Starting phenix.real_space_refine on Sun Feb 8 04:35:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8src_40726/02_2026/8src_40726.cif Found real_map, /net/cci-nas-00/data/ceres_data/8src_40726/02_2026/8src_40726.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8src_40726/02_2026/8src_40726.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8src_40726/02_2026/8src_40726.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8src_40726/02_2026/8src_40726.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8src_40726/02_2026/8src_40726.map" } resolution = 2.92 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= 0.198 sd= 1.779 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 17 9.91 5 P 16 5.49 5 S 208 5.16 5 C 26020 2.51 5 N 6936 2.21 5 O 7084 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 40281 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 9909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1366, 9909 Classifications: {'peptide': 1366} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 270} Link IDs: {'PCIS': 2, 'PTRANS': 53, 'TRANS': 1310} Chain breaks: 4 Unresolved non-hydrogen bonds: 943 Unresolved non-hydrogen angles: 1158 Unresolved non-hydrogen dihedrals: 759 Unresolved non-hydrogen chiralities: 42 Planarities with less than four sites: {'GLU:plan': 40, 'ASP:plan': 51, 'ARG:plan': 18, 'ASN:plan1': 18, 'GLN:plan1': 15, 'PHE:plan': 7, 'HIS:plan': 7, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 601 Chain: "B" Number of atoms: 9909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1366, 9909 Classifications: {'peptide': 1366} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 270} Link IDs: {'PCIS': 2, 'PTRANS': 53, 'TRANS': 1310} Chain breaks: 4 Unresolved non-hydrogen bonds: 943 Unresolved non-hydrogen angles: 1158 Unresolved non-hydrogen dihedrals: 759 Unresolved non-hydrogen chiralities: 42 Planarities with less than four sites: {'GLU:plan': 40, 'ASP:plan': 51, 'ARG:plan': 18, 'ASN:plan1': 18, 'GLN:plan1': 15, 'PHE:plan': 7, 'HIS:plan': 7, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 601 Chain: "C" Number of atoms: 9909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1366, 9909 Classifications: {'peptide': 1366} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 270} Link IDs: {'PCIS': 2, 'PTRANS': 53, 'TRANS': 1310} Chain breaks: 4 Unresolved non-hydrogen bonds: 943 Unresolved non-hydrogen angles: 1158 Unresolved non-hydrogen dihedrals: 759 Unresolved non-hydrogen chiralities: 42 Planarities with less than four sites: {'GLU:plan': 40, 'ASP:plan': 51, 'ARG:plan': 18, 'ASN:plan1': 18, 'GLN:plan1': 15, 'PHE:plan': 7, 'HIS:plan': 7, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 601 Chain: "D" Number of atoms: 9909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1366, 9909 Classifications: {'peptide': 1366} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 270} Link IDs: {'PCIS': 2, 'PTRANS': 53, 'TRANS': 1310} Chain breaks: 4 Unresolved non-hydrogen bonds: 943 Unresolved non-hydrogen angles: 1158 Unresolved non-hydrogen dihedrals: 759 Unresolved non-hydrogen chiralities: 42 Planarities with less than four sites: {'GLU:plan': 40, 'ASP:plan': 51, 'ARG:plan': 18, 'ASN:plan1': 18, 'GLN:plan1': 15, 'PHE:plan': 7, 'HIS:plan': 7, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 601 Chain: "A" Number of atoms: 161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 161 Unusual residues: {' CA': 5, 'APR': 2, 'CLR': 3} Classifications: {'undetermined': 10} Link IDs: {None: 9} Chain: "B" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 160 Unusual residues: {' CA': 4, 'APR': 2, 'CLR': 3} Classifications: {'undetermined': 9} Link IDs: {None: 8} Chain: "C" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 160 Unusual residues: {' CA': 4, 'APR': 2, 'CLR': 3} Classifications: {'undetermined': 9} Link IDs: {None: 8} Chain: "D" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 160 Unusual residues: {' CA': 4, 'APR': 2, 'CLR': 3} Classifications: {'undetermined': 9} Link IDs: {None: 8} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 10.27, per 1000 atoms: 0.25 Number of scatterers: 40281 At special positions: 0 Unit cell: (147.768, 147.768, 187.592, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 17 19.99 S 208 16.00 P 16 15.00 O 7084 8.00 N 6936 7.00 C 26020 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 997 " - pdb=" SG CYS A1006 " distance=2.03 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 Simple disulfide: pdb=" SG CYS D 997 " - pdb=" SG CYS D1006 " 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: 4.18 Conformation dependent library (CDL) restraints added in 1.9 seconds 10848 Ramachandran restraints generated. 5424 Oldfield, 0 Emsley, 5424 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10288 Finding SS restraints... Secondary structure from input PDB file: 244 helices and 32 sheets defined 60.6% alpha, 8.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.98 Creating SS restraints... Processing helix chain 'A' and resid 72 through 77 Processing helix chain 'A' and resid 118 through 135 Processing helix chain 'A' and resid 157 through 176 Processing helix chain 'A' and resid 186 through 203 removed outlier: 3.626A pdb=" N LYS A 190 " --> pdb=" O THR A 186 " (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 287 Processing helix chain 'A' and resid 298 through 311 removed outlier: 3.832A pdb=" N LEU A 302 " --> pdb=" O GLY A 298 " (cutoff:3.500A) removed outlier: 3.619A 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 340 through 344 removed outlier: 3.855A pdb=" N SER A 344 " --> pdb=" O ARG A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 359 Processing helix chain 'A' and resid 362 through 377 removed outlier: 3.656A pdb=" N VAL A 377 " --> pdb=" O ALA A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 381 removed outlier: 6.438A pdb=" N ASN A 381 " --> pdb=" O GLN A 378 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 378 through 381' Processing helix chain 'A' and resid 395 through 406 Processing helix chain 'A' and resid 410 through 421 Processing helix chain 'A' and resid 423 through 437 removed outlier: 3.503A pdb=" N ALA A 427 " --> pdb=" O GLN A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 457 removed outlier: 4.776A pdb=" N ASN A 448 " --> pdb=" O ALA A 444 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N ASP A 449 " --> pdb=" O ALA A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 469 Processing helix chain 'A' and resid 472 through 476 removed outlier: 3.515A pdb=" N GLU A 475 " --> pdb=" O LYS A 472 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LEU A 476 " --> pdb=" O ILE A 473 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 472 through 476' Processing helix chain 'A' and resid 487 through 492 Processing helix chain 'A' and resid 494 through 509 removed outlier: 3.562A pdb=" N LEU A 498 " --> pdb=" O PRO A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 523 removed outlier: 3.633A pdb=" N ARG A 517 " --> pdb=" O SER A 513 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ASN A 523 " --> pdb=" O VAL A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 569 removed outlier: 3.632A pdb=" N SER A 569 " --> pdb=" O ALA A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 586 removed outlier: 3.865A pdb=" N ILE A 580 " --> pdb=" O ASP A 577 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N SER A 583 " --> pdb=" O ILE A 580 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N LYS A 584 " --> pdb=" O TYR A 581 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TYR A 585 " --> pdb=" O ASP A 582 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASP A 586 " --> pdb=" O SER A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 590 through 610 removed outlier: 3.583A 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: 3.697A pdb=" N THR A 642 " --> pdb=" O GLU A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 643 through 647 removed outlier: 3.578A pdb=" N GLN A 647 " --> pdb=" O ARG A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 650 No H-bonds generated for 'chain 'A' and resid 648 through 650' Processing helix chain 'A' and resid 651 through 680 Processing helix chain 'A' and resid 680 through 689 Processing helix chain 'A' and resid 692 through 696 removed outlier: 3.680A pdb=" N PHE A 695 " --> pdb=" O ASN A 692 " (cutoff:3.500A) removed outlier: 3.568A 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: 3.517A pdb=" N LEU A 750 " --> pdb=" O PRO A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 788 through 800 removed outlier: 3.711A pdb=" N ARG A 793 " --> pdb=" O HIS A 789 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 826 removed outlier: 3.501A pdb=" N ARG A 805 " --> pdb=" O ALA A 801 " (cutoff:3.500A) Processing helix chain 'A' and resid 833 through 857 Processing helix chain 'A' and resid 859 through 866 removed outlier: 3.906A pdb=" N ASP A 866 " --> pdb=" O GLU A 862 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 889 removed outlier: 3.565A pdb=" N ARG A 870 " --> pdb=" O ASP A 866 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ASP A 889 " --> pdb=" O THR A 885 " (cutoff:3.500A) Processing helix chain 'A' and resid 892 through 914 removed outlier: 4.054A pdb=" N PHE A 905 " --> pdb=" O GLY A 901 " (cutoff:3.500A) Processing helix chain 'A' and resid 915 through 921 removed outlier: 3.993A pdb=" N LEU A 920 " --> pdb=" O TYR A 917 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 961 removed outlier: 3.661A pdb=" N LYS A 927 " --> pdb=" O ASN A 923 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N LYS A 936 " --> pdb=" O MET A 932 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N ASP A 937 " --> pdb=" O GLU A 933 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ILE A 947 " --> pdb=" O PHE A 943 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N PHE A 948 " --> pdb=" O LEU A 944 " (cutoff:3.500A) Processing helix chain 'A' and resid 967 through 981 removed outlier: 3.695A pdb=" N PHE A 971 " --> pdb=" O SER A 967 " (cutoff:3.500A) removed outlier: 4.467A 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 1009 through 1012 Processing helix chain 'A' and resid 1013 through 1026 removed outlier: 3.879A pdb=" N LEU A1023 " --> pdb=" O ALA A1019 " (cutoff:3.500A) Processing helix chain 'A' and resid 1028 through 1066 removed outlier: 5.966A pdb=" N GLU A1046 " --> pdb=" O MET A1042 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N ALA A1047 " --> pdb=" O LYS A1043 " (cutoff:3.500A) Processing helix chain 'A' and resid 1070 through 1072 No H-bonds generated for 'chain 'A' and resid 1070 through 1072' Processing helix chain 'A' and resid 1073 through 1090 removed outlier: 4.097A 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 1166 Processing helix chain 'A' and resid 1203 through 1208 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 1413 Processing helix chain 'A' and resid 1449 through 1453 Processing helix chain 'A' and resid 1478 through 1491 Processing helix chain 'B' and resid 72 through 77 Processing helix chain 'B' and resid 118 through 135 Processing helix chain 'B' and resid 157 through 176 Processing helix chain 'B' and resid 186 through 203 removed outlier: 3.626A pdb=" N LYS B 190 " --> pdb=" O THR B 186 " (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 287 Processing helix chain 'B' and resid 298 through 311 removed outlier: 3.832A pdb=" N LEU B 302 " --> pdb=" O GLY B 298 " (cutoff:3.500A) removed outlier: 3.619A 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 340 through 344 removed outlier: 3.855A pdb=" N SER B 344 " --> pdb=" O ARG B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 359 Processing helix chain 'B' and resid 362 through 377 removed outlier: 3.656A pdb=" N VAL B 377 " --> pdb=" O ALA B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 378 through 381 removed outlier: 6.437A pdb=" N ASN B 381 " --> pdb=" O GLN B 378 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 378 through 381' Processing helix chain 'B' and resid 395 through 406 Processing helix chain 'B' and resid 410 through 421 Processing helix chain 'B' and resid 423 through 437 removed outlier: 3.503A pdb=" N ALA B 427 " --> pdb=" O GLN B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 457 removed outlier: 4.776A pdb=" N ASN B 448 " --> pdb=" O ALA B 444 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N ASP B 449 " --> pdb=" O ALA B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 469 Processing helix chain 'B' and resid 472 through 476 removed outlier: 3.514A pdb=" N GLU B 475 " --> pdb=" O LYS B 472 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LEU B 476 " --> pdb=" O ILE B 473 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 472 through 476' Processing helix chain 'B' and resid 487 through 492 Processing helix chain 'B' and resid 494 through 509 removed outlier: 3.562A pdb=" N LEU B 498 " --> pdb=" O PRO B 494 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 523 removed outlier: 3.633A pdb=" N ARG B 517 " --> pdb=" O SER B 513 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ASN B 523 " --> pdb=" O VAL B 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 569 removed outlier: 3.632A pdb=" N SER B 569 " --> pdb=" O ALA B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 577 through 586 removed outlier: 3.865A pdb=" N ILE B 580 " --> pdb=" O ASP B 577 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N SER B 583 " --> pdb=" O ILE B 580 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N LYS B 584 " --> pdb=" O TYR B 581 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TYR B 585 " --> pdb=" O ASP B 582 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASP B 586 " --> pdb=" O SER B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 590 through 610 removed outlier: 3.584A 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: 3.697A pdb=" N THR B 642 " --> pdb=" O GLU B 638 " (cutoff:3.500A) Processing helix chain 'B' and resid 643 through 647 removed outlier: 3.579A pdb=" N GLN B 647 " --> pdb=" O ARG B 644 " (cutoff:3.500A) Processing helix chain 'B' and resid 648 through 650 No H-bonds generated for 'chain 'B' and resid 648 through 650' Processing helix chain 'B' and resid 651 through 680 Processing helix chain 'B' and resid 680 through 689 Processing helix chain 'B' and resid 692 through 696 removed outlier: 3.680A pdb=" N PHE B 695 " --> pdb=" O ASN B 692 " (cutoff:3.500A) removed outlier: 3.568A 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: 3.518A pdb=" N LEU B 750 " --> pdb=" O PRO B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 788 through 800 removed outlier: 3.711A pdb=" N ARG B 793 " --> pdb=" O HIS B 789 " (cutoff:3.500A) Processing helix chain 'B' and resid 801 through 826 removed outlier: 3.501A pdb=" N ARG B 805 " --> pdb=" O ALA B 801 " (cutoff:3.500A) Processing helix chain 'B' and resid 833 through 857 Processing helix chain 'B' and resid 859 through 866 removed outlier: 3.906A pdb=" N ASP B 866 " --> pdb=" O GLU B 862 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 889 removed outlier: 3.565A pdb=" N ARG B 870 " --> pdb=" O ASP B 866 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ASP B 889 " --> pdb=" O THR B 885 " (cutoff:3.500A) Processing helix chain 'B' and resid 892 through 914 removed outlier: 4.054A pdb=" N PHE B 905 " --> pdb=" O GLY B 901 " (cutoff:3.500A) Processing helix chain 'B' and resid 915 through 921 removed outlier: 3.993A pdb=" N LEU B 920 " --> pdb=" O TYR B 917 " (cutoff:3.500A) Processing helix chain 'B' and resid 923 through 961 removed outlier: 3.661A pdb=" N LYS B 927 " --> pdb=" O ASN B 923 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N LYS B 936 " --> pdb=" O MET B 932 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N ASP B 937 " --> pdb=" O GLU B 933 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ILE B 947 " --> pdb=" O PHE B 943 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N PHE B 948 " --> pdb=" O LEU B 944 " (cutoff:3.500A) Processing helix chain 'B' and resid 967 through 981 removed outlier: 3.694A pdb=" N PHE B 971 " --> pdb=" O SER B 967 " (cutoff:3.500A) removed outlier: 4.466A 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 1009 through 1012 Processing helix chain 'B' and resid 1013 through 1026 removed outlier: 3.879A pdb=" N LEU B1023 " --> pdb=" O ALA B1019 " (cutoff:3.500A) Processing helix chain 'B' and resid 1028 through 1066 removed outlier: 5.965A pdb=" N GLU B1046 " --> pdb=" O MET B1042 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N ALA B1047 " --> pdb=" O LYS B1043 " (cutoff:3.500A) Processing helix chain 'B' and resid 1070 through 1072 No H-bonds generated for 'chain 'B' and resid 1070 through 1072' Processing helix chain 'B' and resid 1073 through 1090 removed outlier: 4.096A 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 1166 Processing helix chain 'B' and resid 1203 through 1208 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 1413 Processing helix chain 'B' and resid 1449 through 1453 Processing helix chain 'B' and resid 1478 through 1491 Processing helix chain 'C' and resid 72 through 77 Processing helix chain 'C' and resid 118 through 135 Processing helix chain 'C' and resid 157 through 176 Processing helix chain 'C' and resid 186 through 203 removed outlier: 3.626A pdb=" N LYS C 190 " --> pdb=" O THR C 186 " (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 287 Processing helix chain 'C' and resid 298 through 311 removed outlier: 3.832A pdb=" N LEU C 302 " --> pdb=" O GLY C 298 " (cutoff:3.500A) removed outlier: 3.620A 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 340 through 344 removed outlier: 3.855A pdb=" N SER C 344 " --> pdb=" O ARG C 341 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 359 Processing helix chain 'C' and resid 362 through 377 removed outlier: 3.656A pdb=" N VAL C 377 " --> pdb=" O ALA C 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 378 through 381 removed outlier: 6.438A pdb=" N ASN C 381 " --> pdb=" O GLN C 378 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 378 through 381' Processing helix chain 'C' and resid 395 through 406 Processing helix chain 'C' and resid 410 through 421 Processing helix chain 'C' and resid 423 through 437 removed outlier: 3.502A pdb=" N ALA C 427 " --> pdb=" O GLN C 423 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 457 removed outlier: 4.776A pdb=" N ASN C 448 " --> pdb=" O ALA C 444 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N ASP C 449 " --> pdb=" O ALA C 445 " (cutoff:3.500A) Processing helix chain 'C' and resid 459 through 469 Processing helix chain 'C' and resid 472 through 476 removed outlier: 3.515A pdb=" N GLU C 475 " --> pdb=" O LYS C 472 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LEU C 476 " --> pdb=" O ILE C 473 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 472 through 476' Processing helix chain 'C' and resid 487 through 492 Processing helix chain 'C' and resid 494 through 509 removed outlier: 3.562A pdb=" N LEU C 498 " --> pdb=" O PRO C 494 " (cutoff:3.500A) Processing helix chain 'C' and resid 513 through 523 removed outlier: 3.633A pdb=" N ARG C 517 " --> pdb=" O SER C 513 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ASN C 523 " --> pdb=" O VAL C 519 " (cutoff:3.500A) Processing helix chain 'C' and resid 556 through 569 removed outlier: 3.632A pdb=" N SER C 569 " --> pdb=" O ALA C 565 " (cutoff:3.500A) Processing helix chain 'C' and resid 577 through 586 removed outlier: 3.864A pdb=" N ILE C 580 " --> pdb=" O ASP C 577 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N SER C 583 " --> pdb=" O ILE C 580 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N LYS C 584 " --> pdb=" O TYR C 581 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N TYR C 585 " --> pdb=" O ASP C 582 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASP C 586 " --> pdb=" O SER C 583 " (cutoff:3.500A) Processing helix chain 'C' and resid 590 through 610 removed outlier: 3.583A 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: 3.697A pdb=" N THR C 642 " --> pdb=" O GLU C 638 " (cutoff:3.500A) Processing helix chain 'C' and resid 643 through 647 removed outlier: 3.578A pdb=" N GLN C 647 " --> pdb=" O ARG C 644 " (cutoff:3.500A) Processing helix chain 'C' and resid 648 through 650 No H-bonds generated for 'chain 'C' and resid 648 through 650' Processing helix chain 'C' and resid 651 through 680 Processing helix chain 'C' and resid 680 through 