Starting phenix.real_space_refine on Tue Aug 26 18:05:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sr8_40722/08_2025/8sr8_40722.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sr8_40722/08_2025/8sr8_40722.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8sr8_40722/08_2025/8sr8_40722.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sr8_40722/08_2025/8sr8_40722.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8sr8_40722/08_2025/8sr8_40722.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sr8_40722/08_2025/8sr8_40722.map" } resolution = 2.77 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= 0.181 sd= 1.441 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: 4 Type Number sf(0) Gaussians S 196 5.16 5 C 25316 2.51 5 N 6768 2.21 5 O 6968 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 39248 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 9728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1353, 9728 Classifications: {'peptide': 1353} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 290} Link IDs: {'PCIS': 2, 'PTRANS': 53, 'TRANS': 1297} Chain breaks: 4 Unresolved non-hydrogen bonds: 1055 Unresolved non-hydrogen angles: 1323 Unresolved non-hydrogen dihedrals: 876 Unresolved non-hydrogen chiralities: 58 Planarities with less than four sites: {'ARG:plan': 25, 'GLN:plan1': 14, 'GLU:plan': 34, 'ASP:plan': 43, 'HIS:plan': 7, 'ASN:plan1': 17, 'TYR:plan': 7, 'PHE:plan': 6, 'TRP:plan': 6} Unresolved non-hydrogen planarities: 671 Chain: "B" Number of atoms: 9728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1353, 9728 Classifications: {'peptide': 1353} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 290} Link IDs: {'PCIS': 2, 'PTRANS': 53, 'TRANS': 1297} Chain breaks: 4 Unresolved non-hydrogen bonds: 1055 Unresolved non-hydrogen angles: 1323 Unresolved non-hydrogen dihedrals: 876 Unresolved non-hydrogen chiralities: 58 Planarities with less than four sites: {'ARG:plan': 25, 'GLN:plan1': 14, 'GLU:plan': 34, 'ASP:plan': 43, 'HIS:plan': 7, 'ASN:plan1': 17, 'TYR:plan': 7, 'PHE:plan': 6, 'TRP:plan': 6} Unresolved non-hydrogen planarities: 671 Chain: "C" Number of atoms: 9728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1353, 9728 Classifications: {'peptide': 1353} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 290} Link IDs: {'PCIS': 2, 'PTRANS': 53, 'TRANS': 1297} Chain breaks: 4 Unresolved non-hydrogen bonds: 1055 Unresolved non-hydrogen angles: 1323 Unresolved non-hydrogen dihedrals: 876 Unresolved non-hydrogen chiralities: 58 Planarities with less than four sites: {'ARG:plan': 25, 'GLN:plan1': 14, 'GLU:plan': 34, 'ASP:plan': 43, 'HIS:plan': 7, 'ASN:plan1': 17, 'TYR:plan': 7, 'PHE:plan': 6, 'TRP:plan': 6} Unresolved non-hydrogen planarities: 671 Chain: "D" Number of atoms: 9728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1353, 9728 Classifications: {'peptide': 1353} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 290} Link IDs: {'PCIS': 2, 'PTRANS': 53, 'TRANS': 1297} Chain breaks: 4 Unresolved non-hydrogen bonds: 1055 Unresolved non-hydrogen angles: 1323 Unresolved non-hydrogen dihedrals: 876 Unresolved non-hydrogen chiralities: 58 Planarities with less than four sites: {'ARG:plan': 25, 'GLN:plan1': 14, 'GLU:plan': 34, 'ASP:plan': 43, 'HIS:plan': 7, 'ASN:plan1': 17, 'TYR:plan': 7, 'PHE:plan': 6, 'TRP:plan': 6} Unresolved non-hydrogen planarities: 671 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 84 Unusual residues: {'CLR': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 84 Unusual residues: {'CLR': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 84 Unusual residues: {'CLR': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 84 Unusual residues: {'CLR': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 9.72, per 1000 atoms: 0.25 Number of scatterers: 39248 At special positions: 0 Unit cell: (158.248, 158.248, 187.592, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 196 16.00 O 6968 8.00 N 6768 7.00 C 25316 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: 2.98 Conformation dependent library (CDL) restraints added in 1.8 seconds Enol-peptide restraints added in 715.3 nanoseconds 10744 Ramachandran restraints generated. 5372 Oldfield, 0 Emsley, 5372 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10184 Finding SS restraints... Secondary structure from input PDB file: 240 helices and 36 sheets defined 61.0% alpha, 9.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.96 Creating SS restraints... Processing helix chain 'A' and resid 72 through 77 removed outlier: 3.874A pdb=" N LYS A 77 " --> pdb=" O GLN A 73 " (cutoff:3.500A) 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: 3.530A pdb=" N LYS A 190 " --> pdb=" O THR A 186 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ALA A 198 " --> pdb=" O GLN A 194 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU A 199 " --> pdb=" O ILE A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 219 No H-bonds generated for 'chain 'A' and resid 217 through 219' Processing helix chain 'A' and resid 221 through 227 Processing helix chain 'A' and resid 271 through 287 Processing helix chain 'A' and resid 298 through 311 removed outlier: 3.721A pdb=" N LEU A 302 " --> pdb=" O GLY A 298 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLY A 303 " --> pdb=" O PRO A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 337 Processing helix chain 'A' and resid 339 through 343 Processing helix chain 'A' and resid 346 through 359 Processing helix chain 'A' and resid 362 through 377 removed outlier: 3.993A pdb=" N VAL A 377 " --> pdb=" O ALA A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 408 Processing helix chain 'A' and resid 410 through 421 removed outlier: 3.594A pdb=" N LYS A 414 " --> pdb=" O LYS A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 437 Processing helix chain 'A' and resid 439 through 457 removed outlier: 4.673A pdb=" N ASN A 448 " --> pdb=" O ALA A 444 " (cutoff:3.500A) removed outlier: 5.345A 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: 3.777A pdb=" N LEU A 476 " --> pdb=" O ILE A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 492 Processing helix chain 'A' and resid 494 through 509 removed outlier: 3.577A pdb=" N LEU A 498 " --> pdb=" O PRO A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 523 removed outlier: 3.842A pdb=" N ARG A 517 " --> pdb=" O SER A 513 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ASN A 523 " --> pdb=" O VAL A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 553 Processing helix chain 'A' and resid 556 through 569 removed outlier: 3.504A pdb=" N MET A 560 " --> pdb=" O ASN A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 586 removed outlier: 4.007A pdb=" N ILE A 580 " --> pdb=" O ASP A 577 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TYR A 581 " --> pdb=" O PHE A 578 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N SER A 583 " --> pdb=" O ILE A 580 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N LYS A 584 " --> pdb=" O TYR A 581 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASP A 586 " --> pdb=" O SER A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 590 through 610 Processing helix chain 'A' and resid 612 through 623 Processing helix chain 'A' and resid 625 through 642 removed outlier: 3.763A pdb=" N THR A 642 " --> pdb=" O GLU A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 643 through 647 removed outlier: 3.711A pdb=" N GLN A 647 " --> pdb=" O ARG A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 651 through 680 removed outlier: 4.056A pdb=" N LEU A 673 " --> pdb=" O ALA A 669 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 689 Processing helix chain 'A' and resid 692 through 696 removed outlier: 3.570A pdb=" N PHE A 695 " --> pdb=" O ASN A 692 " (cutoff:3.500A) removed outlier: 3.651A 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 726 Processing helix chain 'A' and resid 727 through 729 No H-bonds generated for 'chain 'A' and resid 727 through 729' Processing helix chain 'A' and resid 735 through 745 removed outlier: 3.540A pdb=" N VAL A 739 " --> pdb=" O SER A 735 " (cutoff:3.500A) Processing helix chain 'A' and resid 745 through 750 removed outlier: 3.644A pdb=" N VAL A 749 " --> pdb=" O PHE A 745 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU A 750 " --> pdb=" O PRO A 746 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 745 through 750' Processing helix chain 'A' and resid 788 through 799 removed outlier: 3.706A pdb=" N ARG A 793 " --> pdb=" O HIS A 789 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 826 Processing helix chain 'A' and resid 833 through 857 Processing helix chain 'A' and resid 859 through 866 removed outlier: 3.825A pdb=" N ASP A 866 " --> pdb=" O GLU A 862 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 889 removed outlier: 3.687A pdb=" N ARG A 870 " --> pdb=" O ASP A 866 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ASP A 889 " --> pdb=" O THR A 885 " (cutoff:3.500A) Processing helix chain 'A' and resid 892 through 914 removed outlier: 4.056A pdb=" N PHE A 905 " --> pdb=" O GLY A 901 " (cutoff:3.500A) Processing helix chain 'A' and resid 915 through 921 removed outlier: 3.924A pdb=" N LEU A 920 " --> pdb=" O TYR A 917 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 961 removed outlier: 4.005A pdb=" N LYS A 927 " --> pdb=" O ASN A 923 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N LYS A 936 " --> pdb=" O MET A 932 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N ASP A 937 " --> pdb=" O GLU A 933 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ILE A 947 " --> pdb=" O PHE A 943 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N PHE A 948 " --> pdb=" O LEU A 944 " (cutoff:3.500A) Processing helix chain 'A' and resid 967 through 981 removed outlier: 3.688A pdb=" N PHE A 971 " --> pdb=" O SER A 967 " (cutoff:3.500A) removed outlier: 4.550A 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: 3.766A pdb=" N LEU A1023 " --> pdb=" O ALA A1019 " (cutoff:3.500A) Processing helix chain 'A' and resid 1028 through 1066 removed outlier: 5.675A pdb=" N GLU A1046 " --> pdb=" O MET A1042 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N ALA A1047 " --> pdb=" O LYS A1043 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N TYR A1057 " --> pdb=" O ARG A1053 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASP A1065 " --> pdb=" O ALA A1061 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG A1066 " --> pdb=" O GLU A1062 " (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: 3.894A 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 1167 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 removed outlier: 3.550A pdb=" N ARG A1452 " --> pdb=" O HIS A1449 " (cutoff:3.500A) Processing helix chain 'A' and resid 1478 through 1491 removed outlier: 3.565A pdb=" N LEU A1482 " --> pdb=" O SER A1478 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 77 removed outlier: 3.874A pdb=" N LYS B 77 " --> pdb=" O GLN B 73 " (cutoff:3.500A) 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: 3.530A pdb=" N LYS B 190 " --> pdb=" O THR B 186 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ALA B 198 " --> pdb=" O GLN B 194 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU B 199 " --> pdb=" O ILE B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 219 No H-bonds generated for 'chain 'B' and resid 217 through 219' Processing helix chain 'B' and resid 221 through 227 Processing helix chain 'B' and resid 271 through 287 Processing helix chain 'B' and resid 298 through 311 removed outlier: 3.721A pdb=" N LEU B 302 " --> pdb=" O GLY B 298 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLY B 303 " --> pdb=" O PRO B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 337 Processing helix chain 'B' and resid 339 through 343 Processing helix chain 'B' and resid 346 through 359 Processing helix chain 'B' and resid 362 through 377 removed outlier: 3.992A pdb=" N VAL B 377 " --> pdb=" O ALA B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 408 Processing helix chain 'B' and resid 410 through 421 removed outlier: 3.594A pdb=" N LYS B 414 " --> pdb=" O LYS B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 437 Processing helix chain 'B' and resid 439 through 457 removed outlier: 4.673A pdb=" N ASN B 448 " --> pdb=" O ALA B 444 " (cutoff:3.500A) removed outlier: 5.345A 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: 3.777A pdb=" N LEU B 476 " --> pdb=" O ILE B 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 492 Processing helix chain 'B' and resid 494 through 509 removed outlier: 3.577A pdb=" N LEU B 498 " --> pdb=" O PRO B 494 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 523 removed outlier: 3.842A pdb=" N ARG B 517 " --> pdb=" O SER B 513 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ASN B 523 " --> pdb=" O VAL B 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 553 Processing helix chain 'B' and resid 556 through 569 removed outlier: 3.504A pdb=" N MET B 560 " --> pdb=" O ASN B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 577 through 586 removed outlier: 4.007A pdb=" N ILE B 580 " --> pdb=" O ASP B 577 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TYR B 581 " --> pdb=" O PHE B 578 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N SER B 583 " --> pdb=" O ILE B 580 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N LYS B 584 " --> pdb=" O TYR B 581 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASP B 586 " --> pdb=" O SER B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 590 through 610 Processing helix chain 'B' and resid 612 through 623 Processing helix chain 'B' and resid 625 through 642 removed outlier: 3.763A pdb=" N THR B 642 " --> pdb=" O GLU B 638 " (cutoff:3.500A) Processing helix chain 'B' and resid 643 through 647 removed outlier: 3.711A pdb=" N GLN B 647 " --> pdb=" O ARG B 644 " (cutoff:3.500A) Processing helix chain 'B' and resid 651 through 680 removed outlier: 4.055A pdb=" N LEU B 673 " --> pdb=" O ALA B 669 " (cutoff:3.500A) Processing helix chain 'B' and resid 680 through 689 Processing helix chain 'B' and resid 692 through 696 removed outlier: 3.570A pdb=" N PHE B 695 " --> pdb=" O ASN B 692 " (cutoff:3.500A) removed outlier: 3.651A 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 726 Processing helix chain 'B' and resid 727 through 729 No H-bonds generated for 'chain 'B' and resid 727 through 729' Processing helix chain 'B' and resid 735 through 745 removed outlier: 3.540A pdb=" N VAL B 739 " --> pdb=" O SER B 735 " (cutoff:3.500A) Processing helix chain 'B' and resid 745 through 750 removed outlier: 3.644A pdb=" N VAL B 749 " --> pdb=" O PHE B 745 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU B 750 " --> pdb=" O PRO B 746 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 745 through 750' Processing helix chain 'B' and resid 788 through 799 removed outlier: 3.706A pdb=" N ARG B 793 " --> pdb=" O HIS B 789 " (cutoff:3.500A) Processing helix chain 'B' and resid 801 through 826 Processing helix chain 'B' and resid 833 through 857 Processing helix chain 'B' and resid 859 through 866 removed outlier: 3.824A pdb=" N ASP B 866 " --> pdb=" O GLU B 862 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 889 removed outlier: 3.687A pdb=" N ARG B 870 " --> pdb=" O ASP B 866 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ASP B 889 " --> pdb=" O THR B 885 " (cutoff:3.500A) Processing helix chain 'B' and resid 892 through 914 removed outlier: 4.056A pdb=" N PHE B 905 " --> pdb=" O GLY B 901 " (cutoff:3.500A) Processing helix chain 'B' and resid 915 through 921 removed outlier: 3.924A pdb=" N LEU B 920 " --> pdb=" O TYR B 917 " (cutoff:3.500A) Processing helix chain 'B' and resid 923 through 961 removed outlier: 4.005A pdb=" N LYS B 927 " --> pdb=" O ASN B 923 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N LYS B 936 " --> pdb=" O MET B 932 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N ASP B 937 " --> pdb=" O GLU B 933 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ILE B 947 " --> pdb=" O PHE B 943 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N PHE B 948 " --> pdb=" O LEU B 944 " (cutoff:3.500A) Processing helix chain 'B' and resid 967 through 981 removed outlier: 3.689A pdb=" N PHE B 971 " --> pdb=" O SER B 967 " (cutoff:3.500A) removed outlier: 4.550A 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: 3.766A pdb=" N LEU B1023 " --> pdb=" O ALA B1019 " (cutoff:3.500A) Processing helix chain 'B' and resid 1028 through 1066 removed outlier: 5.675A pdb=" N GLU B1046 " --> pdb=" O MET B1042 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N ALA B1047 " --> pdb=" O LYS B1043 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N TYR B1057 " --> pdb=" O ARG B1053 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASP B1065 " --> pdb=" O ALA B1061 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG B1066 " --> pdb=" O GLU B1062 " (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: 3.894A 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 1167 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 removed outlier: 3.550A pdb=" N ARG B1452 " --> pdb=" O HIS B1449 " (cutoff:3.500A) Processing helix chain 'B' and resid 1478 through 1491 removed outlier: 3.564A pdb=" N LEU B1482 " --> pdb=" O SER B1478 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 77 removed outlier: 3.875A pdb=" N LYS C 77 " --> pdb=" O GLN C 73 " (cutoff:3.500A) 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: 3.530A pdb=" N LYS C 190 " --> pdb=" O THR C 186 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ALA C 198 " --> pdb=" O GLN C 194 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU C 199 " --> pdb=" O ILE C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 219 No H-bonds generated for 'chain 'C' and resid 217 through 219' Processing helix chain 'C' and resid 221 through 227 Processing helix chain 'C' and resid 271 through 287 Processing helix chain 'C' and resid 298 through 311 removed outlier: 3.722A pdb=" N LEU C 302 " --> pdb=" O GLY C 298 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLY C 303 " --> pdb=" O PRO C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 337 Processing helix chain 'C' and resid 339 through 343 Processing helix chain 'C' and resid 346 through 359 Processing helix chain 'C' and resid 362 through 377 removed outlier: 3.992A pdb=" N VAL C 377 " --> pdb=" O ALA C 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 395 through 408 Processing helix chain 'C' and resid 410 through 421 removed outlier: 3.594A pdb=" N LYS C 414 " --> pdb=" O LYS C 410 " (cutoff:3.500A) Processing helix chain 'C' and resid 423 through 437 Processing helix chain 'C' and resid 439 through 457 removed outlier: 4.673A pdb=" N ASN C 448 " --> pdb=" O ALA C 444 " (cutoff:3.500A) removed outlier: 5.345A 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: 3.777A pdb=" N LEU C 476 " --> pdb=" O ILE C 473 " (cutoff:3.500A) Processing helix chain 'C' and resid 487 through 492 Processing