Starting phenix.real_space_refine on Tue Aug 26 13:08:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sra_40724/08_2025/8sra_40724.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sra_40724/08_2025/8sra_40724.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8sra_40724/08_2025/8sra_40724.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sra_40724/08_2025/8sra_40724.map" model { file = "/net/cci-nas-00/data/ceres_data/8sra_40724/08_2025/8sra_40724.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sra_40724/08_2025/8sra_40724.cif" } resolution = 2.93 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= 0.140 sd= 1.451 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 Ca 8 9.91 5 S 164 5.16 5 C 23484 2.51 5 N 6516 2.21 5 O 6524 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: 36696 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 9088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1348, 9088 Classifications: {'peptide': 1348} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 480} Link IDs: {'PCIS': 2, 'PTRANS': 53, 'TRANS': 1292} Chain breaks: 4 Unresolved chain link angles: 12 Unresolved non-hydrogen bonds: 1683 Unresolved non-hydrogen angles: 2134 Unresolved non-hydrogen dihedrals: 1371 Unresolved non-hydrogen chiralities: 141 Planarities with less than four sites: {'GLU:plan': 47, 'ASN:plan1': 27, 'ASP:plan': 56, 'ARG:plan': 31, 'GLN:plan1': 22, 'PHE:plan': 19, 'HIS:plan': 10, 'TYR:plan': 9, 'TRP:plan': 6} Unresolved non-hydrogen planarities: 961 Chain: "D" Number of atoms: 9088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1348, 9088 Classifications: {'peptide': 1348} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 480} Link IDs: {'PCIS': 2, 'PTRANS': 53, 'TRANS': 1292} Chain breaks: 4 Unresolved chain link angles: 12 Unresolved non-hydrogen bonds: 1683 Unresolved non-hydrogen angles: 2134 Unresolved non-hydrogen dihedrals: 1371 Unresolved non-hydrogen chiralities: 141 Planarities with less than four sites: {'GLU:plan': 47, 'ASN:plan1': 27, 'ASP:plan': 56, 'ARG:plan': 31, 'GLN:plan1': 22, 'PHE:plan': 19, 'HIS:plan': 10, 'TYR:plan': 9, 'TRP:plan': 6} Unresolved non-hydrogen planarities: 961 Chain: "A" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 86 Unusual residues: {' CA': 2, 'CLR': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "D" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 86 Unusual residues: {' CA': 2, 'CLR': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Restraints were copied for chains: B, C Time building chain proxies: 12.44, per 1000 atoms: 0.34 Number of scatterers: 36696 At special positions: 0 Unit cell: (147.854, 147.854, 186.676, 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) Ca 8 19.99 S 164 16.00 O 6524 8.00 N 6516 7.00 C 23484 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 997 " - pdb=" SG CYS A1006 " distance=2.03 Simple disulfide: pdb=" SG CYS B 446 " - pdb=" SG CYS B 446 " distance=0.00 Simple disulfide: pdb=" SG CYS B 609 " - pdb=" SG CYS B 609 " distance=0.00 Simple disulfide: pdb=" SG CYS B 676 " - pdb=" SG CYS B 676 " distance=0.00 Simple disulfide: pdb=" SG CYS B 817 " - pdb=" SG CYS B 817 " distance=0.00 Simple disulfide: pdb=" SG CYS B 997 " - pdb=" SG CYS B1006 " distance=2.03 Simple disulfide: pdb=" SG CYS B 997 " - pdb=" SG CYS B 997 " distance=0.00 Simple disulfide: pdb=" SG CYS B 997 " - pdb=" SG CYS B1006 " distance=2.03 Simple disulfide: pdb=" SG CYS B1006 " - pdb=" SG CYS B 997 " distance=2.03 Simple disulfide: pdb=" SG CYS B1006 " - pdb=" SG CYS B1006 " distance=0.00 Simple disulfide: pdb=" SG CYS B1060 " - pdb=" SG CYS B1060 " distance=0.00 Simple disulfide: pdb=" SG CYS B1439 " - pdb=" SG CYS B1439 " distance=0.00 Simple disulfide: pdb=" SG CYS B 997 " - pdb=" SG CYS B1006 " distance=2.03 Simple disulfide: pdb=" SG CYS C 997 " - pdb=" SG CYS C1006 " distance=2.03 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: 3.07 Conformation dependent library (CDL) restraints added in 1.9 seconds Enol-peptide restraints added in 1.4 microseconds 10704 Ramachandran restraints generated. 5352 Oldfield, 0 Emsley, 5352 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10144 Finding SS restraints... Secondary structure from input PDB file: 224 helices and 36 sheets defined 59.8% alpha, 9.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.61 Creating SS restraints... Processing helix chain 'A' and resid 72 through 76 Processing helix chain 'A' and resid 118 through 135 removed outlier: 3.550A pdb=" N ALA A 122 " --> pdb=" O ASP A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 176 Processing helix chain 'A' and resid 186 through 203 removed outlier: 3.603A pdb=" N LYS A 190 " --> pdb=" O THR A 186 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ALA A 198 " --> pdb=" O GLN A 194 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N LEU A 199 " --> pdb=" O ILE A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 219 No H-bonds generated for 'chain 'A' and resid 217 through 219' Processing helix chain 'A' and resid 221 through 227 Processing helix chain 'A' and resid 271 through 286 Processing helix chain 'A' and resid 298 through 311 removed outlier: 3.815A pdb=" N LEU A 302 " --> pdb=" O GLY A 298 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLY A 303 " --> pdb=" O PRO A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 336 Processing helix chain 'A' and resid 339 through 343 removed outlier: 3.554A pdb=" N PHE A 342 " --> pdb=" O LEU A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 358 Processing helix chain 'A' and resid 362 through 377 removed outlier: 3.636A pdb=" N VAL A 377 " --> pdb=" O ALA A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 408 Processing helix chain 'A' and resid 410 through 421 Processing helix chain 'A' and resid 423 through 437 Processing helix chain 'A' and resid 439 through 457 removed outlier: 3.625A pdb=" N ILE A 443 " --> pdb=" O GLN A 439 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ASN A 448 " --> pdb=" O ALA A 444 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N ASP A 449 " --> pdb=" O ALA A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 469 removed outlier: 3.535A pdb=" N PHE A 469 " --> pdb=" O LEU A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 476 removed outlier: 3.593A pdb=" N GLU A 475 " --> pdb=" O LYS A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 492 Processing helix chain 'A' and resid 494 through 509 removed outlier: 3.584A pdb=" N LEU A 498 " --> pdb=" O PRO A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 522 removed outlier: 3.868A pdb=" N ARG A 517 " --> pdb=" O SER A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 553 Processing helix chain 'A' and resid 556 through 569 Processing helix chain 'A' and resid 577 through 586 removed outlier: 3.948A pdb=" N ILE A 580 " --> pdb=" O ASP A 577 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N SER A 583 " --> pdb=" O ILE A 580 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N LYS A 584 " --> pdb=" O TYR A 581 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TYR A 585 " --> pdb=" O ASP A 582 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASP A 586 " --> pdb=" O SER A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 590 through 610 removed outlier: 3.520A pdb=" N ARG A 594 " --> pdb=" O GLY A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 623 Processing helix chain 'A' and resid 625 through 642 removed outlier: 3.506A pdb=" N THR A 642 " --> pdb=" O GLU A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 680 Processing helix chain 'A' and resid 680 through 689 Processing helix chain 'A' and resid 692 through 696 removed outlier: 3.507A pdb=" N PHE A 695 " --> pdb=" O ASN A 692 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASN A 696 " --> pdb=" O ASP A 693 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 692 through 696' Processing helix chain 'A' and resid 699 through 707 Processing helix chain 'A' and resid 709 through 714 Processing helix chain 'A' and resid 715 through 728 Processing helix chain 'A' and resid 735 through 745 Processing helix chain 'A' and resid 745 through 750 removed outlier: 3.645A pdb=" N VAL A 749 " --> pdb=" O PHE A 745 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU A 750 " --> pdb=" O PRO A 746 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 745 through 750' Processing helix chain 'A' and resid 788 through 799 removed outlier: 4.039A pdb=" N ARG A 793 " --> pdb=" O HIS A 789 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 826 Processing helix chain 'A' and resid 833 through 856 Processing helix chain 'A' and resid 859 through 866 removed outlier: 4.055A pdb=" N ASP A 866 " --> pdb=" O GLU A 862 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 889 removed outlier: 3.525A pdb=" N ARG A 870 " --> pdb=" O ASP A 866 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ASP A 889 " --> pdb=" O THR A 885 " (cutoff:3.500A) Processing helix chain 'A' and resid 892 through 914 removed outlier: 4.082A pdb=" N PHE A 905 " --> pdb=" O GLY A 901 " (cutoff:3.500A) Processing helix chain 'A' and resid 915 through 921 removed outlier: 4.003A pdb=" N LEU A 920 " --> pdb=" O TYR A 917 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 961 removed outlier: 4.242A pdb=" N LYS A 927 " --> pdb=" O ASN A 923 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N LYS A 936 " --> pdb=" O MET A 932 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N ASP A 937 " --> pdb=" O GLU A 933 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ILE A 947 " --> pdb=" O PHE A 943 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N PHE A 948 " --> pdb=" O LEU A 944 " (cutoff:3.500A) Processing helix chain 'A' and resid 967 through 981 removed outlier: 3.686A pdb=" N PHE A 971 " --> pdb=" O SER A 967 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ARG A 977 " --> pdb=" O GLY A 973 " (cutoff:3.500A) Proline residue: A 978 - end of helix Processing helix chain 'A' and resid 982 through 984 No H-bonds generated for 'chain 'A' and resid 982 through 984' Processing helix chain 'A' and resid 987 through 995 Processing helix chain 'A' and resid 1010 through 1012 No H-bonds generated for 'chain 'A' and resid 1010 through 1012' Processing helix chain 'A' and resid 1013 through 1026 removed outlier: 3.710A pdb=" N LEU A1023 " --> pdb=" O ALA A1019 " (cutoff:3.500A) Processing helix chain 'A' and resid 1028 through 1066 removed outlier: 5.689A pdb=" N GLU A1046 " --> pdb=" O MET A1042 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N ALA A1047 " --> pdb=" O LYS A1043 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N TYR A1057 " --> pdb=" O ARG A1053 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ASP A1065 " --> pdb=" O ALA A1061 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ARG A1066 " --> pdb=" O GLU A1062 " (cutoff:3.500A) Processing helix chain 'A' and resid 1073 through 1090 removed outlier: 4.081A pdb=" N ALA A1077 " --> pdb=" O PHE A1073 " (cutoff:3.500A) Processing helix chain 'A' and resid 1102 through 1130 Processing helix chain 'A' and resid 1131 through 1168 Processing helix chain 'A' and resid 1255 through 1260 Processing helix chain 'A' and resid 1378 through 1391 Processing helix chain 'A' and resid 1403 through 1414 Processing helix chain 'A' and resid 1478 through 1491 removed outlier: 3.539A pdb=" N LEU A1482 " --> pdb=" O SER A1478 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 76 Processing helix chain 'B' and resid 118 through 135 removed outlier: 3.550A pdb=" N ALA B 122 " --> pdb=" O ASP B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 176 Processing helix chain 'B' and resid 186 through 203 removed outlier: 3.603A pdb=" N LYS B 190 " --> pdb=" O THR B 186 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ALA B 198 " --> pdb=" O GLN B 194 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N LEU B 199 " --> pdb=" O ILE B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 219 No H-bonds generated for 'chain 'B' and resid 217 through 219' Processing helix chain 'B' and resid 221 through 227 Processing helix chain 'B' and resid 271 through 286 Processing helix chain 'B' and resid 298 through 311 removed outlier: 3.815A pdb=" N LEU B 302 " --> pdb=" O GLY B 298 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLY B 303 " --> pdb=" O PRO B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 336 Processing helix chain 'B' and resid 339 through 343 removed outlier: 3.553A pdb=" N PHE B 342 " --> pdb=" O LEU B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 358 Processing helix chain 'B' and resid 362 through 377 removed outlier: 3.636A pdb=" N VAL B 377 " --> pdb=" O ALA B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 408 Processing helix chain 'B' and resid 410 through 421 Processing helix chain 'B' and resid 423 through 437 Processing helix chain 'B' and resid 439 through 457 removed outlier: 3.625A pdb=" N ILE B 443 " --> pdb=" O GLN B 439 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ASN B 448 " --> pdb=" O ALA B 444 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N ASP B 449 " --> pdb=" O ALA B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 469 removed outlier: 3.535A pdb=" N PHE B 469 " --> pdb=" O LEU B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 476 removed outlier: 3.592A pdb=" N GLU B 475 " --> pdb=" O LYS B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 492 Processing helix chain 'B' and resid 494 through 509 removed outlier: 3.584A pdb=" N LEU B 498 " --> pdb=" O PRO B 494 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 522 removed outlier: 3.868A pdb=" N ARG B 517 " --> pdb=" O SER B 513 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 553 Processing helix chain 'B' and resid 556 through 569 Processing helix chain 'B' and resid 577 through 586 removed outlier: 3.949A pdb=" N ILE B 580 " --> pdb=" O ASP B 577 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N SER B 583 " --> pdb=" O ILE B 580 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N LYS B 584 " --> pdb=" O TYR B 581 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TYR B 585 " --> pdb=" O ASP B 582 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASP B 586 " --> pdb=" O SER B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 590 through 610 removed outlier: 3.519A pdb=" N ARG B 594 " --> pdb=" O GLY B 590 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 623 Processing helix chain 'B' and resid 625 through 642 removed outlier: 3.506A pdb=" N THR B 642 " --> pdb=" O GLU B 638 " (cutoff:3.500A) Processing helix chain 'B' and resid 652 through 680 Processing helix chain 'B' and resid 680 through 689 Processing helix chain 'B' and resid 692 through 696 removed outlier: 3.508A pdb=" N PHE B 695 " --> pdb=" O ASN B 692 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASN B 696 " --> pdb=" O ASP B 693 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 692 through 696' Processing helix chain 'B' and resid 699 through 707 Processing helix chain 'B' and resid 709 through 714 Processing helix chain 'B' and resid 715 through 728 Processing helix chain 'B' and resid 735 through 745 Processing helix chain 'B' and resid 745 through 750 removed outlier: 3.644A pdb=" N VAL B 749 " --> pdb=" O PHE B 745 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU B 750 " --> pdb=" O PRO B 746 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 745 through 750' Processing helix chain 'B' and resid 788 through 799 removed outlier: 4.039A pdb=" N ARG B 793 " --> pdb=" O HIS B 789 " (cutoff:3.500A) Processing helix chain 'B' and resid 801 through 826 Processing helix chain 'B' and resid 833 through 856 Processing helix chain 'B' and resid 859 through 866 removed outlier: 4.054A pdb=" N ASP B 866 " --> pdb=" O GLU B 862 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 889 removed outlier: 3.525A pdb=" N ARG B 870 " --> pdb=" O ASP B 866 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ASP B 889 " --> pdb=" O THR B 885 " (cutoff:3.500A) Processing helix chain 'B' and resid 892 through 914 removed outlier: 4.082A pdb=" N PHE B 905 " --> pdb=" O GLY B 901 " (cutoff:3.500A) Processing helix chain 'B' and resid 915 through 921 removed outlier: 4.003A pdb=" N LEU B 920 " --> pdb=" O TYR B 917 " (cutoff:3.500A) Processing helix chain 'B' and resid 923 through 961 removed outlier: 4.242A pdb=" N LYS B 927 " --> pdb=" O ASN B 923 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N LYS B 936 " --> pdb=" O MET B 932 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N ASP B 937 " --> pdb=" O GLU B 933 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ILE B 947 " --> pdb=" O PHE B 943 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N PHE B 948 " --> pdb=" O LEU B 944 " (cutoff:3.500A) Processing helix chain 'B' and resid 967 through 981 removed outlier: 3.685A pdb=" N PHE B 971 " --> pdb=" O SER B 967 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ARG B 977 " --> pdb=" O GLY B 973 " (cutoff:3.500A) Proline residue: B 978 - end of helix Processing helix chain 'B' and resid 982 through 984 No H-bonds generated for 'chain 'B' and resid 982 through 984' Processing helix chain 'B' and resid 987 through 995 Processing helix chain 'B' and resid 1010 through 1012 No H-bonds generated for 'chain 'B' and resid 1010 through 1012' Processing helix chain 'B' and resid 1013 through 1026 removed outlier: 3.710A pdb=" N LEU B1023 " --> pdb=" O ALA B1019 " (cutoff:3.500A) Processing helix chain 'B' and resid 1028 through 1066 removed outlier: 5.689A pdb=" N GLU B1046 " --> pdb=" O MET B1042 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N ALA B1047 " --> pdb=" O LYS B1043 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N TYR B1057 " --> pdb=" O ARG B1053 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASP B1065 " --> pdb=" O ALA B1061 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ARG B1066 " --> pdb=" O GLU B1062 " (cutoff:3.500A) Processing helix chain 'B' and resid 1073 through 1090 removed outlier: 4.081A pdb=" N ALA B1077 " --> pdb=" O PHE B1073 " (cutoff:3.500A) Processing helix chain 'B' and resid 1102 through 1130 Processing helix chain 'B' and resid 1131 through 1168 Processing helix chain 'B' and resid 1255 through 1260 Processing helix chain 'B' and resid 1378 through 1391 Processing