689 Processing helix chain 'C' and resid 692 through 696 removed outlier: 3.680A pdb=" N PHE C 695 " --> pdb=" O ASN C 692 " (cutoff:3.500A) removed outlier: 3.567A 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: 3.516A pdb=" N LEU C 750 " --> pdb=" O PRO C 746 " (cutoff:3.500A) Processing helix chain 'C' and resid 788 through 800 removed outlier: 3.710A pdb=" N ARG C 793 " --> pdb=" O HIS C 789 " (cutoff:3.500A) Processing helix chain 'C' and resid 801 through 826 removed outlier: 3.502A pdb=" N ARG C 805 " --> pdb=" O ALA C 801 " (cutoff:3.500A) Processing helix chain 'C' and resid 833 through 857 Processing helix chain 'C' and resid 859 through 866 removed outlier: 3.906A pdb=" N ASP C 866 " --> pdb=" O GLU C 862 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 889 removed outlier: 3.565A pdb=" N ARG C 870 " --> pdb=" O ASP C 866 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ASP C 889 " --> pdb=" O THR C 885 " (cutoff:3.500A) Processing helix chain 'C' and resid 892 through 914 removed outlier: 4.054A pdb=" N PHE C 905 " --> pdb=" O GLY C 901 " (cutoff:3.500A) Processing helix chain 'C' and resid 915 through 921 removed outlier: 3.993A pdb=" N LEU C 920 " --> pdb=" O TYR C 917 " (cutoff:3.500A) Processing helix chain 'C' and resid 923 through 961 removed outlier: 3.661A pdb=" N LYS C 927 " --> pdb=" O ASN C 923 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N LYS C 936 " --> pdb=" O MET C 932 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N ASP C 937 " --> pdb=" O GLU C 933 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ILE C 947 " --> pdb=" O PHE C 943 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N PHE C 948 " --> pdb=" O LEU C 944 " (cutoff:3.500A) Processing helix chain 'C' and resid 967 through 981 removed outlier: 3.694A pdb=" N PHE C 971 " --> pdb=" O SER C 967 " (cutoff:3.500A) removed outlier: 4.467A 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 1009 through 1012 Processing helix chain 'C' and resid 1013 through 1026 removed outlier: 3.879A pdb=" N LEU C1023 " --> pdb=" O ALA C1019 " (cutoff:3.500A) Processing helix chain 'C' and resid 1028 through 1066 removed outlier: 5.965A pdb=" N GLU C1046 " --> pdb=" O MET C1042 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N ALA C1047 " --> pdb=" O LYS C1043 " (cutoff:3.500A) Processing helix chain 'C' and resid 1070 through 1072 No H-bonds generated for 'chain 'C' and resid 1070 through 1072' Processing helix chain 'C' and resid 1073 through 1090 removed outlier: 4.097A 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 1166 Processing helix chain 'C' and resid 1203 through 1208 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 1413 Processing helix chain 'C' and resid 1449 through 1453 Processing helix chain 'C' and resid 1478 through 1491 Processing helix chain 'D' and resid 72 through 77 Processing helix chain 'D' and resid 118 through 135 Processing helix chain 'D' and resid 157 through 176 Processing helix chain 'D' and resid 186 through 203 removed outlier: 3.626A pdb=" N LYS D 190 " --> pdb=" O THR D 186 " (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 287 Processing helix chain 'D' and resid 298 through 311 removed outlier: 3.832A pdb=" N LEU D 302 " --> pdb=" O GLY D 298 " (cutoff:3.500A) removed outlier: 3.620A 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 340 through 344 removed outlier: 3.855A pdb=" N SER D 344 " --> pdb=" O ARG D 341 " (cutoff:3.500A) Processing helix chain 'D' and resid 346 through 359 Processing helix chain 'D' and resid 362 through 377 removed outlier: 3.656A pdb=" N VAL D 377 " --> pdb=" O ALA D 373 " (cutoff:3.500A) Processing helix chain 'D' and resid 378 through 381 removed outlier: 6.438A pdb=" N ASN D 381 " --> pdb=" O GLN D 378 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 378 through 381' Processing helix chain 'D' and resid 395 through 406 Processing helix chain 'D' and resid 410 through 421 Processing helix chain 'D' and resid 423 through 437 removed outlier: 3.503A pdb=" N ALA D 427 " --> pdb=" O GLN D 423 " (cutoff:3.500A) Processing helix chain 'D' and resid 439 through 457 removed outlier: 4.776A pdb=" N ASN D 448 " --> pdb=" O ALA D 444 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N ASP D 449 " --> pdb=" O ALA D 445 " (cutoff:3.500A) Processing helix chain 'D' and resid 459 through 469 Processing helix chain 'D' and resid 472 through 476 removed outlier: 3.516A pdb=" N GLU D 475 " --> pdb=" O LYS D 472 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LEU D 476 " --> pdb=" O ILE D 473 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 472 through 476' Processing helix chain 'D' and resid 487 through 492 Processing helix chain 'D' and resid 494 through 509 removed outlier: 3.562A pdb=" N LEU D 498 " --> pdb=" O PRO D 494 " (cutoff:3.500A) Processing helix chain 'D' and resid 513 through 523 removed outlier: 3.633A pdb=" N ARG D 517 " --> pdb=" O SER D 513 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ASN D 523 " --> pdb=" O VAL D 519 " (cutoff:3.500A) Processing helix chain 'D' and resid 556 through 569 removed outlier: 3.631A pdb=" N SER D 569 " --> pdb=" O ALA D 565 " (cutoff:3.500A) Processing helix chain 'D' and resid 577 through 586 removed outlier: 3.864A pdb=" N ILE D 580 " --> pdb=" O ASP D 577 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N SER D 583 " --> pdb=" O ILE D 580 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N LYS D 584 " --> pdb=" O TYR D 581 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TYR D 585 " --> pdb=" O ASP D 582 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASP D 586 " --> pdb=" O SER D 583 " (cutoff:3.500A) Processing helix chain 'D' and resid 590 through 610 removed outlier: 3.583A 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: 3.697A pdb=" N THR D 642 " --> pdb=" O GLU D 638 " (cutoff:3.500A) Processing helix chain 'D' and resid 643 through 647 removed outlier: 3.578A pdb=" N GLN D 647 " --> pdb=" O ARG D 644 " (cutoff:3.500A) Processing helix chain 'D' and resid 648 through 650 No H-bonds generated for 'chain 'D' and resid 648 through 650' Processing helix chain 'D' and resid 651 through 680 Processing helix chain 'D' and resid 680 through 689 Processing helix chain 'D' and resid 692 through 696 removed outlier: 3.680A pdb=" N PHE D 695 " --> pdb=" O ASN D 692 " (cutoff:3.500A) removed outlier: 3.568A 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: 3.518A pdb=" N LEU D 750 " --> pdb=" O PRO D 746 " (cutoff:3.500A) Processing helix chain 'D' and resid 788 through 800 removed outlier: 3.711A pdb=" N ARG D 793 " --> pdb=" O HIS D 789 " (cutoff:3.500A) Processing helix chain 'D' and resid 801 through 826 removed outlier: 3.501A pdb=" N ARG D 805 " --> pdb=" O ALA D 801 " (cutoff:3.500A) Processing helix chain 'D' and resid 833 through 857 Processing helix chain 'D' and resid 859 through 866 removed outlier: 3.906A pdb=" N ASP D 866 " --> pdb=" O GLU D 862 " (cutoff:3.500A) Processing helix chain 'D' and resid 866 through 889 removed outlier: 3.565A pdb=" N ARG D 870 " --> pdb=" O ASP D 866 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ASP D 889 " --> pdb=" O THR D 885 " (cutoff:3.500A) Processing helix chain 'D' and resid 892 through 914 removed outlier: 4.054A pdb=" N PHE D 905 " --> pdb=" O GLY D 901 " (cutoff:3.500A) Processing helix chain 'D' and resid 915 through 921 removed outlier: 3.993A pdb=" N LEU D 920 " --> pdb=" O TYR D 917 " (cutoff:3.500A) Processing helix chain 'D' and resid 923 through 961 removed outlier: 3.661A pdb=" N LYS D 927 " --> pdb=" O ASN D 923 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N LYS D 936 " --> pdb=" O MET D 932 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N ASP D 937 " --> pdb=" O GLU D 933 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ILE D 947 " --> pdb=" O PHE D 943 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N PHE D 948 " --> pdb=" O LEU D 944 " (cutoff:3.500A) Processing helix chain 'D' and resid 967 through 981 removed outlier: 3.695A pdb=" N PHE D 971 " --> pdb=" O SER D 967 " (cutoff:3.500A) removed outlier: 4.466A 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 1009 through 1012 Processing helix chain 'D' and resid 1013 through 1026 removed outlier: 3.879A pdb=" N LEU D1023 " --> pdb=" O ALA D1019 " (cutoff:3.500A) Processing helix chain 'D' and resid 1028 through 1066 removed outlier: 5.965A pdb=" N GLU D1046 " --> pdb=" O MET D1042 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N ALA D1047 " --> pdb=" O LYS D1043 " (cutoff:3.500A) Processing helix chain 'D' and resid 1070 through 1072 No H-bonds generated for 'chain 'D' and resid 1070 through 1072' Processing helix chain 'D' and resid 1073 through 1090 removed outlier: 4.097A 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 1166 Processing helix chain 'D' and resid 1203 through 1208 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 1413 Processing helix chain 'D' and resid 1449 through 1453 Processing helix chain 'D' and resid 1478 through 1491 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: 6.680A pdb=" N ILE A 233 " --> pdb=" O TRP A 96 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N THR A 98 " --> pdb=" O ILE A 233 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N LEU A 259 " --> pdb=" O PRO A 109 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N LEU A 111 " --> pdb=" O LEU A 259 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N ASP A 261 " --> pdb=" O LEU A 111 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N LEU A 113 " --> pdb=" O ASP A 261 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N THR A 210 " --> pdb=" O LEU A 256 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N LEU A 258 " --> pdb=" O THR A 210 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N GLY A 212 " --> pdb=" O LEU A 258 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N VAL A 260 " --> pdb=" O GLY A 212 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ALA A 214 " --> pdb=" O VAL A 260 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N VAL A 179 " --> pdb=" O ILE A 211 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N ILE A 213 " --> pdb=" O VAL A 179 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N THR A 181 " --> pdb=" O ILE A 213 " (cutoff:3.500A) removed outlier: 8.673A pdb=" N THR A 215 " --> pdb=" O THR A 181 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N ILE A 144 " --> pdb=" O VAL A 291 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N ILE A 293 " --> pdb=" O ILE A 144 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N SER A 146 " --> pdb=" O ILE A 293 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N VAL A 295 " --> pdb=" O SER A 146 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N THR A 148 " --> pdb=" O VAL A 295 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ILE A 315 " --> pdb=" O VAL A 384 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N TYR A 386 " --> pdb=" O ILE A 315 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N VAL A 317 " --> pdb=" O TYR A 386 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1199 through 1200 removed outlier: 7.045A pdb=" N GLY B1416 " --> pdb=" O HIS B1443 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N HIS B1443 " --> pdb=" O GLY B1416 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N ILE B1418 " --> pdb=" O ASN B1441 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ASN B1441 " --> pdb=" O ILE B1418 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ALA B1420 " --> pdb=" O CYS B1439 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N TRP B1336 " --> pdb=" O ASP B1444 " (cutoff:3.500A) removed outlier: 17.596A pdb=" N ALA B1329 " --> pdb=" O ARG B1360 " (cutoff:3.500A) removed outlier: 13.719A pdb=" N ARG B1360 " --> pdb=" O ALA B1329 " (cutoff:3.500A) removed outlier: 11.377A pdb=" N THR B1331 " --> pdb=" O ILE B1358 " (cutoff:3.500A) removed outlier: 8.190A pdb=" N ILE B1358 " --> pdb=" O THR B1331 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N VAL B1333 " --> pdb=" O VAL B1356 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 1366 through 1367 removed outlier: 5.487A pdb=" N VAL B1333 " --> pdb=" O VAL B1356 " (cutoff:3.500A) removed outlier: 8.190A pdb=" N ILE B1358 " --> pdb=" O THR B1331 " (cutoff:3.500A) removed outlier: 11.377A pdb=" N THR B1331 " --> pdb=" O ILE B1358 " (cutoff:3.500A) removed outlier: 13.719A pdb=" N ARG B1360 " --> pdb=" O ALA B1329 " (cutoff:3.500A) removed outlier: 17.596A pdb=" N ALA B1329 " --> pdb=" O ARG B1360 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1251 through 1254 removed outlier: 3.890A pdb=" N ARG A1317 " --> pdb=" O TYR A1253 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1279 through 1281 Processing sheet with id=AA8, first strand: chain 'A' and resid 1366 through 1367 removed outlier: 5.487A pdb=" N VAL A1333 " --> pdb=" O VAL A1356 " (cutoff:3.500A) removed outlier: 8.190A pdb=" N ILE A1358 " --> pdb=" O THR A1331 " (cutoff:3.500A) removed outlier: 11.376A pdb=" N THR A1331 " --> pdb=" O ILE A1358 " (cutoff:3.500A) removed outlier: 13.719A pdb=" N ARG A1360 " --> pdb=" O ALA A1329 " (cutoff:3.500A) removed outlier: 17.597A pdb=" N ALA A1329 " --> pdb=" O ARG A1360 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1370 through 1372 removed outlier: 17.597A pdb=" N ALA A1329 " --> pdb=" O ARG A1360 " (cutoff:3.500A) removed outlier: 13.719A pdb=" N ARG A1360 " --> pdb=" O ALA A1329 " (cutoff:3.500A) removed outlier: 11.376A pdb=" N THR A1331 " --> pdb=" O ILE A1358 " (cutoff:3.500A) removed outlier: 8.190A pdb=" N ILE A1358 " --> pdb=" O THR A1331 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N VAL A1333 " --> pdb=" O VAL A1356 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 1353 through 1360 current: chain 'A' and resid 1416 through 1423 Processing sheet with id=AB1, first strand: chain 'A' and resid 1346 through 1347 Processing sheet with id=AB2, first strand: chain 'B' and resid 56 through 60 Processing sheet with id=AB3, first strand: chain 'B' and resid 80 through 81 Processing sheet with id=AB4, first strand: chain 'B' and resid 232 through 236 removed outlier: 6.680A pdb=" N ILE B 233 " --> pdb=" O TRP B 96 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N THR B 98 " --> pdb=" O ILE B 233 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N LEU B 259 " --> pdb=" O PRO B 109 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N LEU B 111 " --> pdb=" O LEU B 259 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N ASP B 261 " --> pdb=" O LEU B 111 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N LEU B 113 " --> pdb=" O ASP B 261 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N THR B 210 " --> pdb=" O LEU B 256 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N LEU B 258 " --> pdb=" O THR B 210 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N GLY B 212 " --> pdb=" O LEU B 258 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N VAL B 260 " --> pdb=" O GLY B 212 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ALA B 214 " --> pdb=" O VAL B 260 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N VAL B 179 " --> pdb=" O ILE B 211 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N ILE B 213 " --> pdb=" O VAL B 179 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N THR B 181 " --> pdb=" O ILE B 213 " (cutoff:3.500A) removed outlier: 8.672A pdb=" N THR B 215 " --> pdb=" O THR B 181 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N ILE B 144 " --> pdb=" O VAL B 291 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N ILE B 293 " --> pdb=" O ILE B 144 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N SER B 146 " --> pdb=" O ILE B 293 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N VAL B 295 " --> pdb=" O SER B 146 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N THR B 148 " --> pdb=" O VAL B 295 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ILE B 315 " --> pdb=" O VAL B 384 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N TYR B 386 " --> pdb=" O ILE B 315 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N VAL B 317 " --> pdb=" O TYR B 386 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 1199 through 1200 removed outlier: 7.045A pdb=" N GLY C1416 " --> pdb=" O HIS C1443 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N HIS C1443 " --> pdb=" O GLY C1416 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N ILE C1418 " --> pdb=" O ASN C1441 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ASN C1441 " --> pdb=" O ILE C1418 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ALA C1420 " --> pdb=" O CYS C1439 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N TRP C1336 " --> pdb=" O ASP C1444 " (cutoff:3.500A) removed outlier: 17.597A pdb=" N ALA C1329 " --> pdb=" O ARG C1360 " (cutoff:3.500A) removed outlier: 13.719A pdb=" N ARG C1360 " --> pdb=" O ALA C1329 " (cutoff:3.500A) removed outlier: 11.377A pdb=" N THR C1331 " --> pdb=" O ILE C1358 " (cutoff:3.500A) removed outlier: 8.190A pdb=" N ILE C1358 " --> pdb=" O THR C1331 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N VAL C1333 " --> pdb=" O VAL C1356 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 1366 through 1367 removed outlier: 5.487A pdb=" N VAL C1333 " --> pdb=" O VAL C1356 " (cutoff:3.500A) removed outlier: 8.190A pdb=" N ILE C1358 " --> pdb=" O THR C1331 " (cutoff:3.500A) removed outlier: 11.377A pdb=" N THR C1331 " --> pdb=" O ILE C1358 " (cutoff:3.500A) removed outlier: 13.719A pdb=" N ARG C1360 " --> pdb=" O ALA C1329 " (cutoff:3.500A) removed outlier: 17.597A pdb=" N ALA C1329 " --> pdb=" O ARG C1360 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 1251 through 1254 removed outlier: 3.890A pdb=" N ARG B1317 " --> pdb=" O TYR B1253 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 1279 through 1281 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: 6.680A pdb=" N ILE C 233 " --> pdb=" O TRP C 96 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N THR C 98 " --> pdb=" O ILE C 233 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N LEU C 259 " --> pdb=" O PRO C 109 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N LEU C 111 " --> pdb=" O LEU C 259 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N ASP C 261 " --> pdb=" O LEU C 111 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N LEU C 113 " --> pdb=" O ASP C 261 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N THR C 210 " --> pdb=" O LEU C 256 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N LEU C 258 " --> pdb=" O THR C 210 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N GLY C 212 " --> pdb=" O LEU C 258 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N VAL C 260 " --> pdb=" O GLY C 212 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ALA C 214 " --> pdb=" O VAL C 260 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N VAL C 179 " --> pdb=" O ILE C 211 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N ILE C 213 " --> pdb=" O VAL C 179 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N THR C 181 " --> pdb=" O ILE C 213 " (cutoff:3.500A) removed outlier: 8.673A pdb=" N THR C 215 " --> pdb=" O THR C 181 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N ILE C 144 " --> pdb=" O VAL C 291 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N ILE C 293 " --> pdb=" O ILE C 144 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N SER C 146 " --> pdb=" O ILE C 293 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N VAL C 295 " --> pdb=" O SER C 146 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N THR C 148 " --> pdb=" O VAL C 295 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ILE C 315 " --> pdb=" O VAL C 384 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N TYR C 386 " --> pdb=" O ILE C 315 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N VAL C 317 " --> pdb=" O TYR C 386 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 1199 through 1200 removed outlier: 7.044A pdb=" N GLY D1416 " --> pdb=" O HIS D1443 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N HIS D1443 " --> pdb=" O GLY D1416 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N ILE D1418 " --> pdb=" O ASN D1441 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ASN D1441 " --> pdb=" O ILE D1418 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ALA D1420 " --> pdb=" O CYS D1439 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N TRP D1336 " --> pdb=" O ASP D1444 " (cutoff:3.500A) removed