helix chain 'C' and resid 494 through 509 removed outlier: 3.577A pdb=" N LEU C 498 " --> pdb=" O PRO C 494 " (cutoff:3.500A) Processing helix chain 'C' and resid 513 through 523 removed outlier: 3.843A pdb=" N ARG C 517 " --> pdb=" O SER C 513 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ASN C 523 " --> pdb=" O VAL C 519 " (cutoff:3.500A) Processing helix chain 'C' and resid 547 through 553 Processing helix chain 'C' and resid 556 through 569 removed outlier: 3.505A pdb=" N MET C 560 " --> pdb=" O ASN C 556 " (cutoff:3.500A) Processing helix chain 'C' and resid 577 through 586 removed outlier: 4.007A pdb=" N ILE C 580 " --> pdb=" O ASP C 577 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TYR C 581 " --> pdb=" O PHE C 578 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N SER C 583 " --> pdb=" O ILE C 580 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N LYS C 584 " --> pdb=" O TYR C 581 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASP C 586 " --> pdb=" O SER C 583 " (cutoff:3.500A) Processing helix chain 'C' and resid 590 through 610 Processing helix chain 'C' and resid 612 through 623 Processing helix chain 'C' and resid 625 through 642 removed outlier: 3.763A pdb=" N THR C 642 " --> pdb=" O GLU C 638 " (cutoff:3.500A) Processing helix chain 'C' and resid 643 through 647 removed outlier: 3.712A pdb=" N GLN C 647 " --> pdb=" O ARG C 644 " (cutoff:3.500A) Processing helix chain 'C' and resid 651 through 680 removed outlier: 4.056A pdb=" N LEU C 673 " --> pdb=" O ALA C 669 " (cutoff:3.500A) Processing helix chain 'C' and resid 680 through 689 Processing helix chain 'C' and resid 692 through 696 removed outlier: 3.570A pdb=" N PHE C 695 " --> pdb=" O ASN C 692 " (cutoff:3.500A) removed outlier: 3.651A 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 726 Processing helix chain 'C' and resid 727 through 729 No H-bonds generated for 'chain 'C' and resid 727 through 729' Processing helix chain 'C' and resid 735 through 745 removed outlier: 3.540A pdb=" N VAL C 739 " --> pdb=" O SER C 735 " (cutoff:3.500A) Processing helix chain 'C' and resid 745 through 750 removed outlier: 3.644A pdb=" N VAL C 749 " --> pdb=" O PHE C 745 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU C 750 " --> pdb=" O PRO C 746 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 745 through 750' Processing helix chain 'C' and resid 788 through 799 removed outlier: 3.705A pdb=" N ARG C 793 " --> pdb=" O HIS C 789 " (cutoff:3.500A) Processing helix chain 'C' and resid 801 through 826 Processing helix chain 'C' and resid 833 through 857 Processing helix chain 'C' and resid 859 through 866 removed outlier: 3.825A pdb=" N ASP C 866 " --> pdb=" O GLU C 862 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 889 removed outlier: 3.687A pdb=" N ARG C 870 " --> pdb=" O ASP C 866 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ASP C 889 " --> pdb=" O THR C 885 " (cutoff:3.500A) Processing helix chain 'C' and resid 892 through 914 removed outlier: 4.057A pdb=" N PHE C 905 " --> pdb=" O GLY C 901 " (cutoff:3.500A) Processing helix chain 'C' and resid 915 through 921 removed outlier: 3.924A pdb=" N LEU C 920 " --> pdb=" O TYR C 917 " (cutoff:3.500A) Processing helix chain 'C' and resid 923 through 961 removed outlier: 4.006A pdb=" N LYS C 927 " --> pdb=" O ASN C 923 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N LYS C 936 " --> pdb=" O MET C 932 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N ASP C 937 " --> pdb=" O GLU C 933 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ILE C 947 " --> pdb=" O PHE C 943 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N PHE C 948 " --> pdb=" O LEU C 944 " (cutoff:3.500A) Processing helix chain 'C' and resid 967 through 981 removed outlier: 3.689A pdb=" N PHE C 971 " --> pdb=" O SER C 967 " (cutoff:3.500A) removed outlier: 4.550A 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: 3.767A pdb=" N LEU C1023 " --> pdb=" O ALA C1019 " (cutoff:3.500A) Processing helix chain 'C' and resid 1028 through 1066 removed outlier: 5.676A pdb=" N GLU C1046 " --> pdb=" O MET C1042 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N ALA C1047 " --> pdb=" O LYS C1043 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N TYR C1057 " --> pdb=" O ARG C1053 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASP C1065 " --> pdb=" O ALA C1061 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG C1066 " --> pdb=" O GLU C1062 " (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: 3.893A 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 1167 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 removed outlier: 3.549A pdb=" N ARG C1452 " --> pdb=" O HIS C1449 " (cutoff:3.500A) Processing helix chain 'C' and resid 1478 through 1491 removed outlier: 3.565A pdb=" N LEU C1482 " --> pdb=" O SER C1478 " (cutoff:3.500A) Processing helix chain 'D' and resid 72 through 77 removed outlier: 3.874A pdb=" N LYS D 77 " --> pdb=" O GLN D 73 " (cutoff:3.500A) 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: 3.530A pdb=" N LYS D 190 " --> pdb=" O THR D 186 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ALA D 198 " --> pdb=" O GLN D 194 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU D 199 " --> pdb=" O ILE D 195 " (cutoff:3.500A) Processing helix chain 'D' and resid 217 through 219 No H-bonds generated for 'chain 'D' and resid 217 through 219' Processing helix chain 'D' and resid 221 through 227 Processing helix chain 'D' and resid 271 through 287 Processing helix chain 'D' and resid 298 through 311 removed outlier: 3.721A pdb=" N LEU D 302 " --> pdb=" O GLY D 298 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLY D 303 " --> pdb=" O PRO D 299 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 337 Processing helix chain 'D' and resid 339 through 343 Processing helix chain 'D' and resid 346 through 359 Processing helix chain 'D' and resid 362 through 377 removed outlier: 3.993A pdb=" N VAL D 377 " --> pdb=" O ALA D 373 " (cutoff:3.500A) Processing helix chain 'D' and resid 395 through 408 Processing helix chain 'D' and resid 410 through 421 removed outlier: 3.595A pdb=" N LYS D 414 " --> pdb=" O LYS D 410 " (cutoff:3.500A) Processing helix chain 'D' and resid 423 through 437 Processing helix chain 'D' and resid 439 through 457 removed outlier: 4.672A pdb=" N ASN D 448 " --> pdb=" O ALA D 444 " (cutoff:3.500A) removed outlier: 5.345A 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: 3.777A pdb=" N LEU D 476 " --> pdb=" O ILE D 473 " (cutoff:3.500A) Processing helix chain 'D' and resid 487 through 492 Processing helix chain 'D' and resid 494 through 509 removed outlier: 3.577A pdb=" N LEU D 498 " --> pdb=" O PRO D 494 " (cutoff:3.500A) Processing helix chain 'D' and resid 513 through 523 removed outlier: 3.842A pdb=" N ARG D 517 " --> pdb=" O SER D 513 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ASN D 523 " --> pdb=" O VAL D 519 " (cutoff:3.500A) Processing helix chain 'D' and resid 547 through 553 Processing helix chain 'D' and resid 556 through 569 removed outlier: 3.504A pdb=" N MET D 560 " --> pdb=" O ASN D 556 " (cutoff:3.500A) Processing helix chain 'D' and resid 577 through 586 removed outlier: 4.006A pdb=" N ILE D 580 " --> pdb=" O ASP D 577 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TYR D 581 " --> pdb=" O PHE D 578 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N SER D 583 " --> pdb=" O ILE D 580 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N LYS D 584 " --> pdb=" O TYR D 581 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASP D 586 " --> pdb=" O SER D 583 " (cutoff:3.500A) Processing helix chain 'D' and resid 590 through 610 Processing helix chain 'D' and resid 612 through 623 Processing helix chain 'D' and resid 625 through 642 removed outlier: 3.763A pdb=" N THR D 642 " --> pdb=" O GLU D 638 " (cutoff:3.500A) Processing helix chain 'D' and resid 643 through 647 removed outlier: 3.711A pdb=" N GLN D 647 " --> pdb=" O ARG D 644 " (cutoff:3.500A) Processing helix chain 'D' and resid 651 through 680 removed outlier: 4.056A pdb=" N LEU D 673 " --> pdb=" O ALA D 669 " (cutoff:3.500A) Processing helix chain 'D' and resid 680 through 689 Processing helix chain 'D' and resid 692 through 696 removed outlier: 3.570A pdb=" N PHE D 695 " --> pdb=" O ASN D 692 " (cutoff:3.500A) removed outlier: 3.651A 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 726 Processing helix chain 'D' and resid 727 through 729 No H-bonds generated for 'chain 'D' and resid 727 through 729' Processing helix chain 'D' and resid 735 through 745 removed outlier: 3.540A pdb=" N VAL D 739 " --> pdb=" O SER D 735 " (cutoff:3.500A) Processing helix chain 'D' and resid 745 through 750 removed outlier: 3.644A pdb=" N VAL D 749 " --> pdb=" O PHE D 745 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU D 750 " --> pdb=" O PRO D 746 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 745 through 750' Processing helix chain 'D' and resid 788 through 799 removed outlier: 3.706A pdb=" N ARG D 793 " --> pdb=" O HIS D 789 " (cutoff:3.500A) Processing helix chain 'D' and resid 801 through 826 Processing helix chain 'D' and resid 833 through 857 Processing helix chain 'D' and resid 859 through 866 removed outlier: 3.825A pdb=" N ASP D 866 " --> pdb=" O GLU D 862 " (cutoff:3.500A) Processing helix chain 'D' and resid 866 through 889 removed outlier: 3.687A pdb=" N ARG D 870 " --> pdb=" O ASP D 866 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ASP D 889 " --> pdb=" O THR D 885 " (cutoff:3.500A) Processing helix chain 'D' and resid 892 through 914 removed outlier: 4.056A pdb=" N PHE D 905 " --> pdb=" O GLY D 901 " (cutoff:3.500A) Processing helix chain 'D' and resid 915 through 921 removed outlier: 3.924A pdb=" N LEU D 920 " --> pdb=" O TYR D 917 " (cutoff:3.500A) Processing helix chain 'D' and resid 923 through 961 removed outlier: 4.005A pdb=" N LYS D 927 " --> pdb=" O ASN D 923 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N LYS D 936 " --> pdb=" O MET D 932 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N ASP D 937 " --> pdb=" O GLU D 933 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ILE D 947 " --> pdb=" O PHE D 943 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N PHE D 948 " --> pdb=" O LEU D 944 " (cutoff:3.500A) Processing helix chain 'D' and resid 967 through 981 removed outlier: 3.687A pdb=" N PHE D 971 " --> pdb=" O SER D 967 " (cutoff:3.500A) removed outlier: 4.549A 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: 3.765A pdb=" N LEU D1023 " --> pdb=" O ALA D1019 " (cutoff:3.500A) Processing helix chain 'D' and resid 1028 through 1066 removed outlier: 5.675A pdb=" N GLU D1046 " --> pdb=" O MET D1042 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N ALA D1047 " --> pdb=" O LYS D1043 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N TYR D1057 " --> pdb=" O ARG D1053 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASP D1065 " --> pdb=" O ALA D1061 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG D1066 " --> pdb=" O GLU D1062 " (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: 3.894A 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 1167 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 removed outlier: 3.549A pdb=" N ARG D1452 " --> pdb=" O HIS D1449 " (cutoff:3.500A) Processing helix chain 'D' and resid 1478 through 1491 removed outlier: 3.565A pdb=" N LEU D1482 " --> pdb=" O SER D1478 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 56 through 60 Processing sheet with id=AA2, first strand: chain 'A' and resid 80 through 81 Processing sheet with id=AA3, first strand: chain 'A' and resid 232 through 236 removed outlier: 6.458A pdb=" N ILE A 233 " --> pdb=" O TRP A 96 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N THR A 98 " --> pdb=" O ILE A 233 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N LEU A 259 " --> pdb=" O PRO A 109 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N LEU A 111 " --> pdb=" O LEU A 259 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N ASP A 261 " --> pdb=" O LEU A 111 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N LEU A 113 " --> pdb=" O ASP A 261 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N THR A 210 " --> pdb=" O LEU A 256 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N LEU A 258 " --> pdb=" O THR A 210 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N GLY A 212 " --> pdb=" O LEU A 258 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N VAL A 260 " --> pdb=" O GLY A 212 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ALA A 214 " --> pdb=" O VAL A 260 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ILE A 144 " --> pdb=" O VAL A 291 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N ILE A 293 " --> pdb=" O ILE A 144 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N SER A 146 " --> pdb=" O ILE A 293 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N VAL A 295 " --> pdb=" O SER A 146 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N THR A 148 " --> pdb=" O VAL A 295 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ILE A 315 " --> pdb=" O VAL A 384 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N TYR A 386 " --> pdb=" O ILE A 315 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N VAL A 317 " --> pdb=" O TYR A 386 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1251 through 1252 removed outlier: 6.470A pdb=" N VAL A1251 " --> pdb=" O THR A1315 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 1279 through 1281 Processing sheet with id=AA6, first strand: chain 'A' and resid 1297 through 1298 removed outlier: 3.917A pdb=" N SER A1297 " --> pdb=" O ILE A1306 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1366 through 1367 removed outlier: 5.396A pdb=" N VAL A1333 " --> pdb=" O VAL A1356 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N ILE A1358 " --> pdb=" O THR A1331 " (cutoff:3.500A) removed outlier: 11.485A pdb=" N THR A1331 " --> pdb=" O ILE A1358 " (cutoff:3.500A) removed outlier: 14.259A pdb=" N ARG A1360 " --> pdb=" O ALA A1329 " (cutoff:3.500A) removed outlier: 18.220A pdb=" N ALA A1329 " --> pdb=" O ARG A1360 " (cutoff:3.500A) removed outlier: 5.728A pdb=" N GLY A1324 " --> pdb=" O TRP A1434 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N GLU A1436 " --> pdb=" O GLY A1324 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N ASN A1326 " --> pdb=" O GLU A1436 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N THR A1438 " --> pdb=" O ASN A1326 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ALA A1328 " --> pdb=" O THR A1438 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N VAL A1440 " --> pdb=" O ALA A1328 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ASP A1330 " --> pdb=" O VAL A1440 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N PHE A1442 " --> pdb=" O ASP A1330 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL A1332 " --> pdb=" O PHE A1442 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N ASP A1444 " --> pdb=" O VAL A1332 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N THR A1334 " --> pdb=" O ASP A1444 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ALA A1420 " --> pdb=" O CYS A1439 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N ASN A1441 " --> pdb=" O ILE A1418 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ILE A1418 " --> pdb=" O ASN A1441 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1370 through 1372 removed outlier: 18.220A pdb=" N ALA A1329 " --> pdb=" O ARG A1360 " (cutoff:3.500A) removed outlier: 14.259A pdb=" N ARG A1360 " --> pdb=" O ALA A1329 " (cutoff:3.500A) removed outlier: 11.485A pdb=" N THR A1331 " --> pdb=" O ILE A1358 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N ILE A1358 " --> pdb=" O THR A1331 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N VAL A1333 " --> pdb=" O VAL A1356 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N LEU A1353 " --> pdb=" O MET A1468 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N MET A1468 " --> pdb=" O LEU A1353 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N PHE A1355 " --> pdb=" O TRP A1466 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N TRP A1466 " --> pdb=" O PHE A1355 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ALA A1357 " --> pdb=" O ALA A1464 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ALA A1464 " --> pdb=" O ALA A1357 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N GLN A1359 " --> pdb=" O GLU A1462 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1346 through 1347 Processing sheet with id=AB1, first strand: chain 'B' and resid 56 through 60 Processing sheet with id=AB2, first strand: chain 'B' and resid 80 through 81 Processing sheet with id=AB3, first strand: chain 'B' and resid 232 through 236 removed outlier: 6.458A pdb=" N ILE B 233 " --> pdb=" O TRP B 96 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N THR B 98 " --> pdb=" O ILE B 233 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N LEU B 259 " --> pdb=" O PRO B 109 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N LEU B 111 " --> pdb=" O LEU B 259 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N ASP B 261 " --> pdb=" O LEU B 111 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N LEU B 113 " --> pdb=" O ASP B 261 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N THR B 210 " --> pdb=" O LEU B 256 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N LEU B 258 " --> pdb=" O THR B 210 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N GLY B 212 " --> pdb=" O LEU B 258 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N VAL B 260 " --> pdb=" O GLY B 212 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ALA B 214 " --> pdb=" O VAL B 260 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ILE B 144 " --> pdb=" O VAL B 291 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N ILE B 293 " --> pdb=" O ILE B 144 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N SER B 146 " --> pdb=" O ILE B 293 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N VAL B 295 " --> pdb=" O SER B 146 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N THR B 148 " --> pdb=" O VAL B 295 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ILE B 315 " --> pdb=" O VAL B 384 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N TYR B 386 " --> pdb=" O ILE B 315 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N VAL B 317 " --> pdb=" O TYR B 386 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 1251 through 1252 removed outlier: 6.470A pdb=" N VAL B1251 " --> pdb=" O THR B1315 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 1279 through 1281 Processing sheet with id=AB6, first strand: chain 'B' and resid 1297 through 1298 removed outlier: 3.918A pdb=" N SER B1297 " --> pdb=" O ILE B1306 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 1366 through 1367 removed outlier: 5.396A pdb=" N VAL B1333 " --> pdb=" O VAL B1356 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N ILE B1358 " --> pdb=" O THR B1331 " (cutoff:3.500A) removed outlier: 11.485A pdb=" N THR B1331 " --> pdb=" O ILE B1358 " (cutoff:3.500A) removed outlier: 14.259A pdb=" N ARG B1360 " --> pdb=" O ALA B1329 " (cutoff:3.500A) removed outlier: 18.221A pdb=" N ALA B1329 " --> pdb=" O ARG B1360 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N GLY B1324 " --> pdb=" O TRP B1434 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N GLU B1436 " --> pdb=" O GLY B1324 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N ASN B1326 " --> pdb=" O GLU B1436 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N THR B1438 " --> pdb=" O ASN B1326 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ALA B1328 " --> pdb=" O THR B1438 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N VAL B1440 " --> pdb=" O ALA B1328 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ASP B1330 " --> pdb=" O VAL B1440 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N PHE B1442 " --> pdb=" O ASP B1330 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL B1332 " --> pdb=" O PHE B1442 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N ASP B1444 " --> pdb=" O VAL B1332 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N THR B1334 " --> pdb=" O ASP B1444 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ALA B1420 " --> pdb=" O CYS B1439 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N ASN B1441 " --> pdb=" O ILE B1418 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ILE B1418 " --> pdb=" O ASN B1441 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 1370 through 1372 removed outlier: 18.221A pdb=" N ALA B1329 " --> pdb=" O ARG B1360 " (cutoff:3.500A) removed outlier: 14.259A pdb=" N ARG B1360 " --> pdb=" O ALA B1329 " (cutoff:3.500A) removed outlier: 11.485A pdb=" N THR B1331 " --> pdb=" O ILE B1358 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N ILE B1358 " --> pdb=" O THR B1331 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N VAL B1333 " --> pdb=" O VAL B1356 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N LEU B1353 " --> pdb=" O MET B1468 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N MET B1468 " --> pdb=" O LEU B1353 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N PHE B1355 " --> pdb=" O TRP B1466 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N TRP B1466 " --> pdb=" O PHE B1355 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ALA B1357 " --> pdb=" O ALA B1464 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ALA B1464 " --> pdb=" O ALA B1357 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N GLN B1359 " --> pdb=" O GLU B1462 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 1346 through 1347 Processing sheet with id=AC1, first strand: chain 'C' and resid 56 through 60 Processing sheet with id=AC2, first strand: chain 'C' and resid 80 through 81 Processing sheet with id=AC3, first strand: chain 'C' and resid 232 through 236 removed outlier: 6.458A pdb=" N ILE C 233 " --> pdb=" O TRP C 96 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N THR C 98 " --> pdb=" O ILE C 233 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N LEU C 259 " --> pdb=" O PRO C 109 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N LEU C 111 " --> pdb=" O LEU C 259 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N ASP C 261 " --> pdb=" O LEU C 111 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N LEU C 113 " --> pdb=" O ASP C 261 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N THR C 210 " --> pdb=" O LEU C 256 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N LEU C 258 " --> pdb=" O THR C 210 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N GLY C 212 " --> pdb=" O LEU C 258 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N VAL C 260 " --> pdb=" O GLY C 212 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ALA C 214 " --> pdb=" O VAL C 260 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N ILE C 144 " --> pdb=" O VAL C 291 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N ILE C 293 " --> pdb=" O ILE C 144 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N SER C 146 " --> pdb=" O ILE C 293 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N VAL C 295 " --> pdb=" O SER C 146 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N THR C 148 " --> pdb=" O VAL C 295 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ILE C 315 " --> pdb=" O VAL C 384 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N TYR C 386 " --> pdb=" O ILE C 315 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N VAL C 317 " --> pdb=" O TYR C 386 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 1251 through 1252 removed outlier: 6.470A pdb=" N VAL C1251 " --> pdb=" O THR C1315 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'C' and resid 1279 through 1281 Processing sheet with id=AC6, first strand: chain 'C' and resid 1297 through 1298 removed outlier: 3.916A pdb=" N SER C1297 " --> pdb=" O ILE C1306 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 1366 through 1367 removed outlier: 5.396A pdb=" N VAL C1333 " --> pdb=" O VAL C1356 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N ILE C1358 " --> pdb=" O THR C1331 " (cutoff:3.500A) removed outlier: 11.485A pdb=" N THR C1331 " --> pdb=" O ILE C1358 " (cutoff:3.500A) removed outlier: 14.260A pdb=" N ARG C1360 " --> pdb=" O ALA C1329 " (cutoff:3.500A) removed outlier: 18.221A pdb=" N ALA C1329 " --> pdb=" O ARG C1360 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N GLY C1324 " --> pdb=" O TRP C1434 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N GLU C1436 " --> pdb=" O GLY C1324 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N ASN C1326 " --> pdb=" O GLU C1436 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N THR C1438 " --> pdb=" O ASN C1326 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ALA C1328 " --> pdb=" O THR C1438 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N VAL C1440 " --> pdb=" O ALA C1328 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ASP C1330 " --> pdb=" O VAL C1440 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N PHE C1442 " --> pdb=" O ASP C1330 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N VAL C1332 " --> pdb=" O PHE C1442 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N ASP C1444 " --> pdb=" O VAL C1332 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N THR C1334 " --> pdb=" O ASP C1444 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ALA C1420 " --> pdb=" O CYS C1439 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N ASN C1441 " --> pdb=" O ILE C1418 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ILE C1418 " --> pdb=" O ASN C1441 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 1370 through 1372 removed outlier: 18.221A pdb=" N ALA C1329 " --> pdb=" O ARG C1360 " (cutoff:3.500A) removed outlier: 14.260A pdb=" N ARG C1360 " --> pdb=" O ALA C1329 " (cutoff:3.500A) removed outlier: 11.485A pdb=" N THR C1331 " --> pdb=" O ILE C1358 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N ILE C1358 " --> pdb=" O THR C1331 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N VAL C1333 " --> pdb=" O VAL C1356 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N LEU C1353 " --> pdb=" O MET C1468 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N MET C1468 " --> pdb=" O LEU C1353 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N PHE C1355 " --> pdb=" O TRP C1466 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N TRP C1466 " --> pdb=" O PHE C1355 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ALA C1357 " --> pdb=" O ALA C1464 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ALA C1464 " --> pdb=" O ALA C1357 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N GLN C1359 " --> pdb=" O GLU C1462 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 1346 through 1347 Processing sheet with id=AD1, first strand: chain 'D' and resid 56 through 60 Processing sheet with id=AD2, first strand: chain 'D' and resid 80 through 81 Processing sheet with id=AD3, first strand: chain 'D' and resid 232 through 236 removed outlier: 6.458A pdb=" N ILE D 233 " --> pdb=" O TRP D 96 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N THR D 98 " --> pdb=" O ILE D 233 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N LEU D 259 " --> pdb=" O PRO D 109 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LEU D 111 " --> pdb=" O LEU D 259 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N ASP D 261 " --> pdb=" O LEU D 111 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N LEU D 113 " --> pdb=" O ASP D 261 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N THR D 210 " --> pdb=" O LEU D 256 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N LEU D 258 " --> pdb=" O THR D 210 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N GLY D 212 " --> pdb=" O LEU D 258 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N VAL D 260 " --> pdb=" O GLY D 212 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ALA D 214 " --> pdb=" O VAL D 260 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N ILE D 144 " --> pdb=" O VAL D 291 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N ILE D 293 " --> pdb=" O ILE D 144 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N SER D 146 " --> pdb=" O ILE D 293 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N VAL D 295 " --> pdb=" O SER D 146 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N THR D 148 " --> pdb=" O VAL D 295 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ILE D 315 " --> pdb=" O VAL D 