR cc_start: 0.5948 (p) cc_final: 0.5314 (t) REVERT: A 288 LYS cc_start: 0.6892 (ttpp) cc_final: 0.6649 (pttp) REVERT: A 317 HIS cc_start: 0.4912 (m90) cc_final: 0.4682 (t-90) REVERT: A 322 ARG cc_start: 0.6635 (mtt90) cc_final: 0.6422 (mtt90) REVERT: A 354 ASP cc_start: 0.6624 (t70) cc_final: 0.6066 (t70) REVERT: A 377 ARG cc_start: 0.7413 (mtm-85) cc_final: 0.7113 (mtm-85) REVERT: A 379 GLU cc_start: 0.7383 (mp0) cc_final: 0.7158 (mp0) REVERT: A 401 ASN cc_start: 0.5920 (m110) cc_final: 0.5497 (m110) REVERT: A 402 GLU cc_start: 0.6057 (mp0) cc_final: 0.5688 (tp30) REVERT: A 449 MET cc_start: 0.6655 (tpt) cc_final: 0.6444 (tpt) REVERT: A 487 ARG cc_start: 0.6629 (ttp-110) cc_final: 0.6360 (ptp90) REVERT: A 491 GLU cc_start: 0.7082 (mt-10) cc_final: 0.6689 (mt-10) REVERT: A 505 LYS cc_start: 0.6002 (mtpt) cc_final: 0.5730 (tppp) REVERT: A 546 GLU cc_start: 0.8097 (tt0) cc_final: 0.7433 (mt-10) REVERT: A 624 ASN cc_start: 0.7855 (p0) cc_final: 0.7641 (m-40) REVERT: A 653 ARG cc_start: 0.7248 (mtm-85) cc_final: 0.7025 (mtp180) REVERT: A 696 LYS cc_start: 0.7435 (tttp) cc_final: 0.7164 (ttpt) REVERT: A 738 GLU cc_start: 0.5123 (mm-30) cc_final: 0.4908 (mm-30) REVERT: B 26 LEU cc_start: 0.5024 (tp) cc_final: 0.4823 (mt) REVERT: B 36 ASN cc_start: 0.5349 (m-40) cc_final: 0.5038 (m-40) REVERT: B 57 VAL cc_start: 0.5711 (t) cc_final: 0.5490 (p) REVERT: B 60 LYS cc_start: 0.4805 (mmtm) cc_final: 0.4297 (mppt) REVERT: B 174 CYS cc_start: 0.4541 (m) cc_final: 0.4094 (p) REVERT: B 288 LYS cc_start: 0.6775 (ttpp) cc_final: 0.6566 (pttp) REVERT: B 305 GLU cc_start: 0.7591 (mt-10) cc_final: 0.7294 (mt-10) REVERT: B 386 LYS cc_start: 0.7183 (mtpt) cc_final: 0.6601 (mmtm) REVERT: B 401 ASN cc_start: 0.5993 (m110) cc_final: 0.5589 (m110) REVERT: B 402 GLU cc_start: 0.6133 (mp0) cc_final: 0.5697 (tp30) REVERT: B 449 MET cc_start: 0.6667 (tpt) cc_final: 0.6442 (tpt) REVERT: B 491 GLU cc_start: 0.6982 (mt-10) cc_final: 0.6662 (mt-10) REVERT: B 546 GLU cc_start: 0.8109 (tt0) cc_final: 0.7477 (mt-10) REVERT: B 590 ILE cc_start: 0.2565 (OUTLIER) cc_final: 0.2362 (tt) REVERT: B 624 ASN cc_start: 0.7844 (p0) cc_final: 0.7585 (m-40) REVERT: B 696 LYS cc_start: 0.7476 (tttp) cc_final: 0.7228 (ttpt) REVERT: B 733 ARG cc_start: 0.4302 (ttt180) cc_final: 0.3595 (ttp-170) REVERT: C 36 ASN cc_start: 0.5230 (m-40) cc_final: 0.4729 (m110) REVERT: C 46 MET cc_start: 0.2572 (mmt) cc_final: 0.2329 (mmm) REVERT: C 60 LYS cc_start: 0.4811 (mmtm) cc_final: 0.4289 (mppt) REVERT: C 101 SER cc_start: 0.4735 (t) cc_final: 0.4509 (m) REVERT: C 110 TYR cc_start: 0.4001 (m-10) cc_final: 0.3705 (m-10) REVERT: C 122 THR cc_start: 0.5854 (p) cc_final: 0.5242 (t) REVERT: C 174 CYS cc_start: 0.4561 (m) cc_final: 0.4140 (p) REVERT: C 291 GLU cc_start: 0.5850 (tm-30) cc_final: 0.4930 (tm-30) REVERT: C 377 ARG cc_start: 0.7434 (mtm-85) cc_final: 0.6968 (mtm180) REVERT: C 386 LYS cc_start: 0.7163 (mtpt) cc_final: 0.6550 (mmtm) REVERT: C 401 ASN cc_start: 0.5966 (m110) cc_final: 0.5607 (m110) REVERT: C 402 GLU cc_start: 0.6122 (mp0) cc_final: 0.5814 (tp30) REVERT: C 491 GLU cc_start: 0.6939 (mt-10) cc_final: 0.6585 (mt-10) REVERT: C 505 LYS cc_start: 0.6000 (mtpt) cc_final: 0.5720 (tppp) REVERT: C 546 GLU cc_start: 0.8165 (tt0) cc_final: 0.7580 (mt-10) REVERT: C 624 ASN cc_start: 0.7862 (p0) cc_final: 0.7637 (p0) REVERT: C 696 LYS cc_start: 0.7461 (tttp) cc_final: 0.7186 (ttpt) REVERT: D 36 ASN cc_start: 0.5314 (m-40) cc_final: 0.4892 (m110) REVERT: D 46 MET cc_start: 0.2686 (mmt) cc_final: 0.2412 (mmm) REVERT: D 56 THR cc_start: 0.5794 (p) cc_final: 0.4981 (m) REVERT: D 57 VAL cc_start: 0.5703 (t) cc_final: 0.5477 (p) REVERT: D 60 LYS cc_start: 0.4734 (mmtm) cc_final: 0.4243 (mppt) REVERT: D 110 TYR cc_start: 0.3835 (m-10) cc_final: 0.3440 (m-10) REVERT: D 122 THR cc_start: 0.5944 (p) cc_final: 0.5314 (t) REVERT: D 288 LYS cc_start: 0.6876 (ttpp) cc_final: 0.6646 (pttp) REVERT: D 322 ARG cc_start: 0.6621 (mtt90) cc_final: 0.6420 (mtt90) REVERT: D 354 ASP cc_start: 0.6628 (t70) cc_final: 0.6104 (t70) REVERT: D 377 ARG cc_start: 0.7417 (mtm-85) cc_final: 0.7121 (mtm-85) REVERT: D 379 GLU cc_start: 0.7381 (mp0) cc_final: 0.7156 (mp0) REVERT: D 401 ASN cc_start: 0.5949 (m110) cc_final: 0.5529 (m110) REVERT: D 402 GLU cc_start: 0.6031 (mp0) cc_final: 0.5662 (tp30) REVERT: D 449 MET cc_start: 0.6648 (tpt) cc_final: 0.6440 (tpt) REVERT: D 487 ARG cc_start: 0.6643 (ttp-110) cc_final: 0.6366 (ptp90) REVERT: D 491 GLU cc_start: 0.7096 (mt-10) cc_final: 0.6701 (mt-10) REVERT: D 505 LYS cc_start: 0.5995 (mtpt) cc_final: 0.5728 (tppp) REVERT: D 546 GLU cc_start: 0.8089 (tt0) cc_final: 0.7454 (mt-10) REVERT: D 624 ASN cc_start: 0.7841 (p0) cc_final: 0.7636 (m-40) REVERT: D 653 ARG cc_start: 0.7255 (mtm-85) cc_final: 0.7040 (mtp180) REVERT: D 696 LYS cc_start: 0.7456 (tttp) cc_final: 0.7174 (ttpt) REVERT: D 738 GLU cc_start: 0.5113 (mm-30) cc_final: 0.4883 (mm-30) REVERT: E 26 LEU cc_start: 0.5025 (tp) cc_final: 0.4820 (mt) REVERT: E 36 ASN cc_start: 0.5375 (m-40) cc_final: 0.4914 (m110) REVERT: E 57 VAL cc_start: 0.5672 (t) cc_final: 0.5452 (p) REVERT: E 60 LYS cc_start: 0.4822 (mmtm) cc_final: 0.4311 (mppt) REVERT: E 110 TYR cc_start: 0.3729 (m-10) cc_final: 0.3478 (m-10) REVERT: E 174 CYS cc_start: 0.4516 (m) cc_final: 0.4045 (p) REVERT: E 288 LYS cc_start: 0.6777 (ttpp) cc_final: 0.6569 (pttp) REVERT: E 305 GLU cc_start: 0.7585 (mt-10) cc_final: 0.7292 (mt-10) REVERT: E 386 LYS cc_start: 0.7190 (mtpt) cc_final: 0.6586 (mmtm) REVERT: E 401 ASN cc_start: 0.5993 (m110) cc_final: 0.5603 (m110) REVERT: E 402 GLU cc_start: 0.6154 (mp0) cc_final: 0.5692 (tp30) REVERT: E 491 GLU cc_start: 0.6989 (mt-10) cc_final: 0.6676 (mt-10) REVERT: E 546 GLU cc_start: 0.8112 (tt0) cc_final: 0.7480 (mt-10) REVERT: E 590 ILE cc_start: 0.2579 (OUTLIER) cc_final: 0.2366 (tt) REVERT: E 624 ASN cc_start: 0.7845 (p0) cc_final: 0.7584 (m-40) REVERT: E 696 LYS cc_start: 0.7488 (tttp) cc_final: 0.7244 (ttpt) REVERT: E 733 ARG cc_start: 0.4357 (ttt180) cc_final: 0.3640 (ttp-170) REVERT: F 36 ASN cc_start: 0.5243 (m-40) cc_final: 0.4745 (m110) REVERT: F 46 MET cc_start: 0.2587 (mmt) cc_final: 0.2343 (mmm) REVERT: F 60 LYS cc_start: 0.4824 (mmtm) cc_final: 0.4295 (mppt) REVERT: F 101 SER cc_start: 0.4737 (t) cc_final: 0.4510 (m) REVERT: F 110 TYR cc_start: 0.3996 (m-10) cc_final: 0.3701 (m-10) REVERT: F 122 THR cc_start: 0.5825 (p) cc_final: 0.5232 (t) REVERT: F 174 CYS cc_start: 0.4551 (m) cc_final: 0.4146 (p) REVERT: F 291 GLU cc_start: 0.5851 (tm-30) cc_final: 0.4931 (tm-30) REVERT: F 377 ARG cc_start: 0.7427 (mtm-85) cc_final: 0.6956 (mtm180) REVERT: F 386 LYS cc_start: 0.7160 (mtpt) cc_final: 0.6547 (mmtm) REVERT: F 401 ASN cc_start: 0.5967 (m110) cc_final: 0.5607 (m110) REVERT: F 402 GLU cc_start: 0.6119 (mp0) cc_final: 0.5811 (tp30) REVERT: F 491 GLU cc_start: 0.6939 (mt-10) cc_final: 0.6592 (mt-10) REVERT: F 505 LYS cc_start: 0.6004 (mtpt) cc_final: 0.5725 (tppp) REVERT: F 546 GLU cc_start: 0.8164 (tt0) cc_final: 0.7579 (mt-10) REVERT: F 624 ASN cc_start: 0.7861 (p0) cc_final: 0.7636 (p0) REVERT: F 696 LYS cc_start: 0.7460 (tttp) cc_final: 0.7185 (ttpt) outliers start: 24 outliers final: 6 residues processed: 929 average time/residue: 0.7738 time to fit residues: 834.2394 Evaluate side-chains 535 residues out of total 3690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 527 time to evaluate : 1.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 590 ILE Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain D residue 367 VAL Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 590 ILE Chi-restraints excluded: chain F residue 367 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 197 optimal weight: 5.9990 chunk 388 optimal weight: 5.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 0.7980 chunk 401 optimal weight: 0.0050 chunk 424 optimal weight: 0.8980 chunk 155 optimal weight: 8.9990 overall best weight: 1.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 129 ASN A 285 ASN A 536 GLN A 558 ASN A 568 GLN A 616 ASN B 129 ASN B 285 ASN B 536 GLN B 558 ASN B 568 GLN B 616 ASN B 692 GLN B 750 ASN C 129 ASN C 285 ASN C 536 GLN C 568 GLN C 616 ASN C 692 GLN C 750 ASN D 129 ASN D 285 ASN D 536 GLN D 558 ASN D 568 GLN D 616 ASN E 129 ASN E 285 ASN E 536 GLN E 558 ASN E 568 GLN E 616 ASN E 692 GLN E 750 ASN F 129 ASN F 285 ASN F 317 HIS F 536 GLN F 568 GLN F 616 ASN F 692 GLN F 750 ASN Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4647 r_free = 0.4647 target = 0.235143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.210765 restraints weight = 41741.318| |-----------------------------------------------------------------------------| r_work (start): 0.4414 rms_B_bonded: 1.52 r_work: 0.4173 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.4061 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.4061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6774 moved from start: 0.2856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 34854 Z= 0.165 Angle : 0.785 14.067 47142 Z= 0.403 Chirality : 0.048 0.181 5316 Planarity : 0.005 0.053 6186 Dihedral : 8.772 114.152 4846 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 2.66 % Allowed : 11.68 % Favored : 85.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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 aren not related in a simple way. whole: -2.63 (0.11), residues: 4314 helix: -1.45 (0.11), residues: 1680 sheet: -1.60 (0.16), residues: 714 loop : -1.95 (0.12), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 93 TYR 0.018 0.002 TYR E 755 PHE 0.016 0.002 PHE C 674 TRP 0.012 0.002 TRP F 551 HIS 0.006 0.001 HIS A 499 Details of bonding type rmsd covalent geometry : bond 0.00359 (34854) covalent geometry : angle 0.78538 (47142) hydrogen bonds : bond 0.05239 ( 1392) hydrogen bonds : angle 5.74437 ( 3906) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8628 Ramachandran restraints generated. 4314 Oldfield, 0 Emsley, 4314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8628 Ramachandran restraints generated. 4314 Oldfield, 0 Emsley, 4314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 740 residues out of total 3690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 642 time to evaluate : 0.997 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 36 ASN cc_start: 0.5672 (m-40) cc_final: 0.5366 (m110) REVERT: A 56 THR cc_start: 0.5777 (p) cc_final: 0.5063 (m) REVERT: A 60 LYS cc_start: 0.4576 (mmtm) cc_final: 0.4152 (mppt) REVERT: A 82 ILE cc_start: 0.5068 (OUTLIER) cc_final: 0.4822 (pp) REVERT: A 360 PHE cc_start: 0.5701 (m-10) cc_final: 0.5358 (t80) REVERT: A 653 ARG cc_start: 0.7166 (mtm-85) cc_final: 0.6794 (mtp180) REVERT: A 733 ARG cc_start: 0.4457 (ttt180) cc_final: 0.3786 (ttp-170) REVERT: B 36 ASN cc_start: 0.5474 (m-40) cc_final: 0.5181 (m110) REVERT: B 56 THR cc_start: 0.5631 (p) cc_final: 0.4982 (m) REVERT: B 57 VAL cc_start: 0.5323 (t) cc_final: 0.5020 (p) REVERT: B 82 ILE cc_start: 0.5229 (pt) cc_final: 0.5006 (pp) REVERT: B 360 PHE cc_start: 0.5740 (m-10) cc_final: 0.5350 (t80) REVERT: B 611 MET cc_start: 0.6419 (ttm) cc_final: 0.6128 (ttm) REVERT: B 733 ARG cc_start: 0.4451 (ttt180) cc_final: 0.3814 (ttp-170) REVERT: B 758 PHE cc_start: 0.6110 (t80) cc_final: 0.5817 (t80) REVERT: C 36 ASN cc_start: 0.5460 (m-40) cc_final: 0.5050 (m110) REVERT: C 56 THR cc_start: 0.5733 (p) cc_final: 0.5024 (m) REVERT: C 60 LYS cc_start: 0.4815 (mmtm) cc_final: 0.4386 (mppt) REVERT: C 82 ILE cc_start: 0.5098 (OUTLIER) cc_final: 0.4824 (pp) REVERT: C 101 SER cc_start: 0.4575 (t) cc_final: 0.4201 (m) REVERT: C 360 PHE cc_start: 0.5645 (m-10) cc_final: 0.5289 (t80) REVERT: C 505 LYS cc_start: 0.6204 (mtpt) cc_final: 0.5909 (tppp) REVERT: C 733 ARG cc_start: 0.4493 (ttt180) cc_final: 0.3946 (ttp-170) REVERT: C 758 PHE cc_start: 0.6031 (t80) cc_final: 0.5830 (t80) REVERT: D 36 ASN cc_start: 0.5661 (m-40) cc_final: 0.5341 (m110) REVERT: D 56 THR cc_start: 0.5757 (p) cc_final: 0.5059 (m) REVERT: D 60 LYS cc_start: 0.4610 (mmtm) cc_final: 0.4185 (mppt) REVERT: D 82 ILE cc_start: 0.5138 (OUTLIER) cc_final: 0.4881 (pp) REVERT: D 360 PHE cc_start: 0.5713 (m-10) cc_final: 0.5340 (t80) REVERT: D 560 ARG cc_start: 0.7413 (ttt-90) cc_final: 0.7205 (ttm-80) REVERT: D 653 ARG cc_start: 0.7158 (mtm-85) cc_final: 0.6789 (mtp180) REVERT: D 733 ARG cc_start: 0.4420 (ttt180) cc_final: 0.3768 (ttp-170) REVERT: E 36 ASN cc_start: 0.5436 (m-40) cc_final: 0.5096 (m110) REVERT: E 56 THR cc_start: 0.5602 (p) cc_final: 0.4941 (m) REVERT: E 57 VAL cc_start: 0.5312 (t) cc_final: 0.5014 (p) REVERT: E 82 ILE cc_start: 0.5227 (pt) cc_final: 0.5012 (pp) REVERT: E 360 PHE cc_start: 0.5731 (m-10) cc_final: 0.5356 (t80) REVERT: E 733 ARG cc_start: 0.4498 (ttt180) cc_final: 0.3882 (ttp-170) REVERT: E 758 PHE cc_start: 0.6107 (t80) cc_final: 0.5828 (t80) REVERT: F 36 ASN cc_start: 0.5459 (m-40) cc_final: 0.5061 (m110) REVERT: F 56 THR cc_start: 0.5734 (p) cc_final: 0.5022 (m) REVERT: F 60 LYS cc_start: 0.4811 (mmtm) cc_final: 0.4382 (mppt) REVERT: F 82 ILE cc_start: 0.5096 (OUTLIER) cc_final: 0.4823 (pp) REVERT: F 101 SER cc_start: 0.4562 (t) cc_final: 0.4188 (m) REVERT: F 360 PHE cc_start: 0.5637 (m-10) cc_final: 0.5294 (t80) REVERT: F 491 GLU cc_start: 0.7138 (mt-10) cc_final: 0.6816 (mt-10) REVERT: F 505 LYS cc_start: 0.6198 (mtpt) cc_final: 0.5909 (tppp) REVERT: F 733 ARG cc_start: 0.4489 (ttt180) cc_final: 0.3929 (ttp-170) REVERT: F 758 PHE cc_start: 0.6038 (t80) cc_final: 0.5817 (t80) outliers start: 98 outliers final: 28 residues processed: 717 average time/residue: 0.7723 time to fit residues: 648.3427 Evaluate side-chains 511 residues out of total 3690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 479 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 349 ARG Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 590 ILE Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 590 ILE Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain C residue 394 VAL Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain D residue 349 ARG Chi-restraints excluded: chain D residue 394 VAL Chi-restraints excluded: chain D residue 590 ILE Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain E residue 342 ILE Chi-restraints excluded: chain E residue 394 VAL Chi-restraints excluded: chain E residue 590 ILE Chi-restraints excluded: chain F residue 82 ILE Chi-restraints excluded: chain F residue 284 SER Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain F residue 342 ILE Chi-restraints excluded: chain F residue 347 THR Chi-restraints excluded: chain F residue 394 VAL Chi-restraints excluded: chain F residue 633 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 317 optimal weight: 0.0980 chunk 61 optimal weight: 5.9990 chunk 308 optimal weight: 1.9990 chunk 12 optimal weight: 9.9990 chunk 140 optimal weight: 5.9990 chunk 305 optimal weight: 20.0000 chunk 3 optimal weight: 2.9990 chunk 19 optimal weight: 7.9990 chunk 174 optimal weight: 10.0000 chunk 335 optimal weight: 4.9990 chunk 70 optimal weight: 8.9990 overall best weight: 3.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 401 ASN A 536 GLN A 616 ASN A 624 ASN B 115 HIS ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 401 ASN B 490 GLN B 536 GLN B 616 ASN B 624 ASN ** C 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 536 GLN C 558 ASN C 616 ASN C 624 ASN ** D 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 401 ASN D 490 GLN D 536 GLN D 616 ASN D 624 ASN E 115 HIS ** E 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 401 ASN E 490 GLN E 536 GLN E 616 ASN E 624 ASN F 317 HIS ** F 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 401 ASN F 536 GLN F 558 ASN F 616 ASN F 624 ASN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4634 r_free = 0.4634 target = 0.233923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.209522 restraints weight = 41880.536| |-----------------------------------------------------------------------------| r_work (start): 0.4395 rms_B_bonded: 1.61 r_work: 0.4153 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.4047 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.4047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6787 moved from start: 0.3501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 34854 Z= 0.159 Angle : 0.736 11.204 47142 Z= 0.372 Chirality : 0.047 0.180 5316 Planarity : 0.005 0.045 6186 Dihedral : 8.187 105.062 4840 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.21 % Favored : 93.65 % Rotamer: Outliers : 2.98 % Allowed : 15.64 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.29 % 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 aren not related in a simple way. whole: -1.89 (0.12), residues: 4314 helix: -0.69 (0.12), residues: 1680 sheet: -1.30 (0.18), residues: 714 loop : -1.64 (0.13), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 560 TYR 0.015 0.002 TYR E 755 PHE 0.014 0.002 PHE F 290 TRP 0.008 0.002 TRP F 551 HIS 0.004 0.001 HIS D 317 Details of bonding type rmsd covalent geometry : bond 0.00359 (34854) covalent geometry : angle 0.73626 (47142) hydrogen bonds : bond 0.04605 ( 1392) hydrogen bonds : angle 5.39066 ( 3906) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8628 Ramachandran restraints generated. 4314 Oldfield, 0 Emsley, 4314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8628 Ramachandran restraints generated. 4314 Oldfield, 0 Emsley, 4314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 656 residues out of total 3690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 546 time to evaluate : 1.263 Fit side-chains REVERT: A 36 ASN cc_start: 0.5651 (m-40) cc_final: 0.5370 (m110) REVERT: A 56 THR cc_start: 0.5832 (p) cc_final: 0.5118 (m) REVERT: A 57 VAL cc_start: 0.5396 (t) cc_final: 0.5083 (p) REVERT: A 82 ILE cc_start: 0.5055 (OUTLIER) cc_final: 0.4844 (pp) REVERT: A 150 ASP cc_start: 0.4271 (m-30) cc_final: 0.3765 (p0) REVERT: A 294 GLU cc_start: 0.5825 (OUTLIER) cc_final: 0.5563 (tt0) REVERT: A 321 GLU cc_start: 0.6595 (OUTLIER) cc_final: 0.6348 (mp0) REVERT: A 360 PHE cc_start: 0.5655 (m-10) cc_final: 0.5284 (t80) REVERT: A 388 MET cc_start: 0.5695 (mtt) cc_final: 0.5165 (mtt) REVERT: A 442 MET cc_start: 0.5346 (mtp) cc_final: 0.5133 (mtp) REVERT: A 478 ASP cc_start: 0.7200 (OUTLIER) cc_final: 0.6773 (m-30) REVERT: A 653 ARG cc_start: 0.7217 (mtm-85) cc_final: 0.6964 (mtp180) REVERT: A 758 PHE cc_start: 0.5788 (t80) cc_final: 0.5533 (t80) REVERT: B 36 ASN cc_start: 0.5601 (m-40) cc_final: 0.5306 (m110) REVERT: B 56 THR cc_start: 0.5614 (p) cc_final: 0.4981 (m) REVERT: B 57 VAL cc_start: 0.5323 (t) cc_final: 0.4983 (p) REVERT: B 442 MET cc_start: 0.5258 (mtp) cc_final: 0.5042 (mtp) REVERT: B 478 ASP cc_start: 0.7170 (OUTLIER) cc_final: 0.6762 (m-30) REVERT: B 653 ARG cc_start: 0.7191 (mtp180) cc_final: 0.6624 (mtm110) REVERT: C 36 ASN cc_start: 0.5506 (m-40) cc_final: 0.5211 (m110) REVERT: C 53 ARG cc_start: 0.3556 (ptp90) cc_final: 0.3262 (mtt-85) REVERT: C 56 THR cc_start: 0.5835 (p) cc_final: 0.5124 (m) REVERT: C 57 VAL cc_start: 0.5175 (t) cc_final: 0.4837 (p) REVERT: C 82 ILE cc_start: 0.5065 (OUTLIER) cc_final: 0.4836 (pp) REVERT: C 101 SER cc_start: 0.4633 (t) cc_final: 0.4354 (m) REVERT: C 110 TYR cc_start: 0.3972 (m-10) cc_final: 0.3147 (m-10) REVERT: C 360 PHE cc_start: 0.5456 (m-10) cc_final: 0.5221 (t80) REVERT: C 478 ASP cc_start: 0.7118 (OUTLIER) cc_final: 0.6716 (m-30) REVERT: C 505 LYS cc_start: 0.6153 (mtpt) cc_final: 0.5892 (tppp) REVERT: C 653 ARG cc_start: 0.7248 (mtp180) cc_final: 0.6669 (mtm110) REVERT: D 36 ASN cc_start: 0.5656 (m-40) cc_final: 0.5369 (m110) REVERT: D 56 THR cc_start: 0.5865 (p) cc_final: 0.5145 (m) REVERT: D 57 VAL cc_start: 0.5414 (t) cc_final: 0.5101 (p) REVERT: D 150 ASP cc_start: 0.4297 (m-30) cc_final: 0.3768 (p0) REVERT: D 294 GLU cc_start: 0.5809 (OUTLIER) cc_final: 0.5538 (tt0) REVERT: D 360 PHE cc_start: 0.5628 (m-10) cc_final: 0.5270 (t80) REVERT: D 478 ASP cc_start: 0.7125 (OUTLIER) cc_final: 0.6693 (m-30) REVERT: D 653 ARG cc_start: 0.7218 (mtm-85) cc_final: 0.6964 (mtp180) REVERT: D 758 PHE cc_start: 0.5814 (t80) cc_final: 0.5529 (t80) REVERT: E 36 ASN cc_start: 0.5594 (m-40) cc_final: 0.5281 (m110) REVERT: E 56 THR cc_start: 0.5580 (p) cc_final: 0.4968 (m) REVERT: E 57 VAL cc_start: 0.5324 (t) cc_final: 0.5006 (p) REVERT: E 478 ASP cc_start: 0.7121 (OUTLIER) cc_final: 0.6705 (m-30) REVERT: E 653 ARG cc_start: 0.7187 (mtp180) cc_final: 0.6615 (mtm110) REVERT: E 758 PHE cc_start: 0.6025 (t80) cc_final: 0.5816 (t80) REVERT: F 36 ASN cc_start: 0.5509 (m-40) cc_final: 0.5215 (m110) REVERT: F 53 ARG cc_start: 0.3567 (ptp90) cc_final: 0.3275 (mtt-85) REVERT: F 56 THR cc_start: 0.5817 (p) cc_final: 0.5114 (m) REVERT: F 57 VAL cc_start: 0.5176 (t) cc_final: 0.4840 (p) REVERT: F 101 SER cc_start: 0.4658 (t) cc_final: 0.4378 (m) REVERT: F 110 TYR cc_start: 0.3969 (m-10) cc_final: 0.3229 (m-10) REVERT: F 360 PHE cc_start: 0.5453 (m-10) cc_final: 0.5205 (t80) REVERT: F 478 ASP cc_start: 0.7153 (OUTLIER) cc_final: 0.6758 (m-30) REVERT: F 505 LYS cc_start: 0.6176 (mtpt) cc_final: 0.5902 (tppp) REVERT: F 653 ARG cc_start: 0.7215 (mtp180) cc_final: 0.6641 (mtm110) outliers start: 110 outliers final: 54 residues processed: 606 average time/residue: 0.7077 time to fit residues: 507.7282 Evaluate side-chains 555 residues out of total 3690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 490 time to evaluate : 1.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 327 GLN Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 349 ARG Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 478 ASP Chi-restraints excluded: chain A residue 487 ARG Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 590 ILE Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 327 GLN Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 478 ASP Chi-restraints excluded: chain B residue 487 ARG Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain C residue 394 VAL Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain C residue 473 GLN Chi-restraints excluded: chain C residue 478 ASP Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain D residue 294 GLU Chi-restraints excluded: chain D residue 327 GLN Chi-restraints excluded: chain D residue 342 ILE Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 349 ARG Chi-restraints excluded: chain D residue 394 VAL Chi-restraints excluded: chain D residue 478 ASP Chi-restraints excluded: chain D residue 487 ARG Chi-restraints excluded: chain D residue 497 VAL Chi-restraints excluded: chain D residue 590 ILE Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 229 LEU Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain E residue 327 GLN Chi-restraints excluded: chain E residue 342 ILE Chi-restraints excluded: chain E residue 394 VAL Chi-restraints excluded: chain E residue 478 ASP Chi-restraints excluded: chain E residue 487 ARG Chi-restraints excluded: chain E residue 497 VAL Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain F residue 284 SER Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain F residue 342 ILE Chi-restraints excluded: chain F residue 347 THR Chi-restraints excluded: chain F residue 394 VAL Chi-restraints excluded: chain F residue 423 ILE Chi-restraints excluded: chain F residue 473 GLN Chi-restraints excluded: chain F residue 478 ASP Chi-restraints excluded: chain F residue 497 VAL Chi-restraints excluded: chain F residue 633 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 196 optimal weight: 5.9990 chunk 380 optimal weight: 8.9990 chunk 181 optimal weight: 10.0000 chunk 180 optimal weight: 6.9990 chunk 159 optimal weight: 10.0000 chunk 349 optimal weight: 8.9990 chunk 172 optimal weight: 7.9990 chunk 74 optimal weight: 2.9990 chunk 111 optimal weight: 30.0000 chunk 15 optimal weight: 40.0000 chunk 131 optimal weight: 10.