helix chain 'B' and resid 1403 through 1414 Processing helix chain 'B' and resid 1478 through 1491 removed outlier: 3.539A pdb=" N LEU B1482 " --> pdb=" O SER B1478 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 76 Processing helix chain 'C' and resid 118 through 135 removed outlier: 3.550A pdb=" N ALA C 122 " --> pdb=" O ASP C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 176 Processing helix chain 'C' and resid 186 through 203 removed outlier: 3.603A pdb=" N LYS C 190 " --> pdb=" O THR C 186 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ALA C 198 " --> pdb=" O GLN C 194 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N LEU C 199 " --> pdb=" O ILE C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 219 No H-bonds generated for 'chain 'C' and resid 217 through 219' Processing helix chain 'C' and resid 221 through 227 Processing helix chain 'C' and resid 271 through 286 Processing helix chain 'C' and resid 298 through 311 removed outlier: 3.815A pdb=" N LEU C 302 " --> pdb=" O GLY C 298 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLY C 303 " --> pdb=" O PRO C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 336 Processing helix chain 'C' and resid 339 through 343 removed outlier: 3.554A pdb=" N PHE C 342 " --> pdb=" O LEU C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 358 Processing helix chain 'C' and resid 362 through 377 removed outlier: 3.636A pdb=" N VAL C 377 " --> pdb=" O ALA C 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 395 through 408 Processing helix chain 'C' and resid 410 through 421 Processing helix chain 'C' and resid 423 through 437 Processing helix chain 'C' and resid 439 through 457 removed outlier: 3.625A pdb=" N ILE C 443 " --> pdb=" O GLN C 439 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ASN C 448 " --> pdb=" O ALA C 444 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N ASP C 449 " --> pdb=" O ALA C 445 " (cutoff:3.500A) Processing helix chain 'C' and resid 459 through 469 removed outlier: 3.535A pdb=" N PHE C 469 " --> pdb=" O LEU C 465 " (cutoff:3.500A) Processing helix chain 'C' and resid 472 through 476 removed outlier: 3.593A pdb=" N GLU C 475 " --> pdb=" O LYS C 472 " (cutoff:3.500A) Processing helix chain 'C' and resid 487 through 492 Processing helix chain 'C' and resid 494 through 509 removed outlier: 3.584A pdb=" N LEU C 498 " --> pdb=" O PRO C 494 " (cutoff:3.500A) Processing helix chain 'C' and resid 513 through 522 removed outlier: 3.867A pdb=" N ARG C 517 " --> pdb=" O SER C 513 " (cutoff:3.500A) Processing helix chain 'C' and resid 547 through 553 Processing helix chain 'C' and resid 556 through 569 Processing helix chain 'C' and resid 577 through 586 removed outlier: 3.947A pdb=" N ILE C 580 " --> pdb=" O ASP C 577 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N SER C 583 " --> pdb=" O ILE C 580 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N LYS C 584 " --> pdb=" O TYR C 581 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TYR C 585 " --> pdb=" O ASP C 582 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASP C 586 " --> pdb=" O SER C 583 " (cutoff:3.500A) Processing helix chain 'C' and resid 590 through 610 removed outlier: 3.520A pdb=" N ARG C 594 " --> pdb=" O GLY C 590 " (cutoff:3.500A) Processing helix chain 'C' and resid 612 through 623 Processing helix chain 'C' and resid 625 through 642 removed outlier: 3.507A pdb=" N THR C 642 " --> pdb=" O GLU C 638 " (cutoff:3.500A) Processing helix chain 'C' and resid 652 through 680 Processing helix chain 'C' and resid 680 through 689 Processing helix chain 'C' and resid 692 through 696 removed outlier: 3.507A pdb=" N PHE C 695 " --> pdb=" O ASN C 692 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASN C 696 " --> pdb=" O ASP C 693 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 692 through 696' Processing helix chain 'C' and resid 699 through 707 Processing helix chain 'C' and resid 709 through 714 Processing helix chain 'C' and resid 715 through 728 Processing helix chain 'C' and resid 735 through 745 Processing helix chain 'C' and resid 745 through 750 removed outlier: 3.645A pdb=" N VAL C 749 " --> pdb=" O PHE C 745 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU C 750 " --> pdb=" O PRO C 746 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 745 through 750' Processing helix chain 'C' and resid 788 through 799 removed outlier: 4.040A pdb=" N ARG C 793 " --> pdb=" O HIS C 789 " (cutoff:3.500A) Processing helix chain 'C' and resid 801 through 826 Processing helix chain 'C' and resid 833 through 856 Processing helix chain 'C' and resid 859 through 866 removed outlier: 4.055A pdb=" N ASP C 866 " --> pdb=" O GLU C 862 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 889 removed outlier: 3.526A pdb=" N ARG C 870 " --> pdb=" O ASP C 866 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ASP C 889 " --> pdb=" O THR C 885 " (cutoff:3.500A) Processing helix chain 'C' and resid 892 through 914 removed outlier: 4.082A pdb=" N PHE C 905 " --> pdb=" O GLY C 901 " (cutoff:3.500A) Processing helix chain 'C' and resid 915 through 921 removed outlier: 4.003A pdb=" N LEU C 920 " --> pdb=" O TYR C 917 " (cutoff:3.500A) Processing helix chain 'C' and resid 923 through 961 removed outlier: 4.242A pdb=" N LYS C 927 " --> pdb=" O ASN C 923 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N LYS C 936 " --> pdb=" O MET C 932 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N ASP C 937 " --> pdb=" O GLU C 933 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ILE C 947 " --> pdb=" O PHE C 943 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N PHE C 948 " --> pdb=" O LEU C 944 " (cutoff:3.500A) Processing helix chain 'C' and resid 967 through 981 removed outlier: 3.686A pdb=" N PHE C 971 " --> pdb=" O SER C 967 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ARG C 977 " --> pdb=" O GLY C 973 " (cutoff:3.500A) Proline residue: C 978 - end of helix Processing helix chain 'C' and resid 982 through 984 No H-bonds generated for 'chain 'C' and resid 982 through 984' Processing helix chain 'C' and resid 987 through 995 Processing helix chain 'C' and resid 1010 through 1012 No H-bonds generated for 'chain 'C' and resid 1010 through 1012' Processing helix chain 'C' and resid 1013 through 1026 removed outlier: 3.710A pdb=" N LEU C1023 " --> pdb=" O ALA C1019 " (cutoff:3.500A) Processing helix chain 'C' and resid 1028 through 1066 removed outlier: 5.689A pdb=" N GLU C1046 " --> pdb=" O MET C1042 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N ALA C1047 " --> pdb=" O LYS C1043 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N TYR C1057 " --> pdb=" O ARG C1053 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASP C1065 " --> pdb=" O ALA C1061 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ARG C1066 " --> pdb=" O GLU C1062 " (cutoff:3.500A) Processing helix chain 'C' and resid 1073 through 1090 removed outlier: 4.081A pdb=" N ALA C1077 " --> pdb=" O PHE C1073 " (cutoff:3.500A) Processing helix chain 'C' and resid 1102 through 1130 Processing helix chain 'C' and resid 1131 through 1168 Processing helix chain 'C' and resid 1255 through 1260 Processing helix chain 'C' and resid 1378 through 1391 Processing helix chain 'C' and resid 1403 through 1414 Processing helix chain 'C' and resid 1478 through 1491 removed outlier: 3.539A pdb=" N LEU C1482 " --> pdb=" O SER C1478 " (cutoff:3.500A) Processing helix chain 'D' and resid 72 through 76 Processing helix chain 'D' and resid 118 through 135 removed outlier: 3.550A pdb=" N ALA D 122 " --> pdb=" O ASP D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 176 Processing helix chain 'D' and resid 186 through 203 removed outlier: 3.603A pdb=" N LYS D 190 " --> pdb=" O THR D 186 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ALA D 198 " --> pdb=" O GLN D 194 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N LEU D 199 " --> pdb=" O ILE D 195 " (cutoff:3.500A) Processing helix chain 'D' and resid 217 through 219 No H-bonds generated for 'chain 'D' and resid 217 through 219' Processing helix chain 'D' and resid 221 through 227 Processing helix chain 'D' and resid 271 through 286 Processing helix chain 'D' and resid 298 through 311 removed outlier: 3.815A pdb=" N LEU D 302 " --> pdb=" O GLY D 298 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLY D 303 " --> pdb=" O PRO D 299 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 336 Processing helix chain 'D' and resid 339 through 343 removed outlier: 3.553A pdb=" N PHE D 342 " --> pdb=" O LEU D 339 " (cutoff:3.500A) Processing helix chain 'D' and resid 346 through 358 Processing helix chain 'D' and resid 362 through 377 removed outlier: 3.636A pdb=" N VAL D 377 " --> pdb=" O ALA D 373 " (cutoff:3.500A) Processing helix chain 'D' and resid 395 through 408 Processing helix chain 'D' and resid 410 through 421 Processing helix chain 'D' and resid 423 through 437 Processing helix chain 'D' and resid 439 through 457 removed outlier: 3.625A pdb=" N ILE D 443 " --> pdb=" O GLN D 439 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ASN D 448 " --> pdb=" O ALA D 444 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N ASP D 449 " --> pdb=" O ALA D 445 " (cutoff:3.500A) Processing helix chain 'D' and resid 459 through 469 removed outlier: 3.534A pdb=" N PHE D 469 " --> pdb=" O LEU D 465 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 476 removed outlier: 3.592A pdb=" N GLU D 475 " --> pdb=" O LYS D 472 " (cutoff:3.500A) Processing helix chain 'D' and resid 487 through 492 Processing helix chain 'D' and resid 494 through 509 removed outlier: 3.585A pdb=" N LEU D 498 " --> pdb=" O PRO D 494 " (cutoff:3.500A) Processing helix chain 'D' and resid 513 through 522 removed outlier: 3.868A pdb=" N ARG D 517 " --> pdb=" O SER D 513 " (cutoff:3.500A) Processing helix chain 'D' and resid 547 through 553 Processing helix chain 'D' and resid 556 through 569 Processing helix chain 'D' and resid 577 through 586 removed outlier: 3.947A pdb=" N ILE D 580 " --> pdb=" O ASP D 577 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N SER D 583 " --> pdb=" O ILE D 580 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N LYS D 584 " --> pdb=" O TYR D 581 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TYR D 585 " --> pdb=" O ASP D 582 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASP D 586 " --> pdb=" O SER D 583 " (cutoff:3.500A) Processing helix chain 'D' and resid 590 through 610 removed outlier: 3.519A pdb=" N ARG D 594 " --> pdb=" O GLY D 590 " (cutoff:3.500A) Processing helix chain 'D' and resid 612 through 623 Processing helix chain 'D' and resid 625 through 642 removed outlier: 3.506A pdb=" N THR D 642 " --> pdb=" O GLU D 638 " (cutoff:3.500A) Processing helix chain 'D' and resid 652 through 680 Processing helix chain 'D' and resid 680 through 689 Processing helix chain 'D' and resid 692 through 696 removed outlier: 3.508A pdb=" N PHE D 695 " --> pdb=" O ASN D 692 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASN D 696 " --> pdb=" O ASP D 693 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 692 through 696' Processing helix chain 'D' and resid 699 through 707 Processing helix chain 'D' and resid 709 through 714 Processing helix chain 'D' and resid 715 through 728 Processing helix chain 'D' and resid 735 through 745 Processing helix chain 'D' and resid 745 through 750 removed outlier: 3.645A pdb=" N VAL D 749 " --> pdb=" O PHE D 745 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU D 750 " --> pdb=" O PRO D 746 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 745 through 750' Processing helix chain 'D' and resid 788 through 799 removed outlier: 4.038A pdb=" N ARG D 793 " --> pdb=" O HIS D 789 " (cutoff:3.500A) Processing helix chain 'D' and resid 801 through 826 Processing helix chain 'D' and resid 833 through 856 Processing helix chain 'D' and resid 859 through 866 removed outlier: 4.054A pdb=" N ASP D 866 " --> pdb=" O GLU D 862 " (cutoff:3.500A) Processing helix chain 'D' and resid 866 through 889 removed outlier: 3.526A pdb=" N ARG D 870 " --> pdb=" O ASP D 866 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ASP D 889 " --> pdb=" O THR D 885 " (cutoff:3.500A) Processing helix chain 'D' and resid 892 through 914 removed outlier: 4.082A pdb=" N PHE D 905 " --> pdb=" O GLY D 901 " (cutoff:3.500A) Processing helix chain 'D' and resid 915 through 921 removed outlier: 4.003A pdb=" N LEU D 920 " --> pdb=" O TYR D 917 " (cutoff:3.500A) Processing helix chain 'D' and resid 923 through 961 removed outlier: 4.242A pdb=" N LYS D 927 " --> pdb=" O ASN D 923 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N LYS D 936 " --> pdb=" O MET D 932 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N ASP D 937 " --> pdb=" O GLU D 933 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ILE D 947 " --> pdb=" O PHE D 943 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N PHE D 948 " --> pdb=" O LEU D 944 " (cutoff:3.500A) Processing helix chain 'D' and resid 967 through 981 removed outlier: 3.685A pdb=" N PHE D 971 " --> pdb=" O SER D 967 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ARG D 977 " --> pdb=" O GLY D 973 " (cutoff:3.500A) Proline residue: D 978 - end of helix Processing helix chain 'D' and resid 982 through 984 No H-bonds generated for 'chain 'D' and resid 982 through 984' Processing helix chain 'D' and resid 987 through 995 Processing helix chain 'D' and resid 1010 through 1012 No H-bonds generated for 'chain 'D' and resid 1010 through 1012' Processing helix chain 'D' and resid 1013 through 1026 removed outlier: 3.710A pdb=" N LEU D1023 " --> pdb=" O ALA D1019 " (cutoff:3.500A) Processing helix chain 'D' and resid 1028 through 1066 removed outlier: 5.689A pdb=" N GLU D1046 " --> pdb=" O MET D1042 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N ALA D1047 " --> pdb=" O LYS D1043 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N TYR D1057 " --> pdb=" O ARG D1053 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ASP D1065 " --> pdb=" O ALA D1061 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ARG D1066 " --> pdb=" O GLU D1062 " (cutoff:3.500A) Processing helix chain 'D' and resid 1073 through 1090 removed outlier: 4.081A pdb=" N ALA D1077 " --> pdb=" O PHE D1073 " (cutoff:3.500A) Processing helix chain 'D' and resid 1102 through 1130 Processing helix chain 'D' and resid 1131 through 1168 Processing helix chain 'D' and resid 1255 through 1260 Processing helix chain 'D' and resid 1378 through 1391 Processing helix chain 'D' and resid 1403 through 1414 Processing helix chain 'D' and resid 1478 through 1491 removed outlier: 3.538A pdb=" N LEU D1482 " --> pdb=" O SER D1478 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 56 through 60 Processing sheet with id=AA2, first strand: chain 'A' and resid 80 through 81 Processing sheet with id=AA3, first strand: chain 'A' and resid 232 through 236 removed outlier: 6.047A pdb=" N ILE A 233 " --> pdb=" O TRP A 96 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N THR A 98 " --> pdb=" O ILE A 233 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N LEU A 259 " --> pdb=" O PRO A 109 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LEU A 111 " --> pdb=" O LEU A 259 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N ASP A 261 " --> pdb=" O LEU A 111 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N LEU A 113 " --> pdb=" O ASP A 261 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N THR A 210 " --> pdb=" O LEU A 256 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N LEU A 258 " --> pdb=" O THR A 210 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N GLY A 212 " --> pdb=" O LEU A 258 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N VAL A 260 " --> pdb=" O GLY A 212 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N ALA A 214 " --> pdb=" O VAL A 260 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N VAL A 316 " --> pdb=" O VAL A 290 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N THR A 292 " --> pdb=" O VAL A 316 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N VAL A 318 " --> pdb=" O THR A 292 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N VAL A 294 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N ILE A 315 " --> pdb=" O VAL A 384 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N TYR A 386 " --> pdb=" O ILE A 315 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N VAL A 317 " --> pdb=" O TYR A 386 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1251 through 1252 removed outlier: 6.491A pdb=" N VAL A1251 " --> pdb=" O THR A1315 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 1279 through 1281 Processing sheet with id=AA6, first strand: chain 'A' and resid 1297 through 1298 removed outlier: 3.922A pdb=" N SER A1297 " --> pdb=" O ILE A1306 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1366 through 1367 removed outlier: 5.200A pdb=" N VAL A1333 " --> pdb=" O VAL A1356 " (cutoff:3.500A) removed outlier: 8.257A pdb=" N ILE A1358 " --> pdb=" O THR A1331 " (cutoff:3.500A) removed outlier: 11.244A pdb=" N THR A1331 " --> pdb=" O ILE A1358 " (cutoff:3.500A) removed outlier: 13.847A pdb=" N ARG A1360 " --> pdb=" O ALA A1329 " (cutoff:3.500A) removed outlier: 17.866A pdb=" N ALA A1329 " --> pdb=" O ARG A1360 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N GLY A1324 " --> pdb=" O TRP A1434 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N GLU A1436 " --> pdb=" O GLY A1324 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N ASN A1326 " --> pdb=" O GLU A1436 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N THR A1438 " --> pdb=" O ASN A1326 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ALA A1328 " --> pdb=" O THR A1438 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N VAL A1440 " --> pdb=" O ALA A1328 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ASP A1330 " --> pdb=" O VAL A1440 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N PHE A1442 " --> pdb=" O ASP A1330 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N VAL A1332 " --> pdb=" O PHE A1442 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N ASP A1444 " --> pdb=" O VAL A1332 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N THR A1334 " --> pdb=" O ASP A1444 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ALA A1420 " --> pdb=" O CYS A1439 