outlier: 17.596A pdb=" N ALA D1329 " --> pdb=" O ARG D1360 " (cutoff:3.500A) removed outlier: 13.720A pdb=" N ARG D1360 " --> pdb=" O ALA D1329 " (cutoff:3.500A) removed outlier: 11.376A pdb=" N THR D1331 " --> pdb=" O ILE D1358 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N ILE D1358 " --> pdb=" O THR D1331 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N VAL D1333 " --> pdb=" O VAL D1356 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 1366 through 1367 removed outlier: 5.488A pdb=" N VAL D1333 " --> pdb=" O VAL D1356 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N ILE D1358 " --> pdb=" O THR D1331 " (cutoff:3.500A) removed outlier: 11.376A pdb=" N THR D1331 " --> pdb=" O ILE D1358 " (cutoff:3.500A) removed outlier: 13.720A pdb=" N ARG D1360 " --> pdb=" O ALA D1329 " (cutoff:3.500A) removed outlier: 17.596A pdb=" N ALA D1329 " --> pdb=" O ARG D1360 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 1251 through 1254 removed outlier: 3.891A pdb=" N ARG C1317 " --> pdb=" O TYR C1253 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 1279 through 1281 Processing sheet with id=AC8, first strand: chain 'C' and resid 1346 through 1347 Processing sheet with id=AC9, first strand: chain 'D' and resid 56 through 60 Processing sheet with id=AD1, first strand: chain 'D' and resid 80 through 81 Processing sheet with id=AD2, first strand: chain 'D' and resid 232 through 236 removed outlier: 6.680A pdb=" N ILE D 233 " --> pdb=" O TRP D 96 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N THR D 98 " --> pdb=" O ILE D 233 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N LEU D 259 " --> pdb=" O PRO D 109 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N LEU D 111 " --> pdb=" O LEU D 259 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N ASP D 261 " --> pdb=" O LEU D 111 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N LEU D 113 " --> pdb=" O ASP D 261 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N THR D 210 " --> pdb=" O LEU D 256 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N LEU D 258 " --> pdb=" O THR D 210 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N GLY D 212 " --> pdb=" O LEU D 258 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N VAL D 260 " --> pdb=" O GLY D 212 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ALA D 214 " --> pdb=" O VAL D 260 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N VAL D 179 " --> pdb=" O ILE D 211 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N ILE D 213 " --> pdb=" O VAL D 179 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N THR D 181 " --> pdb=" O ILE D 213 " (cutoff:3.500A) removed outlier: 8.673A pdb=" N THR D 215 " --> pdb=" O THR D 181 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N ILE D 144 " --> pdb=" O VAL D 291 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N ILE D 293 " --> pdb=" O ILE D 144 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N SER D 146 " --> pdb=" O ILE D 293 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N VAL D 295 " --> pdb=" O SER D 146 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N THR D 148 " --> pdb=" O VAL D 295 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ILE D 315 " --> pdb=" O VAL D 384 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N TYR D 386 " --> pdb=" O ILE D 315 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N VAL D 317 " --> pdb=" O TYR D 386 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 1251 through 1254 removed outlier: 3.890A pdb=" N ARG D1317 " --> pdb=" O TYR D1253 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 1279 through 1281 Processing sheet with id=AD5, first strand: chain 'D' and resid 1346 through 1347 2388 hydrogen bonds defined for protein. 6972 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: 11.43 Time building geometry restraints manager: 5.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 6320 1.31 - 1.44: 11328 1.44 - 1.56: 23184 1.56 - 1.69: 52 1.69 - 1.81: 372 Bond restraints: 41256 Sorted by residual: bond pdb=" C LEU A1069 " pdb=" N PRO A1070 " ideal model delta sigma weight residual 1.330 1.385 -0.055 1.25e-02 6.40e+03 1.96e+01 bond pdb=" C LEU D1069 " pdb=" N PRO D1070 " ideal model delta sigma weight residual 1.330 1.385 -0.055 1.25e-02 6.40e+03 1.96e+01 bond pdb=" C LEU C1069 " pdb=" N PRO C1070 " ideal model delta sigma weight residual 1.330 1.385 -0.055 1.25e-02 6.40e+03 1.96e+01 bond pdb=" C LEU B1069 " pdb=" N PRO B1070 " ideal model delta sigma weight residual 1.330 1.385 -0.055 1.25e-02 6.40e+03 1.93e+01 bond pdb=" C GLY A 648 " pdb=" N PRO A 649 " ideal model delta sigma weight residual 1.335 1.388 -0.053 1.28e-02 6.10e+03 1.71e+01 ... (remaining 41251 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.38: 49658 2.38 - 4.76: 5784 4.76 - 7.14: 828 7.14 - 9.52: 166 9.52 - 11.91: 16 Bond angle restraints: 56452 Sorted by residual: angle pdb=" N SER C1163 " pdb=" CA SER C1163 " pdb=" C SER C1163 " ideal model delta sigma weight residual 112.38 104.04 8.34 1.22e+00 6.72e-01 4.68e+01 angle pdb=" N SER D1163 " pdb=" CA SER D1163 " pdb=" C SER D1163 " ideal model delta sigma weight residual 112.38 104.06 8.32 1.22e+00 6.72e-01 4.65e+01 angle pdb=" N SER A1163 " pdb=" CA SER A1163 " pdb=" C SER A1163 " ideal model delta sigma weight residual 112.38 104.06 8.32 1.22e+00 6.72e-01 4.65e+01 angle pdb=" N SER B1163 " pdb=" CA SER B1163 " pdb=" C SER B1163 " ideal model delta sigma weight residual 112.38 104.06 8.32 1.22e+00 6.72e-01 4.65e+01 angle pdb=" N PRO D1002 " pdb=" CA PRO D1002 " pdb=" C PRO D1002 " ideal model delta sigma weight residual 113.47 123.15 -9.68 1.43e+00 4.89e-01 4.58e+01 ... (remaining 56447 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.47: 22794 17.47 - 34.93: 1646 34.93 - 52.40: 328 52.40 - 69.86: 120 69.86 - 87.33: 48 Dihedral angle restraints: 24936 sinusoidal: 9052 harmonic: 15884 Sorted by residual: dihedral pdb=" C TYR D1063 " pdb=" N TYR D1063 " pdb=" CA TYR D1063 " pdb=" CB TYR D1063 " ideal model delta harmonic sigma weight residual -122.60 -136.20 13.60 0 2.50e+00 1.60e-01 2.96e+01 dihedral pdb=" C TYR A1063 " pdb=" N TYR A1063 " pdb=" CA TYR A1063 " pdb=" CB TYR A1063 " ideal model delta harmonic sigma weight residual -122.60 -136.18 13.58 0 2.50e+00 1.60e-01 2.95e+01 dihedral pdb=" C TYR C1063 " pdb=" N TYR C1063 " pdb=" CA TYR C1063 " pdb=" CB TYR C1063 " ideal model delta harmonic sigma weight residual -122.60 -136.16 13.56 0 2.50e+00 1.60e-01 2.94e+01 ... (remaining 24933 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 5157 0.098 - 0.196: 1239 0.196 - 0.293: 188 0.293 - 0.391: 20 0.391 - 0.489: 24 Chirality restraints: 6628 Sorted by residual: chirality pdb=" CB THR B1331 " pdb=" CA THR B1331 " pdb=" OG1 THR B1331 " pdb=" CG2 THR B1331 " both_signs ideal model delta sigma weight residual False 2.55 2.06 0.49 2.00e-01 2.50e+01 5.98e+00 chirality pdb=" CB THR D1331 " pdb=" CA THR D1331 " pdb=" OG1 THR D1331 " pdb=" CG2 THR D1331 " both_signs ideal model delta sigma weight residual False 2.55 2.06 0.49 2.00e-01 2.50e+01 5.98e+00 chirality pdb=" CB THR C1331 " pdb=" CA THR C1331 " pdb=" OG1 THR C1331 " pdb=" CG2 THR C1331 " both_signs ideal model delta sigma weight residual False 2.55 2.06 0.49 2.00e-01 2.50e+01 5.96e+00 ... (remaining 6625 not shown) Planarity restraints: 7116 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU D 199 " -0.024 2.00e-02 2.50e+03 4.73e-02 2.24e+01 pdb=" C LEU D 199 " 0.082 2.00e-02 2.50e+03 pdb=" O LEU D 199 " -0.031 2.00e-02 2.50e+03 pdb=" N SER D 200 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 199 " 0.023 2.00e-02 2.50e+03 4.73e-02 2.24e+01 pdb=" C LEU A 199 " -0.082 2.00e-02 2.50e+03 pdb=" O LEU A 199 " 0.031 2.00e-02 2.50e+03 pdb=" N SER A 200 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 199 " 0.023 2.00e-02 2.50e+03 4.73e-02 2.24e+01 pdb=" C LEU B 199 " -0.082 2.00e-02 2.50e+03 pdb=" O LEU B 199 " 0.031 2.00e-02 2.50e+03 pdb=" N SER B 200 " 0.027 2.00e-02 2.50e+03 ... (remaining 7113 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 692 2.69 - 3.25: 36887 3.25 - 3.80: 62803 3.80 - 4.35: 80623 4.35 - 4.90: 137050 Nonbonded interactions: 318055 Sorted by model distance: nonbonded pdb="CA CA A1705 " pdb=" O1A APR A1707 " model vdw 2.142 2.510 nonbonded pdb="CA CA B1705 " pdb=" O1A APR B1707 " model vdw 2.142 2.510 nonbonded pdb="CA CA D6007 " pdb=" O1A APR D6009 " model vdw 2.142 2.510 nonbonded pdb="CA CA C1705 " pdb=" O1A APR C1707 " model vdw 2.142 2.510 nonbonded pdb=" O LEU A 621 " pdb="CA CA A1703 " model vdw 2.161 2.510 ... (remaining 318050 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 52 through 1494 or resid 1704 through 1705 or resid 1708)) \ selection = (chain 'B' and (resid 52 through 1494 or resid 1704 through 1705 or resid 1708)) \ selection = (chain 'C' and (resid 52 through 1494 or resid 1704 through 1705 or resid 1708)) \ selection = (chain 'D' and (resid 52 through 1494 or resid 6004 through 6005 or resid 6008)) \ } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.570 Check model and map are aligned: 0.130 Set scattering table: 0.110 Process input model: 43.160 Find NCS groups from input model: 1.270 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5908 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.082 41260 Z= 0.663 Angle : 1.615 11.906 56460 Z= 1.066 Chirality : 0.088 0.489 6628 Planarity : 0.011 0.074 7116 Dihedral : 13.797 87.329 14636 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.56 % Allowed : 2.51 % Favored : 96.93 % Cbeta Deviations : 0.47 % 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 are not related in a simple way. whole: 0.23 (0.11), residues: 5424 helix: 0.75 (0.09), residues: 2964 sheet: -0.86 (0.23), residues: 408 loop : -0.36 (0.14), residues: 2052 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG C1135 TYR 0.054 0.005 TYR C 466 PHE 0.049 0.006 PHE A 941 TRP 0.020 0.003 TRP A 606 HIS 0.012 0.003 HIS D 82 Details of bonding type rmsd covalent geometry : bond 0.01123 (41256) covalent geometry : angle 1.61451 (56452) SS BOND : bond 0.00070 ( 4) SS BOND : angle 1.69475 ( 8) hydrogen bonds : bond 0.17047 ( 2376) hydrogen bonds : angle 7.39287 ( 6972) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10848 Ramachandran restraints generated. 5424 Oldfield, 0 Emsley, 5424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10848 Ramachandran restraints generated. 5424 Oldfield, 0 Emsley, 5424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 788 residues out of total 4664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 768 time to evaluate : 1.547 Fit side-chains REVERT: A 70 MET cc_start: 0.4402 (ttt) cc_final: 0.3795 (ttp) REVERT: A 110 TYR cc_start: 0.5732 (p90) cc_final: 0.5386 (p90) REVERT: A 129 MET cc_start: 0.5103 (OUTLIER) cc_final: 0.4893 (tmt) REVERT: A 169 ARG cc_start: 0.5008 (ttm170) cc_final: 0.4768 (mtp-110) REVERT: A 184 THR cc_start: 0.6372 (m) cc_final: 0.6139 (m) REVERT: A 266 ASN cc_start: 0.5650 (m-40) cc_final: 0.5081 (t0) REVERT: A 311 GLN cc_start: 0.7259 (mt0) cc_final: 0.6699 (pt0) REVERT: A 349 ASP cc_start: 0.6615 (t70) cc_final: 0.6311 (t0) REVERT: A 402 LYS cc_start: 0.6601 (ttmm) cc_final: 0.6241 (tttm) REVERT: A 416 LYS cc_start: 0.5604 (tttm) cc_final: 0.5308 (mttm) REVERT: A 594 ARG cc_start: 0.5065 (mtp-110) cc_final: 0.4853 (ttp-170) REVERT: A 614 ARG cc_start: 0.5570 (mtp180) cc_final: 0.5058 (mtm-85) REVERT: A 666 GLU cc_start: 0.6231 (tt0) cc_final: 0.5456 (mt-10) REVERT: A 683 MET cc_start: 0.6251 (tpt) cc_final: 0.5574 (tpp) REVERT: A 686 GLU cc_start: 0.6335 (tp30) cc_final: 0.5969 (tt0) REVERT: A 854 MET cc_start: 0.5368 (mtm) cc_final: 0.5080 (mtt) REVERT: A 916 ARG cc_start: 0.7027 (ttt90) cc_final: 0.6731 (tpp-160) REVERT: A 922 LYS cc_start: 0.6463 (mppt) cc_final: 0.5970 (mmtm) REVERT: A 932 MET cc_start: 0.7106 (mmt) cc_final: 0.6338 (mpt) REVERT: A 935 MET cc_start: 0.6293 (mmm) cc_final: 0.5885 (mmt) REVERT: A 936 LYS cc_start: 0.5601 (mttt) cc_final: 0.5361 (mttt) REVERT: A 964 GLU cc_start: 0.6267 (tp30) cc_final: 0.5643 (tm-30) REVERT: A 969 ARG cc_start: 0.6624 (mtm110) cc_final: 0.5886 (mtm110) REVERT: A 990 ASP cc_start: 0.6116 (m-30) cc_final: 0.5641 (m-30) REVERT: A 1046 GLU cc_start: 0.5109 (mm-30) cc_final: 0.4218 (pm20) REVERT: A 1051 LEU cc_start: 0.6938 (tp) cc_final: 0.6733 (tt) REVERT: A 1126 ARG cc_start: 0.5329 (ttp-110) cc_final: 0.4936 (ttp80) REVERT: A 1131 MET cc_start: 0.5837 (mmm) cc_final: 0.5163 (mtm) REVERT: A 1133 GLU cc_start: 0.5853 (mp0) cc_final: 0.5472 (mm-30) REVERT: A 1149 MET cc_start: 0.7032 (mtp) cc_final: 0.6832 (mtp) REVERT: A 1155 GLU cc_start: 0.6973 (tp30) cc_final: 0.6297 (tm-30) REVERT: A 1207 HIS cc_start: 0.4666 (m170) cc_final: 0.4369 (m170) REVERT: A 1251 VAL cc_start: 0.6856 (m) cc_final: 0.6470 (p) REVERT: A 1388 MET cc_start: 0.6850 (mtp) cc_final: 0.6626 (mtm) REVERT: B 110 TYR cc_start: 0.5734 (p90) cc_final: 0.5391 (p90) REVERT: B 169 ARG cc_start: 0.5008 (ttm170) cc_final: 0.4765 (mtp-110) REVERT: B 184 THR cc_start: 0.6369 (m) cc_final: 0.6141 (m) REVERT: B 266 ASN cc_start: 0.5644 (m-40) cc_final: 0.5083 (t0) REVERT: B 311 GLN cc_start: 0.7264 (mt0) cc_final: 0.6699 (pt0) REVERT: B 349 ASP cc_start: 0.6627 (t70) cc_final: 0.6311 (t0) REVERT: B 402 LYS cc_start: 0.6599 (ttmm) cc_final: 0.6239 (tttm) REVERT: B 416 LYS cc_start: 0.5574 (tttm) cc_final: 0.5279 (mttm) REVERT: B 594 ARG cc_start: 0.5062 (mtp-110) cc_final: 0.4842 (ttp-110) REVERT: B 614 ARG cc_start: 0.5571 (mtp180) cc_final: 0.5058 (mtm-85) REVERT: B 666 GLU cc_start: 0.6229 (tt0) cc_final: 0.5456 (mt-10) REVERT: B 683 MET cc_start: 0.6251 (tpt) cc_final: 0.5578 (tpp) REVERT: B 686 GLU cc_start: 0.6339 (tp30) cc_final: 0.5982 (tt0) REVERT: B 854 MET cc_start: 0.5366 (mtm) cc_final: 0.5079 (mtt) REVERT: B 916 ARG cc_start: 0.7034 (ttt90) cc_final: 0.6741 (tpp-160) REVERT: B 922 LYS cc_start: 0.6458 (mppt) cc_final: 0.5966 (mmtm) REVERT: B 932 MET cc_start: 0.7105 (mmt) cc_final: 0.6465 (mpt) REVERT: B 935 MET cc_start: 0.6288 (mmm) cc_final: 0.5881 (mmt) REVERT: B 936 LYS cc_start: 0.5596 (mttt) cc_final: 0.5358 (mttt) REVERT: B 964 GLU cc_start: 0.6247 (tp30) cc_final: 0.5631 (tm-30) REVERT: B 969 ARG cc_start: 0.6624 (mtm110) cc_final: 0.5882 (mtm110) REVERT: B 990 ASP cc_start: 0.6123 (m-30) cc_final: 0.5648 (m-30) REVERT: B 1046 GLU cc_start: 0.5110 (mm-30) cc_final: 0.4218 (pm20) REVERT: B 1051 LEU cc_start: 0.6937 (tp) cc_final: 0.6732 (tt) REVERT: B 1126 ARG cc_start: 0.5330 (ttp-110) cc_final: 0.4934 (ttp80) REVERT: B 1131 MET cc_start: 0.5843 (mmm) cc_final: 0.5169 (mtm) REVERT: B 1133 GLU cc_start: 0.5855 (mp0) cc_final: 0.5476 (mm-30) REVERT: B 1149 MET cc_start: 0.7041 (mtp) cc_final: 0.6838 (mtp) REVERT: B 1155 GLU cc_start: 0.6948 (tp30) cc_final: 0.6274 (tm-30) REVERT: B 1207 HIS cc_start: 0.4662 (m170) cc_final: 0.4362 (m170) REVERT: B 1251 VAL cc_start: 0.6854 (m) cc_final: 0.6467 (p) REVERT: B 1388 MET cc_start: 0.6788 (mtp) cc_final: 0.6570 (mtm) REVERT: C 110 TYR cc_start: 0.5664 (p90) cc_final: 0.5292 (p90) REVERT: C 129 MET cc_start: 0.5099 (OUTLIER) cc_final: 0.4885 (tmt) REVERT: C 169 ARG cc_start: 0.5004 (ttm170) cc_final: 0.4763 (mtp-110) REVERT: C 184 THR cc_start: 0.6363 (m) cc_final: 0.6135 (m) REVERT: C 266 ASN cc_start: 0.5685 (m-40) cc_final: 0.5112 (t0) REVERT: C 311 GLN cc_start: 0.7262 (mt0) cc_final: 0.6697 (pt0) REVERT: C 349 ASP cc_start: 0.6632 (t70) cc_final: 0.6281 (t0) REVERT: C 402 LYS cc_start: 0.6596 (ttmm) cc_final: 0.6239 (tttm) REVERT: C 416 LYS cc_start: 0.5573 (tttm) cc_final: 0.5277 (mttm) REVERT: C 594 ARG cc_start: 0.5060 (mtp-110) cc_final: 0.4848 (ttp-170) REVERT: C 614 ARG cc_start: 0.5571 (mtp180) cc_final: 0.5058 (mtm-85) REVERT: C 666 GLU cc_start: 0.6226 (tt0) cc_final: 0.5450 (mt-10) REVERT: C 683 MET cc_start: 0.6248 (tpt) cc_final: 0.5578 (tpp) REVERT: C 686 GLU cc_start: 0.6338 (tp30) cc_final: 0.5979 (tt0) REVERT: C 854 MET cc_start: 0.5363 (mtm) cc_final: 0.5074 (mtt) REVERT: C 916 ARG cc_start: 0.7199 (ttt90) cc_final: 0.6882 (tpp-160) REVERT: C 922 LYS cc_start: 0.6453 (mppt) cc_final: 0.5960 (mmtm) REVERT: C 932 MET cc_start: 0.7107 (mmt) cc_final: 0.6464 (mpt) REVERT: C 935 MET cc_start: 0.6260 (mmm) cc_final: 0.5846 (mmt) REVERT: C 936 LYS cc_start: 0.5594 (mttt) cc_final: 0.5358 (mttt) REVERT: C 964 GLU cc_start: 0.6254 (tp30) cc_final: 0.5634 (tm-30) REVERT: C 969 ARG cc_start: 0.6625 (mtm110) cc_final: 0.5883 (mtm110) REVERT: C 990 ASP cc_start: 0.6117 (m-30) cc_final: 0.5645 (m-30) REVERT: C 1046 GLU cc_start: 0.5111 (mm-30) cc_final: 0.4218 (pm20) REVERT: C 1051 LEU cc_start: 0.6936 (tp) cc_final: 0.6728 (tt) REVERT: C 1126 ARG cc_start: 0.5329 (ttp-110) cc_final: 0.4933 (ttp80) REVERT: C 1131 MET cc_start: 0.5847 (mmm) cc_final: 0.5179 (mtm) REVERT: C 1133 GLU cc_start: 0.5771 (mp0) cc_final: 0.5407 (mm-30) REVERT: C 1149 MET cc_start: 0.7056 (mtp) cc_final: 0.6855 (mtp) REVERT: C 1155 GLU cc_start: 0.6948 (tp30) cc_final: 0.6276 (tm-30) REVERT: C 1207 HIS cc_start: 0.4656 (m170) cc_final: 0.4356 (m170) REVERT: C 1251 VAL cc_start: 0.6850 (m) cc_final: 0.6463 (p) REVERT: C 1388 MET cc_start: 0.6786 (mtp) cc_final: 0.6568 (mtm) REVERT: D 110 TYR cc_start: 0.5727 (p90) cc_final: 0.5352 (p90) REVERT: D 169 ARG cc_start: 0.5004 (ttm170) cc_final: 0.4763 (mtp-110) REVERT: D 184 THR cc_start: 0.6364 (m) cc_final: 0.6136 (m) REVERT: D 266 ASN cc_start: 0.5687 (m-40) cc_final: 0.5112 (t0) REVERT: D 311 GLN cc_start: 0.7263 (mt0) cc_final: 0.6697 (pt0) REVERT: D 402 LYS cc_start: 0.6597 (ttmm) cc_final: 0.6240 (tttm) REVERT: D 416 LYS cc_start: 0.5572 (tttm) cc_final: 0.5277 (mttm) REVERT: D 594 ARG cc_start: 0.5059 (mtp-110) cc_final: 0.4839 (ttp-110) REVERT: D 614 ARG cc_start: 0.5573 (mtp180) cc_final: 0.5059 (mtm-85) REVERT: D 666 GLU cc_start: 0.6225 (tt0) cc_final: 0.5465 (mt-10) REVERT: D 683 MET cc_start: 0.6248 (tpt) cc_final: 0.5578 (tpp) REVERT: D 686 GLU cc_start: 0.6338 (tp30) cc_final: 0.5980 (tt0) REVERT: D 854 MET cc_start: 0.5362 (mtm) cc_final: 0.5072 (mtt) REVERT: D 916 ARG cc_start: 0.7198 (ttt90) cc_final: 0.6882 (tpp-160) REVERT: D 922 LYS cc_start: 0.6453 (mppt) cc_final: 0.5960 (mmtm) REVERT: D 932 MET cc_start: 0.7108 (mmt) cc_final: 0.6466 (mpt) REVERT: D 935 MET cc_start: 0.6259 (mmm) cc_final: 0.5845 (mmt) REVERT: D 936 LYS cc_start: 0.5593 (mttt) cc_final: 0.5357 (mttt) REVERT: D 964 GLU cc_start: 0.6256 (tp30) cc_final: 0.5637 (tm-30) REVERT: D 969 ARG cc_start: 0.6626 (mtm110) cc_final: 0.5885 (mtm110) REVERT: D 990 ASP cc_start: 0.6117 (m-30) cc_final: 0.5644 (m-30) REVERT: D 1046 GLU cc_start: 0.5112 (mm-30) cc_final: 0.4220 (pm20) REVERT: D 1051 LEU cc_start: 0.6936 (tp) cc_final: 0.6729 (tt) REVERT: D 1126 ARG cc_start: 0.5329 (ttp-110) cc_final: 0.4934 (ttp80) REVERT: D 1131 MET cc_start: 0.5848 (mmm) cc_final: 0.5177 (mtm) REVERT: D 1133 GLU cc_start: 0.5770 (mp0) cc_final: 0.5408 (mm-30) REVERT: D 1149 MET cc_start: 0.7053 (mtp) cc_final: 0.6851 (mtp) REVERT: D 1155 GLU cc_start: 0.6949 (tp30) cc_final: 0.6276 (tm-30) REVERT: D 1207 HIS cc_start: 0.4665 (m170) cc_final: 0.4364 (m170) REVERT: D 1251 VAL cc_start: 0.6924 (m) cc_final: 0.6521 (p) REVERT: D 1388 MET cc_start: 0.6785 (mtp) cc_final: 0.6566 (mtm) outliers start: 20 outliers final: 0 residues processed: 780 average time/residue: 0.7595 time to fit residues: 717.5414 Evaluate side-chains 441 residues out of total 4664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 439 time to evaluate : 1.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 MET Chi-restraints excluded: chain C residue 129 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 544 random chunks: chunk 394 optimal weight: 0.7980 chunk 430 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 265 optimal weight: 0.9990 chunk 523 optimal weight: 2.9990 chunk 497 optimal weight: 0.5980 chunk 414 optimal weight: 10.0000 chunk 310 optimal weight: 1.9990 chunk 488 optimal weight: 0.9980 chunk 366 optimal weight: 0.8980 chunk 223 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 378 GLN A 461 HIS B 378 GLN B 461 HIS C 378 GLN C 461 HIS D 378 GLN D 461 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.164979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.127189 restraints weight = 57132.982| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 2.01 r_work: 0.3245 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7405 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 41260 Z= 0.122 Angle : 0.523 7.337 56460 Z= 0.277 Chirality : 0.038 0.168 6628 Planarity : 0.004 0.046 7116 Dihedral : 8.278 88.420 6998 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.04 % Allowed : 10.35 % Favored : 87.61 % 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 are not related in a simple way. whole: 1.56 (0.11), residues: 5424 helix: 2.02 (0.09), residues: 2960 sheet: -0.40 (0.24), residues: 404 loop : -0.06 (0.14), residues: 2060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 310 TYR 0.026 0.002 TYR A 420 PHE 0.016 0.001 PHE B 971 TRP 0.010 0.001 TRP D1124 HIS 0.006 0.001 HIS C 660 Details of bonding type rmsd covalent geometry : bond 0.00254 (41256) covalent geometry : angle 0.52346 (56452) SS BOND : bond 0.00026 ( 4) SS BOND : angle 0.37147 ( 8) hydrogen bonds : bond 0.04704 ( 2376) hydrogen bonds : angle 4.32870 ( 6972) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10848 Ramachandran restraints generated. 