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 536 GLN A 568 GLN ** B 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 536 GLN ** C 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 536 GLN ** D 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 536 GLN D 568 GLN ** E 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 536 GLN F 317 HIS ** F 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 536 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4603 r_free = 0.4603 target = 0.231053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.206305 restraints weight = 41314.796| |-----------------------------------------------------------------------------| r_work (start): 0.4365 rms_B_bonded: 1.56 r_work: 0.4135 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.4028 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.4028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6849 moved from start: 0.3683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 34854 Z= 0.216 Angle : 0.823 9.932 47142 Z= 0.414 Chirality : 0.050 0.181 5316 Planarity : 0.006 0.047 6186 Dihedral : 8.696 101.693 4836 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 14.69 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.23 % Favored : 92.63 % Rotamer: Outliers : 4.31 % Allowed : 16.80 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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 aren not related in a simple way. whole: -1.98 (0.12), residues: 4314 helix: -0.76 (0.12), residues: 1692 sheet: -1.11 (0.19), residues: 654 loop : -1.82 (0.13), residues: 1968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 93 TYR 0.014 0.002 TYR D 110 PHE 0.019 0.002 PHE D 139 TRP 0.009 0.002 TRP F 551 HIS 0.006 0.002 HIS E 406 Details of bonding type rmsd covalent geometry : bond 0.00498 (34854) covalent geometry : angle 0.82330 (47142) hydrogen bonds : bond 0.04995 ( 1392) hydrogen bonds : angle 5.63391 ( 3906) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8628 Ramachandran restraints generated. 4314 Oldfield, 0 Emsley, 4314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8628 Ramachandran restraints generated. 4314 Oldfield, 0 Emsley, 4314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 647 residues out of total 3690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 159 poor density : 488 time to evaluate : 1.346 Fit side-chains revert: symmetry clash REVERT: A 36 ASN cc_start: 0.5662 (m-40) cc_final: 0.5399 (m110) REVERT: A 51 LEU cc_start: 0.2540 (OUTLIER) cc_final: 0.2172 (tp) REVERT: A 56 THR cc_start: 0.5899 (p) cc_final: 0.5089 (m) REVERT: A 82 ILE cc_start: 0.5239 (OUTLIER) cc_final: 0.4944 (pp) REVERT: A 150 ASP cc_start: 0.4307 (m-30) cc_final: 0.3745 (p0) REVERT: A 294 GLU cc_start: 0.5857 (OUTLIER) cc_final: 0.5532 (tt0) REVERT: A 426 LYS cc_start: 0.6180 (OUTLIER) cc_final: 0.5554 (mttt) REVERT: A 449 MET cc_start: 0.6754 (tpt) cc_final: 0.6393 (tpp) REVERT: A 478 ASP cc_start: 0.7127 (OUTLIER) cc_final: 0.6817 (m-30) REVERT: A 653 ARG cc_start: 0.7212 (mtm-85) cc_final: 0.6620 (mtm110) REVERT: B 36 ASN cc_start: 0.5666 (m-40) cc_final: 0.5355 (m110) REVERT: B 56 THR cc_start: 0.5628 (p) cc_final: 0.4946 (m) REVERT: B 57 VAL cc_start: 0.5379 (t) cc_final: 0.5036 (p) REVERT: B 294 GLU cc_start: 0.5603 (OUTLIER) cc_final: 0.5347 (tt0) REVERT: B 426 LYS cc_start: 0.6128 (OUTLIER) cc_final: 0.5654 (mttt) REVERT: B 478 ASP cc_start: 0.7362 (OUTLIER) cc_final: 0.7020 (m-30) REVERT: B 611 MET cc_start: 0.6649 (ttm) cc_final: 0.6434 (ttm) REVERT: B 758 PHE cc_start: 0.5984 (t80) cc_final: 0.5775 (t80) REVERT: C 36 ASN cc_start: 0.5713 (m-40) cc_final: 0.5357 (m110) REVERT: C 56 THR cc_start: 0.5816 (p) cc_final: 0.5062 (m) REVERT: C 82 ILE cc_start: 0.5307 (OUTLIER) cc_final: 0.4970 (pp) REVERT: C 110 TYR cc_start: 0.4035 (m-10) cc_final: 0.3276 (m-10) REVERT: C 378 LEU cc_start: 0.7076 (tp) cc_final: 0.6876 (mt) REVERT: C 426 LYS cc_start: 0.6242 (OUTLIER) cc_final: 0.5717 (mttt) REVERT: C 478 ASP cc_start: 0.7103 (OUTLIER) cc_final: 0.6757 (m-30) REVERT: C 758 PHE cc_start: 0.5924 (t80) cc_final: 0.5659 (t80) REVERT: D 36 ASN cc_start: 0.5666 (m-40) cc_final: 0.5411 (m110) REVERT: D 56 THR cc_start: 0.5915 (p) cc_final: 0.5106 (m) REVERT: D 150 ASP cc_start: 0.4282 (m-30) cc_final: 0.3727 (p0) REVERT: D 294 GLU cc_start: 0.5889 (OUTLIER) cc_final: 0.5572 (tt0) REVERT: D 449 MET cc_start: 0.6763 (tpt) cc_final: 0.6420 (tpp) REVERT: D 451 ASP cc_start: 0.5639 (m-30) cc_final: 0.5381 (m-30) REVERT: D 478 ASP cc_start: 0.7126 (OUTLIER) cc_final: 0.6832 (m-30) REVERT: D 653 ARG cc_start: 0.7229 (mtm-85) cc_final: 0.6659 (mtm110) REVERT: E 36 ASN cc_start: 0.5644 (m-40) cc_final: 0.5332 (m110) REVERT: E 56 THR cc_start: 0.5564 (p) cc_final: 0.4901 (m) REVERT: E 110 TYR cc_start: 0.3793 (m-10) cc_final: 0.3112 (m-10) REVERT: E 150 ASP cc_start: 0.4271 (m-30) cc_final: 0.3656 (p0) REVERT: E 426 LYS cc_start: 0.6159 (OUTLIER) cc_final: 0.5705 (mttt) REVERT: E 478 ASP cc_start: 0.7331 (OUTLIER) cc_final: 0.6981 (m-30) REVERT: F 36 ASN cc_start: 0.5707 (m-40) cc_final: 0.5351 (m110) REVERT: F 56 THR cc_start: 0.5814 (p) cc_final: 0.5054 (m) REVERT: F 60 LYS cc_start: 0.4912 (mmtm) cc_final: 0.4479 (mppt) REVERT: F 110 TYR cc_start: 0.4050 (m-10) cc_final: 0.3273 (m-10) REVERT: F 426 LYS cc_start: 0.6300 (OUTLIER) cc_final: 0.5757 (mttt) REVERT: F 478 ASP cc_start: 0.7089 (OUTLIER) cc_final: 0.6726 (m-30) REVERT: F 758 PHE cc_start: 0.5920 (t80) cc_final: 0.5659 (t80) outliers start: 159 outliers final: 65 residues processed: 606 average time/residue: 0.6863 time to fit residues: 495.4900 Evaluate side-chains 531 residues out of total 3690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 449 time to evaluate : 1.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 327 GLN Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 349 ARG Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 426 LYS Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 478 ASP Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 590 ILE Chi-restraints excluded: chain A residue 652 SER Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 294 GLU Chi-restraints excluded: chain B residue 327 GLN Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 426 LYS Chi-restraints excluded: chain B residue 478 ASP Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 652 SER Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain C residue 394 VAL Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain C residue 426 LYS Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 473 GLN Chi-restraints excluded: chain C residue 478 ASP Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 590 ILE Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 652 SER Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain D residue 294 GLU Chi-restraints excluded: chain D residue 327 GLN Chi-restraints excluded: chain D residue 342 ILE Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 349 ARG Chi-restraints excluded: chain D residue 394 VAL Chi-restraints excluded: chain D residue 423 ILE Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 478 ASP Chi-restraints excluded: chain D residue 497 VAL Chi-restraints excluded: chain D residue 590 ILE Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 652 SER Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain E residue 327 GLN Chi-restraints excluded: chain E residue 342 ILE Chi-restraints excluded: chain E residue 394 VAL Chi-restraints excluded: chain E residue 426 LYS Chi-restraints excluded: chain E residue 478 ASP Chi-restraints excluded: chain E residue 497 VAL Chi-restraints excluded: chain E residue 652 SER Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain F residue 284 SER Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain F residue 342 ILE Chi-restraints excluded: chain F residue 347 THR Chi-restraints excluded: chain F residue 394 VAL Chi-restraints excluded: chain F residue 423 ILE Chi-restraints excluded: chain F residue 426 LYS Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 473 GLN Chi-restraints excluded: chain F residue 478 ASP Chi-restraints excluded: chain F residue 497 VAL Chi-restraints excluded: chain F residue 590 ILE Chi-restraints excluded: chain F residue 633 ILE Chi-restraints excluded: chain F residue 652 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 112 optimal weight: 3.9990 chunk 246 optimal weight: 0.6980 chunk 136 optimal weight: 20.0000 chunk 238 optimal weight: 8.9990 chunk 419 optimal weight: 9.9990 chunk 82 optimal weight: 7.9990 chunk 71 optimal weight: 9.9990 chunk 152 optimal weight: 8.9990 chunk 115 optimal weight: 8.9990 chunk 425 optimal weight: 20.0000 chunk 324 optimal weight: 6.9990 overall best weight: 5.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 536 GLN A 568 GLN ** B 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 536 GLN ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 443 ASN C 536 GLN ** D 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 536 GLN ** E 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 536 GLN ** F 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 443 ASN F 536 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4610 r_free = 0.4610 target = 0.231688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.207097 restraints weight = 41394.464| |-----------------------------------------------------------------------------| r_work (start): 0.4372 rms_B_bonded: 1.50 r_work: 0.4145 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.4040 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.4040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6838 moved from start: 0.3993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 34854 Z= 0.194 Angle : 0.781 10.119 47142 Z= 0.392 Chirality : 0.049 0.215 5316 Planarity : 0.006 0.048 6186 Dihedral : 8.442 99.063 4836 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.35 % Favored : 92.51 % Rotamer: Outliers : 4.61 % Allowed : 18.37 % Favored : 77.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.29 % 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 aren not related in a simple way. whole: -1.87 (0.12), residues: 4314 helix: -0.60 (0.12), residues: 1698 sheet: -1.01 (0.20), residues: 618 loop : -1.83 (0.13), residues: 1998 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 377 TYR 0.013 0.002 TYR B 755 PHE 0.015 0.002 PHE B 139 TRP 0.007 0.002 TRP B 551 HIS 0.005 0.002 HIS E 735 Details of bonding type rmsd covalent geometry : bond 0.00450 (34854) covalent geometry : angle 0.78092 (47142) hydrogen bonds : bond 0.04592 ( 1392) hydrogen bonds : angle 5.48634 ( 3906) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8628 Ramachandran restraints generated. 4314 Oldfield, 0 Emsley, 4314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8628 Ramachandran restraints generated. 