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N ASN A1441 " --> pdb=" O ILE A1418 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ILE A1418 " --> pdb=" O ASN A1441 " (cutoff:3.500A) removed outlier: 8.192A pdb=" N HIS A1443 " --> pdb=" O GLY A1416 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N GLY A1416 " --> pdb=" O HIS A1443 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1370 through 1372 removed outlier: 17.866A pdb=" N ALA A1329 " --> pdb=" O ARG A1360 " (cutoff:3.500A) removed outlier: 13.847A pdb=" N ARG A1360 " --> pdb=" O ALA A1329 " (cutoff:3.500A) removed outlier: 11.244A pdb=" N THR A1331 " --> pdb=" O ILE A1358 " (cutoff:3.500A) removed outlier: 8.257A pdb=" N ILE A1358 " --> pdb=" O THR A1331 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N VAL A1333 " --> pdb=" O VAL A1356 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N LEU A1353 " --> pdb=" O MET A1468 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N MET A1468 " --> pdb=" O LEU A1353 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N PHE A1355 " --> pdb=" O TRP A1466 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N TRP A1466 " --> pdb=" O PHE A1355 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ALA A1357 " --> pdb=" O ALA A1464 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N ALA A1464 " --> pdb=" O ALA A1357 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N GLN A1359 " --> pdb=" O GLU A1462 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1346 through 1347 Processing sheet with id=AB1, first strand: chain 'B' and resid 56 through 60 Processing sheet with id=AB2, first strand: chain 'B' and resid 80 through 81 Processing sheet with id=AB3, first strand: chain 'B' and resid 232 through 236 removed outlier: 6.047A pdb=" N ILE B 233 " --> pdb=" O TRP B 96 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N THR B 98 " --> pdb=" O ILE B 233 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N LEU B 259 " --> pdb=" O PRO B 109 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LEU B 111 " --> pdb=" O LEU B 259 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N ASP B 261 " --> pdb=" O LEU B 111 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N LEU B 113 " --> pdb=" O ASP B 261 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N THR B 210 " --> pdb=" O LEU B 256 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N LEU B 258 " --> pdb=" O THR B 210 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N GLY B 212 " --> pdb=" O LEU B 258 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N VAL B 260 " --> pdb=" O GLY B 212 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ALA B 214 " --> pdb=" O VAL B 260 " (cutoff:3.500A) removed outlier: 8.195A pdb=" N VAL B 316 " --> pdb=" O VAL B 290 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N THR B 292 " --> pdb=" O VAL B 316 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N VAL B 318 " --> pdb=" O THR B 292 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N VAL B 294 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N ILE B 315 " --> pdb=" O VAL B 384 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N TYR B 386 " --> pdb=" O ILE B 315 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N VAL B 317 " --> pdb=" O TYR B 386 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 1251 through 1252 removed outlier: 6.491A pdb=" N VAL B1251 " --> pdb=" O THR B1315 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 1279 through 1281 Processing sheet with id=AB6, first strand: chain 'B' and resid 1297 through 1298 removed outlier: 3.922A pdb=" N SER B1297 " --> pdb=" O ILE B1306 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 1366 through 1367 removed outlier: 5.200A pdb=" N VAL B1333 " --> pdb=" O VAL B1356 " (cutoff:3.500A) removed outlier: 8.258A pdb=" N ILE B1358 " --> pdb=" O THR B1331 " (cutoff:3.500A) removed outlier: 11.245A pdb=" N THR B1331 " --> pdb=" O ILE B1358 " (cutoff:3.500A) removed outlier: 13.847A pdb=" N ARG B1360 " --> pdb=" O ALA B1329 " (cutoff:3.500A) removed outlier: 17.866A pdb=" N ALA B1329 " --> pdb=" O ARG B1360 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N GLY B1324 " --> pdb=" O TRP B1434 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N GLU B1436 " --> pdb=" O GLY B1324 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N ASN B1326 " --> pdb=" O GLU B1436 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N THR B1438 " --> pdb=" O ASN B1326 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ALA B1328 " --> pdb=" O THR B1438 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N VAL B1440 " --> pdb=" O ALA B1328 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ASP B1330 " --> pdb=" O VAL B1440 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N PHE B1442 " --> pdb=" O ASP B1330 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N VAL B1332 " --> pdb=" O PHE B1442 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N ASP B1444 " --> pdb=" O VAL B1332 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N THR B1334 " --> pdb=" O ASP B1444 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ALA B1420 " --> pdb=" O CYS B1439 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N ASN B1441 " --> pdb=" O ILE B1418 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ILE B1418 " --> pdb=" O ASN B1441 " (cutoff:3.500A) removed outlier: 8.192A pdb=" N HIS B1443 " --> pdb=" O GLY B1416 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N GLY B1416 " --> pdb=" O HIS B1443 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 1370 through 1372 removed outlier: 17.866A pdb=" N ALA B1329 " --> pdb=" O ARG B1360 " (cutoff:3.500A) removed outlier: 13.847A pdb=" N ARG B1360 " --> pdb=" O ALA B1329 " (cutoff:3.500A) removed outlier: 11.245A pdb=" N THR B1331 " --> pdb=" O ILE B1358 " (cutoff:3.500A) removed outlier: 8.258A pdb=" N ILE B1358 " --> pdb=" O THR B1331 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N VAL B1333 " --> pdb=" O VAL B1356 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N LEU B1353 " --> pdb=" O MET B1468 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N MET B1468 " --> pdb=" O LEU B1353 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N PHE B1355 " --> pdb=" O TRP B1466 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N TRP B1466 " --> pdb=" O PHE B1355 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ALA B1357 " --> pdb=" O ALA B1464 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N ALA B1464 " --> pdb=" O ALA B1357 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N GLN B1359 " --> pdb=" O GLU B1462 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 1346 through 1347 Processing sheet with id=AC1, first strand: chain 'C' and resid 56 through 60 Processing sheet with id=AC2, first strand: chain 'C' and resid 80 through 81 Processing sheet with id=AC3, first strand: chain 'C' and resid 232 through 236 removed outlier: 6.047A pdb=" N ILE C 233 " --> pdb=" O TRP C 96 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N THR C 98 " --> pdb=" O ILE C 233 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N LEU C 259 " --> pdb=" O PRO C 109 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LEU C 111 " --> pdb=" O LEU C 259 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N ASP C 261 " --> pdb=" O LEU C 111 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N LEU C 113 " --> pdb=" O ASP C 261 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N THR C 210 " --> pdb=" O LEU C 256 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N LEU C 258 " --> pdb=" O THR C 210 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N GLY C 212 " --> pdb=" O LEU C 258 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N VAL C 260 " --> pdb=" O GLY C 212 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ALA C 214 " --> pdb=" O VAL C 260 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N VAL C 316 " --> pdb=" O VAL C 290 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N THR C 292 " --> pdb=" O VAL C 316 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N VAL C 318 " --> pdb=" O THR C 292 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N VAL C 294 " --> pdb=" O VAL C 318 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N ILE C 315 " --> pdb=" O VAL C 384 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N TYR C 386 " --> pdb=" O ILE C 315 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N VAL C 317 " --> pdb=" O TYR C 386 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 1251 through 1252 removed outlier: 6.490A pdb=" N VAL C1251 " --> pdb=" O THR C1315 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'C' and resid 1279 through 1281 Processing sheet with id=AC6, first strand: chain 'C' and resid 1297 through 1298 removed outlier: 3.922A pdb=" N SER C1297 " --> pdb=" O ILE C1306 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 1366 through 1367 removed outlier: 5.201A pdb=" N VAL C1333 " --> pdb=" O VAL C1356 " (cutoff:3.500A) removed outlier: 8.257A pdb=" N ILE C1358 " --> pdb=" O THR C1331 " (cutoff:3.500A) removed outlier: 11.245A pdb=" N THR C1331 " --> pdb=" O ILE C1358 " (cutoff:3.500A) removed outlier: 13.846A pdb=" N ARG C1360 " --> pdb=" O ALA C1329 " (cutoff:3.500A) removed outlier: 17.866A pdb=" N ALA C1329 " --> pdb=" O ARG C1360 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N GLY C1324 " --> pdb=" O TRP C1434 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N GLU C1436 " --> pdb=" O GLY C1324 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N ASN C1326 " --> pdb=" O GLU C1436 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N THR C1438 " --> pdb=" O ASN C1326 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ALA C1328 " --> pdb=" O THR C1438 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N VAL C1440 " --> pdb=" O ALA C1328 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ASP C1330 " --> pdb=" O VAL C1440 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N PHE C1442 " --> pdb=" O ASP C1330 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N VAL C1332 " --> pdb=" O PHE C1442 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N ASP C1444 " --> pdb=" O VAL C1332 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N THR C1334 " --> pdb=" O ASP C1444 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ALA C1420 " --> pdb=" O CYS C1439 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N ASN C1441 " --> pdb=" O ILE C1418 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ILE C1418 " --> pdb=" O ASN C1441 " (cutoff:3.500A) removed outlier: 8.192A pdb=" N HIS C1443 " --> pdb=" O GLY C1416 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N GLY C1416 " --> pdb=" O HIS C1443 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 1370 through 1372 removed outlier: 17.866A pdb=" N ALA C1329 " --> pdb=" O ARG C1360 " (cutoff:3.500A) removed outlier: 13.846A pdb=" N ARG C1360 " --> pdb=" O ALA C1329 " (cutoff:3.500A) removed outlier: 11.245A pdb=" N THR C1331 " --> pdb=" O ILE C1358 " (cutoff:3.500A) removed outlier: 8.257A pdb=" N ILE C1358 " --> pdb=" O THR C1331 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N VAL C1333 " --> pdb=" O VAL C1356 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N LEU C1353 " --> pdb=" O MET C1468 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N MET C1468 " --> pdb=" O LEU C1353 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N PHE C1355 " --> pdb=" O TRP C1466 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N TRP C1466 " --> pdb=" O PHE C1355 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ALA C1357 " --> pdb=" O ALA C1464 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N ALA C1464 " --> pdb=" O ALA C1357 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N GLN C1359 " --> pdb=" O GLU C1462 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 1346 through 1347 Processing sheet with id=AD1, first strand: chain 'D' and resid 56 through 60 Processing sheet with id=AD2, first strand: chain 'D' and resid 80 through 81 Processing sheet with id=AD3, first strand: chain 'D' and resid 232 through 236 removed outlier: 6.048A pdb=" N ILE D 233 " --> pdb=" O TRP D 96 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N THR D 98 " --> pdb=" O ILE D 233 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N LEU D 259 " --> pdb=" O PRO D 109 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LEU D 111 " --> pdb=" O LEU D 259 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N ASP D 261 " --> pdb=" O LEU D 111 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LEU D 113 " --> pdb=" O ASP D 261 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N THR D 210 " --> pdb=" O LEU D 256 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N LEU D 258 " --> pdb=" O THR D 210 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N GLY D 212 " --> pdb=" O LEU D 258 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N VAL D 260 " --> pdb=" O GLY D 212 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N ALA D 214 " --> pdb=" O VAL D 260 " (cutoff:3.500A) removed outlier: 8.195A pdb=" N VAL D 316 " --> pdb=" O VAL D 290 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N THR D 292 " --> pdb=" O VAL D 316 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N VAL D 318 " --> pdb=" O THR D 292 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N VAL D 294 " --> pdb=" O VAL D 318 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N ILE D 315 " --> pdb=" O VAL D 384 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N TYR D 386 " --> pdb=" O ILE D 315 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N VAL D 317 " --> pdb=" O TYR D 386 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 1251 through 1252 removed outlier: 6.491A pdb=" N VAL D1251 " --> pdb=" O THR D1315 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'D' and resid 1279 through 1281 Processing sheet with id=AD6, first strand: chain 'D' and resid 1297 through 1298 removed outlier: 3.922A pdb=" N SER D1297 " --> pdb=" O ILE D1306 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 1366 through 1367 removed outlier: 5.200A pdb=" N VAL D1333 " --> pdb=" O VAL D1356 " (cutoff:3.500A) removed outlier: 8.257A pdb=" N ILE D1358 " --> pdb=" O THR D1331 " (cutoff:3.500A) removed outlier: 11.244A pdb=" N THR D1331 " --> pdb=" O ILE D1358 " (cutoff:3.500A) removed outlier: 13.847A pdb=" N ARG D1360 " --> pdb=" O ALA D1329 " (cutoff:3.500A) removed outlier: 17.866A pdb=" N ALA D1329 " --> pdb=" O ARG D1360 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N GLY D1324 " --> pdb=" O TRP D1434 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N GLU D1436 " --> pdb=" O GLY D1324 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N ASN D1326 " --> pdb=" O GLU D1436 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N THR D1438 " --> pdb=" O ASN D1326 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ALA D1328 " --> pdb=" O THR D1438 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N VAL D1440 " --> pdb=" O ALA D1328 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ASP D1330 " --> pdb=" O VAL D1440 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N PHE D1442 " --> pdb=" O ASP D1330 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N VAL D1332 " --> pdb=" O PHE D1442 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N ASP D1444 " --> pdb=" O VAL D1332 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N THR D1334 " --> pdb=" O ASP D1444 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ALA D1420 " --> pdb=" O CYS D1439 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N ASN D1441 " --> pdb=" O ILE D1418 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ILE D1418 " --> pdb=" O ASN D1441 " (cutoff:3.500A) removed outlier: 8.192A pdb=" N HIS D1443 " --> pdb=" O GLY D1416 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N GLY D1416 " --> pdb=" O HIS D1443 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 1370 through 1372 removed outlier: 17.866A pdb=" N ALA D1329 " --> pdb=" O ARG D1360 " (cutoff:3.500A) removed outlier: 13.847A pdb=" N ARG D1360 " --> pdb=" O ALA D1329 " (cutoff:3.500A) removed outlier: 11.244A pdb=" N THR D1331 " --> pdb=" O ILE D1358 " (cutoff:3.500A) removed outlier: 8.257A pdb=" N ILE D1358 " --> pdb=" O THR D1331 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N VAL D1333 " --> pdb=" O VAL D1356 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N LEU D1353 " --> pdb=" O MET D1468 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N MET D1468 " --> pdb=" O LEU D1353 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N PHE D1355 " --> pdb=" O TRP D1466 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N TRP D1466 " --> pdb=" O PHE D1355 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ALA D1357 " --> pdb=" O ALA D1464 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N ALA D1464 " --> pdb=" O ALA D1357 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N GLN D1359 " --> pdb=" O GLU D1462 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 1346 through 1347 2336 hydrogen bonds defined for protein. 6864 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: 8.61 Time building geometry restraints manager: 3.