5424 Oldfield, 0 Emsley, 5424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10848 Ramachandran restraints generated. 5424 Oldfield, 0 Emsley, 5424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 594 residues out of total 4664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 521 time to evaluate : 1.509 Fit side-chains REVERT: A 169 ARG cc_start: 0.5778 (ttm110) cc_final: 0.5365 (mtp-110) REVERT: A 215 THR cc_start: 0.7686 (m) cc_final: 0.7272 (p) REVERT: A 266 ASN cc_start: 0.5637 (m-40) cc_final: 0.5067 (t0) REVERT: A 561 ASP cc_start: 0.7109 (m-30) cc_final: 0.6748 (t0) REVERT: A 594 ARG cc_start: 0.6179 (mtp-110) cc_final: 0.5955 (ttp-170) REVERT: A 614 ARG cc_start: 0.6909 (mtp180) cc_final: 0.6531 (mtm-85) REVERT: A 666 GLU cc_start: 0.7409 (tt0) cc_final: 0.7010 (mt-10) REVERT: A 675 GLU cc_start: 0.7488 (tp30) cc_final: 0.7119 (tp30) REVERT: A 683 MET cc_start: 0.7549 (tpt) cc_final: 0.7194 (tpp) REVERT: A 854 MET cc_start: 0.6966 (mtm) cc_final: 0.6698 (mtp) REVERT: A 922 LYS cc_start: 0.7049 (mppt) cc_final: 0.6832 (mmtm) REVERT: A 969 ARG cc_start: 0.7673 (mtm110) cc_final: 0.7450 (mtm110) REVERT: A 990 ASP cc_start: 0.8036 (m-30) cc_final: 0.7779 (m-30) REVERT: A 1046 GLU cc_start: 0.7879 (mm-30) cc_final: 0.7354 (pm20) REVERT: A 1131 MET cc_start: 0.7579 (mmm) cc_final: 0.7012 (mtp) REVERT: A 1207 HIS cc_start: 0.4824 (m170) cc_final: 0.4542 (m170) REVERT: A 1253 TYR cc_start: 0.7293 (t80) cc_final: 0.6888 (t80) REVERT: A 1314 MET cc_start: 0.6907 (OUTLIER) cc_final: 0.6438 (tpp) REVERT: B 169 ARG cc_start: 0.5774 (ttm110) cc_final: 0.5366 (mtp-110) REVERT: B 266 ASN cc_start: 0.5630 (m-40) cc_final: 0.5061 (t0) REVERT: B 561 ASP cc_start: 0.7100 (m-30) cc_final: 0.6744 (t0) REVERT: B 594 ARG cc_start: 0.6210 (mtp-110) cc_final: 0.5945 (ttp-170) REVERT: B 614 ARG cc_start: 0.6901 (mtp180) cc_final: 0.6522 (mtm-85) REVERT: B 666 GLU cc_start: 0.7405 (tt0) cc_final: 0.7008 (mt-10) REVERT: B 675 GLU cc_start: 0.7486 (tp30) cc_final: 0.7112 (tp30) REVERT: B 683 MET cc_start: 0.7551 (tpt) cc_final: 0.7196 (tpp) REVERT: B 854 MET cc_start: 0.6938 (mtm) cc_final: 0.6670 (mtp) REVERT: B 922 LYS cc_start: 0.7040 (mppt) cc_final: 0.6817 (mmtm) REVERT: B 969 ARG cc_start: 0.7685 (mtm110) cc_final: 0.7458 (mtm110) REVERT: B 990 ASP cc_start: 0.8038 (m-30) cc_final: 0.7785 (m-30) REVERT: B 1046 GLU cc_start: 0.7875 (mm-30) cc_final: 0.7353 (pm20) REVERT: B 1131 MET cc_start: 0.7559 (mmm) cc_final: 0.6988 (mtp) REVERT: B 1207 HIS cc_start: 0.4819 (m170) cc_final: 0.4531 (m170) REVERT: B 1253 TYR cc_start: 0.7290 (t80) cc_final: 0.6908 (t80) REVERT: B 1314 MET cc_start: 0.6909 (OUTLIER) cc_final: 0.6295 (tpp) REVERT: C 169 ARG cc_start: 0.5823 (ttm110) cc_final: 0.5392 (mtp-110) REVERT: C 266 ASN cc_start: 0.5637 (m-40) cc_final: 0.5056 (t0) REVERT: C 561 ASP cc_start: 0.7095 (m-30) cc_final: 0.6735 (t0) REVERT: C 594 ARG cc_start: 0.6194 (mtp-110) cc_final: 0.5930 (ttp-170) REVERT: C 614 ARG cc_start: 0.6896 (mtp180) cc_final: 0.6522 (mtm-85) REVERT: C 666 GLU cc_start: 0.7402 (tt0) cc_final: 0.7010 (mt-10) REVERT: C 675 GLU cc_start: 0.7482 (tp30) cc_final: 0.7108 (tp30) REVERT: C 683 MET cc_start: 0.7545 (tpt) cc_final: 0.7153 (tpp) REVERT: C 854 MET cc_start: 0.6944 (mtm) cc_final: 0.6675 (mtp) REVERT: C 922 LYS cc_start: 0.7048 (mppt) cc_final: 0.6826 (mmtm) REVERT: C 969 ARG cc_start: 0.7684 (mtm110) cc_final: 0.7459 (mtm110) REVERT: C 990 ASP cc_start: 0.8043 (m-30) cc_final: 0.7792 (m-30) REVERT: C 1046 GLU cc_start: 0.7869 (mm-30) cc_final: 0.7349 (pm20) REVERT: C 1131 MET cc_start: 0.7556 (mmm) cc_final: 0.6995 (mtp) REVERT: C 1207 HIS cc_start: 0.4811 (m170) cc_final: 0.4519 (m170) REVERT: C 1253 TYR cc_start: 0.7289 (t80) cc_final: 0.6895 (t80) REVERT: C 1314 MET cc_start: 0.6919 (OUTLIER) cc_final: 0.6315 (tpp) REVERT: D 169 ARG cc_start: 0.5830 (ttm110) cc_final: 0.5399 (mtp-110) REVERT: D 266 ASN cc_start: 0.5643 (m-40) cc_final: 0.5057 (t0) REVERT: D 561 ASP cc_start: 0.7102 (m-30) cc_final: 0.6739 (t0) REVERT: D 594 ARG cc_start: 0.6278 (mtp-110) cc_final: 0.6019 (ttp-170) REVERT: D 614 ARG cc_start: 0.6901 (mtp180) cc_final: 0.6521 (mtm-85) REVERT: D 666 GLU cc_start: 0.7391 (tt0) cc_final: 0.6997 (mt-10) REVERT: D 675 GLU cc_start: 0.7486 (tp30) cc_final: 0.7114 (tp30) REVERT: D 683 MET cc_start: 0.7545 (tpt) cc_final: 0.7156 (tpp) REVERT: D 854 MET cc_start: 0.6937 (mtm) cc_final: 0.6672 (mtp) REVERT: D 922 LYS cc_start: 0.7046 (mppt) cc_final: 0.6820 (mmtm) REVERT: D 969 ARG cc_start: 0.7687 (mtm110) cc_final: 0.7450 (mtm110) REVERT: D 990 ASP cc_start: 0.8047 (m-30) cc_final: 0.7794 (m-30) REVERT: D 1046 GLU cc_start: 0.7866 (mm-30) cc_final: 0.7355 (pm20) REVERT: D 1131 MET cc_start: 0.7555 (mmm) cc_final: 0.6989 (mtp) REVERT: D 1207 HIS cc_start: 0.4812 (m170) cc_final: 0.4520 (m170) REVERT: D 1253 TYR cc_start: 0.7276 (t80) cc_final: 0.6867 (t80) REVERT: D 1314 MET cc_start: 0.6937 (OUTLIER) cc_final: 0.6323 (tpp) outliers start: 73 outliers final: 20 residues processed: 573 average time/residue: 0.7055 time to fit residues: 491.5097 Evaluate side-chains 420 residues out of total 4664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 396 time to evaluate : 1.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 356 GLN Chi-restraints excluded: chain A residue 1001 THR Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1137 LYS Chi-restraints excluded: chain A residue 1314 MET Chi-restraints excluded: chain B residue 347 ILE Chi-restraints excluded: chain B residue 356 GLN Chi-restraints excluded: chain B residue 1001 THR Chi-restraints excluded: chain B residue 1082 LEU Chi-restraints excluded: chain B residue 1137 LYS Chi-restraints excluded: chain B residue 1314 MET Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain C residue 356 GLN Chi-restraints excluded: chain C residue 1001 THR Chi-restraints excluded: chain C residue 1082 LEU Chi-restraints excluded: chain C residue 1137 LYS Chi-restraints excluded: chain C residue 1314 MET Chi-restraints excluded: chain D residue 347 ILE Chi-restraints excluded: chain D residue 356 GLN Chi-restraints excluded: chain D residue 1001 THR Chi-restraints excluded: chain D residue 1082 LEU Chi-restraints excluded: chain D residue 1137 LYS Chi-restraints excluded: chain D residue 1314 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 544 random chunks: chunk 56 optimal weight: 5.9990 chunk 126 optimal weight: 2.9990 chunk 437 optimal weight: 5.9990 chunk 331 optimal weight: 5.9990 chunk 496 optimal weight: 1.9990 chunk 506 optimal weight: 0.9990 chunk 312 optimal weight: 8.9990 chunk 482 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 405 optimal weight: 7.9990 chunk 436 optimal weight: 0.6980 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 450 ASN A 592 GLN A 702 ASN A 853 GLN A1038 ASN A1078 HIS B 450 ASN B 592 GLN B 702 ASN B 853 GLN B1038 ASN B1078 HIS C 450 ASN C 592 GLN C 702 ASN C 853 GLN C1026 ASN C1038 ASN C1078 HIS D 450 ASN D 592 GLN D 702 ASN D 853 GLN D1038 ASN D1078 HIS Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.161216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.131863 restraints weight = 57327.470| |-----------------------------------------------------------------------------| r_work (start): 0.3704 rms_B_bonded: 1.99 r_work: 0.3283 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.3072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 41260 Z= 0.174 Angle : 0.564 8.200 56460 Z= 0.294 Chirality : 0.040 0.164 6628 Planarity : 0.004 0.041 7116 Dihedral : 7.816 84.767 6992 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 3.91 % Allowed : 13.14 % Favored : 82.95 % 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 are not related in a simple way. whole: 1.40 (0.11), residues: 5424 helix: 1.93 (0.09), residues: 2968 sheet: -0.65 (0.23), residues: 432 loop : -0.16 (0.14), residues: 2024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D1008 TYR 0.031 0.002 TYR D 420 PHE 0.017 0.002 PHE D 879 TRP 0.016 0.002 TRP B 96 HIS 0.007 0.001 HIS B 660 Details of bonding type rmsd covalent geometry : bond 0.00401 (41256) covalent geometry : angle 0.56387 (56452) SS BOND : bond 0.00073 ( 4) SS BOND : angle 0.80695 ( 8) hydrogen bonds : bond 0.05139 ( 2376) hydrogen bonds : angle 4.22338 ( 6972) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10848 Ramachandran restraints generated. 5424 Oldfield, 0 Emsley, 5424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10848 Ramachandran restraints generated. 5424 Oldfield, 0 Emsley, 5424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 557 residues out of total 4664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 417 time to evaluate : 1.023 Fit side-chains REVERT: A 69 ARG cc_start: 0.5140 (mmm160) cc_final: 0.4927 (mmm160) REVERT: A 92 PRO cc_start: 0.6385 (Cg_exo) cc_final: 0.6108 (Cg_endo) REVERT: A 169 ARG cc_start: 0.5907 (ttm110) cc_final: 0.5450 (mtp-110) REVERT: A 215 THR cc_start: 0.7862 (m) cc_final: 0.7460 (p) REVERT: A 266 ASN cc_start: 0.5423 (m-40) cc_final: 0.5040 (t0) REVERT: A 356 GLN cc_start: 0.7064 (OUTLIER) cc_final: 0.6316 (tp40) REVERT: A 431 LEU cc_start: 0.6724 (mt) cc_final: 0.6366 (mp) REVERT: A 506 ARG cc_start: 0.6843 (ttt-90) cc_final: 0.6469 (mmm-85) REVERT: A 561 ASP cc_start: 0.7030 (m-30) cc_final: 0.6698 (t0) REVERT: A 594 ARG cc_start: 0.6314 (mtp-110) cc_final: 0.6049 (ttp-110) REVERT: A 666 GLU cc_start: 0.7581 (tt0) cc_final: 0.7187 (mt-10) REVERT: A 675 GLU cc_start: 0.7390 (tp30) cc_final: 0.7073 (tp30) REVERT: A 683 MET cc_start: 0.7560 (tpt) cc_final: 0.7328 (tpp) REVERT: A 864 ILE cc_start: 0.7392 (mm) cc_final: 0.6870 (mm) REVERT: A 922 LYS cc_start: 0.7103 (mppt) cc_final: 0.6779 (mmtm) REVERT: A 990 ASP cc_start: 0.7739 (m-30) cc_final: 0.7482 (m-30) REVERT: A 1046 GLU cc_start: 0.8052 (mm-30) cc_final: 0.7610 (pm20) REVERT: A 1049 GLU cc_start: 0.7582 (mm-30) cc_final: 0.7298 (mm-30) REVERT: A 1131 MET cc_start: 0.7659 (mmm) cc_final: 0.7240 (mtp) REVERT: A 1201 ASN cc_start: 0.7097 (t0) cc_final: 0.6869 (t0) REVERT: A 1253 TYR cc_start: 0.7212 (t80) cc_final: 0.6994 (t80) REVERT: A 1314 MET cc_start: 0.6891 (OUTLIER) cc_final: 0.6518 (tpp) REVERT: B 69 ARG cc_start: 0.5065 (mmm160) cc_final: 0.4854 (mmm160) REVERT: B 76 MET cc_start: 0.4094 (mmp) cc_final: 0.3532 (mmt) REVERT: B 92 PRO cc_start: 0.6354 (Cg_exo) cc_final: 0.6074 (Cg_endo) REVERT: B 169 ARG cc_start: 0.5917 (ttm110) cc_final: 0.5455 (mtp-110) REVERT: B 215 THR cc_start: 0.7869 (m) cc_final: 0.7468 (p) REVERT: B 266 ASN cc_start: 0.5436 (m-40) cc_final: 0.5042 (t0) REVERT: B 356 GLN cc_start: 0.6967 (OUTLIER) cc_final: 0.6375 (tp40) REVERT: B 431 LEU cc_start: 0.6610 (mt) cc_final: 0.6297 (mp) REVERT: B 506 ARG cc_start: 0.6758 (ttt-90) cc_final: 0.6424 (mmm-85) REVERT: B 561 ASP cc_start: 0.7038 (m-30) cc_final: 0.6691 (t0) REVERT: B 594 ARG cc_start: 0.6250 (mtp-110) cc_final: 0.5987 (ttp-110) REVERT: B 666 GLU cc_start: 0.7588 (tt0) cc_final: 0.7194 (mt-10) REVERT: B 675 GLU cc_start: 0.7394 (tp30) cc_final: 0.7078 (tp30) REVERT: B 683 MET cc_start: 0.7566 (tpt) cc_final: 0.7335 (tpp) REVERT: B 864 ILE cc_start: 0.7421 (mm) cc_final: 0.6903 (mm) REVERT: B 922 LYS cc_start: 0.7108 (mppt) cc_final: 0.6774 (mmtm) REVERT: B 990 ASP cc_start: 0.7727 (m-30) cc_final: 0.7473 (m-30) REVERT: B 1046 GLU cc_start: 0.8051 (mm-30) cc_final: 0.7608 (pm20) REVERT: B 1049 GLU cc_start: 0.7604 (mm-30) cc_final: 0.7322 (mm-30) REVERT: B 1131 MET cc_start: 0.7685 (mmm) cc_final: 0.7258 (mtp) REVERT: B 1201 ASN cc_start: 0.7077 (t0) cc_final: 0.6857 (t0) REVERT: B 1253 TYR cc_start: 0.7213 (t80) cc_final: 0.7005 (t80) REVERT: B 1314 MET cc_start: 0.6946 (OUTLIER) cc_final: 0.6566 (tpp) REVERT: C 69 ARG cc_start: 0.5059 (mmm160) cc_final: 0.4848 (mmm160) REVERT: C 76 MET cc_start: 0.4121 (mmp) cc_final: 0.3554 (mmt) REVERT: C 92 PRO cc_start: 0.6356 (Cg_exo) cc_final: 0.6081 (Cg_endo) REVERT: C 169 ARG cc_start: 0.5898 (ttm110) cc_final: 0.5438 (mtp-110) REVERT: C 215 THR cc_start: 0.7857 (m) cc_final: 0.7457 (p) REVERT: C 266 ASN cc_start: 0.5432 (m-40) cc_final: 0.5039 (t0) REVERT: C 356 GLN cc_start: 0.6946 (OUTLIER) cc_final: 0.6365 (tp40) REVERT: C 431 LEU cc_start: 0.6623 (mt) cc_final: 0.6303 (mp) REVERT: C 506 ARG cc_start: 0.6768 (ttt-90) cc_final: 0.6428 (mmm-85) REVERT: C 561 ASP cc_start: 0.7029 (m-30) cc_final: 0.6694 (t0) REVERT: C 594 ARG cc_start: 0.6225 (mtp-110) cc_final: 0.5964 (ttp-110) REVERT: C 666 GLU cc_start: 0.7606 (tt0) cc_final: 0.7208 (mt-10) REVERT: C 675 GLU cc_start: 0.7385 (tp30) cc_final: 0.7063 (tp30) REVERT: C 683 MET cc_start: 0.7563 (tpt) cc_final: 0.7332 (tpp) REVERT: C 864 ILE cc_start: 0.7409 (mm) cc_final: 0.6890 (mm) REVERT: C 922 LYS cc_start: 0.7102 (mppt) cc_final: 0.6773 (mmtm) REVERT: C 990 ASP cc_start: 0.7718 (m-30) cc_final: 0.7464 (m-30) REVERT: C 1046 GLU cc_start: 0.8016 (mm-30) cc_final: 0.7593 (pm20) REVERT: C 1049 GLU cc_start: 0.7592 (mm-30) cc_final: 0.7308 (mm-30) REVERT: C 1131 MET cc_start: 0.7690 (mmm) cc_final: 0.7270 (mtp) REVERT: C 1201 ASN cc_start: 0.7069 (t0) cc_final: 0.6844 (t0) REVERT: C 1253 TYR cc_start: 0.7207 (t80) cc_final: 0.6991 (t80) REVERT: C 1314 MET cc_start: 0.6934 (OUTLIER) cc_final: 0.6556 (tpp) REVERT: D 69 ARG cc_start: 0.5056 (mmm160) cc_final: 0.4843 (mmm160) REVERT: D 76 MET cc_start: 0.4118 (mmp) cc_final: 0.3551 (mmt) REVERT: D 92 PRO cc_start: 0.6359 (Cg_exo) cc_final: 0.6080 (Cg_endo) REVERT: D 169 ARG cc_start: 0.5903 (ttm110) cc_final: 0.5442 (mtp-110) REVERT: D 215 THR cc_start: 0.7858 (m) cc_final: 0.7458 (p) REVERT: D 266 ASN cc_start: 0.5422 (m-40) cc_final: 0.5036 (t0) REVERT: D 356 GLN cc_start: 0.7004 (OUTLIER) cc_final: 0.6387 (tp40) REVERT: D 431 LEU cc_start: 0.6631 (mt) cc_final: 0.6306 (mp) REVERT: D 506 ARG cc_start: 0.6766 (ttt-90) cc_final: 0.6426 (mmm-85) REVERT: D 561 ASP cc_start: 0.7021 (m-30) cc_final: 0.6687 (t0) REVERT: D 594 ARG cc_start: 0.6254 (mtp-110) cc_final: 0.5980 (ttp-110) REVERT: D 666 GLU cc_start: 0.7591 (tt0) cc_final: 0.7200 (mt-10) REVERT: D 675 GLU cc_start: 0.7383 (tp30) cc_final: 0.7058 (tp30) REVERT: D 683 MET cc_start: 0.7559 (tpt) cc_final: 0.7327 (tpp) REVERT: D 864 ILE cc_start: 0.7421 (mm) cc_final: 0.6904 (mm) REVERT: D 922 LYS cc_start: 0.7100 (mppt) cc_final: 0.6772 (mmtm) REVERT: D 990 ASP cc_start: 0.7725 (m-30) cc_final: 0.7474 (m-30) REVERT: D 1046 GLU cc_start: 0.8028 (mm-30) cc_final: 0.7606 (pm20) REVERT: D 1049 GLU cc_start: 0.7578 (mm-30) cc_final: 0.7295 (mm-30) REVERT: D 1131 MET cc_start: 0.7656 (mmm) cc_final: 0.7246 (mtp) REVERT: D 1157 MET cc_start: 0.8162 (mmt) cc_final: 0.7941 (mmp) REVERT: D 1201 ASN cc_start: 0.7081 (t0) cc_final: 0.6851 (t0) REVERT: D 1253 TYR cc_start: 0.7212 (t80) cc_final: 0.6990 (t80) REVERT: D 1314 MET cc_start: 0.6731 (OUTLIER) cc_final: 0.6350 (tpp) outliers start: 140 outliers final: 46 residues processed: 516 average time/residue: 0.6684 time to fit residues: 424.8511 Evaluate side-chains 438 residues out of total 4664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 384 time to evaluate : 1.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 356 GLN Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain A residue 916 ARG Chi-restraints excluded: chain A residue 1001 THR Chi-restraints excluded: chain A residue 1051 LEU Chi-restraints excluded: chain A residue 1076 LEU Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1137 LYS Chi-restraints excluded: chain A residue 1204 VAL Chi-restraints excluded: chain A residue 1251 VAL Chi-restraints excluded: chain A residue 1314 MET Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 356 GLN Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 456 MET Chi-restraints excluded: chain B residue 916 ARG Chi-restraints excluded: chain B residue 1001 THR Chi-restraints excluded: chain B residue 1051 LEU Chi-restraints excluded: chain B residue 1076 LEU Chi-restraints excluded: chain B residue 1082 LEU Chi-restraints excluded: chain B residue 1137 LYS Chi-restraints excluded: chain B residue 1204 VAL Chi-restraints excluded: chain B residue 1251 VAL Chi-restraints excluded: chain B residue 1314 MET Chi-restraints excluded: chain B residue 1331 THR Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 356 GLN Chi-restraints excluded: chain C residue 372 SER Chi-restraints excluded: chain C residue 456 MET Chi-restraints excluded: chain C residue 916 ARG Chi-restraints excluded: chain C residue 1001 THR Chi-restraints excluded: chain C residue 1051 LEU Chi-restraints excluded: chain C residue 1082 LEU Chi-restraints excluded: chain C residue 1137 LYS Chi-restraints excluded: chain C residue 1204 VAL Chi-restraints excluded: chain C residue 1251 VAL Chi-restraints excluded: chain C residue 1314 MET Chi-restraints excluded: chain C residue 1331 THR Chi-restraints excluded: chain D residue 184 THR Chi-restraints excluded: chain D residue 356 GLN Chi-restraints excluded: chain D residue 372 SER Chi-restraints excluded: chain D residue 456 MET Chi-restraints excluded: chain D residue 916 ARG Chi-restraints excluded: chain D residue 1001 THR Chi-restraints excluded: chain D residue 1051 LEU Chi-restraints excluded: chain D residue 1082 LEU Chi-restraints excluded: chain D residue 1137 LYS Chi-restraints excluded: chain D residue 1204 VAL Chi-restraints excluded: chain D residue 1251 VAL Chi-restraints excluded: chain D residue 1314 MET Chi-restraints excluded: chain D residue 1331 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 544 random chunks: chunk 291 optimal weight: 8.9990 chunk 390 optimal weight: 10.0000 chunk 39 optimal weight: 9.9990 chunk 122 optimal weight: 7.9990 chunk 276 optimal weight: 7.9990 chunk 476 optimal weight: 9.9990 chunk 54 optimal weight: 2.9990 chunk 289 optimal weight: 20.0000 chunk 282 optimal weight: 7.9990 chunk 247 optimal weight: 0.0030 chunk 161 optimal weight: 5.9990 overall best weight: 4.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 ASN A 440 HIS A 514 HIS A 702 ASN A1449 HIS B 337 ASN B 440 HIS B 514 HIS B 702 ASN B1449 HIS C 440 HIS C 514 HIS C 702 ASN D 337 ASN D 440 HIS D 514 HIS D 702 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.157113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.127349 restraints weight = 57440.237| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 2.04 r_work: 0.3240 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work: 0.3136 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.4079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.069 41260 Z= 0.360 Angle : 0.787 9.850 56460 Z= 0.409 Chirality : 0.050 0.220 6628 Planarity : 0.006 0.065 7116 Dihedral : 8.660 81.623 6992 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.36 % Favored : 96.57 % Rotamer: Outliers : 4.30 % Allowed : 14.82 % Favored : 80.89 % 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 are not related in a simple way. whole: 0.07 (0.11), residues: 5424 helix: 0.84 (0.09), residues: 2984 sheet: -1.06 (0.24), residues: 424 loop : -0.81 (0.13), residues: 2016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C1008 TYR 0.029 0.004 TYR A 917 PHE 0.024 0.004 PHE C 943 TRP 0.019 0.003 TRP D1052 HIS 0.007 0.002 HIS A 80 Details of bonding type rmsd covalent geometry : bond 0.00865 (41256) covalent geometry : angle 0.78750 (56452) SS BOND : bond 0.00252 ( 4) SS BOND : angle 0.73090 ( 8) hydrogen bonds : bond 0.07149 ( 2376) hydrogen bonds : angle 4.78805 ( 6972) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10848 Ramachandran restraints generated. 5424 Oldfield, 0 Emsley, 5424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10848 Ramachandran restraints generated. 