4314 Oldfield, 0 Emsley, 4314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 627 residues out of total 3690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 170 poor density : 457 time to evaluate : 1.631 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 36 ASN cc_start: 0.5740 (m-40) cc_final: 0.5535 (m110) REVERT: A 51 LEU cc_start: 0.2437 (OUTLIER) cc_final: 0.2068 (tp) REVERT: A 56 THR cc_start: 0.5901 (p) cc_final: 0.5081 (m) REVERT: A 82 ILE cc_start: 0.5248 (OUTLIER) cc_final: 0.4957 (pp) REVERT: A 150 ASP cc_start: 0.4084 (m-30) cc_final: 0.3589 (p0) REVERT: A 294 GLU cc_start: 0.5818 (OUTLIER) cc_final: 0.5584 (tt0) REVERT: A 426 LYS cc_start: 0.6228 (OUTLIER) cc_final: 0.5582 (mttt) REVERT: A 449 MET cc_start: 0.6731 (tpt) cc_final: 0.6426 (tpp) REVERT: A 470 GLU cc_start: 0.7531 (OUTLIER) cc_final: 0.7241 (pp20) REVERT: A 478 ASP cc_start: 0.7068 (OUTLIER) cc_final: 0.6745 (m-30) REVERT: A 614 LYS cc_start: 0.5588 (OUTLIER) cc_final: 0.5068 (mptp) REVERT: A 738 GLU cc_start: 0.5807 (tp30) cc_final: 0.5528 (tp30) REVERT: B 60 LYS cc_start: 0.4943 (OUTLIER) cc_final: 0.4624 (mmtm) REVERT: B 120 ASP cc_start: 0.0979 (OUTLIER) cc_final: 0.0524 (t0) REVERT: B 150 ASP cc_start: 0.4267 (m-30) cc_final: 0.3660 (p0) REVERT: B 294 GLU cc_start: 0.5662 (OUTLIER) cc_final: 0.5418 (tt0) REVERT: B 426 LYS cc_start: 0.6056 (OUTLIER) cc_final: 0.5566 (mttt) REVERT: B 449 MET cc_start: 0.6856 (tpt) cc_final: 0.6499 (tpp) REVERT: B 478 ASP cc_start: 0.7307 (OUTLIER) cc_final: 0.6963 (m-30) REVERT: B 614 LYS cc_start: 0.5277 (mppt) cc_final: 0.4858 (mptp) REVERT: C 36 ASN cc_start: 0.5824 (m-40) cc_final: 0.5379 (m110) REVERT: C 82 ILE cc_start: 0.5312 (OUTLIER) cc_final: 0.4973 (pp) REVERT: C 110 TYR cc_start: 0.3950 (m-10) cc_final: 0.3215 (m-10) REVERT: C 150 ASP cc_start: 0.4442 (m-30) cc_final: 0.3880 (p0) REVERT: C 360 PHE cc_start: 0.5571 (m-10) cc_final: 0.5229 (t80) REVERT: C 426 LYS cc_start: 0.6172 (OUTLIER) cc_final: 0.5657 (mttt) REVERT: C 478 ASP cc_start: 0.7139 (OUTLIER) cc_final: 0.6796 (m-30) REVERT: C 561 GLU cc_start: 0.7038 (mm-30) cc_final: 0.6756 (tp30) REVERT: C 758 PHE cc_start: 0.5875 (t80) cc_final: 0.5670 (t80) REVERT: D 51 LEU cc_start: 0.2445 (OUTLIER) cc_final: 0.2022 (tp) REVERT: D 56 THR cc_start: 0.5845 (p) cc_final: 0.5033 (m) REVERT: D 150 ASP cc_start: 0.4108 (m-30) cc_final: 0.3628 (p0) REVERT: D 294 GLU cc_start: 0.5813 (OUTLIER) cc_final: 0.5564 (tt0) REVERT: D 442 MET cc_start: 0.5275 (OUTLIER) cc_final: 0.4999 (ttp) REVERT: D 470 GLU cc_start: 0.7580 (OUTLIER) cc_final: 0.7298 (pp20) REVERT: D 478 ASP cc_start: 0.7119 (OUTLIER) cc_final: 0.6808 (m-30) REVERT: D 614 LYS cc_start: 0.5566 (OUTLIER) cc_final: 0.5045 (mptp) REVERT: E 36 ASN cc_start: 0.5757 (m-40) cc_final: 0.5456 (m110) REVERT: E 56 THR cc_start: 0.5681 (p) cc_final: 0.4986 (m) REVERT: E 60 LYS cc_start: 0.4998 (OUTLIER) cc_final: 0.4757 (mmtm) REVERT: E 110 TYR cc_start: 0.3848 (m-10) cc_final: 0.3132 (m-10) REVERT: E 120 ASP cc_start: 0.1056 (OUTLIER) cc_final: 0.0576 (t0) REVERT: E 150 ASP cc_start: 0.4315 (m-30) cc_final: 0.3701 (p0) REVERT: E 426 LYS cc_start: 0.6155 (OUTLIER) cc_final: 0.5659 (mttt) REVERT: E 478 ASP cc_start: 0.7260 (OUTLIER) cc_final: 0.6913 (m-30) REVERT: E 614 LYS cc_start: 0.5221 (mppt) cc_final: 0.4831 (mptp) REVERT: F 36 ASN cc_start: 0.5794 (m-40) cc_final: 0.5343 (m110) REVERT: F 60 LYS cc_start: 0.4910 (mmtm) cc_final: 0.4492 (mppt) REVERT: F 110 TYR cc_start: 0.3953 (m-10) cc_final: 0.3201 (m-10) REVERT: F 150 ASP cc_start: 0.4421 (m-30) cc_final: 0.3854 (p0) REVERT: F 360 PHE cc_start: 0.5557 (m-10) cc_final: 0.5226 (t80) REVERT: F 426 LYS cc_start: 0.6187 (OUTLIER) cc_final: 0.5672 (mttt) REVERT: F 478 ASP cc_start: 0.7096 (OUTLIER) cc_final: 0.6741 (m-30) REVERT: F 758 PHE cc_start: 0.5881 (t80) cc_final: 0.5673 (t80) outliers start: 170 outliers final: 91 residues processed: 584 average time/residue: 0.7148 time to fit residues: 492.8606 Evaluate side-chains 544 residues out of total 3690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 426 time to evaluate : 1.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 219 MET Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 327 GLN Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 349 ARG Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 426 LYS Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 470 GLU Chi-restraints excluded: chain A residue 478 ASP Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 590 ILE Chi-restraints excluded: chain A residue 614 LYS Chi-restraints excluded: chain A residue 652 SER Chi-restraints excluded: chain A residue 691 CYS Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 60 LYS Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 154 VAL Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 294 GLU Chi-restraints excluded: chain B residue 327 GLN Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 426 LYS Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 478 ASP Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 652 SER Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain C residue 394 VAL Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain C residue 426 LYS Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 473 GLN Chi-restraints excluded: chain C residue 478 ASP Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 590 ILE Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 652 SER Chi-restraints excluded: chain C residue 670 VAL Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 219 MET Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain D residue 294 GLU Chi-restraints excluded: chain D residue 327 GLN Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 349 ARG Chi-restraints excluded: chain D residue 353 ILE Chi-restraints excluded: chain D residue 394 VAL Chi-restraints excluded: chain D residue 420 LEU Chi-restraints excluded: chain D residue 423 ILE Chi-restraints excluded: chain D residue 442 MET Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 470 GLU Chi-restraints excluded: chain D residue 478 ASP Chi-restraints excluded: chain D residue 487 ARG Chi-restraints excluded: chain D residue 497 VAL Chi-restraints excluded: chain D residue 590 ILE Chi-restraints excluded: chain D residue 614 LYS Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 652 SER Chi-restraints excluded: chain D residue 691 CYS Chi-restraints excluded: chain E residue 60 LYS Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 166 VAL Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain E residue 327 GLN Chi-restraints excluded: chain E residue 341 VAL Chi-restraints excluded: chain E residue 342 ILE Chi-restraints excluded: chain E residue 347 THR Chi-restraints excluded: chain E residue 394 VAL Chi-restraints excluded: chain E residue 426 LYS Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 478 ASP Chi-restraints excluded: chain E residue 497 VAL Chi-restraints excluded: chain E residue 652 SER Chi-restraints excluded: chain F residue 120 ASP Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 284 SER Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain F residue 342 ILE Chi-restraints excluded: chain F residue 347 THR Chi-restraints excluded: chain F residue 378 LEU Chi-restraints excluded: chain F residue 394 VAL Chi-restraints excluded: chain F residue 423 ILE Chi-restraints excluded: chain F residue 426 LYS Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 473 GLN Chi-restraints excluded: chain F residue 478 ASP Chi-restraints excluded: chain F residue 497 VAL Chi-restraints excluded: chain F residue 590 ILE Chi-restraints excluded: chain F residue 633 ILE Chi-restraints excluded: chain F residue 652 SER Chi-restraints excluded: chain F residue 670 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 349 optimal weight: 7.9990 chunk 97 optimal weight: 9.9990 chunk 171 optimal weight: 8.9990 chunk 377 optimal weight: 5.9990 chunk 303 optimal weight: 3.9990 chunk 294 optimal weight: 9.9990 chunk 190 optimal weight: 5.9990 chunk 82 optimal weight: 0.5980 chunk 383 optimal weight: 8.9990 chunk 335 optimal weight: 8.9990 chunk 154 optimal weight: 9.9990 overall best weight: 4.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 115 HIS ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 536 GLN ** B 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 536 GLN ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 HIS C 327 GLN ** C 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 536 GLN D 36 ASN D 115 HIS ** D 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 536 GLN ** E 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 536 GLN F 115 HIS F 327 GLN ** F 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 536 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4614 r_free = 0.4614 target = 0.232222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.207907 restraints weight = 41213.895| |-----------------------------------------------------------------------------| r_work (start): 0.4380 rms_B_bonded: 1.48 r_work: 0.4149 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.4042 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.4042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6831 moved from start: 0.4242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 34854 Z= 0.178 Angle : 0.753 9.799 47142 Z= 0.375 Chirality : 0.048 0.168 5316 Planarity : 0.005 0.049 6186 Dihedral : 8.275 99.115 4836 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.77 % Favored : 92.10 % Rotamer: Outliers : 5.09 % Allowed : 19.02 % Favored : 75.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.29 % 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 aren not related in a simple way. whole: -1.91 (0.12), residues: 4314 helix: -0.72 (0.12), residues: 1770 sheet: -1.00 (0.20), residues: 618 loop : -1.81 (0.13), residues: 1926 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 93 TYR 0.013 0.002 TYR D 755 PHE 0.014 0.002 PHE D 139 TRP 0.007 0.002 TRP B 551 HIS 0.004 0.001 HIS E 735 Details of bonding type rmsd covalent geometry : bond 0.00410 (34854) covalent geometry : angle 0.75328 (47142) hydrogen bonds : bond 0.04361 ( 1392) hydrogen bonds : angle 5.38157 ( 3906) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8628 Ramachandran restraints generated. 4314 Oldfield, 0 Emsley, 4314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8628 Ramachandran restraints generated. 4314 Oldfield, 0 Emsley, 4314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 660 residues out of total 3690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 188 poor density : 472 time to evaluate : 1.399 Fit side-chains revert: symmetry clash REVERT: A 56 THR cc_start: 0.5745 (p) cc_final: 0.4939 (m) REVERT: A 82 ILE cc_start: 0.5237 (OUTLIER) cc_final: 0.4959 (pp) REVERT: A 141 GLU cc_start: 0.1813 (OUTLIER) cc_final: 0.1611 (pt0) REVERT: A 150 ASP cc_start: 0.4094 (m-30) cc_final: 0.3629 (p0) REVERT: A 294 GLU cc_start: 0.5828 (OUTLIER) cc_final: 0.5611 (tt0) REVERT: A 426 LYS cc_start: 0.6227 (OUTLIER) cc_final: 0.5623 (mttt) REVERT: A 442 MET cc_start: 0.5272 (OUTLIER) cc_final: 0.5024 (ttp) REVERT: A 470 GLU cc_start: 0.7561 (OUTLIER) cc_final: 0.7309 (pp20) REVERT: A 478 ASP cc_start: 0.7121 (OUTLIER) cc_final: 0.6808 (m-30) REVERT: A 614 LYS cc_start: 0.5598 (OUTLIER) cc_final: 0.5067 (mptp) REVERT: A 738 GLU cc_start: 0.5783 (tp30) cc_final: 0.5476 (mm-30) REVERT: B 51 LEU cc_start: 0.2604 (OUTLIER) cc_final: 0.2177 (tp) REVERT: B 60 LYS cc_start: 0.5034 (OUTLIER) cc_final: 0.4766 (mmtm) REVERT: B 101 SER cc_start: 0.4713 (p) cc_final: 0.4370 (t) REVERT: B 120 ASP cc_start: 0.0950 (OUTLIER) cc_final: 0.0460 (t0) REVERT: B 150 ASP cc_start: 0.4307 (m-30) cc_final: 0.3662 (p0) REVERT: B 294 GLU cc_start: 0.5640 (OUTLIER) cc_final: 0.5397 (tt0) REVERT: B 426 LYS cc_start: 0.6088 (OUTLIER) cc_final: 0.5634 (mttt) REVERT: B 614 LYS cc_start: 0.5214 (OUTLIER) cc_final: 0.4860 (mptp) REVERT: C 82 ILE cc_start: 0.5304 (OUTLIER) cc_final: 0.4971 (pp) REVERT: C 110 TYR cc_start: 0.3993 (m-10) cc_final: 0.3219 (m-10) REVERT: C 141 GLU cc_start: 0.2001 (OUTLIER) cc_final: 0.1752 (pt0) REVERT: C 150 ASP cc_start: 0.4407 (m-30) cc_final: 0.3866 (p0) REVERT: C 360 PHE cc_start: 0.5588 (m-10) cc_final: 0.5267 (t80) REVERT: C 426 LYS cc_start: 0.6127 (OUTLIER) cc_final: 0.5599 (mttt) REVERT: C 470 GLU cc_start: 0.7562 (OUTLIER) cc_final: 0.7191 (pp20) REVERT: C 478 ASP cc_start: 0.7154 (OUTLIER) cc_final: 0.6801 (m-30) REVERT: C 561 GLU cc_start: 0.7059 (mm-30) cc_final: 0.6765 (tp30) REVERT: D 51 LEU cc_start: 0.2357 (OUTLIER) cc_final: 0.1955 (tp) REVERT: D 56 THR cc_start: 0.5762 (p) cc_final: 0.4954 (m) REVERT: D 141 GLU cc_start: 0.2010 (OUTLIER) cc_final: 0.1787 (pt0) REVERT: D 150 ASP cc_start: 0.4062 (m-30) cc_final: 0.3602 (p0) REVERT: D 294 GLU cc_start: 0.5865 (OUTLIER) cc_final: 0.5658 (tt0) REVERT: D 470 GLU cc_start: 0.7586 (OUTLIER) cc_final: 0.7338 (pp20) REVERT: D 478 ASP cc_start: 0.7142 (OUTLIER) cc_final: 0.6844 (m-30) REVERT: D 614 LYS cc_start: 0.5538 (OUTLIER) cc_final: 0.5007 (mptp) REVERT: D 738 GLU cc_start: 0.5751 (tp30) cc_final: 0.5445 (mm-30) REVERT: E 51 LEU cc_start: 0.2637 (OUTLIER) cc_final: 0.2285 (tp) REVERT: E 60 LYS cc_start: 0.5026 (OUTLIER) cc_final: 0.4756 (mmtm) REVERT: E 101 SER cc_start: 0.4745 (p) cc_final: 0.4409 (t) REVERT: E 110 TYR cc_start: 0.3857 (m-10) cc_final: 0.3190 (m-10) REVERT: E 120 ASP cc_start: 0.0966 (OUTLIER) cc_final: 0.0476 (t0) REVERT: E 150 ASP cc_start: 0.4330 (m-30) cc_final: 0.3661 (p0) REVERT: E 426 LYS cc_start: 0.6162 (OUTLIER) cc_final: 0.5657 (mttt) REVERT: E 442 MET cc_start: 0.5179 (OUTLIER) cc_final: 0.4957 (ttp) REVERT: E 614 LYS cc_start: 0.5180 (mppt) cc_final: 0.4839 (mptp) REVERT: F 110 TYR cc_start: 0.4049 (m-10) cc_final: 0.3256 (m-10) REVERT: F 141 GLU cc_start: 0.2005 (OUTLIER) cc_final: 0.1759 (pt0) REVERT: F 150 ASP cc_start: 0.4451 (m-30) cc_final: 0.3889 (p0) REVERT: F 426 LYS cc_start: 0.6135 (OUTLIER) cc_final: 0.5613 (mttt) REVERT: F 470 GLU cc_start: 0.7568 (OUTLIER) cc_final: 0.7182 (pp20) REVERT: F 478 ASP cc_start: 0.7135 (OUTLIER) cc_final: 0.6770 (m-30) REVERT: F 561 GLU cc_start: 0.6981 (mm-30) cc_final: 0.6707 (tp30) REVERT: F 653 ARG cc_start: 0.7248 (mtp180) cc_final: 0.6900 (mtm110) outliers start: 188 outliers final: 85 residues processed: 611 average time/residue: 0.6920 time to fit residues: 501.4324 Evaluate side-chains 560 residues out of total 3690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 441 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 327 GLN Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 349 ARG Chi-restraints excluded: chain A residue 353 ILE Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 426 LYS Chi-restraints excluded: chain A residue 442 MET Chi-restraints excluded: chain A residue 470 GLU Chi-restraints excluded: chain A residue 478 ASP Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 590 ILE Chi-restraints excluded: chain A residue 614 LYS Chi-restraints excluded: chain A residue 652 SER Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 60 LYS Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 294 GLU Chi-restraints excluded: chain B residue 327 GLN Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 423 ILE Chi-restraints excluded: chain B residue 426 LYS Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 590 ILE Chi-restraints excluded: chain B residue 614 LYS Chi-restraints excluded: chain B residue 652 SER Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 141 GLU Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain C residue 426 LYS Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 470 GLU Chi-restraints excluded: chain C residue 473 GLN Chi-restraints excluded: chain C residue 478 ASP Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 590 ILE Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 652 SER Chi-restraints excluded: chain C residue 670 VAL Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 141 GLU Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain D residue 294 GLU Chi-restraints excluded: chain D residue 327 GLN Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 342 ILE Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 349 ARG Chi-restraints excluded: chain D residue 353 ILE Chi-restraints excluded: chain D residue 394 VAL Chi-restraints excluded: chain D residue 423 ILE Chi-restraints excluded: chain D residue 470 GLU Chi-restraints excluded: chain D residue 478 ASP Chi-restraints excluded: chain D residue 487 ARG Chi-restraints excluded: chain D residue 497 VAL Chi-restraints excluded: chain D residue 590 ILE Chi-restraints excluded: chain D residue 614 LYS Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 652 SER Chi-restraints excluded: chain D residue 691 CYS Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 60 LYS Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain E residue 327 GLN Chi-restraints excluded: chain E residue 341 VAL Chi-restraints excluded: chain E residue 342 ILE Chi-restraints excluded: chain E residue 347 THR Chi-restraints excluded: chain E residue 394 VAL Chi-restraints excluded: chain E residue 426 LYS Chi-restraints excluded: chain E residue 442 MET Chi-restraints excluded: chain E residue 497 VAL Chi-restraints excluded: chain E residue 590 ILE Chi-restraints excluded: chain E residue 652 SER Chi-restraints excluded: chain E residue 666 VAL Chi-restraints excluded: chain F residue 120 ASP Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 141 GLU Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 284 SER Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain F residue 342 ILE Chi-restraints excluded: chain F residue 347 THR Chi-restraints excluded: chain F residue 378 LEU Chi-restraints excluded: chain F residue 423 ILE Chi-restraints excluded: chain F residue 426 LYS Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 470 GLU Chi-restraints excluded: chain F residue 473 GLN Chi-restraints excluded: chain F residue 478 ASP Chi-restraints excluded: chain F residue 497 VAL Chi-restraints excluded: chain F residue 590 ILE Chi-restraints excluded: chain F residue 633 ILE Chi-restraints excluded: chain F residue 652 SER Chi-restraints excluded: chain F residue 670 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 310 optimal weight: 8.9990 chunk 300 optimal weight: 6.9990 chunk 105 optimal weight: 6.9990 chunk 93 optimal weight: 0.8980 chunk 329 optimal weight: 6.9990 chunk 132 optimal weight: 0.6980 chunk 416 optimal weight: 7.9990 chunk 54 optimal weight: 7.9990 chunk 52 optimal weight: 5.9990 chunk 379 optimal weight: 10.0000 chunk 262 optimal weight: 6.9990 overall best weight: 4.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 443 ASN ** B 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 443 ASN B 536 GLN ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 536 GLN ** D 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 568 GLN ** E 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 443 ASN E 536 GLN ** F 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 536 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4619 r_free = 0.4619 target = 0.232605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.208351 restraints weight = 41420.981| |-----------------------------------------------------------------------------| r_work (start): 0.4386 rms_B_bonded: 1.50 r_work: 0.4151 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.4042 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.4042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6847 moved from start: 0.4422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 34854 Z= 0.168 Angle : 0.747 10.828 47142 Z= 0.371 Chirality : 0.047 0.214 5316 Planarity : 0.005 0.050 6186 Dihedral : 8.182 97.667 4836 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.21 % Favored : 92.65 % Rotamer: Outliers : 5.07 % Allowed : 20.27 % Favored : 74.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.29 % 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 aren not related in a simple way. whole: -1.79 (0.12), residues: 4314 helix: -0.58 (0.12), residues: 1758 sheet: -1.00 (0.20), residues: 618 loop : -1.75 (0.13), residues: 1938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 239 TYR 0.015 0.002 TYR A 244 PHE 0.011 0.002 PHE D 139 TRP 0.006 0.002 TRP D 551 HIS 0.004 0.001 HIS D 499 Details of bonding type rmsd covalent geometry : bond 0.00387 (34854) covalent geometry : angle 0.74704 (47142) hydrogen bonds : bond 0.04204 ( 1392) hydrogen bonds : angle 5.31844 ( 3906) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8628 Ramachandran restraints generated. 4314 Oldfield, 0 Emsley, 4314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8628 Ramachandran restraints generated. 4314 Oldfield, 0 Emsley, 4314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 645 residues out of total 3690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 187 poor density : 458 time to evaluate : 1.084 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 ILE cc_start: 0.5234 (OUTLIER) cc_final: 0.4945 (pp) REVERT: A 141 GLU cc_start: 0.1974 (OUTLIER) cc_final: 0.1729 (pt0) REVERT: A 150 ASP cc_start: 0.4070 (m-30) cc_final: 0.3621 (p0) REVERT: A 426 LYS cc_start: 0.6283 (OUTLIER) cc_final: 0.5706 (mttt) REVERT: A 442 MET cc_start: 0.5207 (OUTLIER) cc_final: 0.5001 (ttp) REVERT: A 470 GLU cc_start: 0.7583 (OUTLIER) cc_final: 0.7312 (pp20) REVERT: A 473 GLN cc_start: 0.6416 (OUTLIER) cc_final: 0.6185 (mm110) REVERT: A 478 ASP cc_start: 0.7166 (OUTLIER) cc_final: 0.6785 (m-30) REVERT: A 614 LYS cc_start: 0.5511 (OUTLIER) cc_final: 0.4990 (mptp) REVERT: B 51 LEU cc_start: 0.2600 (OUTLIER) cc_final: 0.2179 (tp) REVERT: B 60 LYS cc_start: 0.4993 (OUTLIER) cc_final: 0.4759 (mmtm) REVERT: B 101 SER cc_start: 0.4769 (p) cc_final: 0.4409 (t) REVERT: B 120 ASP cc_start: 0.0901 (OUTLIER) cc_final: 0.0464 (t0) REVERT: B 426 LYS cc_start: 0.6142 (OUTLIER) cc_final: 0.5667 (mttt) REVERT: B 614 LYS cc_start: 0.5236 (mppt) cc_final: 0.4832 (mptp) REVERT: B 738 GLU cc_start: 0.5544 (tp30) cc_final: 0.5225 (tp30) REVERT: C 53 ARG cc_start: 0.3721 (ptp90) cc_final: 0.3469 (mtt-85) REVERT: C 82 ILE cc_start: 0.5308 (OUTLIER) cc_final: 0.4959 (pp) REVERT: C 110 TYR cc_start: 0.4015 (m-10) cc_final: 0.3252 (m-10) REVERT: C 141 GLU cc_start: 0.1999 (OUTLIER) cc_final: 0.1784 (pt0) REVERT: C 150 ASP cc_start: 0.4414 (m-30) cc_final: 0.3856 (p0) REVERT: C 426 LYS cc_start: 0.6126 (OUTLIER) cc_final: 0.5591 (mttt) REVERT: C 470 GLU cc_start: 0.7622 (OUTLIER) cc_final: 0.7253 (pp20) REVERT: C 478 ASP cc_start: 0.7182 (OUTLIER) cc_final: 0.6808 (m-30) REVERT: C 561 GLU cc_start: 0.7085 (mm-30) cc_final: 0.6770 (tp30) REVERT: D 51 LEU cc_start: 0.2388 (OUTLIER) cc_final: 0.1991 (tp) REVERT: D 56 THR cc_start: 0.5767 (p) cc_final: 0.4970 (m) REVERT: D 141 GLU cc_start: 0.1986 (OUTLIER) cc_final: 0.1749 (pt0) REVERT: D 150 ASP cc_start: 0.4053 (m-30) cc_final: 0.3599 (p0) REVERT: D 294 GLU cc_start: 0.5854 (OUTLIER) cc_final: 0.5649 (tt0) REVERT: D 470 GLU cc_start: 0.7565 (OUTLIER) cc_final: 0.7288 (pp20) REVERT: D 473 GLN cc_start: 0.6398 (OUTLIER) cc_final: 0.6157 (mm110) REVERT: D 614 LYS cc_start: 0.5544 (OUTLIER) cc_final: 0.5012 (mptp) REVERT: D 736 PHE cc_start: 0.7387 (m-80) cc_final: 0.7148 (m-80) REVERT: D 738 GLU cc_start: 0.5653 (tp30) cc_final: 0.5388 (mm-30) REVERT: E 51 LEU cc_start: 0.2610 (OUTLIER) cc_final: 0.2180 (tp) REVERT: E 60 LYS cc_start: 0.4983 (OUTLIER) cc_final: 0.4746 (mmtm) REVERT: E 101 SER cc_start: 0.4760 (p) cc_final: 0.4396 (t) REVERT: E 110 TYR cc_start: 0.3887 (m-10) cc_final: 0.3255 (m-10) REVERT: E 120 ASP cc_start: 0.0870 (OUTLIER) cc_final: 0.0449 (t0) REVERT: E 426 LYS cc_start: 0.6128 (OUTLIER) cc_final: 0.5635 (mttt) REVERT: E 442 MET cc_start: 0.5188 (OUTLIER) cc_final: 0.4954 (ttp) REVERT: E 614 LYS cc_start: 0.5153 (OUTLIER) cc_final: 0.4849 (mptp) REVERT: F 51 LEU cc_start: 0.2577 (OUTLIER) cc_final: 0.2042 (tp) REVERT: F 53 ARG cc_start: 0.3700 (ptp90) cc_final: 0.3408 (mtt-85) REVERT: F 57 VAL cc_start: 0.5243 (t) cc_final: 0.5028 (p) REVERT: F 101 SER cc_start: 0.4671 (p) cc_final: 0.4412 (t) REVERT: F 110 TYR cc_start: 0.4021 (m-10) cc_final: 0.3254 (m-10) REVERT: F 141 GLU cc_start: 0.2013 (OUTLIER) cc_final: 0.1791 (pt0) REVERT: F 150 ASP cc_start: 0.4427 (m-30) cc_final: 0.3832 (p0) REVERT: F 426 LYS cc_start: 0.6172 (OUTLIER) cc_final: 0.5660 (mttt) REVERT: F 470 GLU cc_start: 0.7616 (OUTLIER) cc_final: 0.7229 (pp20) REVERT: F 478 ASP cc_start: 0.7153 (OUTLIER) cc_final: 0.6768 (m-30) REVERT: F 561 GLU cc_start: 0.7073 (mm-30) cc_final: 0.6761 (tp30) outliers start: 187 outliers final: 89 residues processed: 600 average time/residue: 0.7101 time to fit residues: 503.2169 Evaluate side-chains 559 residues out of total 3690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 436 time to evaluate : 1.