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 6083 1.31 - 1.44: 9841 1.44 - 1.56: 21236 1.56 - 1.69: 8 1.69 - 1.82: 296 Bond restraints: 37464 Sorted by residual: bond pdb=" C PRO D1015 " pdb=" O PRO D1015 " ideal model delta sigma weight residual 1.238 1.184 0.054 1.24e-02 6.50e+03 1.86e+01 bond pdb=" C PRO A1015 " pdb=" O PRO A1015 " ideal model delta sigma weight residual 1.238 1.184 0.054 1.24e-02 6.50e+03 1.86e+01 bond pdb=" C PRO B1015 " pdb=" O PRO B1015 " ideal model delta sigma weight residual 1.238 1.184 0.054 1.24e-02 6.50e+03 1.86e+01 bond pdb=" C PRO C1015 " pdb=" O PRO C1015 " ideal model delta sigma weight residual 1.238 1.185 0.053 1.24e-02 6.50e+03 1.81e+01 bond pdb=" C PRO B 802 " pdb=" O PRO B 802 " ideal model delta sigma weight residual 1.237 1.186 0.052 1.26e-02 6.30e+03 1.68e+01 ... (remaining 37459 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.82: 42284 1.82 - 3.64: 7128 3.64 - 5.46: 1546 5.46 - 7.28: 290 7.28 - 9.11: 56 Bond angle restraints: 51304 Sorted by residual: angle pdb=" N VAL A 844 " pdb=" CA VAL A 844 " pdb=" C VAL A 844 " ideal model delta sigma weight residual 110.53 104.10 6.43 9.40e-01 1.13e+00 4.68e+01 angle pdb=" N VAL B 844 " pdb=" CA VAL B 844 " pdb=" C VAL B 844 " ideal model delta sigma weight residual 110.53 104.10 6.43 9.40e-01 1.13e+00 4.68e+01 angle pdb=" N VAL C 844 " pdb=" CA VAL C 844 " pdb=" C VAL C 844 " ideal model delta sigma weight residual 110.53 104.10 6.43 9.40e-01 1.13e+00 4.68e+01 angle pdb=" N VAL D 844 " pdb=" CA VAL D 844 " pdb=" C VAL D 844 " ideal model delta sigma weight residual 110.53 104.10 6.43 9.40e-01 1.13e+00 4.68e+01 angle pdb=" CA PHE C1160 " pdb=" CB PHE C1160 " pdb=" CG PHE C1160 " ideal model delta sigma weight residual 113.80 107.31 6.49 1.00e+00 1.00e+00 4.21e+01 ... (remaining 51299 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.14: 20974 17.14 - 34.27: 1251 34.27 - 51.41: 240 51.41 - 68.54: 32 68.54 - 85.68: 16 Dihedral angle restraints: 22513 sinusoidal: 6877 harmonic: 15636 Sorted by residual: dihedral pdb=" C LYS B 698 " pdb=" N LYS B 698 " pdb=" CA LYS B 698 " pdb=" CB LYS B 698 " ideal model delta harmonic sigma weight residual -122.60 -111.32 -11.28 0 2.50e+00 1.60e-01 2.04e+01 dihedral pdb=" C LYS C 698 " pdb=" N LYS C 698 " pdb=" CA LYS C 698 " pdb=" CB LYS C 698 " ideal model delta harmonic sigma weight residual -122.60 -111.33 -11.27 0 2.50e+00 1.60e-01 2.03e+01 dihedral pdb=" C LYS A 698 " pdb=" N LYS A 698 " pdb=" CA LYS A 698 " pdb=" CB LYS A 698 " ideal model delta harmonic sigma weight residual -122.60 -111.35 -11.25 0 2.50e+00 1.60e-01 2.02e+01 ... (remaining 22510 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.122: 5184 0.122 - 0.244: 800 0.244 - 0.366: 72 0.366 - 0.488: 12 0.488 - 0.610: 4 Chirality restraints: 6072 Sorted by residual: chirality pdb=" CB VAL A1011 " pdb=" CA VAL A1011 " pdb=" CG1 VAL A1011 " pdb=" CG2 VAL A1011 " both_signs ideal model delta sigma weight residual False -2.63 -2.02 -0.61 2.00e-01 2.50e+01 9.30e+00 chirality pdb=" CB VAL B1011 " pdb=" CA VAL B1011 " pdb=" CG1 VAL B1011 " pdb=" CG2 VAL B1011 " both_signs ideal model delta sigma weight residual False -2.63 -2.02 -0.61 2.00e-01 2.50e+01 9.30e+00 chirality pdb=" CB VAL D1011 " pdb=" CA VAL D1011 " pdb=" CG1 VAL D1011 " pdb=" CG2 VAL D1011 " both_signs ideal model delta sigma weight residual False -2.63 -2.02 -0.61 2.00e-01 2.50e+01 9.30e+00 ... (remaining 6069 not shown) Planarity restraints: 6688 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER D 91 " 0.019 2.00e-02 2.50e+03 3.85e-02 1.48e+01 pdb=" C SER D 91 " -0.067 2.00e-02 2.50e+03 pdb=" O SER D 91 " 0.025 2.00e-02 2.50e+03 pdb=" N PRO D 92 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER C 91 " -0.019 2.00e-02 2.50e+03 3.84e-02 1.47e+01 pdb=" C SER C 91 " 0.066 2.00e-02 2.50e+03 pdb=" O SER C 91 " -0.025 2.00e-02 2.50e+03 pdb=" N PRO C 92 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 91 " 0.019 2.00e-02 2.50e+03 3.84e-02 1.47e+01 pdb=" C SER A 91 " -0.066 2.00e-02 2.50e+03 pdb=" O SER A 91 " 0.025 2.00e-02 2.50e+03 pdb=" N PRO A 92 " 0.022 2.00e-02 2.50e+03 ... (remaining 6685 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 222 2.61 - 3.18: 29555 3.18 - 3.75: 56429 3.75 - 4.33: 71427 4.33 - 4.90: 123126 Nonbonded interactions: 280759 Sorted by model distance: nonbonded pdb=" SG CYS D 997 " pdb=" SG CYS D1006 " model vdw 2.032 3.760 nonbonded pdb=" O LEU C 621 " pdb="CA CA C3002 " model vdw 2.120 2.510 nonbonded pdb=" O LEU D 621 " pdb="CA CA D6004 " model vdw 2.120 2.510 nonbonded pdb=" O LEU B 621 " pdb="CA CA B3002 " model vdw 2.120 2.510 nonbonded pdb=" O LEU A 621 " pdb="CA CA A3002 " model vdw 2.120 2.510 ... (remaining 280754 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.11 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 52 through 1494 or resid 3005)) selection = (chain 'B' and (resid 52 through 1494 or resid 3005)) selection = (chain 'C' and (resid 52 through 1494 or resid 3005)) selection = (chain 'D' and (resid 52 through 1494 or resid 6005)) } 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: 8.180 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: 0.020 Extract box with map and model: 0.520 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 38.410 Find NCS groups from input model: 1.190 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6686 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 : 0.010 0.088 37467 Z= 0.627 Angle : 1.520 9.106 51318 Z= 1.049 Chirality : 0.086 0.610 6072 Planarity : 0.010 0.039 6688 Dihedral : 11.752 85.679 12344 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 0.30 % Allowed : 2.53 % Favored : 97.18 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.26 (0.11), residues: 5352 helix: 0.22 (0.09), residues: 2972 sheet: -0.92 (0.23), residues: 400 loop : -0.39 (0.14), residues: 1980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 517 TYR 0.037 0.005 TYR A 504 PHE 0.051 0.005 PHE C 941 TRP 0.028 0.003 TRP B1124 HIS 0.029 0.004 HIS B 618 Details of bonding type rmsd covalent geometry : bond 0.01019 (37464) covalent geometry : angle 1.52006 (51304) SS BOND : bond 0.00054 ( 3) SS BOND : angle 0.73820 ( 14) hydrogen bonds : bond 0.16662 ( 2324) hydrogen bonds : angle 7.40020 ( 6864) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10704 Ramachandran restraints generated. 5352 Oldfield, 0 Emsley, 5352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10704 Ramachandran restraints generated. 5352 Oldfield, 0 Emsley, 5352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 721 residues out of total 4612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 713 time to evaluate : 1.138 Fit side-chains REVERT: A 81 MET cc_start: 0.5239 (tpt) cc_final: 0.4834 (tpt) REVERT: A 336 HIS cc_start: 0.7495 (m-70) cc_final: 0.7088 (m-70) REVERT: A 411 LEU cc_start: 0.6670 (tp) cc_final: 0.6469 (OUTLIER) REVERT: A 413 ASN cc_start: 0.7686 (m-40) cc_final: 0.7115 (t160) REVERT: A 449 ASP cc_start: 0.6832 (m-30) cc_final: 0.6560 (m-30) REVERT: A 466 TYR cc_start: 0.6849 (m-10) cc_final: 0.6631 (m-80) REVERT: A 475 GLU cc_start: 0.8020 (mm-30) cc_final: 0.7214 (pt0) REVERT: A 477 LYS cc_start: 0.7296 (mtmt) cc_final: 0.6759 (mptp) REVERT: A 602 MET cc_start: 0.8048 (mtm) cc_final: 0.7703 (mtp) REVERT: A 641 SER cc_start: 0.5712 (t) cc_final: 0.5218 (p) REVERT: A 663 LYS cc_start: 0.6723 (tttp) cc_final: 0.6493 (ptpt) REVERT: A 666 GLU cc_start: 0.6721 (tt0) cc_final: 0.6510 (tt0) REVERT: A 694 MET cc_start: 0.6994 (ttm) cc_final: 0.5970 (tmm) REVERT: A 708 LYS cc_start: 0.6909 (mptt) cc_final: 0.6478 (mmtt) REVERT: A 725 ASP cc_start: 0.7665 (m-30) cc_final: 0.7128 (t0) REVERT: A 730 LEU cc_start: 0.6881 (tp) cc_final: 0.6673 (tp) REVERT: A 873 LEU cc_start: 0.6382 (mt) cc_final: 0.6079 (mt) REVERT: A 928 LEU cc_start: 0.7060 (mt) cc_final: 0.6782 (mp) REVERT: A 932 MET cc_start: 0.5919 (mmt) cc_final: 0.5654 (mmt) REVERT: A 935 MET cc_start: 0.7240 (mmt) cc_final: 0.6929 (mmm) REVERT: A 943 PHE cc_start: 0.8191 (m-10) cc_final: 0.7848 (m-10) REVERT: A 996 ASN cc_start: 0.7689 (m-40) cc_final: 0.7353 (m-40) REVERT: A 1005 GLU cc_start: 0.7821 (mt-10) cc_final: 0.7499 (mt-10) REVERT: A 1082 LEU cc_start: 0.6518 (tp) cc_final: 0.6258 (mm) REVERT: A 1085 ARG cc_start: 0.4696 (tpp-160) cc_final: 0.4087 (tpp80) REVERT: A 1114 GLU cc_start: 0.6375 (mm-30) cc_final: 0.5962 (mm-30) REVERT: A 1124 TRP cc_start: 0.6514 (t60) cc_final: 0.6070 (t60) REVERT: A 1131 MET cc_start: 0.6399 (mmp) cc_final: 0.5412 (ptt) REVERT: A 1145 GLN cc_start: 0.7772 (tt0) cc_final: 0.7486 (tt0) REVERT: A 1150 MET cc_start: 0.6847 (ttm) cc_final: 0.6636 (ttp) REVERT: A 1336 TRP cc_start: 0.6407 (m100) cc_final: 0.5727 (m100) REVERT: A 1346 GLU cc_start: 0.5637 (tp30) cc_final: 0.5335 (pm20) REVERT: B 81 MET cc_start: 0.5233 (tpt) cc_final: 0.4690 (tpt) REVERT: B 336 HIS cc_start: 0.7621 (m-70) cc_final: 0.7175 (m-70) REVERT: B 413 ASN cc_start: 0.7676 (m-40) cc_final: 0.7098 (t160) REVERT: B 424 LEU cc_start: 0.7078 (tp) cc_final: 0.6807 (tm) REVERT: B 449 ASP cc_start: 0.6821 (m-30) cc_final: 0.6547 (m-30) REVERT: B 466 TYR cc_start: 0.6829 (m-10) cc_final: 0.6629 (m-80) REVERT: B 475 GLU cc_start: 0.7940 (mm-30) cc_final: 0.7051 (pt0) REVERT: B 477 LYS cc_start: 0.7312 (mtmt) cc_final: 0.6835 (mptt) REVERT: B 602 MET cc_start: 0.8052 (mtm) cc_final: 0.7723 (mtp) REVERT: B 641 SER cc_start: 0.5594 (t) cc_final: 0.5124 (p) REVERT: B 663 LYS cc_start: 0.6687 (tttp) cc_final: 0.6464 (ptpt) REVERT: B 666 GLU cc_start: 0.6720 (tt0) cc_final: 0.6510 (tt0) REVERT: B 694 MET cc_start: 0.6964 (ttm) cc_final: 0.5937 (tmm) REVERT: B 708 LYS cc_start: 0.6915 (mptt) cc_final: 0.6492 (mmtt) REVERT: B 725 ASP cc_start: 0.7599 (m-30) cc_final: 0.7076 (t0) REVERT: B 730 LEU cc_start: 0.6848 (tp) cc_final: 0.6642 (tp) REVERT: B 873 LEU cc_start: 0.6406 (mt) cc_final: 0.6084 (mt) REVERT: B 928 LEU cc_start: 0.7051 (mt) cc_final: 0.6778 (mp) REVERT: B 932 MET cc_start: 0.5899 (mmt) cc_final: 0.5635 (mmt) REVERT: B 935 MET cc_start: 0.7243 (mmt) cc_final: 0.6930 (mmm) REVERT: B 943 PHE cc_start: 0.8218 (m-10) cc_final: 0.7891 (m-10) REVERT: B 996 ASN cc_start: 0.7693 (m-40) cc_final: 0.7339 (m-40) REVERT: B 1005 GLU cc_start: 0.7827 (mt-10) cc_final: 0.7512 (mt-10) REVERT: B 1082 LEU cc_start: 0.6561 (tp) cc_final: 0.6294 (mm) REVERT: B 1085 ARG cc_start: 0.4681 (tpp-160) cc_final: 0.4085 (tpp80) REVERT: B 1124 TRP cc_start: 0.6516 (t60) cc_final: 0.6073 (t60) REVERT: B 1131 MET cc_start: 0.6468 (mmp) cc_final: 0.5477 (ptt) REVERT: B 1145 GLN cc_start: 0.7799 (tt0) cc_final: 0.7527 (tt0) REVERT: B 1150 MET cc_start: 0.6873 (ttm) cc_final: 0.6446 (mtm) REVERT: B 1336 TRP cc_start: 0.6417 (m100) cc_final: 0.5629 (m100) REVERT: B 1346 GLU cc_start: 0.5611 (tp30) cc_final: 0.5300 (pm20) REVERT: C 81 MET cc_start: 0.5240 (tpt) cc_final: 0.4678 (tpt) REVERT: C 336 HIS cc_start: 0.7490 (m-70) cc_final: 0.7072 (m-70) REVERT: C 411 LEU cc_start: 0.6692 (tp) cc_final: 0.6492 (mt) REVERT: C 413 ASN cc_start: 0.7677 (m-40) cc_final: 0.7098 (t160) REVERT: C 424 LEU cc_start: 0.7078 (tp) cc_final: 0.6801 (tm) REVERT: C 449 ASP cc_start: 0.6821 (m-30) cc_final: 0.6547 (m-30) REVERT: C 466 TYR cc_start: 0.6831 (m-10) cc_final: 0.6629 (m-80) REVERT: C 475 GLU cc_start: 0.7949 (mm-30) cc_final: 0.7071 (pt0) REVERT: C 477 LYS cc_start: 0.7313 (mtmt) cc_final: 0.6835 (mptt) REVERT: C 602 MET cc_start: 0.8050 (mtm) cc_final: 0.7718 (mtp) REVERT: C 641 SER cc_start: 0.5599 (t) cc_final: 0.5125 (p) REVERT: C 663 LYS cc_start: 0.6688 (tttp) cc_final: 0.6465 (ptpt) REVERT: C 666 GLU cc_start: 0.6718 (tt0) cc_final: 0.6506 (tt0) REVERT: C 694 MET cc_start: 0.6991 (ttm) cc_final: 0.5959 (tmm) REVERT: C 708 LYS cc_start: 0.6922 (mptt) cc_final: 0.6500 (mmtt) REVERT: C 725 ASP cc_start: 0.7600 (m-30) cc_final: 0.7077 (t0) REVERT: C 730 LEU cc_start: 0.6882 (tp) cc_final: 0.6672 (tp) REVERT: C 873 LEU cc_start: 0.6410 (mt) cc_final: 0.6089 (mt) REVERT: C 928 LEU cc_start: 0.7059 (mt) cc_final: 0.6777 (mp) REVERT: C 932 MET cc_start: 0.5919 (mmt) cc_final: 0.5662 (mmt) REVERT: C 935 MET cc_start: 0.7242 (mmt) cc_final: 0.6931 (mmm) REVERT: C 943 PHE cc_start: 0.8215 (m-10) cc_final: 0.7888 (m-10) REVERT: C 996 ASN cc_start: 0.7698 (m-40) cc_final: 0.7338 (m-40) REVERT: C 1005 GLU cc_start: 0.7828 (mt-10) cc_final: 0.7513 (mt-10) REVERT: C 1082 LEU cc_start: 0.6547 (tp) cc_final: 0.6287 (mm) REVERT: C 1085 ARG cc_start: 0.4682 (tpp-160) cc_final: 0.4087 (tpp80) REVERT: C 1114 GLU cc_start: 0.6312 (mm-30) cc_final: 0.5893 (mm-30) REVERT: C 1124 TRP cc_start: 0.6516 (t60) cc_final: 0.6071 (t60) REVERT: C 1131 MET cc_start: 0.6463 (mmp) cc_final: 0.5487 (ptt) REVERT: C 1145 GLN cc_start: 0.7802 (tt0) cc_final: 0.7523 (tt0) REVERT: C 1150 MET cc_start: 0.6877 (ttm) cc_final: 0.6436 (mtm) REVERT: C 1336 TRP cc_start: 0.6423 (m100) cc_final: 0.5630 (m100) REVERT: C 1346 GLU cc_start: 0.5617 (tp30) cc_final: 0.5304 (pm20) REVERT: D 81 MET cc_start: 0.5238 (tpt) cc_final: 0.4676 (tpt) REVERT: D 336 HIS cc_start: 0.7575 (m-70) cc_final: 0.7169 (m-70) REVERT: D 413 ASN cc_start: 0.7677 (m-40) cc_final: 0.7099 (t160) REVERT: D 449 ASP cc_start: 0.6821 (m-30) cc_final: 0.6546 (m-30) REVERT: D 466 TYR cc_start: 0.6832 (m-10) cc_final: 0.6630 (m-80) REVERT: D 475 GLU cc_start: 0.7948 (mm-30) cc_final: 0.7072 (pt0) REVERT: D 477 LYS cc_start: 0.7313 (mtmt) cc_final: 0.6836 (mptt) REVERT: D 602 MET cc_start: 0.8052 (mtm) cc_final: 0.7721 (mtp) REVERT: D 641 SER cc_start: 0.5600 (t) cc_final: 0.5128 (p) REVERT: D 663 LYS cc_start: 0.6688 (tttp) cc_final: 0.6465 (ptpt) REVERT: D 666 GLU cc_start: 0.6719 (tt0) cc_final: 0.6507 (tt0) REVERT: D 694 MET cc_start: 0.6992 (ttm) cc_final: 0.5961 (tmm) REVERT: D 708 LYS cc_start: 0.6923 (mptt) cc_final: 0.6499 (mmtt) REVERT: D 725 ASP cc_start: 0.7599 (m-30) cc_final: 0.7077 (t0) REVERT: D 730 LEU cc_start: 0.6882 (tp) cc_final: 0.6670 (tp) REVERT: D 873 LEU cc_start: 0.6409 (mt) cc_final: 0.6089 (mt) REVERT: D 928 LEU cc_start: 0.7061 (mt) cc_final: 0.6780 (mp) REVERT: D 932 MET cc_start: 0.5921 (mmt) cc_final: 0.5664 (mmt) REVERT: D 935 MET cc_start: 0.7243 (mmt) cc_final: 0.6931 (mmm) REVERT: D 943 PHE cc_start: 0.8217 (m-10) cc_final: 0.7888 (m-10) REVERT: D 996 ASN cc_start: 0.7697 (m-40) cc_final: 0.7338 (m-40) REVERT: D 1005 GLU cc_start: 0.7826 (mt-10) cc_final: 0.7511 (mt-10) REVERT: D 1082 LEU cc_start: 0.6547 (tp) cc_final: 0.6279 (mm) REVERT: D 1085 ARG cc_start: 0.4683 (tpp-160) cc_final: 0.4087 (tpp80) REVERT: D 1114 GLU cc_start: 0.6313 (mm-30) cc_final: 0.5895 (mm-30) REVERT: D 1124 TRP cc_start: 0.6517 (t60) cc_final: 0.6071 (t60) REVERT: D 1131 MET cc_start: 0.6464 (mmp) cc_final: 0.5476 (ptt) REVERT: D 1145 GLN cc_start: 0.7803 (tt0) cc_final: 0.7524 (tt0) REVERT: D 1150 MET cc_start: 0.6875 (ttm) cc_final: 0.6510 (mtm) REVERT: D 1336 TRP cc_start: 0.6420 (m100) cc_final: 0.5632 (m100) REVERT: D 1346 GLU cc_start: 0.5614 (tp30) cc_final: 0.5302 (pm20) outliers start: 8 outliers final: 5 residues processed: 717 average time/residue: 0.6021 time to fit residues: 521.0375 Evaluate side-chains 486 residues out of total 4612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 482 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 621 LEU Chi-restraints excluded: chain B residue 621 LEU Chi-restraints excluded: chain C residue 621 LEU Chi-restraints excluded: chain D residue 621 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 394 optimal weight: 5.9990 chunk 430 optimal weight: 6.9990 chunk 41 optimal weight: 0.9980 chunk 265 optimal weight: 8.9990 chunk 523 optimal weight: 1.9990 chunk 497 optimal weight: 0.9980 chunk 414 optimal weight: 0.7980 chunk 310 optimal weight: 5.9990 chunk 488 optimal weight: 0.7980 chunk 366 optimal weight: 1.9990 chunk 223 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 886 HIS A 892 ASN A 923 ASN A1167 GLN ** B 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 886 HIS B 892 ASN B 923 ASN B1167 GLN C 886 HIS C 892 ASN C 923 ASN C1167 GLN D 886 HIS D 892 ASN D 923 ASN D1167 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.183622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.151060 restraints weight = 52520.407| |-----------------------------------------------------------------------------| r_work (start): 0.3913 rms_B_bonded: 2.11 r_work: 0.3491 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.2066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 37467 Z= 0.125 Angle : 0.492 7.759 51318 Z= 0.263 Chirality : 0.039 0.143 6072 Planarity : 0.004 0.031 6688 Dihedral : 4.600 59.238 6452 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 4.38 % Allowed : 9.66 % Favored : 85.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.32 (0.11), residues: 5352 helix: 1.73 (0.09), residues: 2984 sheet: -1.12 (0.23), residues: 400 loop : 0.10 (0.14), residues: 1968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B1123 TYR 0.015 0.001 TYR B1063 PHE 0.022 0.001 PHE A1160 TRP 0.014 0.001 TRP A1124 HIS 0.003 0.001 HIS D 813 Details of bonding type rmsd covalent geometry : bond 0.00267 (37464) covalent geometry : angle 0.49162 (51304) SS BOND : bond 0.00103 ( 3) SS BOND : angle 0.11741 ( 14) hydrogen bonds : bond 0.04427 ( 2324) hydrogen bonds : angle 3.93185 ( 6864) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10704 Ramachandran restraints generated. 5352 Oldfield, 0 Emsley, 5352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10704 Ramachandran restraints generated. 5352 Oldfield, 0 Emsley, 5352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 624 residues out of total 4612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 506 time to evaluate : 1.257 Fit side-chains REVERT: A 81 MET cc_start: 0.5852 (tpt) cc_final: 0.5602 (tpt) REVERT: A 328 LEU cc_start: 0.7405 (OUTLIER) cc_final: 0.7174 (mt) REVERT: A 415 LEU cc_start: 0.8693 (mm) cc_final: 0.8373 (mt) REVERT: A 585 TYR cc_start: 0.6953 (m-80) cc_final: 0.6616 (m-80) REVERT: A 612 ARG cc_start: 0.7767 (OUTLIER) cc_final: 0.7269 (ptp-170) REVERT: A 694 MET cc_start: 0.7838 (ttm) cc_final: 0.7377 (tmm) REVERT: A 809 ASP cc_start: 0.7846 (t0) cc_final: 0.7635 (t0) REVERT: A 996 ASN cc_start: 0.8340 (m-40) cc_final: 0.7936 (m110) REVERT: A 1082 LEU cc_start: 0.7897 (tp) cc_final: 0.7609 (mm) REVERT: A 1085 ARG cc_start: 0.5834 (tpp-160) cc_final: 0.5410 (ttm170) REVERT: A 1144 VAL cc_start: 0.8125 (t) cc_final: 0.7688 (p) REVERT: A 1158 ILE cc_start: 0.7445 (OUTLIER) cc_final: 0.7188 (mp) REVERT: A 1336 TRP cc_start: 0.6048 (m100) cc_final: 0.5749 (m100) REVERT: A 1483 LEU cc_start: 0.6348 (OUTLIER) cc_final: 0.6102 (tp) REVERT: B 328 LEU cc_start: 0.7426 (OUTLIER) cc_final: 0.7219 (mt) REVERT: B 413 ASN cc_start: 0.7191 (m-40) cc_final: 0.6965 (t160) REVERT: B 415 LEU cc_start: 0.8615 (mm) cc_final: 0.8286 (mt) REVERT: B 560 MET cc_start: 0.8757 (mmm) cc_final: 0.8363 (mmm) REVERT: B 585 TYR cc_start: 0.6918 (m-80) cc_final: 0.6588 (m-80) REVERT: B 612 ARG cc_start: 0.7775 (OUTLIER) cc_final: 0.7291 (ptp-170) REVERT: B 694 MET cc_start: 0.7839 (ttm) cc_final: 0.7373 (tmm) REVERT: B 996 ASN cc_start: 0.8308 (m-40) cc_final: 0.7911 (m110) REVERT: B 1082 LEU cc_start: 0.7898 (tp) cc_final: 0.7618 (mm) REVERT: B 1085 ARG cc_start: 0.5841 (tpp-160) cc_final: 0.5410 (ttm170) REVERT: B 1144 VAL cc_start: 0.8087 (t) cc_final: 0.7684 (p) REVERT: B 1158 ILE cc_start: 0.7391 (OUTLIER) cc_final: 0.7108 (mp) REVERT: B 1336 TRP cc_start: 0.6045 (m100) cc_final: 0.5701 (m100) REVERT: B 1483 LEU cc_start: 0.6383 (OUTLIER) cc_final: 0.6136 (tp) REVERT: C 328 LEU cc_start: 0.7420 (OUTLIER) cc_final: 0.7174 (mt) REVERT: C 585 TYR cc_start: 0.6924 (m-80) cc_final: 0.6609 (m-80) REVERT: C 612 ARG cc_start: 0.7772 (OUTLIER) cc_final: 0.7281 (ptp-170) REVERT: C 694 MET cc_start: 0.7842 (ttm) cc_final: 0.7377 (tmm) REVERT: C 996 ASN cc_start: 0.8281 (m-40) cc_final: 0.7865 (m110) REVERT: C 1082 LEU cc_start: 0.7906 (tp) cc_final: 0.7624 (mm) REVERT: C 1085 ARG cc_start: 0.5822 (tpp-160) cc_final: 0.5407 (ttm170) REVERT: C 1144 VAL cc_start: 0.8091 (t) cc_final: 0.7672 (p) REVERT: C 1158 ILE cc_start: 0.7440 (OUTLIER) cc_final: 0.7190 (mp) REVERT: C 1336 TRP cc_start: 0.6057 (m100) cc_final: 0.5717 (m100) REVERT: C 1483 LEU cc_start: 0.6390 (OUTLIER) cc_final: 0.6141 (tp) REVERT: D 328 LEU cc_start: 0.7425 (OUTLIER) cc_final: 0.7173 (mt) REVERT: D 413 ASN cc_start: 0.7198 (m-40) cc_final: 0.6974 (t160) REVERT: D 415 LEU cc_start: 0.8629 (mm) cc_final: 0.8292 (mt) REVERT: D 517 ARG cc_start: 0.6466 (mpp80) cc_final: 0.6195 (ttp-110) REVERT: D 585 TYR cc_start: 0.6932 (m-80) cc_final: 0.6621 (m-80) REVERT: D 612 ARG cc_start: 0.7776 (OUTLIER) cc_final: 0.7286 (ptp-170) REVERT: D 694 MET cc_start: 0.7827 (ttm) cc_final: 0.7374 (tmm) REVERT: D 1082 LEU cc_start: 0.7898 (tp) cc_final: 0.7619 (mm) REVERT: D 1085 ARG cc_start: 0.5842 (tpp-160) cc_final: 0.5421 (ttm170) REVERT: D 1144 VAL cc_start: 0.8076 (t) cc_final: 0.7661 (p) REVERT: D 1158 ILE cc_start: 0.7421 (OUTLIER) cc_final: 0.7110 (mp) REVERT: D 1336 TRP cc_start: 0.6061 (m100) cc_final: 0.5724 (m100) REVERT: D 1483 LEU cc_start: 0.6380 (OUTLIER) cc_final: 0.6136 (tp) outliers start: 118 outliers final: 37 residues processed: 579 average time/residue: 0.5549 time to fit residues: 395.7579 Evaluate side-chains 437 residues out of total 4612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 384 time to evaluate : 1.