5424 Oldfield, 0 Emsley, 5424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 583 residues out of total 4664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 429 time to evaluate : 1.241 Fit side-chains REVERT: A 76 MET cc_start: 0.4111 (mmp) cc_final: 0.3673 (mmt) REVERT: A 215 THR cc_start: 0.7994 (m) cc_final: 0.7674 (p) REVERT: A 266 ASN cc_start: 0.5512 (m-40) cc_final: 0.5211 (t0) REVERT: A 356 GLN cc_start: 0.6998 (OUTLIER) cc_final: 0.6625 (tp40) REVERT: A 398 ASP cc_start: 0.7479 (OUTLIER) cc_final: 0.6963 (t70) REVERT: A 506 ARG cc_start: 0.6965 (ttt-90) cc_final: 0.6689 (mmm-85) REVERT: A 561 ASP cc_start: 0.7200 (m-30) cc_final: 0.6792 (t0) REVERT: A 576 ARG cc_start: 0.7202 (mmt180) cc_final: 0.6890 (mmt180) REVERT: A 594 ARG cc_start: 0.6606 (mtp-110) cc_final: 0.6235 (mtp-110) REVERT: A 666 GLU cc_start: 0.7905 (tt0) cc_final: 0.7449 (mt-10) REVERT: A 675 GLU cc_start: 0.7543 (tp30) cc_final: 0.7290 (tp30) REVERT: A 864 ILE cc_start: 0.7588 (mm) cc_final: 0.7298 (mp) REVERT: A 1046 GLU cc_start: 0.8286 (mm-30) cc_final: 0.7733 (pm20) REVERT: A 1131 MET cc_start: 0.8035 (mmm) cc_final: 0.7670 (mtp) REVERT: A 1284 LYS cc_start: 0.7024 (OUTLIER) cc_final: 0.6460 (mttt) REVERT: A 1314 MET cc_start: 0.7027 (OUTLIER) cc_final: 0.6419 (tpp) REVERT: B 76 MET cc_start: 0.4197 (mmp) cc_final: 0.3739 (mmt) REVERT: B 215 THR cc_start: 0.8001 (m) cc_final: 0.7688 (p) REVERT: B 266 ASN cc_start: 0.5507 (m-40) cc_final: 0.5204 (t0) REVERT: B 356 GLN cc_start: 0.7006 (OUTLIER) cc_final: 0.6625 (tp40) REVERT: B 398 ASP cc_start: 0.7498 (OUTLIER) cc_final: 0.6984 (t70) REVERT: B 424 LEU cc_start: 0.6861 (OUTLIER) cc_final: 0.6484 (mt) REVERT: B 506 ARG cc_start: 0.6966 (ttt-90) cc_final: 0.6700 (mmm-85) REVERT: B 561 ASP cc_start: 0.7241 (m-30) cc_final: 0.6857 (t0) REVERT: B 576 ARG cc_start: 0.7206 (mmt180) cc_final: 0.6883 (mmt180) REVERT: B 594 ARG cc_start: 0.6575 (mtp-110) cc_final: 0.6271 (ttp-110) REVERT: B 615 MET cc_start: 0.8076 (mtp) cc_final: 0.7708 (mmm) REVERT: B 666 GLU cc_start: 0.7909 (tt0) cc_final: 0.7451 (mt-10) REVERT: B 675 GLU cc_start: 0.7568 (tp30) cc_final: 0.7322 (tp30) REVERT: B 864 ILE cc_start: 0.7598 (mm) cc_final: 0.7308 (mp) REVERT: B 1046 GLU cc_start: 0.8292 (mm-30) cc_final: 0.7736 (pm20) REVERT: B 1131 MET cc_start: 0.8027 (mmm) cc_final: 0.7664 (mtp) REVERT: B 1284 LYS cc_start: 0.7025 (OUTLIER) cc_final: 0.6459 (mttt) REVERT: B 1314 MET cc_start: 0.7044 (OUTLIER) cc_final: 0.6579 (tpp) REVERT: C 76 MET cc_start: 0.4180 (mmp) cc_final: 0.3735 (mmt) REVERT: C 215 THR cc_start: 0.7987 (m) cc_final: 0.7676 (p) REVERT: C 266 ASN cc_start: 0.5502 (m-40) cc_final: 0.5204 (t0) REVERT: C 356 GLN cc_start: 0.7026 (OUTLIER) cc_final: 0.6629 (tp40) REVERT: C 398 ASP cc_start: 0.7491 (OUTLIER) cc_final: 0.6977 (t70) REVERT: C 424 LEU cc_start: 0.6857 (OUTLIER) cc_final: 0.6476 (mt) REVERT: C 506 ARG cc_start: 0.6978 (ttt-90) cc_final: 0.6696 (mmm-85) REVERT: C 561 ASP cc_start: 0.7189 (m-30) cc_final: 0.6778 (t0) REVERT: C 576 ARG cc_start: 0.7185 (mmt180) cc_final: 0.6861 (mmt180) REVERT: C 594 ARG cc_start: 0.6561 (mtp-110) cc_final: 0.6199 (mtp-110) REVERT: C 638 GLU cc_start: 0.6522 (mt-10) cc_final: 0.6127 (mt-10) REVERT: C 666 GLU cc_start: 0.7901 (tt0) cc_final: 0.7458 (mt-10) REVERT: C 675 GLU cc_start: 0.7555 (tp30) cc_final: 0.7308 (tp30) REVERT: C 864 ILE cc_start: 0.7600 (mm) cc_final: 0.7308 (mp) REVERT: C 1046 GLU cc_start: 0.8278 (mm-30) cc_final: 0.7724 (pm20) REVERT: C 1131 MET cc_start: 0.8026 (mmm) cc_final: 0.7672 (mtp) REVERT: C 1284 LYS cc_start: 0.6929 (OUTLIER) cc_final: 0.6386 (mttt) REVERT: C 1314 MET cc_start: 0.7175 (OUTLIER) cc_final: 0.6655 (tpp) REVERT: D 76 MET cc_start: 0.4180 (mmp) cc_final: 0.3740 (mmt) REVERT: D 215 THR cc_start: 0.7992 (m) cc_final: 0.7674 (p) REVERT: D 266 ASN cc_start: 0.5492 (m-40) cc_final: 0.5195 (t0) REVERT: D 356 GLN cc_start: 0.7034 (OUTLIER) cc_final: 0.6612 (tp40) REVERT: D 398 ASP cc_start: 0.7474 (OUTLIER) cc_final: 0.6964 (t70) REVERT: D 424 LEU cc_start: 0.6851 (OUTLIER) cc_final: 0.6473 (mt) REVERT: D 506 ARG cc_start: 0.6975 (ttt-90) cc_final: 0.6696 (mmm-85) REVERT: D 561 ASP cc_start: 0.7192 (m-30) cc_final: 0.6777 (t0) REVERT: D 576 ARG cc_start: 0.7151 (mmt180) cc_final: 0.6822 (mmt180) REVERT: D 594 ARG cc_start: 0.6566 (mtp-110) cc_final: 0.6213 (mtp-110) REVERT: D 638 GLU cc_start: 0.6504 (mt-10) cc_final: 0.6107 (mt-10) REVERT: D 666 GLU cc_start: 0.7908 (tt0) cc_final: 0.7467 (mt-10) REVERT: D 675 GLU cc_start: 0.7553 (tp30) cc_final: 0.7302 (tp30) REVERT: D 864 ILE cc_start: 0.7591 (mm) cc_final: 0.7298 (mp) REVERT: D 1046 GLU cc_start: 0.8265 (mm-30) cc_final: 0.7726 (pm20) REVERT: D 1131 MET cc_start: 0.8022 (mmm) cc_final: 0.7669 (mtp) REVERT: D 1284 LYS cc_start: 0.6932 (OUTLIER) cc_final: 0.6377 (mttt) REVERT: D 1314 MET cc_start: 0.7087 (OUTLIER) cc_final: 0.6603 (tpp) outliers start: 154 outliers final: 76 residues processed: 539 average time/residue: 0.6632 time to fit residues: 443.0282 Evaluate side-chains 492 residues out of total 4664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 397 time to evaluate : 1.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 337 ASN Chi-restraints excluded: chain A residue 356 GLN Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 398 ASP Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 628 ILE Chi-restraints excluded: chain A residue 1001 THR Chi-restraints excluded: chain A residue 1010 THR Chi-restraints excluded: chain A residue 1044 VAL Chi-restraints excluded: chain A residue 1051 LEU Chi-restraints excluded: chain A residue 1076 LEU Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1137 LYS Chi-restraints excluded: chain A residue 1204 VAL Chi-restraints excluded: chain A residue 1251 VAL Chi-restraints excluded: chain A residue 1284 LYS Chi-restraints excluded: chain A residue 1314 MET Chi-restraints excluded: chain A residue 1414 SER Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 337 ASN Chi-restraints excluded: chain B residue 356 GLN Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 456 MET Chi-restraints excluded: chain B residue 628 ILE Chi-restraints excluded: chain B residue 1001 THR Chi-restraints excluded: chain B residue 1010 THR Chi-restraints excluded: chain B residue 1044 VAL Chi-restraints excluded: chain B residue 1051 LEU Chi-restraints excluded: chain B residue 1076 LEU Chi-restraints excluded: chain B residue 1082 LEU Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1137 LYS Chi-restraints excluded: chain B residue 1204 VAL Chi-restraints excluded: chain B residue 1251 VAL Chi-restraints excluded: chain B residue 1284 LYS Chi-restraints excluded: chain B residue 1314 MET Chi-restraints excluded: chain B residue 1331 THR Chi-restraints excluded: chain B residue 1365 MET Chi-restraints excluded: chain B residue 1414 SER Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain C residue 356 GLN Chi-restraints excluded: chain C residue 372 SER Chi-restraints excluded: chain C residue 398 ASP Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 456 MET Chi-restraints excluded: chain C residue 628 ILE Chi-restraints excluded: chain C residue 1001 THR Chi-restraints excluded: chain C residue 1010 THR Chi-restraints excluded: chain C residue 1044 VAL Chi-restraints excluded: chain C residue 1051 LEU Chi-restraints excluded: chain C residue 1082 LEU Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1137 LYS Chi-restraints excluded: chain C residue 1204 VAL Chi-restraints excluded: chain C residue 1251 VAL Chi-restraints excluded: chain C residue 1284 LYS Chi-restraints excluded: chain C residue 1314 MET Chi-restraints excluded: chain C residue 1331 THR Chi-restraints excluded: chain C residue 1365 MET Chi-restraints excluded: chain C residue 1414 SER Chi-restraints excluded: chain D residue 184 THR Chi-restraints excluded: chain D residue 309 VAL Chi-restraints excluded: chain D residue 337 ASN Chi-restraints excluded: chain D residue 347 ILE Chi-restraints excluded: chain D residue 353 LYS Chi-restraints excluded: chain D residue 356 GLN Chi-restraints excluded: chain D residue 372 SER Chi-restraints excluded: chain D residue 398 ASP Chi-restraints excluded: chain D residue 424 LEU Chi-restraints excluded: chain D residue 456 MET Chi-restraints excluded: chain D residue 628 ILE Chi-restraints excluded: chain D residue 1001 THR Chi-restraints excluded: chain D residue 1010 THR Chi-restraints excluded: chain D residue 1044 VAL Chi-restraints excluded: chain D residue 1051 LEU Chi-restraints excluded: chain D residue 1082 LEU Chi-restraints excluded: chain D residue 1105 THR Chi-restraints excluded: chain D residue 1137 LYS Chi-restraints excluded: chain D residue 1204 VAL Chi-restraints excluded: chain D residue 1251 VAL Chi-restraints excluded: chain D residue 1284 LYS Chi-restraints excluded: chain D residue 1314 MET Chi-restraints excluded: chain D residue 1331 THR Chi-restraints excluded: chain D residue 1365 MET Chi-restraints excluded: chain D residue 1414 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 544 random chunks: chunk 485 optimal weight: 0.9990 chunk 185 optimal weight: 0.9980 chunk 382 optimal weight: 10.0000 chunk 324 optimal weight: 5.9990 chunk 86 optimal weight: 3.9990 chunk 468 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 295 optimal weight: 4.9990 chunk 145 optimal weight: 0.9980 chunk 206 optimal weight: 0.9990 chunk 317 optimal weight: 0.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 ASN A 440 HIS ** B 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 337 ASN B 440 HIS B 461 HIS ** C 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 440 HIS C 461 HIS ** D 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 337 ASN D 440 HIS D 461 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.160717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.130201 restraints weight = 57200.407| |-----------------------------------------------------------------------------| r_work (start): 0.3679 rms_B_bonded: 2.03 r_work: 0.3264 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.3960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 41260 Z= 0.125 Angle : 0.511 7.131 56460 Z= 0.264 Chirality : 0.038 0.165 6628 Planarity : 0.004 0.044 7116 Dihedral : 8.020 84.219 6992 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.24 % Allowed : 16.94 % Favored : 79.83 % 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 are not related in a simple way. whole: 1.04 (0.11), residues: 5424 helix: 1.75 (0.09), residues: 2980 sheet: -1.00 (0.23), residues: 448 loop : -0.47 (0.13), residues: 1996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 174 TYR 0.019 0.002 TYR D 420 PHE 0.014 0.001 PHE C 971 TRP 0.017 0.001 TRP A 96 HIS 0.003 0.001 HIS A 660 Details of bonding type rmsd covalent geometry : bond 0.00274 (41256) covalent geometry : angle 0.51071 (56452) SS BOND : bond 0.00039 ( 4) SS BOND : angle 0.45813 ( 8) hydrogen bonds : bond 0.04501 ( 2376) hydrogen bonds : angle 4.13541 ( 6972) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10848 Ramachandran restraints generated. 5424 Oldfield, 0 Emsley, 5424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10848 Ramachandran restraints generated. 5424 Oldfield, 0 Emsley, 5424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 534 residues out of total 4664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 418 time to evaluate : 1.550 Fit side-chains REVERT: A 76 MET cc_start: 0.4200 (mmp) cc_final: 0.3811 (mmt) REVERT: A 215 THR cc_start: 0.7751 (m) cc_final: 0.7385 (p) REVERT: A 266 ASN cc_start: 0.5486 (m-40) cc_final: 0.5163 (t0) REVERT: A 356 GLN cc_start: 0.6942 (OUTLIER) cc_final: 0.6530 (tp40) REVERT: A 398 ASP cc_start: 0.7263 (t70) cc_final: 0.6864 (m-30) REVERT: A 431 LEU cc_start: 0.6753 (mt) cc_final: 0.6412 (mp) REVERT: A 506 ARG cc_start: 0.6847 (ttt-90) cc_final: 0.6531 (mmm-85) REVERT: A 561 ASP cc_start: 0.6985 (m-30) cc_final: 0.6655 (t0) REVERT: A 576 ARG cc_start: 0.7065 (mmt180) cc_final: 0.6761 (mmt180) REVERT: A 594 ARG cc_start: 0.6365 (mtp-110) cc_final: 0.6091 (ttp-110) REVERT: A 666 GLU cc_start: 0.7548 (tt0) cc_final: 0.7198 (mt-10) REVERT: A 675 GLU cc_start: 0.7402 (tp30) cc_final: 0.7076 (tp30) REVERT: A 864 ILE cc_start: 0.7531 (mm) cc_final: 0.6944 (mm) REVERT: A 990 ASP cc_start: 0.7788 (m-30) cc_final: 0.7501 (m-30) REVERT: A 1046 GLU cc_start: 0.7881 (mm-30) cc_final: 0.7489 (pm20) REVERT: A 1131 MET cc_start: 0.7769 (mmm) cc_final: 0.7400 (mtp) REVERT: A 1314 MET cc_start: 0.6909 (tmm) cc_final: 0.6635 (tpp) REVERT: B 76 MET cc_start: 0.4099 (mmp) cc_final: 0.3616 (mmt) REVERT: B 215 THR cc_start: 0.7796 (m) cc_final: 0.7424 (p) REVERT: B 266 ASN cc_start: 0.5478 (m-40) cc_final: 0.5156 (t0) REVERT: B 356 GLN cc_start: 0.6915 (OUTLIER) cc_final: 0.6546 (tp40) REVERT: B 398 ASP cc_start: 0.7278 (t70) cc_final: 0.6864 (m-30) REVERT: B 424 LEU cc_start: 0.6719 (OUTLIER) cc_final: 0.6336 (mt) REVERT: B 431 LEU cc_start: 0.6681 (mt) cc_final: 0.6365 (mp) REVERT: B 506 ARG cc_start: 0.6836 (ttt-90) cc_final: 0.6529 (mmm-85) REVERT: B 561 ASP cc_start: 0.7043 (m-30) cc_final: 0.6717 (t0) REVERT: B 576 ARG cc_start: 0.7117 (mmt180) cc_final: 0.6842 (mmt180) REVERT: B 594 ARG cc_start: 0.6330 (mtp-110) cc_final: 0.6053 (ttp-110) REVERT: B 615 MET cc_start: 0.7750 (mtp) cc_final: 0.7496 (mmm) REVERT: B 666 GLU cc_start: 0.7558 (tt0) cc_final: 0.7204 (mt-10) REVERT: B 675 GLU cc_start: 0.7430 (tp30) cc_final: 0.7100 (tp30) REVERT: B 864 ILE cc_start: 0.7534 (mm) cc_final: 0.6948 (mm) REVERT: B 990 ASP cc_start: 0.7789 (m-30) cc_final: 0.7505 (m-30) REVERT: B 1046 GLU cc_start: 0.7899 (mm-30) cc_final: 0.7487 (pm20) REVERT: B 1131 MET cc_start: 0.7761 (mmm) cc_final: 0.7387 (mtp) REVERT: B 1314 MET cc_start: 0.6930 (tmm) cc_final: 0.6651 (tpp) REVERT: C 76 MET cc_start: 0.4077 (mmp) cc_final: 0.3606 (mmt) REVERT: C 215 THR cc_start: 0.7788 (m) cc_final: 0.7411 (p) REVERT: C 266 ASN cc_start: 0.5478 (m-40) cc_final: 0.5151 (t0) REVERT: C 356 GLN cc_start: 0.6946 (OUTLIER) cc_final: 0.6564 (tp40) REVERT: C 398 ASP cc_start: 0.7291 (t70) cc_final: 0.6867 (m-30) REVERT: C 424 LEU cc_start: 0.6645 (OUTLIER) cc_final: 0.6256 (mt) REVERT: C 431 LEU cc_start: 0.6725 (mt) cc_final: 0.6412 (mp) REVERT: C 506 ARG cc_start: 0.6869 (ttt-90) cc_final: 0.6546 (mmm-85) REVERT: C 561 ASP cc_start: 0.6989 (m-30) cc_final: 0.6674 (t0) REVERT: C 576 ARG cc_start: 0.7127 (mmt180) cc_final: 0.6845 (mmt180) REVERT: C 594 ARG cc_start: 0.6364 (mtp-110) cc_final: 0.6088 (ttp-110) REVERT: C 666 GLU cc_start: 0.7557 (tt0) cc_final: 0.7201 (mt-10) REVERT: C 675 GLU cc_start: 0.7411 (tp30) cc_final: 0.7076 (tp30) REVERT: C 864 ILE cc_start: 0.7534 (mm) cc_final: 0.6951 (mm) REVERT: C 990 ASP cc_start: 0.7778 (m-30) cc_final: 0.7492 (m-30) REVERT: C 1046 GLU cc_start: 0.7891 (mm-30) cc_final: 0.7496 (pm20) REVERT: C 1076 LEU cc_start: 0.7234 (mt) cc_final: 0.6943 (mp) REVERT: C 1131 MET cc_start: 0.7713 (mmm) cc_final: 0.7355 (mtp) REVERT: C 1314 MET cc_start: 0.6914 (tmm) cc_final: 0.6638 (tpp) REVERT: D 76 MET cc_start: 0.4087 (mmp) cc_final: 0.3615 (mmt) REVERT: D 215 THR cc_start: 0.7783 (m) cc_final: 0.7409 (p) REVERT: D 266 ASN cc_start: 0.5483 (m-40) cc_final: 0.5153 (t0) REVERT: D 356 GLN cc_start: 0.6934 (OUTLIER) cc_final: 0.6594 (tp40) REVERT: D 398 ASP cc_start: 0.7260 (t70) cc_final: 0.6850 (m-30) REVERT: D 424 LEU cc_start: 0.6646 (OUTLIER) cc_final: 0.6254 (mt) REVERT: D 431 LEU cc_start: 0.6723 (mt) cc_final: 0.6413 (mp) REVERT: D 506 ARG cc_start: 0.6851 (ttt-90) cc_final: 0.6529 (mmm-85) REVERT: D 561 ASP cc_start: 0.6979 (m-30) cc_final: 0.6663 (t0) REVERT: D 576 ARG cc_start: 0.7141 (mmt180) cc_final: 0.6855 (mmt180) REVERT: D 594 ARG cc_start: 0.6360 (mtp-110) cc_final: 0.6086 (ttp-110) REVERT: D 666 GLU cc_start: 0.7562 (tt0) cc_final: 0.7207 (mt-10) REVERT: D 675 GLU cc_start: 0.7411 (tp30) cc_final: 0.7081 (tp30) REVERT: D 864 ILE cc_start: 0.7532 (mm) cc_final: 0.6952 (mm) REVERT: D 990 ASP cc_start: 0.7801 (m-30) cc_final: 0.7518 (m-30) REVERT: D 1046 GLU cc_start: 0.7873 (mm-30) cc_final: 0.7490 (pm20) REVERT: D 1076 LEU cc_start: 0.7235 (mt) cc_final: 0.6948 (mp) REVERT: D 1131 MET cc_start: 0.7753 (mmm) cc_final: 0.7398 (mtp) REVERT: D 1314 MET cc_start: 0.6838 (tmm) cc_final: 0.6516 (tpp) outliers start: 116 outliers final: 63 residues processed: 503 average time/residue: 0.6919 time to fit residues: 427.6289 Evaluate side-chains 459 residues out of total 4664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 389 time to evaluate : 1.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 353 LYS Chi-restraints excluded: chain A residue 356 GLN Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain A residue 628 ILE Chi-restraints excluded: chain A residue 907 VAL Chi-restraints excluded: chain A residue 916 ARG Chi-restraints excluded: chain A residue 922 LYS Chi-restraints excluded: chain A residue 1001 THR Chi-restraints excluded: chain A residue 1044 VAL Chi-restraints excluded: chain A residue 1076 LEU Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1137 LYS Chi-restraints excluded: chain A residue 1251 VAL Chi-restraints excluded: chain A residue 1365 MET Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 353 LYS Chi-restraints excluded: chain B residue 356 GLN Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 456 MET Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 628 ILE Chi-restraints excluded: chain B residue 907 VAL Chi-restraints excluded: chain B residue 916 ARG Chi-restraints excluded: chain B residue 922 LYS Chi-restraints excluded: chain B residue 1001 THR Chi-restraints excluded: chain B residue 1044 VAL Chi-restraints excluded: chain B residue 1076 LEU Chi-restraints excluded: chain B residue 1082 LEU Chi-restraints excluded: chain B residue 1137 LYS Chi-restraints excluded: chain B residue 1251 VAL Chi-restraints excluded: chain B residue 1331 THR Chi-restraints excluded: chain B residue 1365 MET Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain C residue 353 LYS Chi-restraints excluded: chain C residue 356 GLN Chi-restraints excluded: chain C residue 372 SER Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 456 MET Chi-restraints excluded: chain C residue 628 ILE Chi-restraints excluded: chain C residue 907 VAL Chi-restraints excluded: chain C residue 916 ARG Chi-restraints excluded: chain C residue 922 LYS Chi-restraints excluded: chain C residue 1001 THR Chi-restraints excluded: chain C residue 1044 VAL Chi-restraints excluded: chain C residue 1082 LEU Chi-restraints excluded: chain C residue 1137 LYS Chi-restraints excluded: chain C residue 1251 VAL Chi-restraints excluded: chain C residue 1331 THR Chi-restraints excluded: chain C residue 1365 MET Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain D residue 347 ILE Chi-restraints excluded: chain D residue 356 GLN Chi-restraints excluded: chain D residue 372 SER Chi-restraints excluded: chain D residue 424 LEU Chi-restraints excluded: chain D residue 456 MET Chi-restraints excluded: chain D residue 628 ILE Chi-restraints excluded: chain D residue 907 VAL Chi-restraints excluded: chain D residue 916 ARG Chi-restraints excluded: chain D residue 922 LYS Chi-restraints excluded: chain D residue 1001 THR Chi-restraints excluded: chain D residue 1044 VAL Chi-restraints excluded: chain D residue 1082 LEU Chi-restraints excluded: chain D residue 1137 LYS Chi-restraints excluded: chain D residue 1251 VAL Chi-restraints excluded: chain D residue 1331 THR Chi-restraints excluded: chain D residue 1365 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 544 random chunks: chunk 161 optimal weight: 6.9990 chunk 472 optimal weight: 1.9990 chunk 409 optimal weight: 20.0000 chunk 84 optimal weight: 2.9990 chunk 162 optimal weight: 4.9990 chunk 335 optimal weight: 4.9990 chunk 458 optimal weight: 8.9990 chunk 404 optimal weight: 9.9990 chunk 142 optimal weight: 8.9990 chunk 351 optimal weight: 0.5980 chunk 324 optimal weight: 9.