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 327 GLN Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 349 ARG Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 426 LYS Chi-restraints excluded: chain A residue 442 MET Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 470 GLU Chi-restraints excluded: chain A residue 473 GLN Chi-restraints excluded: chain A residue 478 ASP Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 590 ILE Chi-restraints excluded: chain A residue 614 LYS Chi-restraints excluded: chain A residue 652 SER Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 60 LYS Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 327 GLN Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 426 LYS Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 590 ILE Chi-restraints excluded: chain B residue 652 SER Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 141 GLU Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain C residue 426 LYS Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 470 GLU Chi-restraints excluded: chain C residue 473 GLN Chi-restraints excluded: chain C residue 478 ASP Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 590 ILE Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 652 SER Chi-restraints excluded: chain C residue 670 VAL Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 141 GLU Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain D residue 294 GLU Chi-restraints excluded: chain D residue 327 GLN Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 394 VAL Chi-restraints excluded: chain D residue 423 ILE Chi-restraints excluded: chain D residue 470 GLU Chi-restraints excluded: chain D residue 473 GLN Chi-restraints excluded: chain D residue 487 ARG Chi-restraints excluded: chain D residue 497 VAL Chi-restraints excluded: chain D residue 590 ILE Chi-restraints excluded: chain D residue 614 LYS Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 652 SER Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 60 LYS Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 166 VAL Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain E residue 327 GLN Chi-restraints excluded: chain E residue 341 VAL Chi-restraints excluded: chain E residue 342 ILE Chi-restraints excluded: chain E residue 347 THR Chi-restraints excluded: chain E residue 394 VAL Chi-restraints excluded: chain E residue 426 LYS Chi-restraints excluded: chain E residue 442 MET Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 497 VAL Chi-restraints excluded: chain E residue 590 ILE Chi-restraints excluded: chain E residue 614 LYS Chi-restraints excluded: chain E residue 652 SER Chi-restraints excluded: chain E residue 666 VAL Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 120 ASP Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 141 GLU Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 284 SER Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain F residue 342 ILE Chi-restraints excluded: chain F residue 347 THR Chi-restraints excluded: chain F residue 365 ARG Chi-restraints excluded: chain F residue 378 LEU Chi-restraints excluded: chain F residue 423 ILE Chi-restraints excluded: chain F residue 426 LYS Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 470 GLU Chi-restraints excluded: chain F residue 473 GLN Chi-restraints excluded: chain F residue 478 ASP Chi-restraints excluded: chain F residue 497 VAL Chi-restraints excluded: chain F residue 590 ILE Chi-restraints excluded: chain F residue 633 ILE Chi-restraints excluded: chain F residue 652 SER Chi-restraints excluded: chain F residue 670 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 201 optimal weight: 10.0000 chunk 344 optimal weight: 8.9990 chunk 401 optimal weight: 0.9990 chunk 428 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 chunk 34 optimal weight: 7.9990 chunk 143 optimal weight: 9.9990 chunk 247 optimal weight: 20.0000 chunk 383 optimal weight: 8.9990 chunk 281 optimal weight: 8.9990 chunk 169 optimal weight: 20.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 536 GLN ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 327 GLN ** C 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 536 GLN ** D 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 536 GLN ** F 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 327 GLN ** F 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 536 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4612 r_free = 0.4612 target = 0.231925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.207119 restraints weight = 41283.074| |-----------------------------------------------------------------------------| r_work (start): 0.4372 rms_B_bonded: 1.51 r_work: 0.4143 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.4029 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.4029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6841 moved from start: 0.4468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 34854 Z= 0.183 Angle : 0.775 12.027 47142 Z= 0.384 Chirality : 0.048 0.191 5316 Planarity : 0.005 0.049 6186 Dihedral : 8.307 100.138 4836 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 13.94 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.32 % Favored : 92.54 % Rotamer: Outliers : 4.34 % Allowed : 21.27 % Favored : 74.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.29 % 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 aren not related in a simple way. whole: -1.83 (0.12), residues: 4314 helix: -0.60 (0.12), residues: 1764 sheet: -1.00 (0.20), residues: 618 loop : -1.80 (0.13), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 358 TYR 0.016 0.002 TYR A 244 PHE 0.012 0.002 PHE D 139 TRP 0.007 0.002 TRP C 551 HIS 0.004 0.001 HIS F 735 Details of bonding type rmsd covalent geometry : bond 0.00424 (34854) covalent geometry : angle 0.77456 (47142) hydrogen bonds : bond 0.04334 ( 1392) hydrogen bonds : angle 5.39909 ( 3906) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8628 Ramachandran restraints generated. 4314 Oldfield, 0 Emsley, 4314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8628 Ramachandran restraints generated. 4314 Oldfield, 0 Emsley, 4314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 609 residues out of total 3690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 160 poor density : 449 time to evaluate : 1.437 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 ILE cc_start: 0.5232 (OUTLIER) cc_final: 0.4922 (pp) REVERT: A 141 GLU cc_start: 0.2089 (OUTLIER) cc_final: 0.1841 (pt0) REVERT: A 150 ASP cc_start: 0.4132 (m-30) cc_final: 0.3628 (p0) REVERT: A 151 ILE cc_start: 0.5894 (OUTLIER) cc_final: 0.5372 (mp) REVERT: A 426 LYS cc_start: 0.6300 (OUTLIER) cc_final: 0.5709 (mttt) REVERT: A 442 MET cc_start: 0.5262 (OUTLIER) cc_final: 0.5033 (ttp) REVERT: A 470 GLU cc_start: 0.7553 (OUTLIER) cc_final: 0.7310 (pp20) REVERT: A 473 GLN cc_start: 0.6390 (OUTLIER) cc_final: 0.6155 (mm110) REVERT: A 614 LYS cc_start: 0.5539 (OUTLIER) cc_final: 0.4964 (mptp) REVERT: A 662 ARG cc_start: 0.5033 (ttm110) cc_final: 0.4671 (mtm110) REVERT: B 51 LEU cc_start: 0.2680 (OUTLIER) cc_final: 0.2235 (tp) REVERT: B 60 LYS cc_start: 0.5098 (OUTLIER) cc_final: 0.4833 (mmtm) REVERT: B 101 SER cc_start: 0.4775 (p) cc_final: 0.4418 (t) REVERT: B 120 ASP cc_start: 0.0795 (OUTLIER) cc_final: 0.0372 (t0) REVERT: B 158 MET cc_start: 0.6693 (OUTLIER) cc_final: 0.6445 (mpp) REVERT: B 426 LYS cc_start: 0.6076 (OUTLIER) cc_final: 0.5611 (mttt) REVERT: B 449 MET cc_start: 0.6693 (tpp) cc_final: 0.6295 (tpp) REVERT: B 554 GLU cc_start: 0.7703 (OUTLIER) cc_final: 0.7322 (mt-10) REVERT: B 614 LYS cc_start: 0.5216 (OUTLIER) cc_final: 0.4863 (mptp) REVERT: C 82 ILE cc_start: 0.5342 (OUTLIER) cc_final: 0.4975 (pp) REVERT: C 141 GLU cc_start: 0.2007 (OUTLIER) cc_final: 0.1785 (pt0) REVERT: C 150 ASP cc_start: 0.4462 (m-30) cc_final: 0.3863 (p0) REVERT: C 151 ILE cc_start: 0.5854 (mm) cc_final: 0.5393 (mp) REVERT: C 426 LYS cc_start: 0.6175 (OUTLIER) cc_final: 0.5677 (mttt) REVERT: C 470 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.7268 (pp20) REVERT: C 561 GLU cc_start: 0.7098 (mm-30) cc_final: 0.6775 (tp30) REVERT: D 51 LEU cc_start: 0.2433 (OUTLIER) cc_final: 0.2051 (tp) REVERT: D 141 GLU cc_start: 0.2107 (OUTLIER) cc_final: 0.1852 (pt0) REVERT: D 150 ASP cc_start: 0.4091 (m-30) cc_final: 0.3604 (p0) REVERT: D 151 ILE cc_start: 0.5888 (OUTLIER) cc_final: 0.5365 (mp) REVERT: D 294 GLU cc_start: 0.5882 (OUTLIER) cc_final: 0.5660 (tt0) REVERT: D 394 VAL cc_start: 0.3828 (OUTLIER) cc_final: 0.3587 (t) REVERT: D 470 GLU cc_start: 0.7531 (OUTLIER) cc_final: 0.7297 (pp20) REVERT: D 473 GLN cc_start: 0.6360 (OUTLIER) cc_final: 0.6109 (mm110) REVERT: D 614 LYS cc_start: 0.5526 (OUTLIER) cc_final: 0.4983 (mptp) REVERT: D 738 GLU cc_start: 0.5732 (tp30) cc_final: 0.5441 (mm-30) REVERT: E 51 LEU cc_start: 0.2659 (OUTLIER) cc_final: 0.2216 (tp) REVERT: E 60 LYS cc_start: 0.5039 (OUTLIER) cc_final: 0.4767 (mmtm) REVERT: E 101 SER cc_start: 0.4766 (p) cc_final: 0.4409 (t) REVERT: E 110 TYR cc_start: 0.3910 (m-10) cc_final: 0.3166 (m-10) REVERT: E 120 ASP cc_start: 0.0860 (OUTLIER) cc_final: 0.0435 (t0) REVERT: E 136 LYS cc_start: 0.4749 (mtpp) cc_final: 0.4163 (mmmt) REVERT: E 426 LYS cc_start: 0.6079 (OUTLIER) cc_final: 0.5572 (mttt) REVERT: E 449 MET cc_start: 0.6756 (tpp) cc_final: 0.6420 (tpp) REVERT: E 614 LYS cc_start: 0.5188 (OUTLIER) cc_final: 0.4879 (mptp) REVERT: E 738 GLU cc_start: 0.5692 (tp30) cc_final: 0.5485 (mm-30) REVERT: F 46 MET cc_start: 0.2610 (mmp) cc_final: 0.2102 (ppp) REVERT: F 53 ARG cc_start: 0.3829 (ptp90) cc_final: 0.3526 (mtt-85) REVERT: F 57 VAL cc_start: 0.5240 (t) cc_final: 0.4966 (p) REVERT: F 110 TYR cc_start: 0.4040 (m-10) cc_final: 0.3246 (m-10) REVERT: F 141 GLU cc_start: 0.2009 (OUTLIER) cc_final: 0.1785 (pt0) REVERT: F 150 ASP cc_start: 0.4487 (m-30) cc_final: 0.3889 (p0) REVERT: F 151 ILE cc_start: 0.5850 (mm) cc_final: 0.5365 (mp) REVERT: F 426 LYS cc_start: 0.6184 (OUTLIER) cc_final: 0.5691 (mttt) REVERT: F 470 GLU cc_start: 0.7598 (OUTLIER) cc_final: 0.7254 (pp20) REVERT: F 561 GLU cc_start: 0.7137 (mm-30) cc_final: 0.6828 (tp30) outliers start: 160 outliers final: 87 residues processed: 570 average time/residue: 0.7483 time to fit residues: 504.8879 Evaluate side-chains 557 residues out of total 3690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 435 time to evaluate : 1.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 327 GLN Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 349 ARG Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 426 LYS Chi-restraints excluded: chain A residue 442 MET Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 470 GLU Chi-restraints excluded: chain A residue 473 GLN Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 590 ILE Chi-restraints excluded: chain A residue 614 LYS Chi-restraints excluded: chain A residue 652 SER Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 60 LYS Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 327 GLN Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 426 LYS Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 590 ILE Chi-restraints excluded: chain B residue 614 LYS Chi-restraints excluded: chain B residue 652 SER Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 141 GLU Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain C residue 426 LYS Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 470 GLU Chi-restraints excluded: chain C residue 473 GLN Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 590 ILE Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 652 SER Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 670 VAL Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 141 GLU Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain D residue 294 GLU Chi-restraints excluded: chain D residue 327 GLN Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 342 ILE Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 394 VAL Chi-restraints excluded: chain D residue 423 ILE Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 470 GLU Chi-restraints excluded: chain D residue 473 GLN Chi-restraints excluded: chain D residue 497 VAL Chi-restraints excluded: chain D residue 590 ILE Chi-restraints excluded: chain D residue 614 LYS Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 652 SER Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 60 LYS Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 166 VAL Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain E residue 327 GLN Chi-restraints excluded: chain E residue 341 VAL Chi-restraints excluded: chain E residue 342 ILE Chi-restraints excluded: chain E residue 347 THR Chi-restraints excluded: chain E residue 426 LYS Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 497 VAL Chi-restraints excluded: chain E residue 590 ILE Chi-restraints excluded: chain E residue 614 LYS Chi-restraints excluded: chain E residue 652 SER Chi-restraints excluded: chain E residue 666 VAL Chi-restraints excluded: chain F residue 120 ASP Chi-restraints excluded: chain F residue 133 VAL Chi-restraints excluded: chain F residue 141 GLU Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 284 SER Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain F residue 342 ILE Chi-restraints excluded: chain F residue 347 THR Chi-restraints excluded: chain F residue 378 LEU Chi-restraints excluded: chain F residue 423 ILE Chi-restraints excluded: chain F residue 426 LYS Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 470 GLU Chi-restraints excluded: chain F residue 473 GLN Chi-restraints excluded: chain F residue 497 VAL Chi-restraints excluded: chain F residue 590 ILE Chi-restraints excluded: chain F residue 633 ILE Chi-restraints excluded: chain F residue 652 SER Chi-restraints excluded: chain F residue 666 VAL Chi-restraints excluded: chain F residue 670 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 40 optimal weight: 9.9990 chunk 74 optimal weight: 10.0000 chunk 409 optimal weight: 10.0000 chunk 351 optimal weight: 6.9990 chunk 247 optimal weight: 10.0000 chunk 116 optimal weight: 7.9990 chunk 64 optimal weight: 7.9990 chunk 94 optimal weight: 4.9990 chunk 176 optimal weight: 9.9990 chunk 150 optimal weight: 8.9990 chunk 307 optimal weight: 5.