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 TRP Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 461 HIS Chi-restraints excluded: chain A residue 513 SER Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 612 ARG Chi-restraints excluded: chain A residue 657 LYS Chi-restraints excluded: chain A residue 864 ILE Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain A residue 1158 ILE Chi-restraints excluded: chain A residue 1417 THR Chi-restraints excluded: chain A residue 1481 THR Chi-restraints excluded: chain A residue 1483 LEU Chi-restraints excluded: chain B residue 96 TRP Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 393 ILE Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 461 HIS Chi-restraints excluded: chain B residue 513 SER Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 612 ARG Chi-restraints excluded: chain B residue 657 LYS Chi-restraints excluded: chain B residue 864 ILE Chi-restraints excluded: chain B residue 1107 ARG Chi-restraints excluded: chain B residue 1158 ILE Chi-restraints excluded: chain B residue 1417 THR Chi-restraints excluded: chain B residue 1483 LEU Chi-restraints excluded: chain C residue 96 TRP Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain C residue 461 HIS Chi-restraints excluded: chain C residue 513 SER Chi-restraints excluded: chain C residue 574 VAL Chi-restraints excluded: chain C residue 612 ARG Chi-restraints excluded: chain C residue 657 LYS Chi-restraints excluded: chain C residue 864 ILE Chi-restraints excluded: chain C residue 1107 ARG Chi-restraints excluded: chain C residue 1158 ILE Chi-restraints excluded: chain C residue 1417 THR Chi-restraints excluded: chain C residue 1483 LEU Chi-restraints excluded: chain D residue 96 TRP Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 393 ILE Chi-restraints excluded: chain D residue 513 SER Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 612 ARG Chi-restraints excluded: chain D residue 657 LYS Chi-restraints excluded: chain D residue 864 ILE Chi-restraints excluded: chain D residue 1107 ARG Chi-restraints excluded: chain D residue 1158 ILE Chi-restraints excluded: chain D residue 1417 THR Chi-restraints excluded: chain D residue 1483 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 290 optimal weight: 3.9990 chunk 395 optimal weight: 10.0000 chunk 501 optimal weight: 3.9990 chunk 89 optimal weight: 0.9990 chunk 252 optimal weight: 50.0000 chunk 360 optimal weight: 0.8980 chunk 499 optimal weight: 0.9980 chunk 185 optimal weight: 8.9990 chunk 530 optimal weight: 4.9990 chunk 427 optimal weight: 10.0000 chunk 153 optimal weight: 9.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 413 ASN A 417 GLN A 562 GLN ** A1443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 417 GLN B 562 GLN ** B1443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 413 ASN C 417 GLN C 562 GLN ** C 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 417 GLN D 562 GLN ** D1443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.179199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.145656 restraints weight = 52486.696| |-----------------------------------------------------------------------------| r_work (start): 0.3838 rms_B_bonded: 2.00 r_work: 0.3359 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.3298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 37467 Z= 0.199 Angle : 0.570 6.389 51318 Z= 0.303 Chirality : 0.042 0.176 6072 Planarity : 0.004 0.042 6688 Dihedral : 5.016 48.766 6444 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 5.27 % Allowed : 13.11 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.14 (0.11), residues: 5352 helix: 1.60 (0.09), residues: 2988 sheet: -1.46 (0.23), residues: 384 loop : 0.05 (0.14), residues: 1980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D1128 TYR 0.016 0.002 TYR A 504 PHE 0.026 0.002 PHE A 879 TRP 0.015 0.002 TRP D 620 HIS 0.006 0.001 HIS B 618 Details of bonding type rmsd covalent geometry : bond 0.00462 (37464) covalent geometry : angle 0.57024 (51304) SS BOND : bond 0.00170 ( 3) SS BOND : angle 0.46958 ( 14) hydrogen bonds : bond 0.04912 ( 2324) hydrogen bonds : angle 4.08550 ( 6864) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10704 Ramachandran restraints generated. 5352 Oldfield, 0 Emsley, 5352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10704 Ramachandran restraints generated. 5352 Oldfield, 0 Emsley, 5352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 538 residues out of total 4612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 396 time to evaluate : 1.139 Fit side-chains REVERT: A 134 TYR cc_start: 0.7685 (m-80) cc_final: 0.7459 (m-80) REVERT: A 328 LEU cc_start: 0.7669 (OUTLIER) cc_final: 0.7121 (mt) REVERT: A 415 LEU cc_start: 0.8713 (mm) cc_final: 0.8355 (mt) REVERT: A 585 TYR cc_start: 0.7007 (m-80) cc_final: 0.6807 (m-80) REVERT: A 694 MET cc_start: 0.8051 (OUTLIER) cc_final: 0.7472 (tmm) REVERT: A 875 MET cc_start: 0.8722 (ptt) cc_final: 0.8430 (ptt) REVERT: A 1066 ARG cc_start: 0.7825 (OUTLIER) cc_final: 0.7565 (mtp-110) REVERT: A 1068 PHE cc_start: 0.6661 (t80) cc_final: 0.5152 (t80) REVERT: A 1082 LEU cc_start: 0.7808 (tp) cc_final: 0.7457 (mm) REVERT: A 1085 ARG cc_start: 0.5666 (tpp-160) cc_final: 0.5119 (tpp80) REVERT: A 1144 VAL cc_start: 0.8124 (t) cc_final: 0.7714 (p) REVERT: A 1158 ILE cc_start: 0.7427 (OUTLIER) cc_final: 0.7221 (mp) REVERT: A 1336 TRP cc_start: 0.6352 (m100) cc_final: 0.5903 (m100) REVERT: B 134 TYR cc_start: 0.7656 (m-80) cc_final: 0.7436 (m-80) REVERT: B 328 LEU cc_start: 0.7659 (OUTLIER) cc_final: 0.7301 (mt) REVERT: B 413 ASN cc_start: 0.7621 (m-40) cc_final: 0.7366 (t160) REVERT: B 415 LEU cc_start: 0.8699 (mm) cc_final: 0.8345 (mt) REVERT: B 559 ARG cc_start: 0.8665 (OUTLIER) cc_final: 0.8461 (ttt90) REVERT: B 694 MET cc_start: 0.8042 (OUTLIER) cc_final: 0.7436 (tmm) REVERT: B 875 MET cc_start: 0.8718 (ptt) cc_final: 0.8426 (ptt) REVERT: B 1066 ARG cc_start: 0.7867 (OUTLIER) cc_final: 0.7593 (mtp-110) REVERT: B 1068 PHE cc_start: 0.6694 (t80) cc_final: 0.5172 (t80) REVERT: B 1082 LEU cc_start: 0.7810 (tp) cc_final: 0.7456 (mm) REVERT: B 1085 ARG cc_start: 0.5639 (tpp-160) cc_final: 0.5087 (ttm170) REVERT: B 1144 VAL cc_start: 0.8111 (t) cc_final: 0.7699 (p) REVERT: B 1158 ILE cc_start: 0.7316 (OUTLIER) cc_final: 0.7030 (mp) REVERT: B 1336 TRP cc_start: 0.6333 (m100) cc_final: 0.5878 (m100) REVERT: C 134 TYR cc_start: 0.7661 (m-80) cc_final: 0.7440 (m-80) REVERT: C 328 LEU cc_start: 0.7695 (OUTLIER) cc_final: 0.7147 (mt) REVERT: C 415 LEU cc_start: 0.8694 (mm) cc_final: 0.8335 (mt) REVERT: C 694 MET cc_start: 0.8046 (OUTLIER) cc_final: 0.7438 (tmm) REVERT: C 875 MET cc_start: 0.8726 (ptt) cc_final: 0.8430 (ptt) REVERT: C 1066 ARG cc_start: 0.7869 (OUTLIER) cc_final: 0.7598 (mtp-110) REVERT: C 1068 PHE cc_start: 0.6692 (t80) cc_final: 0.5190 (t80) REVERT: C 1082 LEU cc_start: 0.7815 (tp) cc_final: 0.7464 (mm) REVERT: C 1085 ARG cc_start: 0.5658 (tpp-160) cc_final: 0.5113 (tpp80) REVERT: C 1144 VAL cc_start: 0.8137 (t) cc_final: 0.7708 (p) REVERT: C 1158 ILE cc_start: 0.7458 (OUTLIER) cc_final: 0.7236 (mp) REVERT: C 1336 TRP cc_start: 0.6358 (m100) cc_final: 0.5907 (m100) REVERT: D 134 TYR cc_start: 0.7661 (m-80) cc_final: 0.7442 (m-80) REVERT: D 328 LEU cc_start: 0.7695 (OUTLIER) cc_final: 0.7140 (mt) REVERT: D 413 ASN cc_start: 0.7592 (m-40) cc_final: 0.7348 (t160) REVERT: D 415 LEU cc_start: 0.8706 (mm) cc_final: 0.8344 (mt) REVERT: D 461 HIS cc_start: 0.7355 (OUTLIER) cc_final: 0.6892 (p-80) REVERT: D 694 MET cc_start: 0.8044 (OUTLIER) cc_final: 0.7500 (tmm) REVERT: D 875 MET cc_start: 0.8723 (ptt) cc_final: 0.8428 (ptt) REVERT: D 1066 ARG cc_start: 0.7859 (OUTLIER) cc_final: 0.7580 (mtp-110) REVERT: D 1068 PHE cc_start: 0.6688 (t80) cc_final: 0.5175 (t80) REVERT: D 1082 LEU cc_start: 0.7828 (tp) cc_final: 0.7473 (mm) REVERT: D 1085 ARG cc_start: 0.5668 (tpp-160) cc_final: 0.5121 (tpp80) REVERT: D 1144 VAL cc_start: 0.8115 (t) cc_final: 0.7692 (p) REVERT: D 1158 ILE cc_start: 0.7355 (OUTLIER) cc_final: 0.7043 (mp) REVERT: D 1336 TRP cc_start: 0.6367 (m100) cc_final: 0.5930 (m100) outliers start: 142 outliers final: 63 residues processed: 500 average time/residue: 0.5128 time to fit residues: 316.5274 Evaluate side-chains 430 residues out of total 4612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 349 time to evaluate : 1.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 461 HIS Chi-restraints excluded: chain A residue 513 SER Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 579 THR Chi-restraints excluded: chain A residue 657 LYS Chi-restraints excluded: chain A residue 685 SER Chi-restraints excluded: chain A residue 694 MET Chi-restraints excluded: chain A residue 864 ILE Chi-restraints excluded: chain A residue 915 MET Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1066 ARG Chi-restraints excluded: chain A residue 1084 MET Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain A residue 1158 ILE Chi-restraints excluded: chain A residue 1417 THR Chi-restraints excluded: chain A residue 1481 THR Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 393 ILE Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 449 ASP Chi-restraints excluded: chain B residue 461 HIS Chi-restraints excluded: chain B residue 513 SER Chi-restraints excluded: chain B residue 527 LEU Chi-restraints excluded: chain B residue 559 ARG Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 657 LYS Chi-restraints excluded: chain B residue 685 SER Chi-restraints excluded: chain B residue 694 MET Chi-restraints excluded: chain B residue 864 ILE Chi-restraints excluded: chain B residue 915 MET Chi-restraints excluded: chain B residue 998 LEU Chi-restraints excluded: chain B residue 1066 ARG Chi-restraints excluded: chain B residue 1084 MET Chi-restraints excluded: chain B residue 1107 ARG Chi-restraints excluded: chain B residue 1158 ILE Chi-restraints excluded: chain B residue 1417 THR Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain C residue 426 VAL Chi-restraints excluded: chain C residue 461 HIS Chi-restraints excluded: chain C residue 513 SER Chi-restraints excluded: chain C residue 527 LEU Chi-restraints excluded: chain C residue 574 VAL Chi-restraints excluded: chain C residue 579 THR Chi-restraints excluded: chain C residue 657 LYS Chi-restraints excluded: chain C residue 685 SER Chi-restraints excluded: chain C residue 694 MET Chi-restraints excluded: chain C residue 864 ILE Chi-restraints excluded: chain C residue 915 MET Chi-restraints excluded: chain C residue 998 LEU Chi-restraints excluded: chain C residue 1042 MET Chi-restraints excluded: chain C residue 1066 ARG Chi-restraints excluded: chain C residue 1084 MET Chi-restraints excluded: chain C residue 1107 ARG Chi-restraints excluded: chain C residue 1158 ILE Chi-restraints excluded: chain C residue 1417 THR Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 393 ILE Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 449 ASP Chi-restraints excluded: chain D residue 461 HIS Chi-restraints excluded: chain D residue 513 SER Chi-restraints excluded: chain D residue 527 LEU Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 579 THR Chi-restraints excluded: chain D residue 657 LYS Chi-restraints excluded: chain D residue 685 SER Chi-restraints excluded: chain D residue 694 MET Chi-restraints excluded: chain D residue 864 ILE Chi-restraints excluded: chain D residue 915 MET Chi-restraints excluded: chain D residue 998 LEU Chi-restraints excluded: chain D residue 1066 ARG Chi-restraints excluded: chain D residue 1084 MET Chi-restraints excluded: chain D residue 1107 ARG Chi-restraints excluded: chain D residue 1158 ILE Chi-restraints excluded: chain D residue 1417 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 102 optimal weight: 0.9980 chunk 182 optimal weight: 6.9990 chunk 512 optimal weight: 8.9990 chunk 395 optimal weight: 10.0000 chunk 181 optimal weight: 2.9990 chunk 110 optimal weight: 7.9990 chunk 20 optimal weight: 10.0000 chunk 460 optimal weight: 9.9990 chunk 489 optimal weight: 2.9990 chunk 490 optimal weight: 0.6980 chunk 204 optimal weight: 0.5980 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 413 ASN A 643 HIS A1152 GLN A1156 HIS ** A1443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 417 GLN B1152 GLN B1156 HIS ** B1443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 413 ASN C1156 HIS ** C1443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 417 GLN D 643 HIS D1152 GLN D1156 HIS ** D1443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.180127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.147270 restraints weight = 52284.737| |-----------------------------------------------------------------------------| r_work (start): 0.3843 rms_B_bonded: 2.12 r_work: 0.3367 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.3598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 37467 Z= 0.157 Angle : 0.497 6.101 51318 Z= 0.263 Chirality : 0.040 0.159 6072 Planarity : 0.003 0.043 6688 Dihedral : 4.863 51.608 6444 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 4.35 % Allowed : 14.71 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.32 (0.11), residues: 5352 helix: 1.77 (0.09), residues: 2984 sheet: -1.50 (0.23), residues: 384 loop : 0.12 (0.14), residues: 1984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B1128 TYR 0.014 0.002 TYR B1063 PHE 0.018 0.002 PHE B 879 TRP 0.014 0.002 TRP D 620 HIS 0.004 0.001 HIS A 813 Details of bonding type rmsd covalent geometry : bond 0.00361 (37464) covalent geometry : angle 0.49676 (51304) SS BOND : bond 0.00174 ( 3) SS BOND : angle 0.31129 ( 14) hydrogen bonds : bond 0.04264 ( 2324) hydrogen bonds : angle 3.87747 ( 6864) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10704 Ramachandran restraints generated. 5352 Oldfield, 0 Emsley, 5352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10704 Ramachandran restraints generated. 