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 440 HIS A 699 ASN B 440 HIS B 699 ASN C 440 HIS C 461 HIS C 699 ASN D 440 HIS D 461 HIS D 699 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.158293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.129745 restraints weight = 57317.598| |-----------------------------------------------------------------------------| r_work (start): 0.3674 rms_B_bonded: 1.97 r_work: 0.3223 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.4264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 41260 Z= 0.241 Angle : 0.639 7.424 56460 Z= 0.331 Chirality : 0.043 0.191 6628 Planarity : 0.005 0.046 7116 Dihedral : 8.251 82.957 6992 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.47 % Favored : 96.46 % Rotamer: Outliers : 4.41 % Allowed : 16.60 % Favored : 78.99 % 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 are not related in a simple way. whole: 0.60 (0.11), residues: 5424 helix: 1.34 (0.09), residues: 3000 sheet: -1.03 (0.24), residues: 444 loop : -0.64 (0.13), residues: 1980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 174 TYR 0.026 0.003 TYR A 917 PHE 0.019 0.003 PHE C 879 TRP 0.022 0.002 TRP A 96 HIS 0.006 0.001 HIS B 660 Details of bonding type rmsd covalent geometry : bond 0.00575 (41256) covalent geometry : angle 0.63934 (56452) SS BOND : bond 0.00077 ( 4) SS BOND : angle 0.77447 ( 8) hydrogen bonds : bond 0.05942 ( 2376) hydrogen bonds : angle 4.40311 ( 6972) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10848 Ramachandran restraints generated. 5424 Oldfield, 0 Emsley, 5424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10848 Ramachandran restraints generated. 5424 Oldfield, 0 Emsley, 5424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 575 residues out of total 4664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 417 time to evaluate : 1.410 Fit side-chains REVERT: A 76 MET cc_start: 0.3971 (mmp) cc_final: 0.3594 (mmt) REVERT: A 215 THR cc_start: 0.7925 (m) cc_final: 0.7560 (p) REVERT: A 266 ASN cc_start: 0.5632 (m-40) cc_final: 0.5223 (t0) REVERT: A 356 GLN cc_start: 0.6961 (OUTLIER) cc_final: 0.6507 (tp40) REVERT: A 398 ASP cc_start: 0.7298 (t70) cc_final: 0.6829 (m-30) REVERT: A 424 LEU cc_start: 0.6698 (OUTLIER) cc_final: 0.6199 (mt) REVERT: A 448 ASN cc_start: 0.5990 (m-40) cc_final: 0.5759 (m-40) REVERT: A 505 LYS cc_start: 0.7449 (OUTLIER) cc_final: 0.7247 (mtpm) REVERT: A 506 ARG cc_start: 0.6890 (ttt-90) cc_final: 0.6543 (mmm-85) REVERT: A 561 ASP cc_start: 0.7088 (m-30) cc_final: 0.6702 (t0) REVERT: A 576 ARG cc_start: 0.7141 (mmt180) cc_final: 0.6783 (mmt180) REVERT: A 594 ARG cc_start: 0.6351 (mtp-110) cc_final: 0.6105 (ttp-170) REVERT: A 615 MET cc_start: 0.7986 (mtp) cc_final: 0.7509 (mmm) REVERT: A 617 ARG cc_start: 0.8152 (ttt-90) cc_final: 0.7828 (ttp80) REVERT: A 638 GLU cc_start: 0.6284 (mt-10) cc_final: 0.5793 (mt-10) REVERT: A 666 GLU cc_start: 0.7561 (tt0) cc_final: 0.7201 (mt-10) REVERT: A 675 GLU cc_start: 0.7347 (tp30) cc_final: 0.7047 (tp30) REVERT: A 864 ILE cc_start: 0.7737 (mm) cc_final: 0.7215 (mm) REVERT: A 893 GLN cc_start: 0.6945 (tp-100) cc_final: 0.6577 (mm110) REVERT: A 990 ASP cc_start: 0.7952 (m-30) cc_final: 0.7668 (m-30) REVERT: A 1046 GLU cc_start: 0.7672 (mm-30) cc_final: 0.7391 (pm20) REVERT: A 1049 GLU cc_start: 0.7873 (mm-30) cc_final: 0.7586 (mm-30) REVERT: A 1131 MET cc_start: 0.7699 (mmm) cc_final: 0.7353 (mtp) REVERT: A 1166 GLN cc_start: 0.6993 (mm-40) cc_final: 0.6626 (mm110) REVERT: A 1284 LYS cc_start: 0.6939 (OUTLIER) cc_final: 0.6422 (mttt) REVERT: A 1314 MET cc_start: 0.7070 (OUTLIER) cc_final: 0.6574 (tpp) REVERT: B 76 MET cc_start: 0.4071 (mmp) cc_final: 0.3754 (mmt) REVERT: B 215 THR cc_start: 0.7937 (m) cc_final: 0.7574 (p) REVERT: B 266 ASN cc_start: 0.5632 (m-40) cc_final: 0.5218 (t0) REVERT: B 356 GLN cc_start: 0.6884 (OUTLIER) cc_final: 0.6514 (tp40) REVERT: B 424 LEU cc_start: 0.6684 (OUTLIER) cc_final: 0.6226 (mt) REVERT: B 448 ASN cc_start: 0.5953 (m-40) cc_final: 0.5725 (m-40) REVERT: B 461 HIS cc_start: 0.6414 (OUTLIER) cc_final: 0.6139 (p90) REVERT: B 506 ARG cc_start: 0.6890 (ttt-90) cc_final: 0.6549 (mmm-85) REVERT: B 561 ASP cc_start: 0.7148 (m-30) cc_final: 0.6767 (t0) REVERT: B 576 ARG cc_start: 0.7116 (mmt180) cc_final: 0.6761 (mmt180) REVERT: B 594 ARG cc_start: 0.6347 (mtp-110) cc_final: 0.6061 (ttp-110) REVERT: B 615 MET cc_start: 0.7947 (mtp) cc_final: 0.7592 (mmm) REVERT: B 617 ARG cc_start: 0.8159 (ttt-90) cc_final: 0.7833 (ttp80) REVERT: B 638 GLU cc_start: 0.6289 (mt-10) cc_final: 0.5792 (mt-10) REVERT: B 666 GLU cc_start: 0.7548 (tt0) cc_final: 0.7190 (mt-10) REVERT: B 675 GLU cc_start: 0.7372 (tp30) cc_final: 0.7069 (tp30) REVERT: B 864 ILE cc_start: 0.7761 (mm) cc_final: 0.7241 (mm) REVERT: B 893 GLN cc_start: 0.6904 (tp-100) cc_final: 0.6528 (mm110) REVERT: B 990 ASP cc_start: 0.7949 (m-30) cc_final: 0.7666 (m-30) REVERT: B 1046 GLU cc_start: 0.7662 (mm-30) cc_final: 0.7392 (pm20) REVERT: B 1049 GLU cc_start: 0.7873 (mm-30) cc_final: 0.7595 (mm-30) REVERT: B 1131 MET cc_start: 0.7698 (mmm) cc_final: 0.7344 (mtp) REVERT: B 1166 GLN cc_start: 0.6996 (mm-40) cc_final: 0.6623 (mm110) REVERT: B 1284 LYS cc_start: 0.6950 (OUTLIER) cc_final: 0.6438 (mttt) REVERT: B 1314 MET cc_start: 0.7059 (OUTLIER) cc_final: 0.6572 (tpp) REVERT: C 76 MET cc_start: 0.4039 (mmp) cc_final: 0.3724 (mmt) REVERT: C 215 THR cc_start: 0.7928 (m) cc_final: 0.7555 (p) REVERT: C 266 ASN cc_start: 0.5627 (m-40) cc_final: 0.5218 (t0) REVERT: C 356 GLN cc_start: 0.6931 (OUTLIER) cc_final: 0.6524 (tp40) REVERT: C 424 LEU cc_start: 0.6675 (OUTLIER) cc_final: 0.6233 (mt) REVERT: C 448 ASN cc_start: 0.6063 (m-40) cc_final: 0.5785 (m-40) REVERT: C 506 ARG cc_start: 0.6892 (ttt-90) cc_final: 0.6550 (mmm-85) REVERT: C 561 ASP cc_start: 0.7117 (m-30) cc_final: 0.6735 (t0) REVERT: C 576 ARG cc_start: 0.7128 (mmt180) cc_final: 0.6758 (mmt180) REVERT: C 594 ARG cc_start: 0.6363 (mtp-110) cc_final: 0.6128 (ttp-170) REVERT: C 615 MET cc_start: 0.7980 (mtp) cc_final: 0.7556 (mmm) REVERT: C 617 ARG cc_start: 0.8161 (ttt-90) cc_final: 0.7841 (ttp80) REVERT: C 638 GLU cc_start: 0.6305 (mt-10) cc_final: 0.5809 (mt-10) REVERT: C 666 GLU cc_start: 0.7549 (tt0) cc_final: 0.7187 (mt-10) REVERT: C 675 GLU cc_start: 0.7360 (tp30) cc_final: 0.7050 (tp30) REVERT: C 864 ILE cc_start: 0.7762 (mm) cc_final: 0.7201 (mm) REVERT: C 893 GLN cc_start: 0.6889 (tp-100) cc_final: 0.6511 (mm110) REVERT: C 990 ASP cc_start: 0.7939 (m-30) cc_final: 0.7653 (m-30) REVERT: C 1046 GLU cc_start: 0.7700 (mm-30) cc_final: 0.7414 (pm20) REVERT: C 1131 MET cc_start: 0.7698 (mmm) cc_final: 0.7356 (mtp) REVERT: C 1166 GLN cc_start: 0.6958 (mm-40) cc_final: 0.6562 (mm110) REVERT: C 1284 LYS cc_start: 0.6966 (OUTLIER) cc_final: 0.6439 (mttt) REVERT: C 1314 MET cc_start: 0.7044 (OUTLIER) cc_final: 0.6560 (tpp) REVERT: D 76 MET cc_start: 0.4051 (mmp) cc_final: 0.3735 (mmt) REVERT: D 215 THR cc_start: 0.7930 (m) cc_final: 0.7561 (p) REVERT: D 266 ASN cc_start: 0.5627 (m-40) cc_final: 0.5212 (t0) REVERT: D 356 GLN cc_start: 0.6942 (OUTLIER) cc_final: 0.6519 (tp40) REVERT: D 424 LEU cc_start: 0.6671 (OUTLIER) cc_final: 0.6171 (mt) REVERT: D 448 ASN cc_start: 0.6058 (m-40) cc_final: 0.5786 (m-40) REVERT: D 506 ARG cc_start: 0.6885 (ttt-90) cc_final: 0.6537 (mmm-85) REVERT: D 561 ASP cc_start: 0.7108 (m-30) cc_final: 0.6727 (t0) REVERT: D 576 ARG cc_start: 0.7122 (mmt180) cc_final: 0.6753 (mmt180) REVERT: D 594 ARG cc_start: 0.6344 (mtp-110) cc_final: 0.6100 (ttp-170) REVERT: D 617 ARG cc_start: 0.8139 (ttt-90) cc_final: 0.7821 (ttp80) REVERT: D 638 GLU cc_start: 0.6281 (mt-10) cc_final: 0.5789 (mt-10) REVERT: D 666 GLU cc_start: 0.7552 (tt0) cc_final: 0.7194 (mt-10) REVERT: D 675 GLU cc_start: 0.7361 (tp30) cc_final: 0.7055 (tp30) REVERT: D 864 ILE cc_start: 0.7760 (mm) cc_final: 0.7243 (mm) REVERT: D 893 GLN cc_start: 0.6885 (tp-100) cc_final: 0.6510 (mm110) REVERT: D 990 ASP cc_start: 0.7956 (m-30) cc_final: 0.7670 (m-30) REVERT: D 1046 GLU cc_start: 0.7669 (mm-30) cc_final: 0.7412 (pm20) REVERT: D 1131 MET cc_start: 0.7719 (mmm) cc_final: 0.7369 (mtp) REVERT: D 1284 LYS cc_start: 0.6985 (OUTLIER) cc_final: 0.6439 (mttt) REVERT: D 1314 MET cc_start: 0.7060 (OUTLIER) cc_final: 0.6550 (tpp) outliers start: 158 outliers final: 93 residues processed: 536 average time/residue: 0.6896 time to fit residues: 455.5071 Evaluate side-chains 515 residues out of total 4664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 404 time to evaluate : 1.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 353 LYS Chi-restraints excluded: chain A residue 356 GLN Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain A residue 505 LYS Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 628 ILE Chi-restraints excluded: chain A residue 641 SER Chi-restraints excluded: chain A residue 703 ILE Chi-restraints excluded: chain A residue 922 LYS Chi-restraints excluded: chain A residue 1001 THR Chi-restraints excluded: chain A residue 1010 THR Chi-restraints excluded: chain A residue 1044 VAL Chi-restraints excluded: chain A residue 1051 LEU Chi-restraints excluded: chain A residue 1076 LEU Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1137 LYS Chi-restraints excluded: chain A residue 1218 VAL Chi-restraints excluded: chain A residue 1251 VAL Chi-restraints excluded: chain A residue 1284 LYS Chi-restraints excluded: chain A residue 1314 MET Chi-restraints excluded: chain A residue 1365 MET Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 353 LYS Chi-restraints excluded: chain B residue 356 GLN Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 456 MET Chi-restraints excluded: chain B residue 461 HIS Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 628 ILE Chi-restraints excluded: chain B residue 641 SER Chi-restraints excluded: chain B residue 703 ILE Chi-restraints excluded: chain B residue 922 LYS Chi-restraints excluded: chain B residue 1001 THR Chi-restraints excluded: chain B residue 1010 THR Chi-restraints excluded: chain B residue 1044 VAL Chi-restraints excluded: chain B residue 1051 LEU Chi-restraints excluded: chain B residue 1076 LEU Chi-restraints excluded: chain B residue 1082 LEU Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1137 LYS Chi-restraints excluded: chain B residue 1218 VAL Chi-restraints excluded: chain B residue 1251 VAL Chi-restraints excluded: chain B residue 1284 LYS Chi-restraints excluded: chain B residue 1314 MET Chi-restraints excluded: chain B residue 1331 THR Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain C residue 353 LYS Chi-restraints excluded: chain C residue 356 GLN Chi-restraints excluded: chain C residue 372 SER Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 456 MET Chi-restraints excluded: chain C residue 574 VAL Chi-restraints excluded: chain C residue 628 ILE Chi-restraints excluded: chain C residue 641 SER Chi-restraints excluded: chain C residue 703 ILE Chi-restraints excluded: chain C residue 922 LYS Chi-restraints excluded: chain C residue 1001 THR Chi-restraints excluded: chain C residue 1010 THR Chi-restraints excluded: chain C residue 1044 VAL Chi-restraints excluded: chain C residue 1051 LEU Chi-restraints excluded: chain C residue 1082 LEU Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1137 LYS Chi-restraints excluded: chain C residue 1218 VAL Chi-restraints excluded: chain C residue 1251 VAL Chi-restraints excluded: chain C residue 1284 LYS Chi-restraints excluded: chain C residue 1314 MET Chi-restraints excluded: chain C residue 1331 THR Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 309 VAL Chi-restraints excluded: chain D residue 347 ILE Chi-restraints excluded: chain D residue 353 LYS Chi-restraints excluded: chain D residue 356 GLN Chi-restraints excluded: chain D residue 372 SER Chi-restraints excluded: chain D residue 424 LEU Chi-restraints excluded: chain D residue 456 MET Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 628 ILE Chi-restraints excluded: chain D residue 641 SER Chi-restraints excluded: chain D residue 703 ILE Chi-restraints excluded: chain D residue 922 LYS Chi-restraints excluded: chain D residue 1001 THR Chi-restraints excluded: chain D residue 1010 THR Chi-restraints excluded: chain D residue 1044 VAL Chi-restraints excluded: chain D residue 1051 LEU Chi-restraints excluded: chain D residue 1082 LEU Chi-restraints excluded: chain D residue 1105 THR Chi-restraints excluded: chain D residue 1137 LYS Chi-restraints excluded: chain D residue 1218 VAL Chi-restraints excluded: chain D residue 1251 VAL Chi-restraints excluded: chain D residue 1284 LYS Chi-restraints excluded: chain D residue 1314 MET Chi-restraints excluded: chain D residue 1331 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 544 random chunks: chunk 97 optimal weight: 0.8980 chunk 113 optimal weight: 7.9990 chunk 482 optimal weight: 0.6980 chunk 539 optimal weight: 9.9990 chunk 492 optimal weight: 0.6980 chunk 478 optimal weight: 0.9980 chunk 506 optimal weight: 1.9990 chunk 362 optimal weight: 0.3980 chunk 270 optimal weight: 6.9990 chunk 20 optimal weight: 5.9990 chunk 514 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 440 HIS B 440 HIS C 440 HIS C1026 ASN D 440 HIS D 461 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.160910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.130743 restraints weight = 57430.249| |-----------------------------------------------------------------------------| r_work (start): 0.3688 rms_B_bonded: 2.03 r_work: 0.3254 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.4190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 41260 Z= 0.110 Angle : 0.489 7.609 56460 Z= 0.250 Chirality : 0.037 0.144 6628 Planarity : 0.003 0.041 7116 Dihedral : 7.844 84.814 6992 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.73 % Allowed : 18.36 % Favored : 78.91 % 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 are not related in a simple way. whole: 1.28 (0.11), residues: 5424 helix: 1.98 (0.09), residues: 2984 sheet: -0.96 (0.24), residues: 448 loop : -0.41 (0.14), residues: 1992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 174 TYR 0.013 0.001 TYR A 420 PHE 0.017 0.001 PHE B 971 TRP 0.021 0.001 TRP A 96 HIS 0.003 0.001 HIS D 660 Details of bonding type rmsd covalent geometry : bond 0.00240 (41256) covalent geometry : angle 0.48949 (56452) SS BOND : bond 0.00003 ( 4) SS BOND : angle 0.42622 ( 8) hydrogen bonds : bond 0.04086 ( 2376) hydrogen bonds : angle 3.96049 ( 6972) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10848 Ramachandran restraints generated. 5424 Oldfield, 0 Emsley, 5424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10848 Ramachandran restraints generated. 5424 Oldfield, 0 Emsley, 5424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 520 residues out of total 4664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 422 time to evaluate : 1.477 Fit side-chains REVERT: A 76 MET cc_start: 0.4093 (mmp) cc_final: 0.3768 (mmt) REVERT: A 215 THR cc_start: 0.7914 (m) cc_final: 0.7503 (p) REVERT: A 266 ASN cc_start: 0.5608 (m-40) cc_final: 0.5208 (t0) REVERT: A 353 LYS cc_start: 0.7706 (OUTLIER) cc_final: 0.7496 (ttmt) REVERT: A 356 GLN cc_start: 0.6885 (OUTLIER) cc_final: 0.6536 (tp40) REVERT: A 398 ASP cc_start: 0.7265 (t70) cc_final: 0.6846 (m-30) REVERT: A 424 LEU cc_start: 0.6530 (OUTLIER) cc_final: 0.6155 (mt) REVERT: A 431 LEU cc_start: 0.6728 (mt) cc_final: 0.6442 (mp) REVERT: A 506 ARG cc_start: 0.7003 (ttt-90) cc_final: 0.6651 (mmm-85) REVERT: A 561 ASP cc_start: 0.7190 (m-30) cc_final: 0.6878 (t0) REVERT: A 576 ARG cc_start: 0.6971 (mmt180) cc_final: 0.6672 (mmt180) REVERT: A 594 ARG cc_start: 0.6266 (mtp-110) cc_final: 0.5908 (mtp-110) REVERT: A 617 ARG cc_start: 0.8106 (ttt-90) cc_final: 0.7537 (ttt-90) REVERT: A 666 GLU cc_start: 0.7535 (tt0) cc_final: 0.7152 (mt-10) REVERT: A 675 GLU cc_start: 0.7312 (tp30) cc_final: 0.6974 (tp30) REVERT: A 864 ILE cc_start: 0.7453 (mm) cc_final: 0.6924 (mm) REVERT: A 990 ASP cc_start: 0.7899 (m-30) cc_final: 0.7595 (m-30) REVERT: A 1010 THR cc_start: 0.8673 (OUTLIER) cc_final: 0.8471 (t) REVERT: A 1046 GLU cc_start: 0.7481 (mm-30) cc_final: 0.7273 (pm20) REVERT: A 1131 MET cc_start: 0.7702 (mmm) cc_final: 0.7337 (mtp) REVERT: A 1284 LYS cc_start: 0.6975 (OUTLIER) cc_final: 0.6489 (mttt) REVERT: A 1314 MET cc_start: 0.6918 (tmm) cc_final: 0.6693 (tpp) REVERT: B 76 MET cc_start: 0.4267 (mmp) cc_final: 0.3884 (mmt) REVERT: B 215 THR cc_start: 0.7923 (m) cc_final: 0.7510 (p) REVERT: B 266 ASN cc_start: 0.5588 (m-40) cc_final: 0.5162 (t0) REVERT: B 353 LYS cc_start: 0.7704 (OUTLIER) cc_final: 0.7500 (ttmt) REVERT: B 356 GLN cc_start: 0.6840 (OUTLIER) cc_final: 0.6482 (tp40) REVERT: B 398 ASP cc_start: 0.7284 (t70) cc_final: 0.6844 (m-30) REVERT: B 424 LEU cc_start: 0.6669 (OUTLIER) cc_final: 0.6187 (mt) REVERT: B 431 LEU cc_start: 0.6715 (mt) cc_final: 0.6432 (mp) REVERT: B 506 ARG cc_start: 0.6973 (ttt-90) cc_final: 0.6620 (mmm-85) REVERT: B 561 ASP cc_start: 0.7167 (m-30) cc_final: 0.6857 (t0) REVERT: B 576 ARG cc_start: 0.6979 (mmt180) cc_final: 0.6676 (mmt180) REVERT: B 594 ARG cc_start: 0.6239 (mtp-110) cc_final: 0.5885 (mtp-110) REVERT: B 617 ARG cc_start: 0.8095 (ttt-90) cc_final: 0.7530 (ttt-90) REVERT: B 666 GLU cc_start: 0.7538 (tt0) cc_final: 0.7156 (mt-10) REVERT: B 675 GLU cc_start: 0.7316 (tp30) cc_final: 0.6978 (tp30) REVERT: B 864 ILE cc_start: 0.7455 (mm) cc_final: 0.6931 (mm) REVERT: B 990 ASP cc_start: 0.7891 (m-30) cc_final: 0.7614 (m-30) REVERT: B 1010 THR cc_start: 0.8675 (OUTLIER) cc_final: 0.8470 (t) REVERT: B 1131 MET cc_start: 0.7638 (mmm) cc_final: 0.7294 (mtp) REVERT: B 1284 LYS cc_start: 0.7003 (OUTLIER) cc_final: 0.6516 (mttt) REVERT: B 1314 MET cc_start: 0.6895 (tmm) cc_final: 0.6671 (tpp) REVERT: C 76 MET cc_start: 0.4259 (mmp) cc_final: 0.3883 (mmt) REVERT: C 215 THR cc_start: 0.7897 (m) cc_final: 0.7491 (p) REVERT: C 266 ASN cc_start: 0.5640 (m-40) cc_final: 0.5238 (t0) REVERT: C 356 GLN cc_start: 0.6965 (OUTLIER) cc_final: 0.6577 (tp40) REVERT: C 398 ASP cc_start: 0.7345 (t70) cc_final: 0.6898 (m-30) REVERT: C 424 LEU cc_start: 0.6622 (OUTLIER) cc_final: 0.6158 (mt) REVERT: C 431 LEU cc_start: 0.6725 (mt) cc_final: 0.6438 (mp) REVERT: C 506 ARG cc_start: 0.7029 (ttt-90) cc_final: 0.6680 (mmm-85) REVERT: C 561 ASP cc_start: 0.7176 (m-30) cc_final: 0.6872 (t0) REVERT: C 576 ARG cc_start: 0.6984 (mmt180) cc_final: 0.6675 (mmt180) REVERT: C 594 ARG cc_start: 0.6254 (mtp-110) cc_final: 0.5895 (mtp-110) REVERT: C 617 ARG cc_start: 0.8096 (ttt-90) cc_final: 0.7526 (ttt-90) REVERT: C 666 GLU cc_start: 0.7538 (tt0) cc_final: 0.7153 (mt-10) REVERT: C 675 GLU cc_start: 0.7311 (tp30) cc_final: 0.6965 (tp30) REVERT: C 864 ILE cc_start: 0.7450 (mm) cc_final: 0.6924 (mm) REVERT: C 990 ASP cc_start: 0.7878 (m-30) cc_final: 0.7602 (m-30) REVERT: C 1010 THR cc_start: 0.8674 (OUTLIER) cc_final: 0.8472 (t) REVERT: C 1046 GLU cc_start: 0.7428 (mm-30) cc_final: 0.7179 (pm20) REVERT: C 1076 LEU cc_start: 0.7334 (mt) cc_final: 0.7061 (mp) REVERT: C 1131 MET cc_start: 0.7649 (mmm) cc_final: 0.7302 (mtp) REVERT: C 1284 LYS cc_start: 0.7002 (OUTLIER) cc_final: 0.6502 (mttt) REVERT: C 1314 MET cc_start: 0.6893 (tmm) cc_final: 0.6675 (tpp) REVERT: D 76 MET cc_start: 0.4257 (mmp) cc_final: 0.3881 (mmt) REVERT: D 215 THR cc_start: 0.7904 (m) cc_final: 0.7501 (p) REVERT: D 266 ASN cc_start: 0.5605 (m-40) cc_final: 0.5196 (t0) REVERT: D 356 GLN cc_start: 0.6766 (OUTLIER) cc_final: 0.6491 (tp40) REVERT: D 398 ASP cc_start: 0.7317 (t70) cc_final: 0.6875 (m-30) REVERT: D 424 LEU cc_start: 0.6625 (OUTLIER) cc_final: 0.6163 (mt) REVERT: D 431 LEU cc_start: 0.6729 (mt) cc_final: 0.6436 (mp) REVERT: D 506 ARG cc_start: 0.7020 (ttt-90) cc_final: 0.6668 (mmm-85) REVERT: D 561 ASP cc_start: 0.7175 (m-30) cc_final: 0.6869 (t0) REVERT: D 576 ARG cc_start: 0.6984 (mmt180) cc_final: 0.6672 (mmt180) REVERT: D 594 ARG cc_start: 0.6264 (mtp-110) cc_final: 0.5907 (mtp-110) REVERT: D 615 MET cc_start: 0.7877 (mtp) cc_final: 0.7419 (mmm) REVERT: D 617 ARG cc_start: 0.8099 (ttt-90) cc_final: 0.7527 (ttt-90) REVERT: D 666 GLU cc_start: 0.7534 (tt0) cc_final: 0.7152 (mt-10) REVERT: D 675 GLU cc_start: 0.7311 (tp30) cc_final: 0.6970 (tp30) REVERT: D 864 ILE cc_start: 0.7455 (mm) cc_final: 0.6929 (mm) REVERT: D 990 ASP cc_start: 0.7891 (m-30) cc_final: 0.7614 (m-30) REVERT: D 1046 GLU cc_start: 0.7429 (mm-30) cc_final: 0.7180 (pm20) REVERT: D 1076 LEU cc_start: 0.7329 (mt) cc_final: 0.7060 (mp) REVERT: D 1131 MET cc_start: 0.7697 (mmm) cc_final: 0.7330 (mtp) REVERT: D 1284 LYS cc_start: 0.7003 (OUTLIER) cc_final: 0.6496 (mttt) REVERT: D 1314 MET cc_start: 0.6728 (tmm) cc_final: 0.6457 (tpp) outliers start: 98 outliers final: 58 residues processed: 504 average time/residue: 0.6637 time to fit residues: 413.6508 Evaluate side-chains 474 residues out of total 4664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 399 time to evaluate : 1.