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 536 GLN ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 536 GLN ** D 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 536 GLN ** F 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 536 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4599 r_free = 0.4599 target = 0.230902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.205325 restraints weight = 41329.070| |-----------------------------------------------------------------------------| r_work (start): 0.4352 rms_B_bonded: 1.62 r_work: 0.4130 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.4025 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.4025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6879 moved from start: 0.4519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 34854 Z= 0.214 Angle : 0.829 12.556 47142 Z= 0.413 Chirality : 0.050 0.189 5316 Planarity : 0.006 0.053 6186 Dihedral : 8.596 102.674 4836 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 14.90 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.58 % Favored : 92.28 % Rotamer: Outliers : 4.28 % Allowed : 21.68 % Favored : 74.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.29 % 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 aren not related in a simple way. whole: -2.02 (0.12), residues: 4314 helix: -0.78 (0.12), residues: 1758 sheet: -1.06 (0.20), residues: 618 loop : -1.90 (0.13), residues: 1938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 93 TYR 0.014 0.002 TYR D 495 PHE 0.011 0.002 PHE F 576 TRP 0.009 0.002 TRP D 476 HIS 0.005 0.002 HIS E 384 Details of bonding type rmsd covalent geometry : bond 0.00498 (34854) covalent geometry : angle 0.82895 (47142) hydrogen bonds : bond 0.04625 ( 1392) hydrogen bonds : angle 5.58769 ( 3906) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8628 Ramachandran restraints generated. 4314 Oldfield, 0 Emsley, 4314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8628 Ramachandran restraints generated. 4314 Oldfield, 0 Emsley, 4314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 613 residues out of total 3690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 455 time to evaluate : 1.459 Fit side-chains revert: symmetry clash REVERT: A 82 ILE cc_start: 0.5249 (OUTLIER) cc_final: 0.4917 (pp) REVERT: A 141 GLU cc_start: 0.2099 (OUTLIER) cc_final: 0.1851 (pt0) REVERT: A 150 ASP cc_start: 0.4063 (m-30) cc_final: 0.3515 (p0) REVERT: A 151 ILE cc_start: 0.5847 (OUTLIER) cc_final: 0.5303 (mp) REVERT: A 426 LYS cc_start: 0.6248 (OUTLIER) cc_final: 0.5663 (mttt) REVERT: A 442 MET cc_start: 0.5283 (OUTLIER) cc_final: 0.4991 (ttp) REVERT: A 470 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.7361 (pp20) REVERT: A 478 ASP cc_start: 0.7123 (OUTLIER) cc_final: 0.6890 (m-30) REVERT: A 614 LYS cc_start: 0.5574 (OUTLIER) cc_final: 0.4943 (mptp) REVERT: A 662 ARG cc_start: 0.5149 (ttm110) cc_final: 0.4724 (mtm110) REVERT: B 51 LEU cc_start: 0.2628 (OUTLIER) cc_final: 0.2190 (tp) REVERT: B 60 LYS cc_start: 0.5175 (OUTLIER) cc_final: 0.4908 (mmtm) REVERT: B 101 SER cc_start: 0.4844 (p) cc_final: 0.4450 (t) REVERT: B 120 ASP cc_start: 0.0792 (OUTLIER) cc_final: 0.0361 (t0) REVERT: B 151 ILE cc_start: 0.5696 (OUTLIER) cc_final: 0.5429 (mp) REVERT: B 388 MET cc_start: 0.6020 (mtp) cc_final: 0.5655 (mtp) REVERT: B 426 LYS cc_start: 0.6014 (OUTLIER) cc_final: 0.5453 (mttt) REVERT: B 554 GLU cc_start: 0.7697 (OUTLIER) cc_final: 0.7290 (mt-10) REVERT: B 614 LYS cc_start: 0.5294 (OUTLIER) cc_final: 0.4924 (mptp) REVERT: C 46 MET cc_start: 0.2601 (mmp) cc_final: 0.2137 (ppp) REVERT: C 82 ILE cc_start: 0.5317 (OUTLIER) cc_final: 0.4923 (pp) REVERT: C 110 TYR cc_start: 0.3932 (m-10) cc_final: 0.3217 (m-10) REVERT: C 141 GLU cc_start: 0.1982 (OUTLIER) cc_final: 0.1769 (pt0) REVERT: C 150 ASP cc_start: 0.4324 (m-30) cc_final: 0.3673 (p0) REVERT: C 151 ILE cc_start: 0.5753 (OUTLIER) cc_final: 0.5213 (mp) REVERT: C 426 LYS cc_start: 0.6237 (OUTLIER) cc_final: 0.5704 (mttt) REVERT: C 470 GLU cc_start: 0.7667 (OUTLIER) cc_final: 0.7288 (pp20) REVERT: C 561 GLU cc_start: 0.7113 (mm-30) cc_final: 0.6800 (tp30) REVERT: D 141 GLU cc_start: 0.2089 (OUTLIER) cc_final: 0.1849 (pt0) REVERT: D 150 ASP cc_start: 0.4072 (m-30) cc_final: 0.3520 (p0) REVERT: D 151 ILE cc_start: 0.5853 (OUTLIER) cc_final: 0.5315 (mp) REVERT: D 294 GLU cc_start: 0.5802 (OUTLIER) cc_final: 0.5527 (tt0) REVERT: D 394 VAL cc_start: 0.3863 (OUTLIER) cc_final: 0.3641 (t) REVERT: D 470 GLU cc_start: 0.7613 (OUTLIER) cc_final: 0.7355 (pp20) REVERT: D 614 LYS cc_start: 0.5605 (OUTLIER) cc_final: 0.4974 (mptp) REVERT: D 662 ARG cc_start: 0.5147 (ttm110) cc_final: 0.4763 (mtm110) REVERT: E 51 LEU cc_start: 0.2657 (OUTLIER) cc_final: 0.2204 (tp) REVERT: E 60 LYS cc_start: 0.5130 (OUTLIER) cc_final: 0.4863 (mmtm) REVERT: E 101 SER cc_start: 0.4767 (p) cc_final: 0.4392 (t) REVERT: E 120 ASP cc_start: 0.0787 (OUTLIER) cc_final: 0.0355 (t0) REVERT: E 151 ILE cc_start: 0.5707 (mm) cc_final: 0.5447 (mp) REVERT: E 388 MET cc_start: 0.6015 (mtp) cc_final: 0.5643 (mtp) REVERT: E 426 LYS cc_start: 0.6067 (OUTLIER) cc_final: 0.5534 (mttt) REVERT: E 614 LYS cc_start: 0.5321 (OUTLIER) cc_final: 0.4956 (mptp) REVERT: E 738 GLU cc_start: 0.5718 (tp30) cc_final: 0.5472 (mm-30) REVERT: F 46 MET cc_start: 0.2640 (mmp) cc_final: 0.2107 (ppp) REVERT: F 101 SER cc_start: 0.4645 (p) cc_final: 0.4350 (t) REVERT: F 110 TYR cc_start: 0.3921 (m-10) cc_final: 0.3248 (m-10) REVERT: F 141 GLU cc_start: 0.1963 (OUTLIER) cc_final: 0.1758 (pt0) REVERT: F 150 ASP cc_start: 0.4365 (m-30) cc_final: 0.3643 (p0) REVERT: F 151 ILE cc_start: 0.5758 (OUTLIER) cc_final: 0.5199 (mp) REVERT: F 426 LYS cc_start: 0.6259 (OUTLIER) cc_final: 0.5753 (mttt) REVERT: F 470 GLU cc_start: 0.7654 (OUTLIER) cc_final: 0.7257 (pp20) REVERT: F 561 GLU cc_start: 0.7146 (mm-30) cc_final: 0.6816 (tp30) outliers start: 158 outliers final: 87 residues processed: 573 average time/residue: 0.7911 time to fit residues: 537.8833 Evaluate side-chains 556 residues out of total 3690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 434 time to evaluate : 1.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 327 GLN Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 349 ARG Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 426 LYS Chi-restraints excluded: chain A residue 442 MET Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 470 GLU Chi-restraints excluded: chain A residue 478 ASP Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 590 ILE Chi-restraints excluded: chain A residue 614 LYS Chi-restraints excluded: chain A residue 652 SER Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 60 LYS Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 327 GLN Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 426 LYS Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 590 ILE Chi-restraints excluded: chain B residue 614 LYS Chi-restraints excluded: chain B residue 652 SER Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 141 GLU Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 394 VAL Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain C residue 426 LYS Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 470 GLU Chi-restraints excluded: chain C residue 473 GLN Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 590 ILE Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 652 SER Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 670 VAL Chi-restraints excluded: chain D residue 141 GLU Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain D residue 294 GLU Chi-restraints excluded: chain D residue 327 GLN Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 342 ILE Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 394 VAL Chi-restraints excluded: chain D residue 423 ILE Chi-restraints excluded: chain D residue 470 GLU Chi-restraints excluded: chain D residue 497 VAL Chi-restraints excluded: chain D residue 590 ILE Chi-restraints excluded: chain D residue 614 LYS Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 652 SER Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 60 LYS Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 166 VAL Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain E residue 327 GLN Chi-restraints excluded: chain E residue 341 VAL Chi-restraints excluded: chain E residue 342 ILE Chi-restraints excluded: chain E residue 347 THR Chi-restraints excluded: chain E residue 426 LYS Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 497 VAL Chi-restraints excluded: chain E residue 590 ILE Chi-restraints excluded: chain E residue 614 LYS Chi-restraints excluded: chain E residue 652 SER Chi-restraints excluded: chain E residue 666 VAL Chi-restraints excluded: chain F residue 120 ASP Chi-restraints excluded: chain F residue 141 GLU Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 284 SER Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain F residue 342 ILE Chi-restraints excluded: chain F residue 347 THR Chi-restraints excluded: chain F residue 378 LEU Chi-restraints excluded: chain F residue 394 VAL Chi-restraints excluded: chain F residue 423 ILE Chi-restraints excluded: chain F residue 426 LYS Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 470 GLU Chi-restraints excluded: chain F residue 473 GLN Chi-restraints excluded: chain F residue 497 VAL Chi-restraints excluded: chain F residue 590 ILE Chi-restraints excluded: chain F residue 633 ILE Chi-restraints excluded: chain F residue 652 SER Chi-restraints excluded: chain F residue 666 VAL Chi-restraints excluded: chain F residue 670 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 428 optimal weight: 4.9990 chunk 363 optimal weight: 9.9990 chunk 224 optimal weight: 4.9990 chunk 308 optimal weight: 0.0870 chunk 266 optimal weight: 5.9990 chunk 43 optimal weight: 8.9990 chunk 240 optimal weight: 9.9990 chunk 106 optimal weight: 8.9990 chunk 413 optimal weight: 9.9990 chunk 66 optimal weight: 9.9990 chunk 47 optimal weight: 6.9990 overall best weight: 4.