5352 Oldfield, 0 Emsley, 5352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 4612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 359 time to evaluate : 1.256 Fit side-chains REVERT: A 134 TYR cc_start: 0.7628 (m-80) cc_final: 0.7389 (m-80) REVERT: A 328 LEU cc_start: 0.7604 (OUTLIER) cc_final: 0.7016 (mt) REVERT: A 415 LEU cc_start: 0.8628 (mm) cc_final: 0.8308 (mt) REVERT: A 694 MET cc_start: 0.7903 (ttm) cc_final: 0.7429 (tmm) REVERT: A 1082 LEU cc_start: 0.7896 (tp) cc_final: 0.7567 (mm) REVERT: A 1085 ARG cc_start: 0.5662 (tpp-160) cc_final: 0.5149 (ttm110) REVERT: A 1144 VAL cc_start: 0.8038 (t) cc_final: 0.7664 (p) REVERT: A 1336 TRP cc_start: 0.6222 (m100) cc_final: 0.5821 (m100) REVERT: B 328 LEU cc_start: 0.7597 (OUTLIER) cc_final: 0.7019 (mt) REVERT: B 415 LEU cc_start: 0.8633 (mm) cc_final: 0.8310 (mt) REVERT: B 694 MET cc_start: 0.7918 (OUTLIER) cc_final: 0.7408 (tmm) REVERT: B 1082 LEU cc_start: 0.7903 (tp) cc_final: 0.7574 (mm) REVERT: B 1085 ARG cc_start: 0.5675 (tpp-160) cc_final: 0.5152 (ttm110) REVERT: B 1140 ASN cc_start: 0.8048 (OUTLIER) cc_final: 0.7747 (m-40) REVERT: B 1144 VAL cc_start: 0.8059 (t) cc_final: 0.7647 (p) REVERT: B 1157 MET cc_start: 0.6610 (tpp) cc_final: 0.6118 (ttm) REVERT: B 1158 ILE cc_start: 0.7459 (OUTLIER) cc_final: 0.7254 (mp) REVERT: B 1336 TRP cc_start: 0.6218 (m100) cc_final: 0.5633 (m100) REVERT: B 1347 ARG cc_start: 0.6670 (OUTLIER) cc_final: 0.6452 (mmp-170) REVERT: C 328 LEU cc_start: 0.7619 (OUTLIER) cc_final: 0.7024 (mt) REVERT: C 415 LEU cc_start: 0.8628 (mm) cc_final: 0.8311 (mt) REVERT: C 694 MET cc_start: 0.7902 (ttm) cc_final: 0.7390 (tmm) REVERT: C 1082 LEU cc_start: 0.7899 (tp) cc_final: 0.7570 (mm) REVERT: C 1085 ARG cc_start: 0.5659 (tpp-160) cc_final: 0.5143 (ttm110) REVERT: C 1144 VAL cc_start: 0.8069 (t) cc_final: 0.7666 (p) REVERT: C 1336 TRP cc_start: 0.6221 (m100) cc_final: 0.5635 (m100) REVERT: D 328 LEU cc_start: 0.7608 (OUTLIER) cc_final: 0.7013 (mt) REVERT: D 415 LEU cc_start: 0.8643 (mm) cc_final: 0.8327 (mt) REVERT: D 461 HIS cc_start: 0.7299 (OUTLIER) cc_final: 0.6974 (p-80) REVERT: D 694 MET cc_start: 0.7914 (OUTLIER) cc_final: 0.7400 (tmm) REVERT: D 1082 LEU cc_start: 0.7879 (tp) cc_final: 0.7554 (mm) REVERT: D 1085 ARG cc_start: 0.5655 (tpp-160) cc_final: 0.5145 (ttm110) REVERT: D 1140 ASN cc_start: 0.7975 (OUTLIER) cc_final: 0.7720 (m-40) REVERT: D 1144 VAL cc_start: 0.8071 (t) cc_final: 0.7654 (p) REVERT: D 1336 TRP cc_start: 0.6224 (m100) cc_final: 0.5658 (m100) outliers start: 117 outliers final: 55 residues processed: 436 average time/residue: 0.5123 time to fit residues: 274.6231 Evaluate side-chains 409 residues out of total 4612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 343 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 461 HIS Chi-restraints excluded: chain A residue 488 THR Chi-restraints excluded: chain A residue 513 SER Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 579 THR Chi-restraints excluded: chain A residue 657 LYS Chi-restraints excluded: chain A residue 685 SER Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1084 MET Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain A residue 1417 THR Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 393 ILE Chi-restraints excluded: chain B residue 449 ASP Chi-restraints excluded: chain B residue 461 HIS Chi-restraints excluded: chain B residue 488 THR Chi-restraints excluded: chain B residue 513 SER Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 657 LYS Chi-restraints excluded: chain B residue 685 SER Chi-restraints excluded: chain B residue 694 MET Chi-restraints excluded: chain B residue 915 MET Chi-restraints excluded: chain B residue 998 LEU Chi-restraints excluded: chain B residue 1084 MET Chi-restraints excluded: chain B residue 1107 ARG Chi-restraints excluded: chain B residue 1140 ASN Chi-restraints excluded: chain B residue 1158 ILE Chi-restraints excluded: chain B residue 1347 ARG Chi-restraints excluded: chain B residue 1417 THR Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain C residue 426 VAL Chi-restraints excluded: chain C residue 461 HIS Chi-restraints excluded: chain C residue 488 THR Chi-restraints excluded: chain C residue 513 SER Chi-restraints excluded: chain C residue 574 VAL Chi-restraints excluded: chain C residue 579 THR Chi-restraints excluded: chain C residue 657 LYS Chi-restraints excluded: chain C residue 685 SER Chi-restraints excluded: chain C residue 915 MET Chi-restraints excluded: chain C residue 998 LEU Chi-restraints excluded: chain C residue 1042 MET Chi-restraints excluded: chain C residue 1084 MET Chi-restraints excluded: chain C residue 1107 ARG Chi-restraints excluded: chain C residue 1417 THR Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 393 ILE Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 449 ASP Chi-restraints excluded: chain D residue 461 HIS Chi-restraints excluded: chain D residue 488 THR Chi-restraints excluded: chain D residue 513 SER Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 579 THR Chi-restraints excluded: chain D residue 657 LYS Chi-restraints excluded: chain D residue 685 SER Chi-restraints excluded: chain D residue 694 MET Chi-restraints excluded: chain D residue 915 MET Chi-restraints excluded: chain D residue 998 LEU Chi-restraints excluded: chain D residue 1084 MET Chi-restraints excluded: chain D residue 1107 ARG Chi-restraints excluded: chain D residue 1140 ASN Chi-restraints excluded: chain D residue 1417 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 336 optimal weight: 2.9990 chunk 361 optimal weight: 1.9990 chunk 521 optimal weight: 0.8980 chunk 528 optimal weight: 5.9990 chunk 20 optimal weight: 10.0000 chunk 69 optimal weight: 0.9990 chunk 195 optimal weight: 7.9990 chunk 243 optimal weight: 20.0000 chunk 452 optimal weight: 0.8980 chunk 109 optimal weight: 10.0000 chunk 334 optimal weight: 5.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 413 ASN A1152 GLN ** A1443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 413 ASN B 417 GLN B 643 HIS B1152 GLN ** B1443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 413 ASN C 592 GLN C 643 HIS ** C1443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 413 ASN D 417 GLN ** D 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1152 GLN ** D1443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.178962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.144655 restraints weight = 52193.015| |-----------------------------------------------------------------------------| r_work (start): 0.3822 rms_B_bonded: 1.98 r_work: 0.3366 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3207 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.3861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 37467 Z= 0.153 Angle : 0.489 6.880 51318 Z= 0.260 Chirality : 0.039 0.160 6072 Planarity : 0.003 0.046 6688 Dihedral : 5.028 58.539 6444 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 4.83 % Allowed : 14.12 % Favored : 81.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.34 (0.11), residues: 5352 helix: 1.87 (0.09), residues: 2960 sheet: -1.63 (0.23), residues: 408 loop : 0.05 (0.14), residues: 1984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D1008 TYR 0.015 0.002 TYR A1063 PHE 0.020 0.002 PHE C1068 TRP 0.013 0.002 TRP C 620 HIS 0.005 0.001 HIS A 813 Details of bonding type rmsd covalent geometry : bond 0.00352 (37464) covalent geometry : angle 0.48905 (51304) SS BOND : bond 0.00157 ( 3) SS BOND : angle 0.30805 ( 14) hydrogen bonds : bond 0.04215 ( 2324) hydrogen bonds : angle 3.82672 ( 6864) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10704 Ramachandran restraints generated. 5352 Oldfield, 0 Emsley, 5352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10704 Ramachandran restraints generated. 5352 Oldfield, 0 Emsley, 5352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 4612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 352 time to evaluate : 1.020 Fit side-chains REVERT: A 134 TYR cc_start: 0.7651 (m-80) cc_final: 0.7370 (m-80) REVERT: A 328 LEU cc_start: 0.7615 (OUTLIER) cc_final: 0.6998 (mt) REVERT: A 415 LEU cc_start: 0.8682 (mm) cc_final: 0.8322 (mt) REVERT: A 466 TYR cc_start: 0.7807 (m-80) cc_final: 0.7551 (m-80) REVERT: A 694 MET cc_start: 0.7974 (OUTLIER) cc_final: 0.7434 (tmm) REVERT: A 1082 LEU cc_start: 0.7866 (tp) cc_final: 0.7526 (mm) REVERT: A 1085 ARG cc_start: 0.5574 (tpp-160) cc_final: 0.5059 (ttm170) REVERT: A 1144 VAL cc_start: 0.8087 (t) cc_final: 0.7698 (p) REVERT: A 1336 TRP cc_start: 0.6272 (m100) cc_final: 0.5842 (m100) REVERT: A 1353 LEU cc_start: 0.7596 (OUTLIER) cc_final: 0.7358 (tp) REVERT: B 328 LEU cc_start: 0.7562 (OUTLIER) cc_final: 0.6966 (mt) REVERT: B 415 LEU cc_start: 0.8687 (mm) cc_final: 0.8333 (mt) REVERT: B 466 TYR cc_start: 0.7810 (m-80) cc_final: 0.7573 (m-80) REVERT: B 694 MET cc_start: 0.7964 (ttm) cc_final: 0.7408 (tmm) REVERT: B 1082 LEU cc_start: 0.7840 (tp) cc_final: 0.7493 (mm) REVERT: B 1085 ARG cc_start: 0.5573 (tpp-160) cc_final: 0.5047 (ttm170) REVERT: B 1140 ASN cc_start: 0.8191 (OUTLIER) cc_final: 0.7911 (m-40) REVERT: B 1144 VAL cc_start: 0.8155 (t) cc_final: 0.7756 (p) REVERT: B 1336 TRP cc_start: 0.6266 (m100) cc_final: 0.5829 (m100) REVERT: C 328 LEU cc_start: 0.7648 (OUTLIER) cc_final: 0.7027 (mt) REVERT: C 415 LEU cc_start: 0.8687 (mm) cc_final: 0.8329 (mt) REVERT: C 466 TYR cc_start: 0.7809 (m-80) cc_final: 0.7556 (m-80) REVERT: C 694 MET cc_start: 0.7968 (OUTLIER) cc_final: 0.7426 (tmm) REVERT: C 1082 LEU cc_start: 0.7864 (tp) cc_final: 0.7523 (mm) REVERT: C 1085 ARG cc_start: 0.5559 (tpp-160) cc_final: 0.5040 (ttm170) REVERT: C 1144 VAL cc_start: 0.8118 (t) cc_final: 0.7701 (p) REVERT: C 1336 TRP cc_start: 0.6282 (m100) cc_final: 0.5890 (m100) REVERT: D 328 LEU cc_start: 0.7646 (OUTLIER) cc_final: 0.7040 (mt) REVERT: D 415 LEU cc_start: 0.8689 (mm) cc_final: 0.8324 (mt) REVERT: D 461 HIS cc_start: 0.7422 (OUTLIER) cc_final: 0.7122 (p-80) REVERT: D 466 TYR cc_start: 0.7801 (m-80) cc_final: 0.7525 (m-80) REVERT: D 694 MET cc_start: 0.7976 (ttm) cc_final: 0.7418 (tmm) REVERT: D 1082 LEU cc_start: 0.7872 (tp) cc_final: 0.7527 (mm) REVERT: D 1085 ARG cc_start: 0.5554 (tpp-160) cc_final: 0.5039 (ttm170) REVERT: D 1144 VAL cc_start: 0.8113 (t) cc_final: 0.7679 (p) REVERT: D 1153 LEU cc_start: 0.7808 (OUTLIER) cc_final: 0.7566 (mt) REVERT: D 1154 LEU cc_start: 0.7474 (OUTLIER) cc_final: 0.7250 (mm) REVERT: D 1336 TRP cc_start: 0.6280 (m100) cc_final: 0.5877 (m100) outliers start: 130 outliers final: 68 residues processed: 441 average time/residue: 0.5136 time to fit residues: 282.3881 Evaluate side-chains 418 residues out of total 4612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 339 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 461 HIS Chi-restraints excluded: chain A residue 488 THR Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 579 THR Chi-restraints excluded: chain A residue 657 LYS Chi-restraints excluded: chain A residue 685 SER Chi-restraints excluded: chain A residue 694 MET Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1042 MET Chi-restraints excluded: chain A residue 1084 MET Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain A residue 1152 GLN Chi-restraints excluded: chain A residue 1353 LEU Chi-restraints excluded: chain A residue 1417 THR Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 393 ILE Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 449 ASP Chi-restraints excluded: chain B residue 461 HIS Chi-restraints excluded: chain B residue 488 THR Chi-restraints excluded: chain B residue 513 SER Chi-restraints excluded: chain B residue 527 LEU Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 657 LYS Chi-restraints excluded: chain B residue 685 SER Chi-restraints excluded: chain B residue 915 MET Chi-restraints excluded: chain B residue 936 LYS Chi-restraints excluded: chain B residue 998 LEU Chi-restraints excluded: chain B residue 1042 MET Chi-restraints excluded: chain B residue 1084 MET Chi-restraints excluded: chain B residue 1107 ARG Chi-restraints excluded: chain B residue 1140 ASN Chi-restraints excluded: chain B residue 1417 THR Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain C residue 426 VAL Chi-restraints excluded: chain C residue 461 HIS Chi-restraints excluded: chain C residue 488 THR Chi-restraints excluded: chain C residue 513 SER Chi-restraints excluded: chain C residue 527 LEU Chi-restraints excluded: chain C residue 574 VAL Chi-restraints excluded: chain C residue 579 THR Chi-restraints excluded: chain C residue 657 LYS Chi-restraints excluded: chain C residue 685 SER Chi-restraints excluded: chain C residue 694 MET Chi-restraints excluded: chain C residue 915 MET Chi-restraints excluded: chain C residue 936 LYS Chi-restraints excluded: chain C residue 998 LEU Chi-restraints excluded: chain C residue 1011 VAL Chi-restraints excluded: chain C residue 1042 MET Chi-restraints excluded: chain C residue 1084 MET Chi-restraints excluded: chain C residue 1107 ARG Chi-restraints excluded: chain C residue 1417 THR Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 393 ILE Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 449 ASP Chi-restraints excluded: chain D residue 461 HIS Chi-restraints excluded: chain D residue 488 THR Chi-restraints excluded: chain D residue 527 LEU Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 579 THR Chi-restraints excluded: chain D residue 657 LYS Chi-restraints excluded: chain D residue 685 SER Chi-restraints excluded: chain D residue 915 MET Chi-restraints excluded: chain D residue 936 LYS Chi-restraints excluded: chain D residue 1011 VAL Chi-restraints excluded: chain D residue 1042 MET Chi-restraints excluded: chain D residue 1084 MET Chi-restraints excluded: chain D residue 1107 ARG Chi-restraints excluded: chain D residue 1152 GLN Chi-restraints excluded: chain D residue 1153 LEU Chi-restraints excluded: chain D residue 1154 LEU Chi-restraints excluded: chain D residue 1417 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 104 optimal weight: 5.9990 chunk 187 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 363 optimal weight: 3.9990 chunk 440 optimal weight: 3.9990 chunk 472 optimal weight: 4.9990 chunk 98 optimal weight: 3.9990 chunk 56 optimal weight: 0.7980 chunk 373 optimal weight: 0.9990 chunk 448 optimal weight: 1.9990 chunk 279 optimal weight: 20.0000 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 413 ASN A 417 GLN ** A1443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 413 ASN B 417 GLN B1152 GLN ** B1443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 413 ASN C 417 GLN C1152 GLN D 413 ASN D 417 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.178866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.146006 restraints weight = 52381.256| |-----------------------------------------------------------------------------| r_work (start): 0.3840 rms_B_bonded: 2.06 r_work: 0.3371 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3204 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.4007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 37467 Z= 0.151 Angle : 0.485 7.157 51318 Z= 0.258 Chirality : 0.039 0.160 6072 Planarity : 0.003 0.047 6688 Dihedral : 5.049 59.731 6444 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 4.31 % Allowed : 15.38 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.34 (0.11), residues: 5352 helix: 1.88 (0.09), residues: 2964 sheet: -1.61 (0.23), residues: 404 loop : 0.03 (0.14), residues: 1984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1128 TYR 0.018 0.002 TYR C1063 PHE 0.018 0.002 PHE C 879 TRP 0.018 0.002 TRP D 96 HIS 0.004 0.001 HIS B 813 Details of bonding type rmsd covalent geometry : bond 0.00349 (37464) covalent geometry : angle 0.48546 (51304) SS BOND : bond 0.00156 ( 3) SS BOND : angle 0.29310 ( 14) hydrogen bonds : bond 0.04174 ( 2324) hydrogen bonds : angle 3.81453 ( 6864) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10704 Ramachandran restraints generated. 5352 Oldfield, 0 Emsley, 5352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10704 Ramachandran restraints generated. 5352 Oldfield, 0 Emsley, 5352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 4612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 355 time to evaluate : 1.054 Fit side-chains REVERT: A 134 TYR cc_start: 0.7666 (m-80) cc_final: 0.7239 (m-80) REVERT: A 328 LEU cc_start: 0.7655 (OUTLIER) cc_final: 0.7023 (mt) REVERT: A 415 LEU cc_start: 0.8613 (mm) cc_final: 0.8237 (mt) REVERT: A 424 LEU cc_start: 0.7728 (OUTLIER) cc_final: 0.7379 (tt) REVERT: A 559 ARG cc_start: 0.8653 (OUTLIER) cc_final: 0.8435 (ttt90) REVERT: A 694 MET cc_start: 0.7997 (OUTLIER) cc_final: 0.7450 (tmm) REVERT: A 1082 LEU cc_start: 0.7834 (tp) cc_final: 0.7507 (mm) REVERT: A 1085 ARG cc_start: 0.5574 (tpp-160) cc_final: 0.5056 (ttm170) REVERT: A 1144 VAL cc_start: 0.8092 (t) cc_final: 0.7727 (p) REVERT: A 1336 TRP cc_start: 0.6310 (m100) cc_final: 0.5914 (m100) REVERT: B 328 LEU cc_start: 0.7614 (OUTLIER) cc_final: 0.6995 (mt) REVERT: B 415 LEU cc_start: 0.8604 (mm) cc_final: 0.8238 (mt) REVERT: B 694 MET cc_start: 0.7993 (OUTLIER) cc_final: 0.7442 (tmm) REVERT: B 1082 LEU cc_start: 0.7841 (tp) cc_final: 0.7506 (mm) REVERT: B 1085 ARG cc_start: 0.5556 (tpp-160) cc_final: 0.5028 (ttm170) REVERT: B 1140 ASN cc_start: 0.8188 (OUTLIER) cc_final: 0.7914 (m-40) REVERT: B 1144 VAL cc_start: 0.8182 (t) cc_final: 0.7797 (p) REVERT: B 1336 TRP cc_start: 0.6295 (m100) cc_final: 0.5861 (m100) REVERT: C 328 LEU cc_start: 0.7653 (OUTLIER) cc_final: 0.7035 (mt) REVERT: C 415 LEU cc_start: 0.8611 (mm) cc_final: 0.8241 (mt) REVERT: C 559 ARG cc_start: 0.8633 (OUTLIER) cc_final: 0.8425 (ttt90) REVERT: C 694 MET cc_start: 0.8004 (OUTLIER) cc_final: 0.7455 (tmm) REVERT: C 809 ASP cc_start: 0.8289 (t0) cc_final: 0.7839 (t0) REVERT: C 1082 LEU cc_start: 0.7837 (tp) cc_final: 0.7503 (mm) REVERT: C 1085 ARG cc_start: 0.5563 (tpp-160) cc_final: 0.5045 (ttm170) REVERT: C 1144 VAL cc_start: 0.8153 (t) cc_final: 0.7734 (p) REVERT: C 1336 TRP cc_start: 0.6303 (m100) cc_final: 0.5871 (m100) REVERT: D 328 LEU cc_start: 0.7656 (OUTLIER) cc_final: 0.7037 (mt) REVERT: D 415 LEU cc_start: 0.8617 (mm) cc_final: 0.8247 (mt) REVERT: D 559 ARG cc_start: 0.8648 (OUTLIER) cc_final: 0.8431 (ttt90) REVERT: D 694 MET cc_start: 0.7994 (OUTLIER) cc_final: 0.7443 (tmm) REVERT: D 1082 LEU cc_start: 0.7841 (tp) cc_final: 0.7507 (mm) REVERT: D 1085 ARG cc_start: 0.5545 (tpp-160) cc_final: 0.5028 (ttm170) REVERT: D 1144 VAL cc_start: 0.8101 (t) cc_final: 0.7698 (p) REVERT: D 1336 TRP cc_start: 0.6297 (m100) cc_final: 0.5864 (m100) outliers start: 116 outliers final: 74 residues processed: 431 average time/residue: 0.4987 time to fit residues: 267.4305 Evaluate side-chains 432 residues out of total 4612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 345 time to evaluate : 1.