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 353 LYS Chi-restraints excluded: chain A residue 356 GLN Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 628 ILE Chi-restraints excluded: chain A residue 691 LYS Chi-restraints excluded: chain A residue 1001 THR Chi-restraints excluded: chain A residue 1010 THR Chi-restraints excluded: chain A residue 1076 LEU Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1137 LYS Chi-restraints excluded: chain A residue 1218 VAL Chi-restraints excluded: chain A residue 1251 VAL Chi-restraints excluded: chain A residue 1284 LYS Chi-restraints excluded: chain A residue 1306 ILE Chi-restraints excluded: chain A residue 1365 MET Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 353 LYS Chi-restraints excluded: chain B residue 356 GLN Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 456 MET Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 628 ILE Chi-restraints excluded: chain B residue 1001 THR Chi-restraints excluded: chain B residue 1010 THR Chi-restraints excluded: chain B residue 1076 LEU Chi-restraints excluded: chain B residue 1137 LYS Chi-restraints excluded: chain B residue 1218 VAL Chi-restraints excluded: chain B residue 1251 VAL Chi-restraints excluded: chain B residue 1284 LYS Chi-restraints excluded: chain B residue 1306 ILE Chi-restraints excluded: chain B residue 1331 THR Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain C residue 356 GLN Chi-restraints excluded: chain C residue 372 SER Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 456 MET Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 574 VAL Chi-restraints excluded: chain C residue 628 ILE Chi-restraints excluded: chain C residue 691 LYS Chi-restraints excluded: chain C residue 1001 THR Chi-restraints excluded: chain C residue 1010 THR Chi-restraints excluded: chain C residue 1137 LYS Chi-restraints excluded: chain C residue 1218 VAL Chi-restraints excluded: chain C residue 1251 VAL Chi-restraints excluded: chain C residue 1284 LYS Chi-restraints excluded: chain C residue 1306 ILE Chi-restraints excluded: chain C residue 1331 THR Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain D residue 347 ILE Chi-restraints excluded: chain D residue 356 GLN Chi-restraints excluded: chain D residue 372 SER Chi-restraints excluded: chain D residue 424 LEU Chi-restraints excluded: chain D residue 456 MET Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 628 ILE Chi-restraints excluded: chain D residue 691 LYS Chi-restraints excluded: chain D residue 1001 THR Chi-restraints excluded: chain D residue 1137 LYS Chi-restraints excluded: chain D residue 1218 VAL Chi-restraints excluded: chain D residue 1251 VAL Chi-restraints excluded: chain D residue 1284 LYS Chi-restraints excluded: chain D residue 1306 ILE Chi-restraints excluded: chain D residue 1331 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 544 random chunks: chunk 423 optimal weight: 9.9990 chunk 117 optimal weight: 3.9990 chunk 289 optimal weight: 8.9990 chunk 291 optimal weight: 4.9990 chunk 328 optimal weight: 0.9980 chunk 116 optimal weight: 2.9990 chunk 161 optimal weight: 0.8980 chunk 372 optimal weight: 9.9990 chunk 391 optimal weight: 9.9990 chunk 276 optimal weight: 10.0000 chunk 538 optimal weight: 0.8980 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 440 HIS B 440 HIS C 440 HIS D 440 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.159326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.127446 restraints weight = 57102.049| |-----------------------------------------------------------------------------| r_work (start): 0.3646 rms_B_bonded: 2.01 r_work: 0.3229 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.4319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 41260 Z= 0.167 Angle : 0.557 8.023 56460 Z= 0.285 Chirality : 0.040 0.161 6628 Planarity : 0.004 0.042 7116 Dihedral : 7.912 83.580 6992 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 3.43 % Allowed : 18.28 % Favored : 78.29 % 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 are not related in a simple way. whole: 1.11 (0.11), residues: 5424 helix: 1.83 (0.09), residues: 2988 sheet: -0.98 (0.24), residues: 444 loop : -0.49 (0.14), residues: 1992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 174 TYR 0.022 0.002 TYR C 420 PHE 0.016 0.002 PHE A 971 TRP 0.024 0.002 TRP A 96 HIS 0.005 0.001 HIS C 660 Details of bonding type rmsd covalent geometry : bond 0.00393 (41256) covalent geometry : angle 0.55741 (56452) SS BOND : bond 0.00048 ( 4) SS BOND : angle 0.61251 ( 8) hydrogen bonds : bond 0.04974 ( 2376) hydrogen bonds : angle 4.08628 ( 6972) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10848 Ramachandran restraints generated. 5424 Oldfield, 0 Emsley, 5424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10848 Ramachandran restraints generated. 5424 Oldfield, 0 Emsley, 5424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 4664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 407 time to evaluate : 1.511 Fit side-chains REVERT: A 76 MET cc_start: 0.3982 (mmp) cc_final: 0.3644 (mmt) REVERT: A 215 THR cc_start: 0.7920 (m) cc_final: 0.7586 (p) REVERT: A 266 ASN cc_start: 0.5629 (m-40) cc_final: 0.5213 (t0) REVERT: A 356 GLN cc_start: 0.6964 (OUTLIER) cc_final: 0.6563 (tp40) REVERT: A 398 ASP cc_start: 0.7204 (t70) cc_final: 0.6760 (m-30) REVERT: A 424 LEU cc_start: 0.6629 (OUTLIER) cc_final: 0.6133 (mt) REVERT: A 431 LEU cc_start: 0.6836 (mt) cc_final: 0.6498 (mp) REVERT: A 461 HIS cc_start: 0.6306 (OUTLIER) cc_final: 0.5994 (p90) REVERT: A 506 ARG cc_start: 0.6988 (ttt-90) cc_final: 0.6628 (mmm-85) REVERT: A 561 ASP cc_start: 0.7181 (m-30) cc_final: 0.6829 (t0) REVERT: A 576 ARG cc_start: 0.7005 (mmt180) cc_final: 0.6677 (mmt180) REVERT: A 594 ARG cc_start: 0.6286 (mtp-110) cc_final: 0.5926 (mtp-110) REVERT: A 615 MET cc_start: 0.8005 (mtp) cc_final: 0.7567 (mmm) REVERT: A 617 ARG cc_start: 0.8133 (ttt-90) cc_final: 0.7550 (ttt-90) REVERT: A 638 GLU cc_start: 0.6298 (mt-10) cc_final: 0.5925 (mm-30) REVERT: A 666 GLU cc_start: 0.7667 (tt0) cc_final: 0.7182 (mt-10) REVERT: A 675 GLU cc_start: 0.7321 (tp30) cc_final: 0.7001 (tp30) REVERT: A 864 ILE cc_start: 0.7721 (mm) cc_final: 0.7222 (mm) REVERT: A 990 ASP cc_start: 0.7934 (m-30) cc_final: 0.7652 (m-30) REVERT: A 1046 GLU cc_start: 0.7597 (mm-30) cc_final: 0.7268 (pm20) REVERT: A 1049 GLU cc_start: 0.7975 (mm-30) cc_final: 0.7691 (mm-30) REVERT: A 1131 MET cc_start: 0.7709 (mmm) cc_final: 0.7330 (mtp) REVERT: A 1284 LYS cc_start: 0.6962 (OUTLIER) cc_final: 0.6453 (mttt) REVERT: A 1314 MET cc_start: 0.6996 (tmm) cc_final: 0.6757 (tpp) REVERT: B 76 MET cc_start: 0.4058 (mmp) cc_final: 0.3758 (mmt) REVERT: B 215 THR cc_start: 0.7926 (m) cc_final: 0.7586 (p) REVERT: B 266 ASN cc_start: 0.5624 (m-40) cc_final: 0.5212 (t0) REVERT: B 356 GLN cc_start: 0.6796 (OUTLIER) cc_final: 0.6496 (tp40) REVERT: B 398 ASP cc_start: 0.7217 (t70) cc_final: 0.6756 (m-30) REVERT: B 424 LEU cc_start: 0.6662 (OUTLIER) cc_final: 0.6189 (mt) REVERT: B 431 LEU cc_start: 0.6830 (mt) cc_final: 0.6497 (mp) REVERT: B 506 ARG cc_start: 0.6967 (ttt-90) cc_final: 0.6615 (mmm-85) REVERT: B 561 ASP cc_start: 0.7247 (m-30) cc_final: 0.6906 (t0) REVERT: B 576 ARG cc_start: 0.7000 (mmt180) cc_final: 0.6675 (mmt180) REVERT: B 594 ARG cc_start: 0.6246 (mtp-110) cc_final: 0.5886 (mtp-110) REVERT: B 615 MET cc_start: 0.7994 (mtp) cc_final: 0.7492 (mmm) REVERT: B 617 ARG cc_start: 0.8126 (ttt-90) cc_final: 0.7547 (ttt-90) REVERT: B 638 GLU cc_start: 0.6302 (mt-10) cc_final: 0.5924 (mm-30) REVERT: B 666 GLU cc_start: 0.7665 (tt0) cc_final: 0.7188 (mt-10) REVERT: B 675 GLU cc_start: 0.7330 (tp30) cc_final: 0.7009 (tp30) REVERT: B 864 ILE cc_start: 0.7726 (mm) cc_final: 0.7235 (mm) REVERT: B 990 ASP cc_start: 0.7924 (m-30) cc_final: 0.7642 (m-30) REVERT: B 1049 GLU cc_start: 0.7940 (mm-30) cc_final: 0.7650 (mm-30) REVERT: B 1131 MET cc_start: 0.7676 (mmm) cc_final: 0.7312 (mtp) REVERT: B 1284 LYS cc_start: 0.6999 (OUTLIER) cc_final: 0.6497 (mttt) REVERT: B 1314 MET cc_start: 0.7001 (tmm) cc_final: 0.6692 (tpp) REVERT: C 76 MET cc_start: 0.4054 (mmp) cc_final: 0.3741 (mmt) REVERT: C 215 THR cc_start: 0.7912 (m) cc_final: 0.7571 (p) REVERT: C 266 ASN cc_start: 0.5634 (m-40) cc_final: 0.5208 (t0) REVERT: C 356 GLN cc_start: 0.6835 (OUTLIER) cc_final: 0.6516 (tp40) REVERT: C 398 ASP cc_start: 0.7215 (t70) cc_final: 0.6748 (m-30) REVERT: C 424 LEU cc_start: 0.6616 (OUTLIER) cc_final: 0.6152 (mt) REVERT: C 431 LEU cc_start: 0.6829 (mt) cc_final: 0.6486 (mp) REVERT: C 506 ARG cc_start: 0.6983 (ttt-90) cc_final: 0.6627 (mmm-85) REVERT: C 561 ASP cc_start: 0.7198 (m-30) cc_final: 0.6845 (t0) REVERT: C 576 ARG cc_start: 0.6998 (mmt180) cc_final: 0.6670 (mmt180) REVERT: C 594 ARG cc_start: 0.6265 (mtp-110) cc_final: 0.5910 (mtp-110) REVERT: C 615 MET cc_start: 0.7996 (mtp) cc_final: 0.7556 (mmm) REVERT: C 617 ARG cc_start: 0.8122 (ttt-90) cc_final: 0.7540 (ttt-90) REVERT: C 638 GLU cc_start: 0.6331 (mt-10) cc_final: 0.5944 (mm-30) REVERT: C 666 GLU cc_start: 0.7654 (tt0) cc_final: 0.7173 (mt-10) REVERT: C 675 GLU cc_start: 0.7338 (tp30) cc_final: 0.7011 (tp30) REVERT: C 864 ILE cc_start: 0.7727 (mm) cc_final: 0.7195 (mm) REVERT: C 990 ASP cc_start: 0.7918 (m-30) cc_final: 0.7636 (m-30) REVERT: C 1046 GLU cc_start: 0.7561 (mm-30) cc_final: 0.7248 (pm20) REVERT: C 1076 LEU cc_start: 0.7261 (mt) cc_final: 0.6976 (mp) REVERT: C 1131 MET cc_start: 0.7650 (mmm) cc_final: 0.7288 (mtp) REVERT: C 1284 LYS cc_start: 0.6961 (OUTLIER) cc_final: 0.6458 (mttt) REVERT: C 1314 MET cc_start: 0.6999 (tmm) cc_final: 0.6694 (tpp) REVERT: D 76 MET cc_start: 0.4054 (mmp) cc_final: 0.3746 (mmt) REVERT: D 215 THR cc_start: 0.7919 (m) cc_final: 0.7565 (p) REVERT: D 266 ASN cc_start: 0.5625 (m-40) cc_final: 0.5202 (t0) REVERT: D 356 GLN cc_start: 0.6867 (OUTLIER) cc_final: 0.6515 (tp40) REVERT: D 398 ASP cc_start: 0.7194 (t70) cc_final: 0.6737 (m-30) REVERT: D 424 LEU cc_start: 0.6631 (OUTLIER) cc_final: 0.6122 (mt) REVERT: D 431 LEU cc_start: 0.6836 (mt) cc_final: 0.6496 (mp) REVERT: D 461 HIS cc_start: 0.6355 (OUTLIER) cc_final: 0.6037 (p90) REVERT: D 506 ARG cc_start: 0.6978 (ttt-90) cc_final: 0.6617 (mmm-85) REVERT: D 561 ASP cc_start: 0.7193 (m-30) cc_final: 0.6836 (t0) REVERT: D 576 ARG cc_start: 0.6999 (mmt180) cc_final: 0.6668 (mmt180) REVERT: D 594 ARG cc_start: 0.6271 (mtp-110) cc_final: 0.5917 (mtp-110) REVERT: D 617 ARG cc_start: 0.8118 (ttt-90) cc_final: 0.7535 (ttt-90) REVERT: D 638 GLU cc_start: 0.6283 (mt-10) cc_final: 0.5914 (mm-30) REVERT: D 666 GLU cc_start: 0.7575 (tt0) cc_final: 0.7165 (mt-10) REVERT: D 675 GLU cc_start: 0.7340 (tp30) cc_final: 0.7015 (tp30) REVERT: D 864 ILE cc_start: 0.7719 (mm) cc_final: 0.7222 (mm) REVERT: D 990 ASP cc_start: 0.7907 (m-30) cc_final: 0.7625 (m-30) REVERT: D 1046 GLU cc_start: 0.7530 (mm-30) cc_final: 0.7251 (pm20) REVERT: D 1076 LEU cc_start: 0.7268 (mt) cc_final: 0.6984 (mp) REVERT: D 1131 MET cc_start: 0.7710 (mmm) cc_final: 0.7329 (mtp) REVERT: D 1284 LYS cc_start: 0.6973 (OUTLIER) cc_final: 0.6465 (mttt) REVERT: D 1314 MET cc_start: 0.6911 (tmm) cc_final: 0.6575 (tpp) outliers start: 123 outliers final: 82 residues processed: 511 average time/residue: 0.6946 time to fit residues: 438.0372 Evaluate side-chains 507 residues out of total 4664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 411 time to evaluate : 1.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 353 LYS Chi-restraints excluded: chain A residue 356 GLN Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain A residue 461 HIS Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 628 ILE Chi-restraints excluded: chain A residue 691 LYS Chi-restraints excluded: chain A residue 922 LYS Chi-restraints excluded: chain A residue 1001 THR Chi-restraints excluded: chain A residue 1010 THR Chi-restraints excluded: chain A residue 1044 VAL Chi-restraints excluded: chain A residue 1051 LEU Chi-restraints excluded: chain A residue 1076 LEU Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1137 LYS Chi-restraints excluded: chain A residue 1218 VAL Chi-restraints excluded: chain A residue 1242 SER Chi-restraints excluded: chain A residue 1251 VAL Chi-restraints excluded: chain A residue 1284 LYS Chi-restraints excluded: chain A residue 1365 MET Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 353 LYS Chi-restraints excluded: chain B residue 356 GLN Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 456 MET Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 628 ILE Chi-restraints excluded: chain B residue 641 SER Chi-restraints excluded: chain B residue 922 LYS Chi-restraints excluded: chain B residue 1001 THR Chi-restraints excluded: chain B residue 1010 THR Chi-restraints excluded: chain B residue 1044 VAL Chi-restraints excluded: chain B residue 1051 LEU Chi-restraints excluded: chain B residue 1076 LEU Chi-restraints excluded: chain B residue 1137 LYS Chi-restraints excluded: chain B residue 1218 VAL Chi-restraints excluded: chain B residue 1242 SER Chi-restraints excluded: chain B residue 1251 VAL Chi-restraints excluded: chain B residue 1284 LYS Chi-restraints excluded: chain B residue 1331 THR Chi-restraints excluded: chain B residue 1365 MET Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain C residue 353 LYS Chi-restraints excluded: chain C residue 356 GLN Chi-restraints excluded: chain C residue 372 SER Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 456 MET Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 574 VAL Chi-restraints excluded: chain C residue 628 ILE Chi-restraints excluded: chain C residue 691 LYS Chi-restraints excluded: chain C residue 922 LYS Chi-restraints excluded: chain C residue 1001 THR Chi-restraints excluded: chain C residue 1010 THR Chi-restraints excluded: chain C residue 1044 VAL Chi-restraints excluded: chain C residue 1051 LEU Chi-restraints excluded: chain C residue 1137 LYS Chi-restraints excluded: chain C residue 1218 VAL Chi-restraints excluded: chain C residue 1242 SER Chi-restraints excluded: chain C residue 1251 VAL Chi-restraints excluded: chain C residue 1284 LYS Chi-restraints excluded: chain C residue 1331 THR Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 347 ILE Chi-restraints excluded: chain D residue 356 GLN Chi-restraints excluded: chain D residue 372 SER Chi-restraints excluded: chain D residue 424 LEU Chi-restraints excluded: chain D residue 456 MET Chi-restraints excluded: chain D residue 461 HIS Chi-restraints excluded: chain D residue 463 VAL Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 628 ILE Chi-restraints excluded: chain D residue 691 LYS Chi-restraints excluded: chain D residue 922 LYS Chi-restraints excluded: chain D residue 1001 THR Chi-restraints excluded: chain D residue 1044 VAL Chi-restraints excluded: chain D residue 1051 LEU Chi-restraints excluded: chain D residue 1137 LYS Chi-restraints excluded: chain D residue 1218 VAL Chi-restraints excluded: chain D residue 1242 SER Chi-restraints excluded: chain D residue 1251 VAL Chi-restraints excluded: chain D residue 1284 LYS Chi-restraints excluded: chain D residue 1331 THR Chi-restraints excluded: chain D residue 1365 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 544 random chunks: chunk 135 optimal weight: 6.9990 chunk 352 optimal weight: 3.9990 chunk 453 optimal weight: 10.0000 chunk 23 optimal weight: 6.9990 chunk 457 optimal weight: 3.9990 chunk 13 optimal weight: 10.0000 chunk 77 optimal weight: 3.9990 chunk 339 optimal weight: 5.9990 chunk 373 optimal weight: 1.9990 chunk 208 optimal weight: 0.9990 chunk 360 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 440 HIS B 440 HIS C 440 HIS D 440 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.158310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.127698 restraints weight = 57487.315| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 2.05 r_work: 0.3234 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.4504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 41260 Z= 0.206 Angle : 0.610 9.349 56460 Z= 0.313 Chirality : 0.042 0.174 6628 Planarity : 0.005 0.044 7116 Dihedral : 8.081 83.728 6992 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.77 % Allowed : 18.08 % Favored : 78.15 % 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 are not related in a simple way. whole: 0.78 (0.11), residues: 5424 helix: 1.54 (0.09), residues: 2984 sheet: -1.07 (0.24), residues: 448 loop : -0.60 (0.13), residues: 1992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 69 TYR 0.023 0.002 TYR A 917 PHE 0.017 0.002 PHE A 879 TRP 0.020 0.002 TRP A 96 HIS 0.006 0.001 HIS A 660 Details of bonding type rmsd covalent geometry : bond 0.00490 (41256) covalent geometry : angle 0.61011 (56452) SS BOND : bond 0.00029 ( 4) SS BOND : angle 0.75079 ( 8) hydrogen bonds : bond 0.05546 ( 2376) hydrogen bonds : angle 4.26026 ( 6972) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10848 Ramachandran restraints generated. 5424 Oldfield, 0 Emsley, 5424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10848 Ramachandran restraints generated. 5424 Oldfield, 0 Emsley, 5424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 553 residues out of total 4664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 418 time to evaluate : 1.634 Fit side-chains REVERT: A 76 MET cc_start: 0.4040 (mmp) cc_final: 0.3828 (mmt) REVERT: A 215 THR cc_start: 0.7959 (m) cc_final: 0.7654 (p) REVERT: A 266 ASN cc_start: 0.5579 (m-40) cc_final: 0.5183 (t0) REVERT: A 356 GLN cc_start: 0.6981 (OUTLIER) cc_final: 0.6612 (tp40) REVERT: A 424 LEU cc_start: 0.6660 (OUTLIER) cc_final: 0.6179 (mt) REVERT: A 506 ARG cc_start: 0.6919 (ttt-90) cc_final: 0.6640 (mmm-85) REVERT: A 561 ASP cc_start: 0.7136 (m-30) cc_final: 0.6773 (t0) REVERT: A 576 ARG cc_start: 0.6947 (mmt180) cc_final: 0.6616 (mmt180) REVERT: A 594 ARG cc_start: 0.6387 (mtp-110) cc_final: 0.6128 (ttp-110) REVERT: A 615 MET cc_start: 0.7996 (mtp) cc_final: 0.7522 (mmm) REVERT: A 617 ARG cc_start: 0.8196 (ttt-90) cc_final: 0.7889 (ttp80) REVERT: A 638 GLU cc_start: 0.6354 (mt-10) cc_final: 0.5914 (mt-10) REVERT: A 666 GLU cc_start: 0.7719 (tt0) cc_final: 0.7329 (mt-10) REVERT: A 675 GLU cc_start: 0.7399 (tp30) cc_final: 0.7101 (tp30) REVERT: A 864 ILE cc_start: 0.7762 (mm) cc_final: 0.7264 (mm) REVERT: A 893 GLN cc_start: 0.6844 (tp-100) cc_final: 0.6590 (mm110) REVERT: A 990 ASP cc_start: 0.7839 (m-30) cc_final: 0.7549 (m-30) REVERT: A 1046 GLU cc_start: 0.7705 (mm-30) cc_final: 0.7430 (pm20) REVERT: A 1049 GLU cc_start: 0.7887 (mm-30) cc_final: 0.7597 (mm-30) REVERT: A 1131 MET cc_start: 0.7740 (mmm) cc_final: 0.7366 (mtp) REVERT: A 1314 MET cc_start: 0.7044 (tmm) cc_final: 0.6763 (tpp) REVERT: B 76 MET cc_start: 0.4165 (mmp) cc_final: 0.3823 (mmt) REVERT: B 215 THR cc_start: 0.7962 (m) cc_final: 0.7664 (p) REVERT: B 266 ASN cc_start: 0.5581 (m-40) cc_final: 0.5195 (t0) REVERT: B 356 GLN cc_start: 0.6871 (OUTLIER) cc_final: 0.6580 (tp40) REVERT: B 424 LEU cc_start: 0.6705 (OUTLIER) cc_final: 0.6272 (mt) REVERT: B 461 HIS cc_start: 0.6391 (OUTLIER) cc_final: 0.6090 (p90) REVERT: B 506 ARG cc_start: 0.6889 (ttt-90) cc_final: 0.6626 (mmm-85) REVERT: B 561 ASP cc_start: 0.7170 (m-30) cc_final: 0.6812 (t0) REVERT: B 576 ARG cc_start: 0.6944 (mmt180) cc_final: 0.6599 (mmt180) REVERT: B 594 ARG cc_start: 0.6335 (mtp-110) cc_final: 0.6064 (ttp-110) REVERT: B 615 MET cc_start: 0.8018 (mtp) cc_final: 0.7631 (mmm) REVERT: B 617 ARG cc_start: 0.8186 (ttt-90) cc_final: 0.7875 (ttp80) REVERT: B 638 GLU cc_start: 0.6349 (mt-10) cc_final: 0.5891 (mt-10) REVERT: B 666 GLU cc_start: 0.7690 (tt0) cc_final: 0.7298 (mt-10) REVERT: B 675 GLU cc_start: 0.7413 (tp30) cc_final: 0.7114 (tp30) REVERT: B 864 ILE cc_start: 0.7772 (mm) cc_final: 0.7279 (mm) REVERT: B 893 GLN cc_start: 0.6847 (tp-100) cc_final: 0.6600 (mm110) REVERT: B 990 ASP cc_start: 0.7817 (m-30) cc_final: 0.7528 (m-30) REVERT: B 1049 GLU cc_start: 0.7844 (mm-30) cc_final: 0.7550 (mm-30) REVERT: B 1131 MET cc_start: 0.7741 (mmm) cc_final: 0.7360 (mtp) REVERT: B 1284 LYS cc_start: 0.6935 (OUTLIER) cc_final: 0.6441 (mttt) REVERT: B 1314 MET cc_start: 0.7043 (tmm) cc_final: 0.6772 (tpp) REVERT: C 76 MET cc_start: 0.4120 (mmp) cc_final: 0.3772 (mmt) REVERT: C 215 THR cc_start: 0.7955 (m) cc_final: 0.7658 (p) REVERT: C 266 ASN cc_start: 0.5572 (m-40) cc_final: 0.5172 (t0) REVERT: C 356 GLN cc_start: 0.6885 (OUTLIER) cc_final: 0.6591 (tp40) REVERT: C 424 LEU cc_start: 0.6708 (OUTLIER) cc_final: 0.6279 (mt) REVERT: C 461 HIS cc_start: 0.6373 (OUTLIER) cc_final: 0.6066 (p90) REVERT: C 506 ARG cc_start: 0.6903 (ttt-90) cc_final: 0.6641 (mmm-85) REVERT: C 561 ASP cc_start: 0.7125 (m-30) cc_final: 0.6752 (t0) REVERT: C 576 ARG cc_start: 0.6961 (mmt180) cc_final: 0.6622 (mmt180) REVERT: C 594 ARG cc_start: 0.6340 (mtp-110) cc_final: 0.6077 (ttp-110) REVERT: C 615 MET cc_start: 0.8002 (mtp) cc_final: 0.7537 (mmm) REVERT: C 617 ARG cc_start: 0.8199 (ttt-90) cc_final: 0.7890 (ttp80) REVERT: C 638 GLU cc_start: 0.6377 (mt-10) cc_final: 0.5928 (mt-10) REVERT: C 666 GLU cc_start: 0.7685 (tt0) cc_final: 0.7293 (mt-10) REVERT: C 675 GLU cc_start: 0.7427 (tp30) cc_final: 0.7117 (tp30) REVERT: C 864 ILE cc_start: 0.7777 (mm) cc_final: 0.7283 (mm) REVERT: C 893 GLN cc_start: 0.6795 (tp-100) cc_final: 0.6542 (mm110) REVERT: C 990 ASP cc_start: 0.7829 (m-30) cc_final: 0.7540 (m-30) REVERT: C 1046 GLU cc_start: 0.7701 (mm-30) cc_final: 0.7426 (pm20) REVERT: C 1076 LEU cc_start: 0.7292 (mt) cc_final: 0.7015 (mp) REVERT: C 1131 MET cc_start: 0.7702 (mmm) cc_final: 0.7342 (mtp) REVERT: C 1284 LYS cc_start: 0.6921 (OUTLIER) cc_final: 0.6430 (mttt) REVERT: C 1314 MET cc_start: 0.7010 (tmm) cc_final: 0.6742 (tpp) REVERT: D 76 MET cc_start: 0.4117 (mmp) cc_final: 0.3776 (mmt) REVERT: D 215 THR cc_start: 0.7954 (m) cc_final: 0.7650 (p) REVERT: D 266 ASN cc_start: 0.5579 (m-40) cc_final: 0.5177 (t0) REVERT: D 356 GLN cc_start: 0.6884 (OUTLIER) cc_final: 0.6605 (tp40) REVERT: D 424 LEU cc_start: 0.6667 (OUTLIER) cc_final: 0.6246 (mt) REVERT: D 506 ARG cc_start: 0.6885 (ttt-90) cc_final: 0.6623 (mmm-85) REVERT: D 561 ASP cc_start: 0.7114 (m-30) cc_final: 0.6738 (t0) REVERT: D 576 ARG cc_start: 0.6958 (mmt180) cc_final: 0.6614 (mmt180) REVERT: D 594 ARG cc_start: 0.6349 (mtp-110) cc_final: 0.6089 (ttp-110) REVERT: D 615 MET cc_start: 0.7948 (mtp) cc_final: 0.7493 (mmm) REVERT: D 617 ARG cc_start: 0.8184 (ttt-90) cc_final: 0.7867 (ttp80) REVERT: D 638 GLU cc_start: 0.6337 (mt-10) cc_final: 0.5892 (mt-10) REVERT: D 666 GLU cc_start: 0.7686 (tt0) cc_final: 0.7299 (mt-10) REVERT: D 675 GLU cc_start: 0.7426 (tp30) cc_final: 0.7126 (tp30) REVERT: D 864 ILE cc_start: 0.7771 (mm) cc_final: 0.7276 (mm) REVERT: D 893 GLN cc_start: 0.6835 (tp-100) cc_final: 0.6583 (mm110) REVERT: D 990 ASP cc_start: 0.7833 (m-30) cc_final: 0.7546 (m-30) REVERT: D 1046 GLU cc_start: 0.7669 (mm-30) cc_final: 0.7419 (pm20) REVERT: D 1131 MET cc_start: 0.7776 (mmm) cc_final: 0.7405 (mtp) REVERT: D 1284 LYS cc_start: 0.6936 (OUTLIER) cc_final: 0.6439 (mttt) REVERT: D 1314 MET cc_start: 0.6935 (tmm) cc_final: 0.6639 (tpp) outliers start: 135 outliers final: 94 residues processed: 523 average time/residue: 0.6618 time to fit residues: 428.2594 Evaluate side-chains 517 residues out of total 4664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 410 time to evaluate : 1.