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 536 GLN ** C 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 536 GLN ** D 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 536 GLN ** F 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 536 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4611 r_free = 0.4611 target = 0.232068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.206205 restraints weight = 41630.468| |-----------------------------------------------------------------------------| r_work (start): 0.4362 rms_B_bonded: 1.65 r_work: 0.4142 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.4036 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.4036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6846 moved from start: 0.4651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 34854 Z= 0.175 Angle : 0.778 13.051 47142 Z= 0.384 Chirality : 0.048 0.230 5316 Planarity : 0.005 0.057 6186 Dihedral : 8.274 98.786 4836 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 14.01 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.23 % Favored : 92.65 % Rotamer: Outliers : 3.63 % Allowed : 22.49 % Favored : 73.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.29 % 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 aren not related in a simple way. whole: -1.88 (0.12), residues: 4314 helix: -0.62 (0.12), residues: 1764 sheet: -1.06 (0.20), residues: 618 loop : -1.83 (0.13), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG C 239 TYR 0.018 0.002 TYR A 244 PHE 0.015 0.002 PHE C 758 TRP 0.011 0.002 TRP E 476 HIS 0.004 0.001 HIS A 499 Details of bonding type rmsd covalent geometry : bond 0.00406 (34854) covalent geometry : angle 0.77793 (47142) hydrogen bonds : bond 0.04223 ( 1392) hydrogen bonds : angle 5.45138 ( 3906) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8628 Ramachandran restraints generated. 4314 Oldfield, 0 Emsley, 4314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8628 Ramachandran restraints generated. 4314 Oldfield, 0 Emsley, 4314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 580 residues out of total 3690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 446 time to evaluate : 1.428 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 ILE cc_start: 0.5190 (OUTLIER) cc_final: 0.4883 (pp) REVERT: A 141 GLU cc_start: 0.2121 (OUTLIER) cc_final: 0.1862 (pt0) REVERT: A 150 ASP cc_start: 0.4080 (m-30) cc_final: 0.3572 (p0) REVERT: A 151 ILE cc_start: 0.5897 (OUTLIER) cc_final: 0.5360 (mp) REVERT: A 426 LYS cc_start: 0.6200 (OUTLIER) cc_final: 0.5577 (mttt) REVERT: A 442 MET cc_start: 0.5265 (OUTLIER) cc_final: 0.5026 (ttp) REVERT: A 470 GLU cc_start: 0.7648 (OUTLIER) cc_final: 0.7398 (pp20) REVERT: A 478 ASP cc_start: 0.7099 (OUTLIER) cc_final: 0.6877 (m-30) REVERT: A 614 LYS cc_start: 0.5407 (OUTLIER) cc_final: 0.4893 (mptp) REVERT: A 662 ARG cc_start: 0.5089 (ttm110) cc_final: 0.4719 (mtm110) REVERT: A 740 MET cc_start: 0.6771 (tpp) cc_final: 0.6413 (mmm) REVERT: B 51 LEU cc_start: 0.2519 (OUTLIER) cc_final: 0.2138 (tp) REVERT: B 101 SER cc_start: 0.4809 (p) cc_final: 0.4474 (t) REVERT: B 120 ASP cc_start: 0.0882 (OUTLIER) cc_final: 0.0458 (t0) REVERT: B 151 ILE cc_start: 0.5778 (OUTLIER) cc_final: 0.5493 (mp) REVERT: B 426 LYS cc_start: 0.6052 (OUTLIER) cc_final: 0.5481 (mttt) REVERT: B 442 MET cc_start: 0.4898 (ttp) cc_final: 0.4647 (ttp) REVERT: B 554 GLU cc_start: 0.7740 (OUTLIER) cc_final: 0.7346 (mt-10) REVERT: B 614 LYS cc_start: 0.5225 (OUTLIER) cc_final: 0.4833 (mptp) REVERT: B 738 GLU cc_start: 0.5614 (tp30) cc_final: 0.5289 (tp30) REVERT: C 46 MET cc_start: 0.2409 (mmp) cc_final: 0.1962 (ppp) REVERT: C 82 ILE cc_start: 0.5239 (OUTLIER) cc_final: 0.4872 (pp) REVERT: C 110 TYR cc_start: 0.4001 (m-10) cc_final: 0.3306 (m-10) REVERT: C 141 GLU cc_start: 0.2002 (OUTLIER) cc_final: 0.1776 (pt0) REVERT: C 150 ASP cc_start: 0.4382 (m-30) cc_final: 0.3677 (p0) REVERT: C 151 ILE cc_start: 0.5753 (OUTLIER) cc_final: 0.5245 (mp) REVERT: C 426 LYS cc_start: 0.6213 (OUTLIER) cc_final: 0.5692 (mttt) REVERT: C 470 GLU cc_start: 0.7625 (OUTLIER) cc_final: 0.7267 (pp20) REVERT: C 561 GLU cc_start: 0.7143 (mm-30) cc_final: 0.6821 (tp30) REVERT: D 141 GLU cc_start: 0.2119 (OUTLIER) cc_final: 0.1867 (pt0) REVERT: D 150 ASP cc_start: 0.4084 (m-30) cc_final: 0.3593 (p0) REVERT: D 151 ILE cc_start: 0.5850 (OUTLIER) cc_final: 0.5320 (mp) REVERT: D 236 LYS cc_start: 0.6440 (mptt) cc_final: 0.6223 (mtpt) REVERT: D 294 GLU cc_start: 0.5813 (OUTLIER) cc_final: 0.5597 (tt0) REVERT: D 470 GLU cc_start: 0.7586 (OUTLIER) cc_final: 0.7333 (pp20) REVERT: D 614 LYS cc_start: 0.5451 (OUTLIER) cc_final: 0.4952 (mptp) REVERT: D 662 ARG cc_start: 0.5091 (ttm110) cc_final: 0.4707 (mtm110) REVERT: D 740 MET cc_start: 0.6883 (tpp) cc_final: 0.6539 (mmm) REVERT: E 51 LEU cc_start: 0.2523 (OUTLIER) cc_final: 0.2134 (tp) REVERT: E 60 LYS cc_start: 0.5001 (OUTLIER) cc_final: 0.4742 (mmtm) REVERT: E 101 SER cc_start: 0.4788 (p) cc_final: 0.4415 (t) REVERT: E 120 ASP cc_start: 0.0889 (OUTLIER) cc_final: 0.0460 (t0) REVERT: E 151 ILE cc_start: 0.5769 (OUTLIER) cc_final: 0.5506 (mp) REVERT: E 158 MET cc_start: 0.6592 (OUTLIER) cc_final: 0.6365 (mpp) REVERT: E 388 MET cc_start: 0.6028 (mtp) cc_final: 0.5737 (mtp) REVERT: E 426 LYS cc_start: 0.6070 (OUTLIER) cc_final: 0.5500 (mttt) REVERT: E 614 LYS cc_start: 0.5216 (OUTLIER) cc_final: 0.4913 (mptp) REVERT: E 738 GLU cc_start: 0.5695 (tp30) cc_final: 0.5480 (mm-30) REVERT: F 46 MET cc_start: 0.2546 (mmp) cc_final: 0.2045 (ppp) REVERT: F 141 GLU cc_start: 0.1985 (OUTLIER) cc_final: 0.1766 (pt0) REVERT: F 150 ASP cc_start: 0.4371 (m-30) cc_final: 0.3722 (p0) REVERT: F 151 ILE cc_start: 0.5745 (OUTLIER) cc_final: 0.5226 (mp) REVERT: F 426 LYS cc_start: 0.6231 (OUTLIER) cc_final: 0.5713 (mttt) REVERT: F 470 GLU cc_start: 0.7644 (OUTLIER) cc_final: 0.7278 (pp20) REVERT: F 561 GLU cc_start: 0.7143 (mm-30) cc_final: 0.6820 (tp30) outliers start: 134 outliers final: 83 residues processed: 552 average time/residue: 0.7867 time to fit residues: 513.2839 Evaluate side-chains 537 residues out of total 3690 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 419 time to evaluate : 1.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 327 GLN Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 423 ILE Chi-restraints excluded: chain A residue 426 LYS Chi-restraints excluded: chain A residue 442 MET Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 470 GLU Chi-restraints excluded: chain A residue 478 ASP Chi-restraints excluded: chain A residue 497 VAL Chi-restraints excluded: chain A residue 590 ILE Chi-restraints excluded: chain A residue 614 LYS Chi-restraints excluded: chain A residue 652 SER Chi-restraints excluded: chain A residue 666 VAL Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 120 ASP Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 327 GLN Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 426 LYS Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 590 ILE Chi-restraints excluded: chain B residue 614 LYS Chi-restraints excluded: chain B residue 652 SER Chi-restraints excluded: chain B residue 666 VAL Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 141 GLU Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 341 VAL Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 347 THR Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 426 LYS Chi-restraints excluded: chain C residue 441 VAL Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 470 GLU Chi-restraints excluded: chain C residue 473 GLN Chi-restraints excluded: chain C residue 497 VAL Chi-restraints excluded: chain C residue 590 ILE Chi-restraints excluded: chain C residue 633 ILE Chi-restraints excluded: chain C residue 652 SER Chi-restraints excluded: chain C residue 666 VAL Chi-restraints excluded: chain C residue 670 VAL Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 141 GLU Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain D residue 294 GLU Chi-restraints excluded: chain D residue 327 GLN Chi-restraints excluded: chain D residue 341 VAL Chi-restraints excluded: chain D residue 342 ILE Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 423 ILE Chi-restraints excluded: chain D residue 470 GLU Chi-restraints excluded: chain D residue 497 VAL Chi-restraints excluded: chain D residue 590 ILE Chi-restraints excluded: chain D residue 614 LYS Chi-restraints excluded: chain D residue 633 ILE Chi-restraints excluded: chain D residue 652 SER Chi-restraints excluded: chain D residue 666 VAL Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 60 LYS Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 158 MET Chi-restraints excluded: chain E residue 166 VAL Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain E residue 327 GLN Chi-restraints excluded: chain E residue 341 VAL Chi-restraints excluded: chain E residue 342 ILE Chi-restraints excluded: chain E residue 347 THR Chi-restraints excluded: chain E residue 426 LYS Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 497 VAL Chi-restraints excluded: chain E residue 590 ILE Chi-restraints excluded: chain E residue 614 LYS Chi-restraints excluded: chain E residue 652 SER Chi-restraints excluded: chain E residue 666 VAL Chi-restraints excluded: chain F residue 120 ASP Chi-restraints excluded: chain F residue 141 GLU Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 284 SER Chi-restraints excluded: chain F residue 335 LEU Chi-restraints excluded: chain F residue 341 VAL Chi-restraints excluded: chain F residue 342 ILE Chi-restraints excluded: chain F residue 347 THR Chi-restraints excluded: chain F residue 378 LEU Chi-restraints excluded: chain F residue 426 LYS Chi-restraints excluded: chain F residue 441 VAL Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 470 GLU Chi-restraints excluded: chain F residue 473 GLN Chi-restraints excluded: chain F residue 497 VAL Chi-restraints excluded: chain F residue 590 ILE Chi-restraints excluded: chain F residue 633 ILE Chi-restraints excluded: chain F residue 652 SER Chi-restraints excluded: chain F residue 670 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 294 optimal weight: 4.9990 chunk 379 optimal weight: 6.9990 chunk 95 optimal weight: 9.9990 chunk 314 optimal weight: 10.0000 chunk 227 optimal weight: 9.9990 chunk 306 optimal weight: 0.2980 chunk 230 optimal weight: 20.0000 chunk 312 optimal weight: 9.9990 chunk 324 optimal weight: 10.0000 chunk 428 optimal weight: 8.9990 chunk 25 optimal weight: 8.9990 overall best weight: 6.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 568 GLN ** B 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 536 GLN ** C 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 536 GLN ** D 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 536 GLN ** F 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 536 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4605 r_free = 0.4605 target = 0.231351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.205941 restraints weight = 41214.573| |-----------------------------------------------------------------------------| r_work (start): 0.4359 rms_B_bonded: 1.57 r_work: 0.4135 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.4027 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.4027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6874 moved from start: 0.4658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 34854 Z= 0.200 Angle : 0.816 12.885 47142 Z= 0.405 Chirality : 0.049 0.207 5316 Planarity : 0.006 0.052 6186 Dihedral : 8.494 101.674 4836 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 14.63 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.35 % Favored : 92.63 % Rotamer: Outliers : 3.74 % Allowed : 22.79 % Favored : 73.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.29 % 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 aren not related in a simple way. whole: -1.96 (0.12), residues: 4314 helix: -0.67 (0.12), residues: 1758 sheet: -1.11 (0.20), residues: 618 loop : -1.90 (0.13), residues: 1938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG F 239 TYR 0.020 0.002 TYR A 244 PHE 0.013 0.002 PHE F 758 TRP 0.013 0.002 TRP E 476 HIS 0.005 0.002 HIS A 384 Details of bonding type rmsd covalent geometry : bond 0.00465 (34854) covalent geometry : angle 0.81617 (47142) hydrogen bonds : bond 0.04497 ( 1392) hydrogen bonds : angle 5.55584 ( 3906) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17297.91 seconds wall clock time: 294 minutes 1.15 seconds (17641.15 seconds total)