384 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N TYR D 386 " --> pdb=" O ILE D 315 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N VAL D 317 " --> pdb=" O TYR D 386 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 1251 through 1252 removed outlier: 6.471A pdb=" N VAL D1251 " --> pdb=" O THR D1315 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'D' and resid 1279 through 1281 Processing sheet with id=AD6, first strand: chain 'D' and resid 1297 through 1298 removed outlier: 3.917A pdb=" N SER D1297 " --> pdb=" O ILE D1306 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 1366 through 1367 removed outlier: 5.396A pdb=" N VAL D1333 " --> pdb=" O VAL D1356 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N ILE D1358 " --> pdb=" O THR D1331 " (cutoff:3.500A) removed outlier: 11.484A pdb=" N THR D1331 " --> pdb=" O ILE D1358 " (cutoff:3.500A) removed outlier: 14.259A pdb=" N ARG D1360 " --> pdb=" O ALA D1329 " (cutoff:3.500A) removed outlier: 18.221A pdb=" N ALA D1329 " --> pdb=" O ARG D1360 " (cutoff:3.500A) removed outlier: 5.728A pdb=" N GLY D1324 " --> pdb=" O TRP D1434 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N GLU D1436 " --> pdb=" O GLY D1324 " (cutoff:3.500A) removed outlier: 5.536A pdb=" N ASN D1326 " --> pdb=" O GLU D1436 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N THR D1438 " --> pdb=" O ASN D1326 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ALA D1328 " --> pdb=" O THR D1438 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N VAL D1440 " --> pdb=" O ALA D1328 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ASP D1330 " --> pdb=" O VAL D1440 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N PHE D1442 " --> pdb=" O ASP D1330 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL D1332 " --> pdb=" O PHE D1442 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N ASP D1444 " --> pdb=" O VAL D1332 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N THR D1334 " --> pdb=" O ASP D1444 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ALA D1420 " --> pdb=" O CYS D1439 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N ASN D1441 " --> pdb=" O ILE D1418 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ILE D1418 " --> pdb=" O ASN D1441 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 1370 through 1372 removed outlier: 18.221A pdb=" N ALA D1329 " --> pdb=" O ARG D1360 " (cutoff:3.500A) removed outlier: 14.259A pdb=" N ARG D1360 " --> pdb=" O ALA D1329 " (cutoff:3.500A) removed outlier: 11.484A pdb=" N THR D1331 " --> pdb=" O ILE D1358 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N ILE D1358 " --> pdb=" O THR D1331 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N VAL D1333 " --> pdb=" O VAL D1356 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N LEU D1353 " --> pdb=" O MET D1468 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N MET D1468 " --> pdb=" O LEU D1353 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N PHE D1355 " --> pdb=" O TRP D1466 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N TRP D1466 " --> pdb=" O PHE D1355 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ALA D1357 " --> pdb=" O ALA D1464 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ALA D1464 " --> pdb=" O ALA D1357 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N GLN D1359 " --> pdb=" O GLU D1462 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 1346 through 1347 2348 hydrogen bonds defined for protein. 6852 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.59 Time building geometry restraints manager: 4.06 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: 6400 1.31 - 1.44: 10560 1.44 - 1.57: 22820 1.57 - 1.69: 8 1.69 - 1.82: 356 Bond restraints: 40144 Sorted by residual: bond pdb=" C PRO C1015 " pdb=" O PRO C1015 " ideal model delta sigma weight residual 1.237 1.190 0.047 1.16e-02 7.43e+03 1.67e+01 bond pdb=" C PRO B1015 " pdb=" O PRO B1015 " ideal model delta sigma weight residual 1.237 1.190 0.047 1.16e-02 7.43e+03 1.63e+01 bond pdb=" C PRO A1015 " pdb=" O PRO A1015 " ideal model delta sigma weight residual 1.237 1.190 0.047 1.16e-02 7.43e+03 1.63e+01 bond pdb=" C PRO D1015 " pdb=" O PRO D1015 " ideal model delta sigma weight residual 1.237 1.190 0.047 1.16e-02 7.43e+03 1.63e+01 bond pdb=" C PRO A 926 " pdb=" O PRO A 926 " ideal model delta sigma weight residual 1.237 1.187 0.050 1.26e-02 6.30e+03 1.58e+01 ... (remaining 40139 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.48: 48778 2.48 - 4.96: 5215 4.96 - 7.44: 715 7.44 - 9.92: 96 9.92 - 12.40: 12 Bond angle restraints: 54816 Sorted by residual: angle pdb=" N PRO B1002 " pdb=" CA PRO B1002 " pdb=" C PRO B1002 " ideal model delta sigma weight residual 113.53 123.90 -10.37 1.39e+00 5.18e-01 5.57e+01 angle pdb=" N PRO C1002 " pdb=" CA PRO C1002 " pdb=" C PRO C1002 " ideal model delta sigma weight residual 113.53 123.90 -10.37 1.39e+00 5.18e-01 5.57e+01 angle pdb=" N PRO D1002 " pdb=" CA PRO D1002 " pdb=" C PRO D1002 " ideal model delta sigma weight residual 113.53 123.90 -10.37 1.39e+00 5.18e-01 5.57e+01 angle pdb=" N PRO A1002 " pdb=" CA PRO A1002 " pdb=" C PRO A1002 " ideal model delta sigma weight residual 113.53 123.90 -10.37 1.39e+00 5.18e-01 5.57e+01 angle pdb=" C VAL A1286 " pdb=" CA VAL A1286 " pdb=" CB VAL A1286 " ideal model delta sigma weight residual 110.82 120.52 -9.70 1.54e+00 4.22e-01 3.97e+01 ... (remaining 54811 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.92: 21988 15.92 - 31.84: 1760 31.84 - 47.76: 368 47.76 - 63.68: 80 63.68 - 79.60: 52 Dihedral angle restraints: 24248 sinusoidal: 8544 harmonic: 15704 Sorted by residual: dihedral pdb=" C THR C 215 " pdb=" N THR C 215 " pdb=" CA THR C 215 " pdb=" CB THR C 215 " ideal model delta harmonic sigma weight residual -122.00 -109.84 -12.16 0 2.50e+00 1.60e-01 2.37e+01 dihedral pdb=" C THR A 215 " pdb=" N THR A 215 " pdb=" CA THR A 215 " pdb=" CB THR A 215 " ideal model delta harmonic sigma weight residual -122.00 -109.87 -12.13 0 2.50e+00 1.60e-01 2.35e+01 dihedral pdb=" C THR D 215 " pdb=" N THR D 215 " pdb=" CA THR D 215 " pdb=" CB THR D 215 " ideal model delta harmonic sigma weight residual -122.00 -109.87 -12.13 0 2.50e+00 1.60e-01 2.35e+01 ... (remaining 24245 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 5062 0.094 - 0.188: 1147 0.188 - 0.281: 147 0.281 - 0.375: 56 0.375 - 0.469: 16 Chirality restraints: 6428 Sorted by residual: chirality pdb=" CA PRO A1002 " pdb=" N PRO A1002 " pdb=" C PRO A1002 " pdb=" CB PRO A1002 " both_signs ideal model delta sigma weight residual False 2.72 2.25 0.47 2.00e-01 2.50e+01 5.50e+00 chirality pdb=" CA PRO B1002 " pdb=" N PRO B1002 " pdb=" C PRO B1002 " pdb=" CB PRO B1002 " both_signs ideal model delta sigma weight residual False 2.72 2.25 0.47 2.00e-01 2.50e+01 5.50e+00 chirality pdb=" CA PRO D1002 " pdb=" N PRO D1002 " pdb=" C PRO D1002 " pdb=" CB PRO D1002 " both_signs ideal model delta sigma weight residual False 2.72 2.25 0.47 2.00e-01 2.50e+01 5.50e+00 ... (remaining 6425 not shown) Planarity restraints: 7036 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU D 651 " 0.020 2.00e-02 2.50e+03 4.01e-02 1.60e+01 pdb=" C LEU D 651 " -0.069 2.00e-02 2.50e+03 pdb=" O LEU D 651 " 0.026 2.00e-02 2.50e+03 pdb=" N ALA D 652 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 651 " 0.020 2.00e-02 2.50e+03 4.01e-02 1.60e+01 pdb=" C LEU A 651 " -0.069 2.00e-02 2.50e+03 pdb=" O LEU A 651 " 0.026 2.00e-02 2.50e+03 pdb=" N ALA A 652 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU C 651 " 0.020 2.00e-02 2.50e+03 4.01e-02 1.60e+01 pdb=" C LEU C 651 " -0.069 2.00e-02 2.50e+03 pdb=" O LEU C 651 " 0.026 2.00e-02 2.50e+03 pdb=" N ALA C 652 " 0.024 2.00e-02 2.50e+03 ... (remaining 7033 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 9894 2.84 - 3.35: 35095 3.35 - 3.87: 65568 3.87 - 4.38: 69588 4.38 - 4.90: 124066 Nonbonded interactions: 304211 Sorted by model distance: nonbonded pdb=" O VAL B 218 " pdb=" OG1 THR B 248 " model vdw 2.322 3.040 nonbonded pdb=" O VAL A 218 " pdb=" OG1 THR A 248 " model vdw 2.322 3.040 nonbonded pdb=" O VAL C 218 " pdb=" OG1 THR C 248 " model vdw 2.322 3.040 nonbonded pdb=" O VAL D 218 " pdb=" OG1 THR D 248 " model vdw 2.322 3.040 nonbonded pdb=" OG1 THR D 215 " pdb=" OE1 GLU D 271 " model vdw 2.358 3.040 ... (remaining 304206 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: 0.12 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 2.540 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: 0.040 Extract box with map and model: 0.590 Check model and map are aligned: 0.120 Set scattering table: 0.110 Process input model: 39.890 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.100 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:6.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6890 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 0.074 40148 Z= 0.639 Angle : 1.576 12.403 54824 Z= 1.059 Chirality : 0.084 0.469 6428 Planarity : 0.010 0.040 7036 Dihedral : 12.887 79.601 14052 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 0.66 % Allowed : 1.76 % Favored : 97.58 % Cbeta Deviations : 0.39 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.22 (0.11), residues: 5372 helix: 0.70 (0.09), residues: 2976 sheet: -0.89 (0.23), residues: 412 loop : -0.28 (0.14), residues: 1984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 517 TYR 0.036 0.004 TYR D 504 PHE 0.047 0.005 PHE A 496 TRP 0.041 0.004 TRP A1052 HIS 0.016 0.003 HIS D 514 Details of bonding type rmsd covalent geometry : bond 0.01054 (40144) covalent geometry : angle 1.57617 (54816) SS BOND : bond 0.00038 ( 4) SS BOND : angle 1.54168 ( 8) hydrogen bonds : bond 0.17550 ( 2336) hydrogen bonds : angle 7.48324 ( 6852) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10744 Ramachandran restraints generated. 