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 461 HIS Chi-restraints excluded: chain A residue 488 THR Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 559 ARG Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 579 THR Chi-restraints excluded: chain A residue 657 LYS Chi-restraints excluded: chain A residue 685 SER Chi-restraints excluded: chain A residue 694 MET Chi-restraints excluded: chain A residue 915 MET Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1011 VAL Chi-restraints excluded: chain A residue 1042 MET Chi-restraints excluded: chain A residue 1044 VAL Chi-restraints excluded: chain A residue 1084 MET Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain A residue 1352 VAL Chi-restraints excluded: chain A residue 1417 THR Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 393 ILE Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 449 ASP Chi-restraints excluded: chain B residue 461 HIS Chi-restraints excluded: chain B residue 488 THR Chi-restraints excluded: chain B residue 513 SER Chi-restraints excluded: chain B residue 527 LEU Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 657 LYS Chi-restraints excluded: chain B residue 685 SER Chi-restraints excluded: chain B residue 694 MET Chi-restraints excluded: chain B residue 915 MET Chi-restraints excluded: chain B residue 936 LYS Chi-restraints excluded: chain B residue 998 LEU Chi-restraints excluded: chain B residue 1011 VAL Chi-restraints excluded: chain B residue 1042 MET Chi-restraints excluded: chain B residue 1044 VAL Chi-restraints excluded: chain B residue 1084 MET Chi-restraints excluded: chain B residue 1107 ARG Chi-restraints excluded: chain B residue 1140 ASN Chi-restraints excluded: chain B residue 1152 GLN Chi-restraints excluded: chain B residue 1417 THR Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain C residue 426 VAL Chi-restraints excluded: chain C residue 461 HIS Chi-restraints excluded: chain C residue 488 THR Chi-restraints excluded: chain C residue 527 LEU Chi-restraints excluded: chain C residue 559 ARG Chi-restraints excluded: chain C residue 574 VAL Chi-restraints excluded: chain C residue 579 THR Chi-restraints excluded: chain C residue 657 LYS Chi-restraints excluded: chain C residue 685 SER Chi-restraints excluded: chain C residue 694 MET Chi-restraints excluded: chain C residue 915 MET Chi-restraints excluded: chain C residue 936 LYS Chi-restraints excluded: chain C residue 998 LEU Chi-restraints excluded: chain C residue 1011 VAL Chi-restraints excluded: chain C residue 1042 MET Chi-restraints excluded: chain C residue 1044 VAL Chi-restraints excluded: chain C residue 1084 MET Chi-restraints excluded: chain C residue 1107 ARG Chi-restraints excluded: chain C residue 1417 THR Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 393 ILE Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 449 ASP Chi-restraints excluded: chain D residue 488 THR Chi-restraints excluded: chain D residue 527 LEU Chi-restraints excluded: chain D residue 559 ARG Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 579 THR Chi-restraints excluded: chain D residue 657 LYS Chi-restraints excluded: chain D residue 685 SER Chi-restraints excluded: chain D residue 694 MET Chi-restraints excluded: chain D residue 915 MET Chi-restraints excluded: chain D residue 936 LYS Chi-restraints excluded: chain D residue 1011 VAL Chi-restraints excluded: chain D residue 1042 MET Chi-restraints excluded: chain D residue 1044 VAL Chi-restraints excluded: chain D residue 1084 MET Chi-restraints excluded: chain D residue 1107 ARG Chi-restraints excluded: chain D residue 1417 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 169 optimal weight: 0.7980 chunk 448 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 chunk 345 optimal weight: 2.9990 chunk 438 optimal weight: 0.9990 chunk 428 optimal weight: 10.0000 chunk 357 optimal weight: 0.6980 chunk 242 optimal weight: 0.0670 chunk 81 optimal weight: 1.9990 chunk 503 optimal weight: 3.9990 chunk 239 optimal weight: 1.9990 overall best weight: 0.9122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 413 ASN A 417 GLN ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 413 ASN B 417 GLN ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1443 HIS C 413 ASN C 417 GLN ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 413 ASN D 417 GLN ** D 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1152 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.179828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.145635 restraints weight = 52281.798| |-----------------------------------------------------------------------------| r_work (start): 0.3835 rms_B_bonded: 2.04 r_work: 0.3382 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3222 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.4051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 37467 Z= 0.113 Angle : 0.446 5.739 51318 Z= 0.235 Chirality : 0.038 0.154 6072 Planarity : 0.003 0.044 6688 Dihedral : 4.669 56.396 6444 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 4.09 % Allowed : 16.57 % Favored : 79.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.58 (0.12), residues: 5352 helix: 2.09 (0.09), residues: 2968 sheet: -1.55 (0.23), residues: 404 loop : 0.10 (0.14), residues: 1980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1128 TYR 0.016 0.001 TYR D1063 PHE 0.015 0.001 PHE A 334 TRP 0.021 0.001 TRP A 96 HIS 0.003 0.001 HIS A 813 Details of bonding type rmsd covalent geometry : bond 0.00251 (37464) covalent geometry : angle 0.44577 (51304) SS BOND : bond 0.00084 ( 3) SS BOND : angle 0.21922 ( 14) hydrogen bonds : bond 0.03698 ( 2324) hydrogen bonds : angle 3.63877 ( 6864) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10704 Ramachandran restraints generated. 5352 Oldfield, 0 Emsley, 5352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10704 Ramachandran restraints generated. 5352 Oldfield, 0 Emsley, 5352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 4612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 363 time to evaluate : 0.929 Fit side-chains REVERT: A 134 TYR cc_start: 0.7664 (m-80) cc_final: 0.7327 (m-80) REVERT: A 328 LEU cc_start: 0.7577 (OUTLIER) cc_final: 0.6958 (mt) REVERT: A 334 PHE cc_start: 0.8248 (t80) cc_final: 0.7895 (t80) REVERT: A 415 LEU cc_start: 0.8633 (mm) cc_final: 0.8277 (mt) REVERT: A 466 TYR cc_start: 0.7781 (m-80) cc_final: 0.7502 (m-80) REVERT: A 694 MET cc_start: 0.7969 (OUTLIER) cc_final: 0.7420 (tmm) REVERT: A 915 MET cc_start: 0.9140 (OUTLIER) cc_final: 0.8904 (ttm) REVERT: A 1082 LEU cc_start: 0.7884 (tp) cc_final: 0.7550 (mm) REVERT: A 1085 ARG cc_start: 0.5632 (tpp-160) cc_final: 0.5130 (ttm170) REVERT: A 1144 VAL cc_start: 0.8052 (t) cc_final: 0.7680 (p) REVERT: A 1336 TRP cc_start: 0.6304 (m100) cc_final: 0.5928 (m100) REVERT: B 328 LEU cc_start: 0.7592 (OUTLIER) cc_final: 0.6988 (mt) REVERT: B 334 PHE cc_start: 0.8253 (t80) cc_final: 0.7891 (t80) REVERT: B 466 TYR cc_start: 0.7759 (m-80) cc_final: 0.7349 (m-80) REVERT: B 694 MET cc_start: 0.7932 (OUTLIER) cc_final: 0.7402 (tmm) REVERT: B 809 ASP cc_start: 0.8183 (t0) cc_final: 0.7803 (t0) REVERT: B 1082 LEU cc_start: 0.7880 (tp) cc_final: 0.7533 (mm) REVERT: B 1085 ARG cc_start: 0.5603 (tpp-160) cc_final: 0.5097 (ttm170) REVERT: B 1140 ASN cc_start: 0.8115 (OUTLIER) cc_final: 0.7854 (m-40) REVERT: B 1144 VAL cc_start: 0.8055 (t) cc_final: 0.7712 (p) REVERT: B 1336 TRP cc_start: 0.6276 (m100) cc_final: 0.5900 (m100) REVERT: C 328 LEU cc_start: 0.7576 (OUTLIER) cc_final: 0.6961 (mt) REVERT: C 334 PHE cc_start: 0.8253 (t80) cc_final: 0.7906 (t80) REVERT: C 415 LEU cc_start: 0.8640 (mm) cc_final: 0.8282 (mt) REVERT: C 466 TYR cc_start: 0.7753 (m-80) cc_final: 0.7409 (m-80) REVERT: C 694 MET cc_start: 0.7978 (OUTLIER) cc_final: 0.7430 (tmm) REVERT: C 1082 LEU cc_start: 0.7876 (tp) cc_final: 0.7539 (mm) REVERT: C 1085 ARG cc_start: 0.5581 (tpp-160) cc_final: 0.5091 (ttm170) REVERT: C 1144 VAL cc_start: 0.8097 (t) cc_final: 0.7686 (p) REVERT: C 1336 TRP cc_start: 0.6285 (m100) cc_final: 0.5920 (m100) REVERT: D 328 LEU cc_start: 0.7606 (OUTLIER) cc_final: 0.6985 (mt) REVERT: D 334 PHE cc_start: 0.8258 (t80) cc_final: 0.7911 (t80) REVERT: D 466 TYR cc_start: 0.7748 (m-80) cc_final: 0.7336 (m-80) REVERT: D 694 MET cc_start: 0.7918 (OUTLIER) cc_final: 0.7393 (tmm) REVERT: D 809 ASP cc_start: 0.8156 (t0) cc_final: 0.7777 (t0) REVERT: D 1082 LEU cc_start: 0.7892 (tp) cc_final: 0.7547 (mm) REVERT: D 1085 ARG cc_start: 0.5595 (tpp-160) cc_final: 0.5096 (ttm170) REVERT: D 1144 VAL cc_start: 0.8076 (t) cc_final: 0.7681 (p) REVERT: D 1157 MET cc_start: 0.6722 (tpt) cc_final: 0.6446 (tpp) REVERT: D 1336 TRP cc_start: 0.6285 (m100) cc_final: 0.5920 (m100) outliers start: 110 outliers final: 64 residues processed: 440 average time/residue: 0.5199 time to fit residues: 284.8779 Evaluate side-chains 439 residues out of total 4612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 365 time to evaluate : 1.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 461 HIS Chi-restraints excluded: chain A residue 488 THR Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 579 THR Chi-restraints excluded: chain A residue 611 ASP Chi-restraints excluded: chain A residue 657 LYS Chi-restraints excluded: chain A residue 685 SER Chi-restraints excluded: chain A residue 694 MET Chi-restraints excluded: chain A residue 915 MET Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1011 VAL Chi-restraints excluded: chain A residue 1084 MET Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain A residue 1417 THR Chi-restraints excluded: chain A residue 1483 LEU Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 393 ILE Chi-restraints excluded: chain B residue 449 ASP Chi-restraints excluded: chain B residue 461 HIS Chi-restraints excluded: chain B residue 488 THR Chi-restraints excluded: chain B residue 527 LEU Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 657 LYS Chi-restraints excluded: chain B residue 685 SER Chi-restraints excluded: chain B residue 694 MET Chi-restraints excluded: chain B residue 915 MET Chi-restraints excluded: chain B residue 998 LEU Chi-restraints excluded: chain B residue 1011 VAL Chi-restraints excluded: chain B residue 1084 MET Chi-restraints excluded: chain B residue 1107 ARG Chi-restraints excluded: chain B residue 1140 ASN Chi-restraints excluded: chain B residue 1352 VAL Chi-restraints excluded: chain B residue 1417 THR Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain C residue 426 VAL Chi-restraints excluded: chain C residue 461 HIS Chi-restraints excluded: chain C residue 488 THR Chi-restraints excluded: chain C residue 527 LEU Chi-restraints excluded: chain C residue 574 VAL Chi-restraints excluded: chain C residue 579 THR Chi-restraints excluded: chain C residue 611 ASP Chi-restraints excluded: chain C residue 657 LYS Chi-restraints excluded: chain C residue 685 SER Chi-restraints excluded: chain C residue 694 MET Chi-restraints excluded: chain C residue 915 MET Chi-restraints excluded: chain C residue 998 LEU Chi-restraints excluded: chain C residue 1042 MET Chi-restraints excluded: chain C residue 1084 MET Chi-restraints excluded: chain C residue 1107 ARG Chi-restraints excluded: chain C residue 1352 VAL Chi-restraints excluded: chain C residue 1417 THR Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 393 ILE Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 449 ASP Chi-restraints excluded: chain D residue 488 THR Chi-restraints excluded: chain D residue 527 LEU Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 579 THR Chi-restraints excluded: chain D residue 657 LYS Chi-restraints excluded: chain D residue 685 SER Chi-restraints excluded: chain D residue 694 MET Chi-restraints excluded: chain D residue 915 MET Chi-restraints excluded: chain D residue 1011 VAL Chi-restraints excluded: chain D residue 1084 MET Chi-restraints excluded: chain D residue 1107 ARG Chi-restraints excluded: chain D residue 1352 VAL Chi-restraints excluded: chain D residue 1417 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 149 optimal weight: 4.9990 chunk 431 optimal weight: 0.8980 chunk 264 optimal weight: 0.0270 chunk 56 optimal weight: 2.9990 chunk 47 optimal weight: 9.9990 chunk 382 optimal weight: 20.0000 chunk 312 optimal weight: 0.7980 chunk 486 optimal weight: 0.7980 chunk 143 optimal weight: 5.9990 chunk 80 optimal weight: 0.9990 chunk 330 optimal weight: 6.9990 overall best weight: 0.7040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 413 ASN A 417 GLN ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1152 GLN ** A1443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 413 ASN B 417 GLN ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1152 GLN C 413 ASN C 417 GLN ** C 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 413 ASN D 417 GLN ** D 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1152 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.180515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.146712 restraints weight = 52071.724| |-----------------------------------------------------------------------------| r_work (start): 0.3848 rms_B_bonded: 2.05 r_work: 0.3386 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3223 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.4102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 37467 Z= 0.100 Angle : 0.433 6.881 51318 Z= 0.227 Chirality : 0.038 0.139 6072 Planarity : 0.003 0.044 6688 Dihedral : 4.437 57.851 6444 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.75 % Allowed : 17.20 % Favored : 79.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.73 (0.12), residues: 5352 helix: 2.22 (0.09), residues: 2992 sheet: -1.43 (0.24), residues: 404 loop : 0.11 (0.14), residues: 1956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D1128 TYR 0.016 0.001 TYR C1063 PHE 0.016 0.001 PHE A 334 TRP 0.024 0.001 TRP A 96 HIS 0.003 0.001 HIS B 813 Details of bonding type rmsd covalent geometry : bond 0.00219 (37464) covalent geometry : angle 0.43332 (51304) SS BOND : bond 0.00096 ( 3) SS BOND : angle 0.17594 ( 14) hydrogen bonds : bond 0.03475 ( 2324) hydrogen bonds : angle 3.51892 ( 6864) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10704 Ramachandran restraints generated. 5352 Oldfield, 0 Emsley, 5352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10704 Ramachandran restraints generated. 5352 Oldfield, 0 Emsley, 5352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 4612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 370 time to evaluate : 1.295 Fit side-chains REVERT: A 134 TYR cc_start: 0.7653 (m-80) cc_final: 0.7374 (m-80) REVERT: A 328 LEU cc_start: 0.7591 (OUTLIER) cc_final: 0.6982 (mt) REVERT: A 334 PHE cc_start: 0.8243 (t80) cc_final: 0.7913 (t80) REVERT: A 415 LEU cc_start: 0.8589 (mm) cc_final: 0.8230 (mt) REVERT: A 466 TYR cc_start: 0.7752 (m-80) cc_final: 0.7509 (m-80) REVERT: A 694 MET cc_start: 0.7911 (OUTLIER) cc_final: 0.7380 (tmm) REVERT: A 915 MET cc_start: 0.9124 (OUTLIER) cc_final: 0.8903 (ttm) REVERT: A 1082 LEU cc_start: 0.7866 (tp) cc_final: 0.7554 (mm) REVERT: A 1085 ARG cc_start: 0.5569 (tpp-160) cc_final: 0.5045 (ttm110) REVERT: A 1144 VAL cc_start: 0.8065 (t) cc_final: 0.7672 (p) REVERT: A 1336 TRP cc_start: 0.6311 (m100) cc_final: 0.6006 (m100) REVERT: A 1490 LEU cc_start: 0.6507 (mt) cc_final: 0.6176 (mt) REVERT: B 328 LEU cc_start: 0.7532 (OUTLIER) cc_final: 0.6927 (mt) REVERT: B 334 PHE cc_start: 0.8258 (t80) cc_final: 0.7845 (t80) REVERT: B 415 LEU cc_start: 0.8572 (mm) cc_final: 0.8208 (mt) REVERT: B 466 TYR cc_start: 0.7741 (m-80) cc_final: 0.7504 (m-80) REVERT: B 694 MET cc_start: 0.7909 (OUTLIER) cc_final: 0.7376 (tmm) REVERT: B 809 ASP cc_start: 0.8168 (t0) cc_final: 0.7755 (t0) REVERT: B 1082 LEU cc_start: 0.7851 (tp) cc_final: 0.7527 (mm) REVERT: B 1085 ARG cc_start: 0.5545 (tpp-160) cc_final: 0.5015 (ttm110) REVERT: B 1144 VAL cc_start: 0.8048 (t) cc_final: 0.7684 (p) REVERT: B 1157 MET cc_start: 0.6712 (tpp) cc_final: 0.5974 (ttm) REVERT: B 1336 TRP cc_start: 0.6295 (m100) cc_final: 0.5914 (m100) REVERT: C 328 LEU cc_start: 0.7588 (OUTLIER) cc_final: 0.6993 (mt) REVERT: C 415 LEU cc_start: 0.8589 (mm) cc_final: 0.8236 (mt) REVERT: C 466 TYR cc_start: 0.7735 (m-80) cc_final: 0.7492 (m-80) REVERT: C 694 MET cc_start: 0.7902 (OUTLIER) cc_final: 0.7373 (tmm) REVERT: C 809 ASP cc_start: 0.8160 (t0) cc_final: 0.7822 (t0) REVERT: C 1082 LEU cc_start: 0.7863 (tp) cc_final: 0.7545 (mm) REVERT: C 1085 ARG cc_start: 0.5555 (tpp-160) cc_final: 0.5029 (ttm110) REVERT: C 1144 VAL cc_start: 0.8113 (t) cc_final: 0.7709 (p) REVERT: C 1157 MET cc_start: 0.6456 (tpp) cc_final: 0.5618 (mtt) REVERT: C 1336 TRP cc_start: 0.6396 (m100) cc_final: 0.6014 (m100) REVERT: C 1490 LEU cc_start: 0.6684 (mt) cc_final: 0.6376 (mt) REVERT: D 328 LEU cc_start: 0.7574 (OUTLIER) cc_final: 0.6981 (mt) REVERT: D 415 LEU cc_start: 0.8578 (mm) cc_final: 0.8222 (mt) REVERT: D 466 TYR cc_start: 0.7741 (m-80) cc_final: 0.7512 (m-80) REVERT: D 611 ASP cc_start: 0.7353 (OUTLIER) cc_final: 0.7122 (t0) REVERT: D 694 MET cc_start: 0.7913 (OUTLIER) cc_final: 0.7376 (tmm) REVERT: D 809 ASP cc_start: 0.8138 (t0) cc_final: 0.7729 (t0) REVERT: D 1082 LEU cc_start: 0.7872 (tp) cc_final: 0.7549 (mm) REVERT: D 1085 ARG cc_start: 0.5541 (tpp-160) cc_final: 0.5018 (ttm110) REVERT: D 1144 VAL cc_start: 0.8064 (t) cc_final: 0.7664 (p) REVERT: D 1336 TRP cc_start: 0.6385 (m100) cc_final: 0.6000 (m100) REVERT: D 1490 LEU cc_start: 0.6651 (mt) cc_final: 0.6372 (mt) outliers start: 101 outliers final: 56 residues processed: 427 average time/residue: 0.4943 time to fit residues: 264.6276 Evaluate side-chains 429 residues out of total 4612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 363 time to evaluate : 1.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 461 HIS Chi-restraints excluded: chain A residue 488 THR Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 579 THR Chi-restraints excluded: chain A residue 612 ARG Chi-restraints excluded: chain A residue 657 LYS Chi-restraints excluded: chain A residue 694 MET Chi-restraints excluded: chain A residue 915 MET Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1011 VAL Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain A residue 1417 THR Chi-restraints excluded: chain A residue 1483 LEU Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 393 ILE Chi-restraints excluded: chain B residue 461 HIS Chi-restraints excluded: chain B residue 488 THR Chi-restraints excluded: chain B residue 527 LEU Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 657 LYS Chi-restraints excluded: chain B residue 694 MET Chi-restraints excluded: chain B residue 998 LEU Chi-restraints excluded: chain B residue 1011 VAL Chi-restraints excluded: chain B residue 1107 ARG Chi-restraints excluded: chain B residue 1352 VAL Chi-restraints excluded: chain B residue 1417 THR Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain C residue 461 HIS Chi-restraints excluded: chain C residue 488 THR Chi-restraints excluded: chain C residue 527 LEU Chi-restraints excluded: chain C residue 574 VAL Chi-restraints excluded: chain C residue 579 THR Chi-restraints excluded: chain C residue 612 ARG Chi-restraints excluded: chain C residue 657 LYS Chi-restraints excluded: chain C residue 694 MET Chi-restraints excluded: chain C residue 998 LEU Chi-restraints excluded: chain C residue 1011 VAL Chi-restraints excluded: chain C residue 1042 MET Chi-restraints excluded: chain C residue 1107 ARG Chi-restraints excluded: chain C residue 1352 VAL Chi-restraints excluded: chain C residue 1417 THR Chi-restraints excluded: chain C residue 1483 LEU Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 393 ILE Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 488 THR Chi-restraints excluded: chain D residue 527 LEU Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 579 THR Chi-restraints excluded: chain D residue 611 ASP Chi-restraints excluded: chain D residue 657 LYS Chi-restraints excluded: chain D residue 694 MET Chi-restraints excluded: chain D residue 998 LEU Chi-restraints excluded: chain D residue 1011 VAL Chi-restraints excluded: chain D residue 1107 ARG Chi-restraints excluded: chain D residue 1352 VAL Chi-restraints excluded: chain D residue 1417 THR Chi-restraints excluded: chain D residue 1483 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 227 optimal weight: 3.9990 chunk 143 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 378 optimal weight: 20.0000 chunk 193 optimal weight: 6.9990 chunk 179 optimal weight: 5.9990 chunk 486 optimal weight: 0.6980 chunk 45 optimal weight: 4.9990 chunk 139 optimal weight: 0.0980 chunk 315 optimal weight: 4.