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 353 LYS Chi-restraints excluded: chain A residue 356 GLN Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 628 ILE Chi-restraints excluded: chain A residue 641 SER Chi-restraints excluded: chain A residue 691 LYS Chi-restraints excluded: chain A residue 922 LYS Chi-restraints excluded: chain A residue 1001 THR Chi-restraints excluded: chain A residue 1010 THR Chi-restraints excluded: chain A residue 1044 VAL Chi-restraints excluded: chain A residue 1051 LEU Chi-restraints excluded: chain A residue 1076 LEU Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1137 LYS Chi-restraints excluded: chain A residue 1218 VAL Chi-restraints excluded: chain A residue 1242 SER Chi-restraints excluded: chain A residue 1251 VAL Chi-restraints excluded: chain A residue 1365 MET Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 353 LYS Chi-restraints excluded: chain B residue 356 GLN Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 456 MET Chi-restraints excluded: chain B residue 461 HIS Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 628 ILE Chi-restraints excluded: chain B residue 641 SER Chi-restraints excluded: chain B residue 922 LYS Chi-restraints excluded: chain B residue 1001 THR Chi-restraints excluded: chain B residue 1010 THR Chi-restraints excluded: chain B residue 1044 VAL Chi-restraints excluded: chain B residue 1051 LEU Chi-restraints excluded: chain B residue 1076 LEU Chi-restraints excluded: chain B residue 1137 LYS Chi-restraints excluded: chain B residue 1218 VAL Chi-restraints excluded: chain B residue 1242 SER Chi-restraints excluded: chain B residue 1251 VAL Chi-restraints excluded: chain B residue 1284 LYS Chi-restraints excluded: chain B residue 1331 THR Chi-restraints excluded: chain B residue 1365 MET Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain C residue 353 LYS Chi-restraints excluded: chain C residue 356 GLN Chi-restraints excluded: chain C residue 372 SER Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 456 MET Chi-restraints excluded: chain C residue 461 HIS Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 574 VAL Chi-restraints excluded: chain C residue 628 ILE Chi-restraints excluded: chain C residue 641 SER Chi-restraints excluded: chain C residue 691 LYS Chi-restraints excluded: chain C residue 922 LYS Chi-restraints excluded: chain C residue 1001 THR Chi-restraints excluded: chain C residue 1010 THR Chi-restraints excluded: chain C residue 1044 VAL Chi-restraints excluded: chain C residue 1051 LEU Chi-restraints excluded: chain C residue 1137 LYS Chi-restraints excluded: chain C residue 1218 VAL Chi-restraints excluded: chain C residue 1242 SER Chi-restraints excluded: chain C residue 1251 VAL Chi-restraints excluded: chain C residue 1284 LYS Chi-restraints excluded: chain C residue 1331 THR Chi-restraints excluded: chain C residue 1365 MET Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 309 VAL Chi-restraints excluded: chain D residue 347 ILE Chi-restraints excluded: chain D residue 356 GLN Chi-restraints excluded: chain D residue 372 SER Chi-restraints excluded: chain D residue 424 LEU Chi-restraints excluded: chain D residue 456 MET Chi-restraints excluded: chain D residue 463 VAL Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 628 ILE Chi-restraints excluded: chain D residue 641 SER Chi-restraints excluded: chain D residue 691 LYS Chi-restraints excluded: chain D residue 835 ILE Chi-restraints excluded: chain D residue 922 LYS Chi-restraints excluded: chain D residue 1001 THR Chi-restraints excluded: chain D residue 1044 VAL Chi-restraints excluded: chain D residue 1051 LEU Chi-restraints excluded: chain D residue 1137 LYS Chi-restraints excluded: chain D residue 1218 VAL Chi-restraints excluded: chain D residue 1242 SER Chi-restraints excluded: chain D residue 1251 VAL Chi-restraints excluded: chain D residue 1284 LYS Chi-restraints excluded: chain D residue 1331 THR Chi-restraints excluded: chain D residue 1365 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 544 random chunks: chunk 46 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 268 optimal weight: 10.0000 chunk 374 optimal weight: 0.8980 chunk 94 optimal weight: 0.7980 chunk 2 optimal weight: 8.9990 chunk 57 optimal weight: 9.9990 chunk 311 optimal weight: 8.9990 chunk 406 optimal weight: 3.9990 chunk 432 optimal weight: 3.9990 chunk 360 optimal weight: 0.6980 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 440 HIS B 440 HIS C 440 HIS D 440 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.159370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.128824 restraints weight = 57222.778| |-----------------------------------------------------------------------------| r_work (start): 0.3663 rms_B_bonded: 2.03 r_work: 0.3248 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.4495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 41260 Z= 0.153 Angle : 0.555 9.865 56460 Z= 0.282 Chirality : 0.039 0.157 6628 Planarity : 0.004 0.043 7116 Dihedral : 7.927 84.755 6992 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.04 % Allowed : 18.92 % Favored : 78.04 % 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 are not related in a simple way. whole: 1.00 (0.11), residues: 5424 helix: 1.76 (0.09), residues: 2984 sheet: -1.04 (0.25), residues: 448 loop : -0.55 (0.14), residues: 1992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 69 TYR 0.020 0.002 TYR C 420 PHE 0.015 0.002 PHE B 971 TRP 0.025 0.001 TRP D 96 HIS 0.004 0.001 HIS D 660 Details of bonding type rmsd covalent geometry : bond 0.00355 (41256) covalent geometry : angle 0.55468 (56452) SS BOND : bond 0.00055 ( 4) SS BOND : angle 0.57778 ( 8) hydrogen bonds : bond 0.04830 ( 2376) hydrogen bonds : angle 4.09741 ( 6972) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10848 Ramachandran restraints generated. 5424 Oldfield, 0 Emsley, 5424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10848 Ramachandran restraints generated. 5424 Oldfield, 0 Emsley, 5424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 519 residues out of total 4664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 410 time to evaluate : 1.554 Fit side-chains REVERT: A 76 MET cc_start: 0.4189 (mmp) cc_final: 0.3761 (mmt) REVERT: A 215 THR cc_start: 0.7945 (m) cc_final: 0.7608 (p) REVERT: A 266 ASN cc_start: 0.5650 (m-40) cc_final: 0.5246 (t0) REVERT: A 274 PHE cc_start: 0.7371 (t80) cc_final: 0.7080 (t80) REVERT: A 356 GLN cc_start: 0.6936 (OUTLIER) cc_final: 0.6607 (tp40) REVERT: A 398 ASP cc_start: 0.7197 (t70) cc_final: 0.6805 (m-30) REVERT: A 424 LEU cc_start: 0.6634 (OUTLIER) cc_final: 0.6143 (mt) REVERT: A 431 LEU cc_start: 0.6799 (mt) cc_final: 0.6500 (mp) REVERT: A 506 ARG cc_start: 0.6976 (ttt-90) cc_final: 0.6671 (mmm-85) REVERT: A 561 ASP cc_start: 0.7149 (m-30) cc_final: 0.6824 (t0) REVERT: A 576 ARG cc_start: 0.6827 (mmt180) cc_final: 0.6550 (mmt180) REVERT: A 594 ARG cc_start: 0.6316 (mtp-110) cc_final: 0.5852 (mtp-110) REVERT: A 615 MET cc_start: 0.7986 (mtp) cc_final: 0.7537 (mmm) REVERT: A 617 ARG cc_start: 0.8149 (ttt-90) cc_final: 0.7589 (ttt-90) REVERT: A 666 GLU cc_start: 0.7575 (tt0) cc_final: 0.7184 (mt-10) REVERT: A 675 GLU cc_start: 0.7347 (tp30) cc_final: 0.7026 (tp30) REVERT: A 694 MET cc_start: 0.6338 (ptm) cc_final: 0.5979 (OUTLIER) REVERT: A 864 ILE cc_start: 0.7735 (mm) cc_final: 0.7221 (mm) REVERT: A 990 ASP cc_start: 0.7854 (m-30) cc_final: 0.7563 (m-30) REVERT: A 1049 GLU cc_start: 0.7814 (mm-30) cc_final: 0.7501 (mm-30) REVERT: A 1131 MET cc_start: 0.7695 (mmm) cc_final: 0.7311 (mtp) REVERT: B 76 MET cc_start: 0.4396 (mmp) cc_final: 0.4047 (mmt) REVERT: B 215 THR cc_start: 0.7950 (m) cc_final: 0.7602 (p) REVERT: B 266 ASN cc_start: 0.5612 (m-40) cc_final: 0.5221 (t0) REVERT: B 356 GLN cc_start: 0.6834 (OUTLIER) cc_final: 0.6595 (tp40) REVERT: B 398 ASP cc_start: 0.7218 (t70) cc_final: 0.6792 (m-30) REVERT: B 424 LEU cc_start: 0.6680 (OUTLIER) cc_final: 0.6262 (mt) REVERT: B 431 LEU cc_start: 0.6765 (mt) cc_final: 0.6460 (mp) REVERT: B 506 ARG cc_start: 0.6922 (ttt-90) cc_final: 0.6632 (mmm-85) REVERT: B 561 ASP cc_start: 0.7183 (m-30) cc_final: 0.6852 (t0) REVERT: B 576 ARG cc_start: 0.6852 (mmt180) cc_final: 0.6537 (mmt180) REVERT: B 594 ARG cc_start: 0.6277 (mtp-110) cc_final: 0.5909 (mtp-110) REVERT: B 617 ARG cc_start: 0.8140 (ttt-90) cc_final: 0.7579 (ttt-90) REVERT: B 638 GLU cc_start: 0.6351 (mt-10) cc_final: 0.5963 (mm-30) REVERT: B 666 GLU cc_start: 0.7552 (tt0) cc_final: 0.7166 (mt-10) REVERT: B 675 GLU cc_start: 0.7359 (tp30) cc_final: 0.7039 (tp30) REVERT: B 694 MET cc_start: 0.6345 (ptm) cc_final: 0.6006 (OUTLIER) REVERT: B 864 ILE cc_start: 0.7737 (mm) cc_final: 0.7228 (mm) REVERT: B 990 ASP cc_start: 0.7842 (m-30) cc_final: 0.7554 (m-30) REVERT: B 1049 GLU cc_start: 0.7776 (mm-30) cc_final: 0.7464 (mm-30) REVERT: B 1131 MET cc_start: 0.7684 (mmm) cc_final: 0.7300 (mtp) REVERT: B 1238 MET cc_start: 0.7485 (ptp) cc_final: 0.7234 (ptp) REVERT: B 1314 MET cc_start: 0.7027 (tmm) cc_final: 0.6751 (tpp) REVERT: C 76 MET cc_start: 0.4518 (mmp) cc_final: 0.4200 (mmt) REVERT: C 215 THR cc_start: 0.7942 (m) cc_final: 0.7607 (p) REVERT: C 266 ASN cc_start: 0.5615 (m-40) cc_final: 0.5217 (t0) REVERT: C 356 GLN cc_start: 0.6830 (OUTLIER) cc_final: 0.6577 (tp40) REVERT: C 398 ASP cc_start: 0.7273 (t70) cc_final: 0.6841 (m-30) REVERT: C 424 LEU cc_start: 0.6680 (OUTLIER) cc_final: 0.6249 (mt) REVERT: C 431 LEU cc_start: 0.6789 (mt) cc_final: 0.6503 (mp) REVERT: C 506 ARG cc_start: 0.6931 (ttt-90) cc_final: 0.6641 (mmm-85) REVERT: C 561 ASP cc_start: 0.7161 (m-30) cc_final: 0.6833 (t0) REVERT: C 576 ARG cc_start: 0.6827 (mmt180) cc_final: 0.6536 (mmt180) REVERT: C 594 ARG cc_start: 0.6311 (mtp-110) cc_final: 0.5938 (mtp-110) REVERT: C 615 MET cc_start: 0.7980 (mtp) cc_final: 0.7532 (mmm) REVERT: C 617 ARG cc_start: 0.8144 (ttt-90) cc_final: 0.7581 (ttt-90) REVERT: C 638 GLU cc_start: 0.6378 (mt-10) cc_final: 0.5963 (mm-30) REVERT: C 666 GLU cc_start: 0.7553 (tt0) cc_final: 0.7167 (mt-10) REVERT: C 675 GLU cc_start: 0.7370 (tp30) cc_final: 0.7054 (tp30) REVERT: C 694 MET cc_start: 0.6346 (ptm) cc_final: 0.5998 (OUTLIER) REVERT: C 864 ILE cc_start: 0.7737 (mm) cc_final: 0.7228 (mm) REVERT: C 990 ASP cc_start: 0.7823 (m-30) cc_final: 0.7535 (m-30) REVERT: C 1076 LEU cc_start: 0.7300 (mt) cc_final: 0.7037 (mp) REVERT: C 1131 MET cc_start: 0.7645 (mmm) cc_final: 0.7282 (mtp) REVERT: C 1238 MET cc_start: 0.7455 (ptp) cc_final: 0.7214 (ptp) REVERT: C 1284 LYS cc_start: 0.6937 (OUTLIER) cc_final: 0.6451 (mttt) REVERT: C 1314 MET cc_start: 0.7005 (tmm) cc_final: 0.6734 (tpp) REVERT: D 76 MET cc_start: 0.4515 (mmp) cc_final: 0.4195 (mmt) REVERT: D 215 THR cc_start: 0.7947 (m) cc_final: 0.7593 (p) REVERT: D 266 ASN cc_start: 0.5633 (m-40) cc_final: 0.5227 (t0) REVERT: D 356 GLN cc_start: 0.6856 (OUTLIER) cc_final: 0.6605 (tp40) REVERT: D 424 LEU cc_start: 0.6686 (OUTLIER) cc_final: 0.6269 (mt) REVERT: D 431 LEU cc_start: 0.6796 (mt) cc_final: 0.6513 (mp) REVERT: D 506 ARG cc_start: 0.6902 (ttt-90) cc_final: 0.6631 (mmm-85) REVERT: D 561 ASP cc_start: 0.7154 (m-30) cc_final: 0.6820 (t0) REVERT: D 576 ARG cc_start: 0.6826 (mmt180) cc_final: 0.6534 (mmt180) REVERT: D 594 ARG cc_start: 0.6309 (mtp-110) cc_final: 0.5858 (mtp-110) REVERT: D 615 MET cc_start: 0.7955 (mtp) cc_final: 0.7516 (mmm) REVERT: D 617 ARG cc_start: 0.8142 (ttt-90) cc_final: 0.7578 (ttt-90) REVERT: D 638 GLU cc_start: 0.6347 (mt-10) cc_final: 0.5967 (mm-30) REVERT: D 666 GLU cc_start: 0.7556 (tt0) cc_final: 0.7168 (mt-10) REVERT: D 675 GLU cc_start: 0.7374 (tp30) cc_final: 0.7066 (tp30) REVERT: D 694 MET cc_start: 0.6352 (ptm) cc_final: 0.6010 (OUTLIER) REVERT: D 864 ILE cc_start: 0.7758 (mm) cc_final: 0.7267 (mm) REVERT: D 990 ASP cc_start: 0.7833 (m-30) cc_final: 0.7545 (m-30) REVERT: D 1076 LEU cc_start: 0.7242 (mt) cc_final: 0.6987 (mp) REVERT: D 1131 MET cc_start: 0.7712 (mmm) cc_final: 0.7321 (mtp) REVERT: D 1284 LYS cc_start: 0.6952 (OUTLIER) cc_final: 0.6459 (mttt) REVERT: D 1314 MET cc_start: 0.6850 (tmm) cc_final: 0.6594 (tpp) outliers start: 109 outliers final: 90 residues processed: 502 average time/residue: 0.6447 time to fit residues: 401.0156 Evaluate side-chains 501 residues out of total 4664 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 405 time to evaluate : 1.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 353 LYS Chi-restraints excluded: chain A residue 356 GLN Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 456 MET Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 628 ILE Chi-restraints excluded: chain A residue 641 SER Chi-restraints excluded: chain A residue 691 LYS Chi-restraints excluded: chain A residue 907 VAL Chi-restraints excluded: chain A residue 922 LYS Chi-restraints excluded: chain A residue 1001 THR Chi-restraints excluded: chain A residue 1010 THR Chi-restraints excluded: chain A residue 1044 VAL Chi-restraints excluded: chain A residue 1076 LEU Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1137 LYS Chi-restraints excluded: chain A residue 1218 VAL Chi-restraints excluded: chain A residue 1251 VAL Chi-restraints excluded: chain A residue 1365 MET Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 353 LYS Chi-restraints excluded: chain B residue 356 GLN Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 424 LEU Chi-restraints excluded: chain B residue 456 MET Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 628 ILE Chi-restraints excluded: chain B residue 922 LYS Chi-restraints excluded: chain B residue 1001 THR Chi-restraints excluded: chain B residue 1010 THR Chi-restraints excluded: chain B residue 1044 VAL Chi-restraints excluded: chain B residue 1076 LEU Chi-restraints excluded: chain B residue 1137 LYS Chi-restraints excluded: chain B residue 1218 VAL Chi-restraints excluded: chain B residue 1251 VAL Chi-restraints excluded: chain B residue 1331 THR Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 181 THR Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 347 ILE Chi-restraints excluded: chain C residue 353 LYS Chi-restraints excluded: chain C residue 356 GLN Chi-restraints excluded: chain C residue 372 SER Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 456 MET Chi-restraints excluded: chain C residue 463 VAL Chi-restraints excluded: chain C residue 574 VAL Chi-restraints excluded: chain C residue 628 ILE Chi-restraints excluded: chain C residue 641 SER Chi-restraints excluded: chain C residue 691 LYS Chi-restraints excluded: chain C residue 922 LYS Chi-restraints excluded: chain C residue 1001 THR Chi-restraints excluded: chain C residue 1010 THR Chi-restraints excluded: chain C residue 1044 VAL Chi-restraints excluded: chain C residue 1051 LEU Chi-restraints excluded: chain C residue 1137 LYS Chi-restraints excluded: chain C residue 1138 MET Chi-restraints excluded: chain C residue 1218 VAL Chi-restraints excluded: chain C residue 1251 VAL Chi-restraints excluded: chain C residue 1284 LYS Chi-restraints excluded: chain C residue 1331 THR Chi-restraints excluded: chain C residue 1365 MET Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 175 THR Chi-restraints excluded: chain D residue 181 THR Chi-restraints excluded: chain D residue 309 VAL Chi-restraints excluded: chain D residue 347 ILE Chi-restraints excluded: chain D residue 356 GLN Chi-restraints excluded: chain D residue 372 SER Chi-restraints excluded: chain D residue 424 LEU Chi-restraints excluded: chain D residue 456 MET Chi-restraints excluded: chain D residue 463 VAL Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 628 ILE Chi-restraints excluded: chain D residue 641 SER Chi-restraints excluded: chain D residue 691 LYS Chi-restraints excluded: chain D residue 907 VAL Chi-restraints excluded: chain D residue 922 LYS Chi-restraints excluded: chain D residue 1001 THR Chi-restraints excluded: chain D residue 1044 VAL Chi-restraints excluded: chain D residue 1051 LEU Chi-restraints excluded: chain D residue 1137 LYS Chi-restraints excluded: chain D residue 1218 VAL Chi-restraints excluded: chain D residue 1251 VAL Chi-restraints excluded: chain D residue 1284 LYS Chi-restraints excluded: chain D residue 1331 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 544 random chunks: chunk 230 optimal weight: 2.9990 chunk 27 optimal weight: 7.9990 chunk 91 optimal weight: 1.9990 chunk 192 optimal weight: 0.9990 chunk 166 optimal weight: 10.0000 chunk 209 optimal weight: 5.9990 chunk 52 optimal weight: 5.9990 chunk 336 optimal weight: 1.9990 chunk 297 optimal weight: 8.9990 chunk 113 optimal weight: 4.9990 chunk 23 optimal weight: 0.7980 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 440 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.159515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.128516 restraints weight = 57343.146| |-----------------------------------------------------------------------------| r_work (start): 0.3655 rms_B_bonded: 2.03 r_work: 0.3228 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.4569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 41260 Z= 0.159 Angle : 0.562 9.580 56460 Z= 0.286 Chirality : 0.040 0.160 6628 Planarity : 0.004 0.043 7116 Dihedral : 7.919 84.507 6992 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.15 % Allowed : 18.97 % Favored : 77.87 % 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 are not related in a simple way. whole: 0.99 (0.11), residues: 5424 helix: 1.73 (0.09), residues: 2984 sheet: -1.02 (0.25), residues: 448 loop : -0.54 (0.14), residues: 1992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 69 TYR 0.021 0.002 TYR B 917 PHE 0.022 0.002 PHE D 75 TRP 0.025 0.002 TRP D 96 HIS 0.005 0.001 HIS D 660 Details of bonding type rmsd covalent geometry : bond 0.00371 (41256) covalent geometry : angle 0.56227 (56452) SS BOND : bond 0.00045 ( 4) SS BOND : angle 0.58660 ( 8) hydrogen bonds : bond 0.04906 ( 2376) hydrogen bonds : angle 4.09361 ( 6972) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12296.09 seconds wall clock time: 210 minutes 22.31 seconds (12622.31 seconds total)