5372 Oldfield, 0 Emsley, 5372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10744 Ramachandran restraints generated. 5372 Oldfield, 0 Emsley, 5372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 654 residues out of total 4632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 631 time to evaluate : 1.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 TRP cc_start: 0.7281 (p-90) cc_final: 0.6442 (p-90) REVERT: A 129 MET cc_start: 0.7713 (mmt) cc_final: 0.7085 (mmp) REVERT: A 197 GLU cc_start: 0.5961 (tt0) cc_final: 0.5718 (pt0) REVERT: A 207 ILE cc_start: 0.7706 (mt) cc_final: 0.7347 (tt) REVERT: A 223 ASP cc_start: 0.7752 (m-30) cc_final: 0.7310 (t70) REVERT: A 235 LEU cc_start: 0.6162 (tp) cc_final: 0.5911 (tt) REVERT: A 330 TYR cc_start: 0.7236 (t80) cc_final: 0.6754 (t80) REVERT: A 342 PHE cc_start: 0.7339 (m-80) cc_final: 0.6886 (m-80) REVERT: A 345 TYR cc_start: 0.7924 (m-10) cc_final: 0.7403 (m-80) REVERT: A 352 GLN cc_start: 0.7128 (tt0) cc_final: 0.6916 (pp30) REVERT: A 560 MET cc_start: 0.7588 (mmm) cc_final: 0.7353 (mmm) REVERT: A 658 MET cc_start: 0.6609 (mtt) cc_final: 0.6355 (mtt) REVERT: A 663 LYS cc_start: 0.6828 (mttp) cc_final: 0.6273 (mppt) REVERT: A 666 GLU cc_start: 0.6887 (tt0) cc_final: 0.6426 (tp30) REVERT: A 683 MET cc_start: 0.8143 (tpp) cc_final: 0.7879 (tpt) REVERT: A 686 GLU cc_start: 0.7210 (tt0) cc_final: 0.6959 (mt-10) REVERT: A 915 MET cc_start: 0.8174 (OUTLIER) cc_final: 0.7928 (mtm) REVERT: A 1083 PHE cc_start: 0.5599 (t80) cc_final: 0.5042 (t80) REVERT: A 1085 ARG cc_start: 0.4907 (tpp80) cc_final: 0.4667 (ttt180) REVERT: A 1128 ARG cc_start: 0.7390 (ttp80) cc_final: 0.7062 (ttm-80) REVERT: A 1157 MET cc_start: 0.8509 (tpp) cc_final: 0.8154 (tpt) REVERT: A 1351 LYS cc_start: 0.4753 (mtmt) cc_final: 0.4249 (mtmp) REVERT: A 1468 MET cc_start: 0.5359 (ppp) cc_final: 0.4948 (ppp) REVERT: B 96 TRP cc_start: 0.7287 (p-90) cc_final: 0.6451 (p-90) REVERT: B 129 MET cc_start: 0.7719 (mmt) cc_final: 0.7086 (mmp) REVERT: B 197 GLU cc_start: 0.5970 (tt0) cc_final: 0.5728 (pt0) REVERT: B 207 ILE cc_start: 0.7715 (mt) cc_final: 0.7351 (tt) REVERT: B 223 ASP cc_start: 0.7758 (m-30) cc_final: 0.7320 (t70) REVERT: B 235 LEU cc_start: 0.6055 (tp) cc_final: 0.5819 (tt) REVERT: B 330 TYR cc_start: 0.7242 (t80) cc_final: 0.6761 (t80) REVERT: B 342 PHE cc_start: 0.7347 (m-80) cc_final: 0.6892 (m-80) REVERT: B 345 TYR cc_start: 0.7923 (m-10) cc_final: 0.7390 (m-80) REVERT: B 352 GLN cc_start: 0.7141 (tt0) cc_final: 0.6923 (pp30) REVERT: B 560 MET cc_start: 0.7593 (mmm) cc_final: 0.7350 (mmm) REVERT: B 658 MET cc_start: 0.6608 (mtt) cc_final: 0.6355 (mtt) REVERT: B 663 LYS cc_start: 0.6829 (mttp) cc_final: 0.6276 (mppt) REVERT: B 666 GLU cc_start: 0.6886 (tt0) cc_final: 0.6428 (tp30) REVERT: B 683 MET cc_start: 0.8147 (tpp) cc_final: 0.7883 (tpt) REVERT: B 686 GLU cc_start: 0.7208 (tt0) cc_final: 0.6958 (mt-10) REVERT: B 915 MET cc_start: 0.8170 (OUTLIER) cc_final: 0.7887 (mtm) REVERT: B 1083 PHE cc_start: 0.5597 (t80) cc_final: 0.5037 (t80) REVERT: B 1085 ARG cc_start: 0.4912 (tpp80) cc_final: 0.4676 (ttt180) REVERT: B 1128 ARG cc_start: 0.7381 (ttp80) cc_final: 0.7066 (ttm-80) REVERT: B 1157 MET cc_start: 0.8556 (tpp) cc_final: 0.8208 (tpt) REVERT: B 1468 MET cc_start: 0.5373 (ppp) cc_final: 0.4959 (ppp) REVERT: C 96 TRP cc_start: 0.7269 (p-90) cc_final: 0.6448 (p-90) REVERT: C 197 GLU cc_start: 0.5930 (tt0) cc_final: 0.5687 (pt0) REVERT: C 207 ILE cc_start: 0.7691 (mt) cc_final: 0.7337 (tt) REVERT: C 223 ASP cc_start: 0.7767 (m-30) cc_final: 0.7278 (t70) REVERT: C 235 LEU cc_start: 0.6103 (tp) cc_final: 0.5854 (tt) REVERT: C 330 TYR cc_start: 0.7213 (t80) cc_final: 0.6771 (t80) REVERT: C 342 PHE cc_start: 0.7219 (m-80) cc_final: 0.6799 (m-80) REVERT: C 345 TYR cc_start: 0.7902 (m-10) cc_final: 0.7402 (m-80) REVERT: C 352 GLN cc_start: 0.7112 (tt0) cc_final: 0.6905 (pp30) REVERT: C 560 MET cc_start: 0.7592 (mmm) cc_final: 0.7358 (mmm) REVERT: C 658 MET cc_start: 0.6605 (mtt) cc_final: 0.6378 (mtt) REVERT: C 663 LYS cc_start: 0.6838 (mttp) cc_final: 0.6291 (mppt) REVERT: C 666 GLU cc_start: 0.6881 (tt0) cc_final: 0.6422 (tp30) REVERT: C 683 MET cc_start: 0.8134 (tpp) cc_final: 0.7868 (tpt) REVERT: C 686 GLU cc_start: 0.7193 (tt0) cc_final: 0.6940 (mt-10) REVERT: C 915 MET cc_start: 0.8162 (OUTLIER) cc_final: 0.7915 (mtm) REVERT: C 1083 PHE cc_start: 0.5592 (t80) cc_final: 0.5024 (t80) REVERT: C 1085 ARG cc_start: 0.4906 (tpp80) cc_final: 0.4671 (ttt180) REVERT: C 1128 ARG cc_start: 0.7420 (ttp80) cc_final: 0.7104 (ttm-80) REVERT: C 1157 MET cc_start: 0.8575 (tpp) cc_final: 0.8170 (tpt) REVERT: C 1351 LYS cc_start: 0.4743 (mtmt) cc_final: 0.4216 (mtmp) REVERT: C 1468 MET cc_start: 0.5361 (ppp) cc_final: 0.4567 (ppp) REVERT: D 96 TRP cc_start: 0.7276 (p-90) cc_final: 0.6442 (p-90) REVERT: D 129 MET cc_start: 0.7713 (mmt) cc_final: 0.7501 (mmp) REVERT: D 197 GLU cc_start: 0.5950 (tt0) cc_final: 0.5700 (pt0) REVERT: D 207 ILE cc_start: 0.7701 (mt) cc_final: 0.7343 (tt) REVERT: D 223 ASP cc_start: 0.7778 (m-30) cc_final: 0.7327 (t70) REVERT: D 235 LEU cc_start: 0.5992 (tp) cc_final: 0.5772 (tt) REVERT: D 330 TYR cc_start: 0.7227 (t80) cc_final: 0.6781 (t80) REVERT: D 342 PHE cc_start: 0.7327 (m-80) cc_final: 0.6880 (m-80) REVERT: D 345 TYR cc_start: 0.7911 (m-10) cc_final: 0.7408 (m-80) REVERT: D 352 GLN cc_start: 0.7125 (tt0) cc_final: 0.6912 (pp30) REVERT: D 560 MET cc_start: 0.7598 (mmm) cc_final: 0.7353 (mmm) REVERT: D 658 MET cc_start: 0.6608 (mtt) cc_final: 0.6357 (mtt) REVERT: D 663 LYS cc_start: 0.6828 (mttp) cc_final: 0.6275 (mppt) REVERT: D 666 GLU cc_start: 0.6881 (tt0) cc_final: 0.6425 (tp30) REVERT: D 683 MET cc_start: 0.8131 (tpp) cc_final: 0.7866 (tpt) REVERT: D 686 GLU cc_start: 0.7193 (tt0) cc_final: 0.6939 (mt-10) REVERT: D 915 MET cc_start: 0.8175 (OUTLIER) cc_final: 0.7891 (mtm) REVERT: D 1083 PHE cc_start: 0.5592 (t80) cc_final: 0.5025 (t80) REVERT: D 1085 ARG cc_start: 0.4911 (tpp80) cc_final: 0.4677 (ttt180) REVERT: D 1128 ARG cc_start: 0.7412 (ttp80) cc_final: 0.7100 (ttm-80) REVERT: D 1157 MET cc_start: 0.8558 (tpp) cc_final: 0.8191 (tpt) REVERT: D 1351 LYS cc_start: 0.4777 (mtmt) cc_final: 0.4324 (mtmp) REVERT: D 1468 MET cc_start: 0.5351 (ppp) cc_final: 0.4549 (ppp) outliers start: 23 outliers final: 4 residues processed: 646 average time/residue: 0.7610 time to fit residues: 594.1832 Evaluate side-chains 410 residues out of total 4632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 402 time to evaluate : 1.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 907 VAL Chi-restraints excluded: chain A residue 915 MET Chi-restraints excluded: chain B residue 907 VAL Chi-restraints excluded: chain B residue 915 MET Chi-restraints excluded: chain C residue 907 VAL Chi-restraints excluded: chain C residue 915 MET Chi-restraints excluded: chain D residue 907 VAL Chi-restraints excluded: chain D residue 915 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 394 optimal weight: 20.0000 chunk 430 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 265 optimal weight: 2.9990 chunk 523 optimal weight: 30.0000 chunk 497 optimal weight: 0.8980 chunk 414 optimal weight: 5.9990 chunk 310 optimal weight: 7.9990 chunk 488 optimal weight: 0.4980 chunk 366 optimal weight: 0.5980 chunk 223 optimal weight: 2.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 GLN A 417 GLN A 440 HIS A 448 ASN A 598 GLN A 702 ASN A 992 ASN A1078 HIS B 284 GLN B 296 GLN B 417 GLN B 448 ASN B 702 ASN B 992 ASN B1078 HIS C 296 GLN C 417 GLN C 448 ASN C 702 ASN C 992 ASN C1078 HIS D 296 GLN D 417 GLN D 448 ASN D 702 ASN D 992 ASN D1045 GLN D1078 HIS D1152 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.166909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.110773 restraints weight = 60580.288| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 2.79 r_work: 0.3117 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 40148 Z= 0.139 Angle : 0.548 8.172 54824 Z= 0.288 Chirality : 0.039 0.150 6428 Planarity : 0.004 0.033 7036 Dihedral : 5.342 59.936 6516 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.59 % Allowed : 9.36 % Favored : 88.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.32 (0.11), residues: 5372 helix: 1.80 (0.09), residues: 3000 sheet: -0.50 (0.24), residues: 376 loop : -0.20 (0.14), residues: 1996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 517 TYR 0.013 0.002 TYR D 979 PHE 0.027 0.002 PHE B1355 TRP 0.020 0.001 TRP C1052 HIS 0.005 0.001 HIS D 660 Details of bonding type rmsd covalent geometry : bond 0.00301 (40144) covalent geometry : angle 0.54796 (54816) SS BOND : bond 0.00055 ( 4) SS BOND : angle 0.47439 ( 8) hydrogen bonds : bond 0.05003 ( 2336) hydrogen bonds : angle 4.35153 ( 6852) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10744 Ramachandran restraints generated. 5372 Oldfield, 0 Emsley, 5372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10744 Ramachandran restraints generated. 