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 413 ASN A 417 GLN A1152 GLN ** A1443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 413 ASN B 417 GLN C 413 ASN C 417 GLN D 413 ASN D 417 GLN ** D 692 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1152 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.178210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.144382 restraints weight = 52491.434| |-----------------------------------------------------------------------------| r_work (start): 0.3819 rms_B_bonded: 2.17 r_work: 0.3349 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.4303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 37467 Z= 0.192 Angle : 0.533 9.588 51318 Z= 0.282 Chirality : 0.041 0.179 6072 Planarity : 0.004 0.051 6688 Dihedral : 5.010 59.303 6444 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.71 % Allowed : 16.98 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.29 (0.11), residues: 5352 helix: 1.82 (0.09), residues: 2968 sheet: -1.65 (0.24), residues: 404 loop : 0.02 (0.14), residues: 1980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 559 TYR 0.028 0.002 TYR B1063 PHE 0.029 0.002 PHE C1160 TRP 0.019 0.002 TRP A 96 HIS 0.006 0.001 HIS A 813 Details of bonding type rmsd covalent geometry : bond 0.00448 (37464) covalent geometry : angle 0.53267 (51304) SS BOND : bond 0.00173 ( 3) SS BOND : angle 0.34161 ( 14) hydrogen bonds : bond 0.04538 ( 2324) hydrogen bonds : angle 3.90047 ( 6864) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10704 Ramachandran restraints generated. 5352 Oldfield, 0 Emsley, 5352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10704 Ramachandran restraints generated. 5352 Oldfield, 0 Emsley, 5352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 4612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 353 time to evaluate : 1.066 Fit side-chains REVERT: A 134 TYR cc_start: 0.7581 (m-80) cc_final: 0.7280 (m-80) REVERT: A 328 LEU cc_start: 0.7667 (OUTLIER) cc_final: 0.7032 (mt) REVERT: A 466 TYR cc_start: 0.7749 (m-80) cc_final: 0.7424 (m-80) REVERT: A 517 ARG cc_start: 0.7120 (OUTLIER) cc_final: 0.6624 (ttm-80) REVERT: A 694 MET cc_start: 0.7852 (OUTLIER) cc_final: 0.7329 (tmm) REVERT: A 809 ASP cc_start: 0.7936 (t0) cc_final: 0.7556 (t0) REVERT: A 1082 LEU cc_start: 0.7864 (tp) cc_final: 0.7566 (mm) REVERT: A 1085 ARG cc_start: 0.5604 (tpp-160) cc_final: 0.5089 (ttm110) REVERT: A 1144 VAL cc_start: 0.8101 (t) cc_final: 0.7693 (p) REVERT: A 1336 TRP cc_start: 0.6301 (m100) cc_final: 0.5819 (m100) REVERT: B 328 LEU cc_start: 0.7648 (OUTLIER) cc_final: 0.7028 (mt) REVERT: B 466 TYR cc_start: 0.7744 (m-80) cc_final: 0.7390 (m-80) REVERT: B 694 MET cc_start: 0.7843 (OUTLIER) cc_final: 0.7318 (tmm) REVERT: B 809 ASP cc_start: 0.7911 (t0) cc_final: 0.7576 (t0) REVERT: B 1082 LEU cc_start: 0.7870 (tp) cc_final: 0.7574 (mm) REVERT: B 1085 ARG cc_start: 0.5595 (tpp-160) cc_final: 0.5084 (ttm110) REVERT: B 1144 VAL cc_start: 0.8116 (t) cc_final: 0.7728 (p) REVERT: B 1157 MET cc_start: 0.6822 (tpp) cc_final: 0.6175 (ttm) REVERT: B 1336 TRP cc_start: 0.6311 (m100) cc_final: 0.5910 (m100) REVERT: C 328 LEU cc_start: 0.7668 (OUTLIER) cc_final: 0.7039 (mt) REVERT: C 466 TYR cc_start: 0.7737 (m-80) cc_final: 0.7416 (m-80) REVERT: C 694 MET cc_start: 0.7841 (OUTLIER) cc_final: 0.7315 (tmm) REVERT: C 809 ASP cc_start: 0.7940 (t0) cc_final: 0.7576 (t0) REVERT: C 1082 LEU cc_start: 0.7864 (tp) cc_final: 0.7542 (mm) REVERT: C 1085 ARG cc_start: 0.5618 (tpp-160) cc_final: 0.5097 (ttm110) REVERT: C 1144 VAL cc_start: 0.8127 (t) cc_final: 0.7699 (p) REVERT: C 1336 TRP cc_start: 0.6322 (m100) cc_final: 0.5960 (m100) REVERT: D 328 LEU cc_start: 0.7667 (OUTLIER) cc_final: 0.7032 (mt) REVERT: D 466 TYR cc_start: 0.7743 (m-80) cc_final: 0.7385 (m-80) REVERT: D 694 MET cc_start: 0.7790 (OUTLIER) cc_final: 0.7297 (tmm) REVERT: D 809 ASP cc_start: 0.7905 (t0) cc_final: 0.7570 (t0) REVERT: D 1082 LEU cc_start: 0.7867 (tp) cc_final: 0.7565 (mm) REVERT: D 1085 ARG cc_start: 0.5601 (tpp-160) cc_final: 0.5089 (ttm110) REVERT: D 1144 VAL cc_start: 0.8061 (t) cc_final: 0.7668 (p) REVERT: D 1336 TRP cc_start: 0.6320 (m100) cc_final: 0.5960 (m100) outliers start: 100 outliers final: 69 residues processed: 425 average time/residue: 0.4888 time to fit residues: 259.9203 Evaluate side-chains 419 residues out of total 4612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 341 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 461 HIS Chi-restraints excluded: chain A residue 488 THR Chi-restraints excluded: chain A residue 517 ARG Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 579 THR Chi-restraints excluded: chain A residue 657 LYS Chi-restraints excluded: chain A residue 694 MET Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1011 VAL Chi-restraints excluded: chain A residue 1042 MET Chi-restraints excluded: chain A residue 1044 VAL Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain A residue 1352 VAL Chi-restraints excluded: chain A residue 1417 THR Chi-restraints excluded: chain A residue 1481 THR Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 393 ILE Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 449 ASP Chi-restraints excluded: chain B residue 461 HIS Chi-restraints excluded: chain B residue 488 THR Chi-restraints excluded: chain B residue 527 LEU Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 657 LYS Chi-restraints excluded: chain B residue 694 MET Chi-restraints excluded: chain B residue 915 MET Chi-restraints excluded: chain B residue 998 LEU Chi-restraints excluded: chain B residue 1011 VAL Chi-restraints excluded: chain B residue 1042 MET Chi-restraints excluded: chain B residue 1044 VAL Chi-restraints excluded: chain B residue 1107 ARG Chi-restraints excluded: chain B residue 1352 VAL Chi-restraints excluded: chain B residue 1417 THR Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain C residue 426 VAL Chi-restraints excluded: chain C residue 461 HIS Chi-restraints excluded: chain C residue 488 THR Chi-restraints excluded: chain C residue 527 LEU Chi-restraints excluded: chain C residue 574 VAL Chi-restraints excluded: chain C residue 579 THR Chi-restraints excluded: chain C residue 657 LYS Chi-restraints excluded: chain C residue 694 MET Chi-restraints excluded: chain C residue 915 MET Chi-restraints excluded: chain C residue 998 LEU Chi-restraints excluded: chain C residue 1011 VAL Chi-restraints excluded: chain C residue 1042 MET Chi-restraints excluded: chain C residue 1044 VAL Chi-restraints excluded: chain C residue 1107 ARG Chi-restraints excluded: chain C residue 1352 VAL Chi-restraints excluded: chain C residue 1417 THR Chi-restraints excluded: chain C residue 1483 LEU Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 393 ILE Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 449 ASP Chi-restraints excluded: chain D residue 488 THR Chi-restraints excluded: chain D residue 527 LEU Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 579 THR Chi-restraints excluded: chain D residue 657 LYS Chi-restraints excluded: chain D residue 694 MET Chi-restraints excluded: chain D residue 915 MET Chi-restraints excluded: chain D residue 998 LEU Chi-restraints excluded: chain D residue 1011 VAL Chi-restraints excluded: chain D residue 1042 MET Chi-restraints excluded: chain D residue 1044 VAL Chi-restraints excluded: chain D residue 1107 ARG Chi-restraints excluded: chain D residue 1352 VAL Chi-restraints excluded: chain D residue 1417 THR Chi-restraints excluded: chain D residue 1483 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 466 optimal weight: 1.9990 chunk 300 optimal weight: 10.0000 chunk 369 optimal weight: 0.6980 chunk 310 optimal weight: 0.9990 chunk 203 optimal weight: 0.3980 chunk 318 optimal weight: 0.9980 chunk 435 optimal weight: 7.9990 chunk 362 optimal weight: 0.7980 chunk 297 optimal weight: 9.9990 chunk 54 optimal weight: 0.6980 chunk 66 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 413 ASN A 417 GLN ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 692 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1152 GLN ** A1443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 413 ASN B 417 GLN ** B 692 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1152 GLN C 413 ASN C 417 GLN ** C 692 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 413 ASN D 417 GLN ** D 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1152 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.180368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.147066 restraints weight = 52293.712| |-----------------------------------------------------------------------------| r_work (start): 0.3850 rms_B_bonded: 2.19 r_work: 0.3378 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.4307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 37467 Z= 0.104 Angle : 0.448 9.448 51318 Z= 0.234 Chirality : 0.038 0.162 6072 Planarity : 0.003 0.044 6688 Dihedral : 4.488 50.123 6444 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.79 % Allowed : 17.72 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.63 (0.12), residues: 5352 helix: 2.12 (0.09), residues: 2972 sheet: -1.55 (0.24), residues: 404 loop : 0.16 (0.14), residues: 1976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 517 TYR 0.019 0.001 TYR D1063 PHE 0.044 0.001 PHE B1160 TRP 0.030 0.001 TRP A 96 HIS 0.004 0.001 HIS D 813 Details of bonding type rmsd covalent geometry : bond 0.00222 (37464) covalent geometry : angle 0.44770 (51304) SS BOND : bond 0.00138 ( 3) SS BOND : angle 0.19041 ( 14) hydrogen bonds : bond 0.03596 ( 2324) hydrogen bonds : angle 3.60888 ( 6864) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10704 Ramachandran restraints generated. 5352 Oldfield, 0 Emsley, 5352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10704 Ramachandran restraints generated. 5352 Oldfield, 0 Emsley, 5352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 4612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 363 time to evaluate : 1.156 Fit side-chains REVERT: A 134 TYR cc_start: 0.7484 (m-80) cc_final: 0.7222 (m-80) REVERT: A 328 LEU cc_start: 0.7553 (OUTLIER) cc_final: 0.6933 (mt) REVERT: A 415 LEU cc_start: 0.8538 (mm) cc_final: 0.8155 (mt) REVERT: A 466 TYR cc_start: 0.7683 (m-80) cc_final: 0.7482 (m-80) REVERT: A 517 ARG cc_start: 0.7072 (OUTLIER) cc_final: 0.6547 (ttm-80) REVERT: A 694 MET cc_start: 0.7784 (OUTLIER) cc_final: 0.7240 (tmm) REVERT: A 809 ASP cc_start: 0.7855 (t0) cc_final: 0.7548 (t0) REVERT: A 916 ARG cc_start: 0.8273 (OUTLIER) cc_final: 0.7682 (tpm170) REVERT: A 1068 PHE cc_start: 0.6724 (t80) cc_final: 0.4853 (t80) REVERT: A 1082 LEU cc_start: 0.7868 (tp) cc_final: 0.7570 (mm) REVERT: A 1085 ARG cc_start: 0.5538 (tpp-160) cc_final: 0.5013 (ttm110) REVERT: A 1144 VAL cc_start: 0.7987 (t) cc_final: 0.7623 (p) REVERT: A 1336 TRP cc_start: 0.6346 (m100) cc_final: 0.6001 (m100) REVERT: A 1490 LEU cc_start: 0.6424 (mp) cc_final: 0.6127 (mt) REVERT: B 328 LEU cc_start: 0.7540 (OUTLIER) cc_final: 0.6936 (mt) REVERT: B 334 PHE cc_start: 0.8204 (t80) cc_final: 0.7798 (t80) REVERT: B 415 LEU cc_start: 0.8537 (mm) cc_final: 0.8155 (mt) REVERT: B 466 TYR cc_start: 0.7688 (m-80) cc_final: 0.7468 (m-80) REVERT: B 694 MET cc_start: 0.7747 (ttm) cc_final: 0.7233 (tmm) REVERT: B 809 ASP cc_start: 0.7872 (t0) cc_final: 0.7544 (t0) REVERT: B 1068 PHE cc_start: 0.6708 (t80) cc_final: 0.4828 (t80) REVERT: B 1082 LEU cc_start: 0.7872 (tp) cc_final: 0.7575 (mm) REVERT: B 1085 ARG cc_start: 0.5533 (tpp-160) cc_final: 0.5009 (ttm110) REVERT: B 1144 VAL cc_start: 0.7952 (t) cc_final: 0.7577 (p) REVERT: B 1157 MET cc_start: 0.6658 (tpp) cc_final: 0.6173 (ttm) REVERT: B 1336 TRP cc_start: 0.6240 (m100) cc_final: 0.5869 (m100) REVERT: B 1490 LEU cc_start: 0.6698 (mp) cc_final: 0.6327 (mt) REVERT: C 328 LEU cc_start: 0.7562 (OUTLIER) cc_final: 0.6946 (mt) REVERT: C 415 LEU cc_start: 0.8541 (mm) cc_final: 0.8160 (mt) REVERT: C 466 TYR cc_start: 0.7697 (m-80) cc_final: 0.7488 (m-80) REVERT: C 694 MET cc_start: 0.7758 (OUTLIER) cc_final: 0.7214 (tmm) REVERT: C 1068 PHE cc_start: 0.6709 (t80) cc_final: 0.4828 (t80) REVERT: C 1082 LEU cc_start: 0.7862 (tp) cc_final: 0.7572 (mm) REVERT: C 1085 ARG cc_start: 0.5540 (tpp-160) cc_final: 0.5015 (ttm110) REVERT: C 1144 VAL cc_start: 0.8044 (t) cc_final: 0.7625 (p) REVERT: C 1336 TRP cc_start: 0.6310 (m100) cc_final: 0.5952 (m100) REVERT: C 1490 LEU cc_start: 0.6745 (mp) cc_final: 0.6326 (mt) REVERT: D 328 LEU cc_start: 0.7554 (OUTLIER) cc_final: 0.6933 (mt) REVERT: D 466 TYR cc_start: 0.7667 (m-80) cc_final: 0.7371 (m-80) REVERT: D 694 MET cc_start: 0.7785 (ttm) cc_final: 0.7275 (tmm) REVERT: D 809 ASP cc_start: 0.7853 (t0) cc_final: 0.7526 (t0) REVERT: D 1068 PHE cc_start: 0.6706 (t80) cc_final: 0.4826 (t80) REVERT: D 1082 LEU cc_start: 0.7873 (tp) cc_final: 0.7573 (mm) REVERT: D 1085 ARG cc_start: 0.5523 (tpp-160) cc_final: 0.5008 (ttm110) REVERT: D 1144 VAL cc_start: 0.7985 (t) cc_final: 0.7599 (p) REVERT: D 1336 TRP cc_start: 0.6306 (m100) cc_final: 0.5946 (m100) REVERT: D 1490 LEU cc_start: 0.6761 (mp) cc_final: 0.6275 (mt) outliers start: 75 outliers final: 54 residues processed: 415 average time/residue: 0.5161 time to fit residues: 267.4300 Evaluate side-chains 416 residues out of total 4612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 354 time to evaluate : 1.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 461 HIS Chi-restraints excluded: chain A residue 488 THR Chi-restraints excluded: chain A residue 517 ARG Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 579 THR Chi-restraints excluded: chain A residue 612 ARG Chi-restraints excluded: chain A residue 657 LYS Chi-restraints excluded: chain A residue 694 MET Chi-restraints excluded: chain A residue 916 ARG Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1011 VAL Chi-restraints excluded: chain A residue 1107 ARG Chi-restraints excluded: chain A residue 1417 THR Chi-restraints excluded: chain A residue 1483 LEU Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 393 ILE Chi-restraints excluded: chain B residue 461 HIS Chi-restraints excluded: chain B residue 488 THR Chi-restraints excluded: chain B residue 527 LEU Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 657 LYS Chi-restraints excluded: chain B residue 998 LEU Chi-restraints excluded: chain B residue 1011 VAL Chi-restraints excluded: chain B residue 1107 ARG Chi-restraints excluded: chain B residue 1352 VAL Chi-restraints excluded: chain B residue 1417 THR Chi-restraints excluded: chain C residue 145 LEU Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain C residue 461 HIS Chi-restraints excluded: chain C residue 488 THR Chi-restraints excluded: chain C residue 527 LEU Chi-restraints excluded: chain C residue 574 VAL Chi-restraints excluded: chain C residue 579 THR Chi-restraints excluded: chain C residue 612 ARG Chi-restraints excluded: chain C residue 657 LYS Chi-restraints excluded: chain C residue 694 MET Chi-restraints excluded: chain C residue 998 LEU Chi-restraints excluded: chain C residue 1011 VAL Chi-restraints excluded: chain C residue 1107 ARG Chi-restraints excluded: chain C residue 1352 VAL Chi-restraints excluded: chain C residue 1417 THR Chi-restraints excluded: chain C residue 1483 LEU Chi-restraints excluded: chain D residue 328 LEU Chi-restraints excluded: chain D residue 393 ILE Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 488 THR Chi-restraints excluded: chain D residue 527 LEU Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 579 THR Chi-restraints excluded: chain D residue 657 LYS Chi-restraints excluded: chain D residue 998 LEU Chi-restraints excluded: chain D residue 1011 VAL Chi-restraints excluded: chain D residue 1107 ARG Chi-restraints excluded: chain D residue 1352 VAL Chi-restraints excluded: chain D residue 1417 THR Chi-restraints excluded: chain D residue 1483 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 261 optimal weight: 8.9990 chunk 376 optimal weight: 0.0770 chunk 493 optimal weight: 3.9990 chunk 88 optimal weight: 0.7980 chunk 136 optimal weight: 9.9990 chunk 269 optimal weight: 20.0000 chunk 197 optimal weight: 1.9990 chunk 218 optimal weight: 1.9990 chunk 191 optimal weight: 5.9990 chunk 244 optimal weight: 20.0000 chunk 16 optimal weight: 0.2980 overall best weight: 1.0342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 413 ASN A 417 GLN ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 692 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1152 GLN ** A1443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 413 ASN B 417 GLN ** B 692 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1038 ASN C 413 ASN C 417 GLN ** C1443 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 413 ASN D 417 GLN D1152 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.179662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.146609 restraints weight = 52003.928| |-----------------------------------------------------------------------------| r_work (start): 0.3847 rms_B_bonded: 2.07 r_work: 0.3378 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3226 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.4364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 37467 Z= 0.120 Angle : 0.460 9.756 51318 Z= 0.240 Chirality : 0.038 0.151 6072 Planarity : 0.003 0.047 6688 Dihedral : 4.344 48.769 6444 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 3.12 % Allowed : 17.42 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.65 (0.12), residues: 5352 helix: 2.14 (0.09), residues: 2972 sheet: -1.47 (0.24), residues: 428 loop : 0.15 (0.14), residues: 1952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1128 TYR 0.020 0.001 TYR D1063 PHE 0.015 0.001 PHE C 879 TRP 0.028 0.001 TRP D 96 HIS 0.004 0.001 HIS D 813 Details of bonding type rmsd covalent geometry : bond 0.00270 (37464) covalent geometry : angle 0.45978 (51304) SS BOND : bond 0.00098 ( 3) SS BOND : angle 0.22939 ( 14) hydrogen bonds : bond 0.03748 ( 2324) hydrogen bonds : angle 3.62035 ( 6864) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11319.46 seconds wall clock time: 192 minutes 45.07 seconds (11565.07 seconds total)