5372 Oldfield, 0 Emsley, 5372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 520 residues out of total 4632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 430 time to evaluate : 1.460 Fit side-chains REVERT: A 96 TRP cc_start: 0.7596 (p-90) cc_final: 0.7189 (p-90) REVERT: A 129 MET cc_start: 0.8167 (mmt) cc_final: 0.7874 (mmp) REVERT: A 197 GLU cc_start: 0.6133 (tt0) cc_final: 0.5869 (pt0) REVERT: A 223 ASP cc_start: 0.7861 (m-30) cc_final: 0.7550 (t70) REVERT: A 235 LEU cc_start: 0.6798 (tp) cc_final: 0.6590 (tt) REVERT: A 313 THR cc_start: 0.8242 (m) cc_final: 0.8019 (m) REVERT: A 342 PHE cc_start: 0.7538 (m-80) cc_final: 0.7161 (m-80) REVERT: A 345 TYR cc_start: 0.8230 (m-10) cc_final: 0.7886 (m-80) REVERT: A 374 LEU cc_start: 0.7718 (mm) cc_final: 0.7476 (mm) REVERT: A 461 HIS cc_start: 0.8018 (OUTLIER) cc_final: 0.7338 (p90) REVERT: A 523 ASN cc_start: 0.8254 (t0) cc_final: 0.7673 (p0) REVERT: A 566 ARG cc_start: 0.8153 (OUTLIER) cc_final: 0.7292 (mtp180) REVERT: A 663 LYS cc_start: 0.8422 (mttp) cc_final: 0.8106 (mppt) REVERT: A 683 MET cc_start: 0.8982 (tpp) cc_final: 0.8758 (mmm) REVERT: A 694 MET cc_start: 0.8351 (ttm) cc_final: 0.8128 (ttm) REVERT: A 865 SER cc_start: 0.8079 (m) cc_final: 0.7839 (p) REVERT: A 1083 PHE cc_start: 0.6099 (t80) cc_final: 0.5644 (t80) REVERT: A 1085 ARG cc_start: 0.5154 (tpp80) cc_final: 0.4863 (ttt180) REVERT: A 1128 ARG cc_start: 0.7993 (ttp80) cc_final: 0.7729 (ttm-80) REVERT: A 1157 MET cc_start: 0.8626 (tpp) cc_final: 0.8248 (tpt) REVERT: A 1468 MET cc_start: 0.5364 (ppp) cc_final: 0.5040 (ppp) REVERT: B 61 ASN cc_start: 0.6138 (m-40) cc_final: 0.5903 (m110) REVERT: B 96 TRP cc_start: 0.7677 (p-90) cc_final: 0.7269 (p-90) REVERT: B 129 MET cc_start: 0.8174 (mmt) cc_final: 0.7878 (mmp) REVERT: B 197 GLU cc_start: 0.6156 (tt0) cc_final: 0.5892 (pt0) REVERT: B 223 ASP cc_start: 0.7882 (m-30) cc_final: 0.7580 (t70) REVERT: B 313 THR cc_start: 0.8234 (m) cc_final: 0.8008 (m) REVERT: B 342 PHE cc_start: 0.7624 (m-80) cc_final: 0.7210 (m-80) REVERT: B 345 TYR cc_start: 0.8232 (m-10) cc_final: 0.7885 (m-80) REVERT: B 374 LEU cc_start: 0.7715 (mm) cc_final: 0.7480 (mm) REVERT: B 461 HIS cc_start: 0.8017 (OUTLIER) cc_final: 0.7329 (p90) REVERT: B 566 ARG cc_start: 0.8166 (OUTLIER) cc_final: 0.7281 (mtp180) REVERT: B 663 LYS cc_start: 0.8417 (mttp) cc_final: 0.8106 (mppt) REVERT: B 683 MET cc_start: 0.8985 (tpp) cc_final: 0.8763 (mmm) REVERT: B 694 MET cc_start: 0.8367 (ttm) cc_final: 0.8147 (ttm) REVERT: B 865 SER cc_start: 0.8082 (m) cc_final: 0.7847 (p) REVERT: B 1083 PHE cc_start: 0.6106 (t80) cc_final: 0.5650 (t80) REVERT: B 1085 ARG cc_start: 0.5151 (tpp80) cc_final: 0.4861 (ttt180) REVERT: B 1128 ARG cc_start: 0.7986 (ttp80) cc_final: 0.7724 (ttm-80) REVERT: B 1149 MET cc_start: 0.8280 (OUTLIER) cc_final: 0.8064 (mtm) REVERT: B 1157 MET cc_start: 0.8584 (tpp) cc_final: 0.8212 (tpt) REVERT: B 1468 MET cc_start: 0.5376 (ppp) cc_final: 0.5037 (ppp) REVERT: C 96 TRP cc_start: 0.7577 (p-90) cc_final: 0.7160 (p-90) REVERT: C 197 GLU cc_start: 0.6103 (tt0) cc_final: 0.5841 (pt0) REVERT: C 223 ASP cc_start: 0.7839 (m-30) cc_final: 0.7556 (t70) REVERT: C 235 LEU cc_start: 0.6900 (tp) cc_final: 0.6700 (tt) REVERT: C 248 THR cc_start: 0.7058 (OUTLIER) cc_final: 0.6744 (t) REVERT: C 313 THR cc_start: 0.8199 (m) cc_final: 0.7977 (m) REVERT: C 342 PHE cc_start: 0.7466 (m-80) cc_final: 0.7095 (m-80) REVERT: C 345 TYR cc_start: 0.8200 (m-10) cc_final: 0.7868 (m-80) REVERT: C 374 LEU cc_start: 0.7554 (mm) cc_final: 0.7307 (mm) REVERT: C 449 ASP cc_start: 0.7917 (OUTLIER) cc_final: 0.7654 (m-30) REVERT: C 461 HIS cc_start: 0.7958 (OUTLIER) cc_final: 0.7246 (p90) REVERT: C 566 ARG cc_start: 0.8149 (OUTLIER) cc_final: 0.7282 (mtp180) REVERT: C 663 LYS cc_start: 0.8405 (mttp) cc_final: 0.8095 (mppt) REVERT: C 683 MET cc_start: 0.8983 (tpp) cc_final: 0.8763 (mmm) REVERT: C 694 MET cc_start: 0.8364 (ttm) cc_final: 0.8140 (ttm) REVERT: C 865 SER cc_start: 0.8073 (m) cc_final: 0.7835 (p) REVERT: C 1083 PHE cc_start: 0.6111 (t80) cc_final: 0.5703 (t80) REVERT: C 1085 ARG cc_start: 0.5159 (tpp80) cc_final: 0.4867 (ttt180) REVERT: C 1128 ARG cc_start: 0.8023 (ttp80) cc_final: 0.7756 (ttm-80) REVERT: C 1157 MET cc_start: 0.8612 (tpp) cc_final: 0.8231 (tpt) REVERT: C 1468 MET cc_start: 0.5350 (ppp) cc_final: 0.4984 (ppp) REVERT: D 96 TRP cc_start: 0.7591 (p-90) cc_final: 0.7161 (p-90) REVERT: D 129 MET cc_start: 0.8180 (mmt) cc_final: 0.7960 (mmp) REVERT: D 197 GLU cc_start: 0.6121 (tt0) cc_final: 0.5857 (pt0) REVERT: D 223 ASP cc_start: 0.7856 (m-30) cc_final: 0.7550 (t70) REVERT: D 313 THR cc_start: 0.8208 (m) cc_final: 0.7987 (m) REVERT: D 342 PHE cc_start: 0.7564 (m-80) cc_final: 0.7183 (m-80) REVERT: D 345 TYR cc_start: 0.8211 (m-10) cc_final: 0.7879 (m-80) REVERT: D 374 LEU cc_start: 0.7702 (mm) cc_final: 0.7460 (mm) REVERT: D 461 HIS cc_start: 0.8015 (OUTLIER) cc_final: 0.7329 (p90) REVERT: D 523 ASN cc_start: 0.8252 (t0) cc_final: 0.7678 (p0) REVERT: D 566 ARG cc_start: 0.8175 (OUTLIER) cc_final: 0.7301 (mtp180) REVERT: D 663 LYS cc_start: 0.8413 (mttp) cc_final: 0.8106 (mppt) REVERT: D 683 MET cc_start: 0.8984 (tpp) cc_final: 0.8758 (mmm) REVERT: D 694 MET cc_start: 0.8378 (ttm) cc_final: 0.8153 (ttm) REVERT: D 865 SER cc_start: 0.8077 (m) cc_final: 0.7839 (p) REVERT: D 1083 PHE cc_start: 0.6107 (t80) cc_final: 0.5700 (t80) REVERT: D 1085 ARG cc_start: 0.5170 (tpp80) cc_final: 0.4877 (ttt180) REVERT: D 1128 ARG cc_start: 0.8020 (ttp80) cc_final: 0.7753 (ttm-80) REVERT: D 1149 MET cc_start: 0.8273 (OUTLIER) cc_final: 0.8068 (mtm) REVERT: D 1157 MET cc_start: 0.8628 (tpp) cc_final: 0.8254 (tpt) REVERT: D 1468 MET cc_start: 0.5337 (ppp) cc_final: 0.4961 (ppp) outliers start: 90 outliers final: 28 residues processed: 486 average time/residue: 0.7219 time to fit residues: 426.8550 Evaluate side-chains 384 residues out of total 4632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 344 time to evaluate : 1.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 189 MET Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 449 ASP Chi-restraints excluded: chain A residue 461 HIS Chi-restraints excluded: chain A residue 566 ARG Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 930 MET Chi-restraints excluded: chain A residue 1115 LEU Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 189 MET Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 449 ASP Chi-restraints excluded: chain B residue 461 HIS Chi-restraints excluded: chain B residue 566 ARG Chi-restraints excluded: chain B residue 750 LEU Chi-restraints excluded: chain B residue 930 MET Chi-restraints excluded: chain B residue 1115 LEU Chi-restraints excluded: chain B residue 1149 MET Chi-restraints excluded: chain C residue 71 GLU Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 189 MET Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 449 ASP Chi-restraints excluded: chain C residue 461 HIS Chi-restraints excluded: chain C residue 566 ARG Chi-restraints excluded: chain C residue 750 LEU Chi-restraints excluded: chain C residue 930 MET Chi-restraints excluded: chain C residue 1115 LEU Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 189 MET Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 449 ASP Chi-restraints excluded: chain D residue 461 HIS Chi-restraints excluded: chain D residue 566 ARG Chi-restraints excluded: chain D residue 750 LEU Chi-restraints excluded: chain D residue 930 MET Chi-restraints excluded: chain D residue 1115 LEU Chi-restraints excluded: chain D residue 1149 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 368 optimal weight: 0.4980 chunk 204 optimal weight: 30.0000 chunk 503 optimal weight: 0.5980 chunk 392 optimal weight: 10.0000 chunk 475 optimal weight: 7.9990 chunk 229 optimal weight: 2.9990 chunk 414 optimal weight: 4.9990 chunk 246 optimal weight: 0.0040 chunk 339 optimal weight: 20.0000 chunk 230 optimal weight: 0.9980 chunk 522 optimal weight: 8.9990 overall best weight: 1.0194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 440 HIS A 992 ASN B 440 HIS B 992 ASN C 440 HIS C 992 ASN D 440 HIS D 992 ASN D1152 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.167096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.113819 restraints weight = 60284.678| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 2.59 r_work: 0.3098 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.2522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 40148 Z= 0.120 Angle : 0.490 7.514 54824 Z= 0.254 Chirality : 0.038 0.151 6428 Planarity : 0.004 0.042 7036 Dihedral : 4.745 54.279 6500 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.82 % Allowed : 11.18 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.73 (0.11), residues: 5372 helix: 2.13 (0.09), residues: 2988 sheet: -0.52 (0.25), residues: 400 loop : 0.05 (0.14), residues: 1984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 517 TYR 0.014 0.001 TYR D 979 PHE 0.017 0.001 PHE A1355 TRP 0.016 0.001 TRP A1052 HIS 0.004 0.001 HIS B 660 Details of bonding type rmsd covalent geometry : bond 0.00260 (40144) covalent geometry : angle 0.49024 (54816) SS BOND : bond 0.00053 ( 4) SS BOND : angle 0.43235 ( 8) hydrogen bonds : bond 0.04196 ( 2336) hydrogen bonds : angle 3.94553 ( 6852) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10744 Ramachandran restraints generated. 5372 Oldfield, 0 Emsley, 5372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10744 Ramachandran restraints generated. 5372 Oldfield, 0 Emsley, 5372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 4632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 366 time to evaluate : 1.558 Fit side-chains REVERT: A 81 MET cc_start: 0.7740 (ptt) cc_final: 0.7421 (ptm) REVERT: A 96 TRP cc_start: 0.7638 (p-90) cc_final: 0.7071 (p-90) REVERT: A 129 MET cc_start: 0.7554 (mmt) cc_final: 0.7312 (mmp) REVERT: A 197 GLU cc_start: 0.6395 (tt0) cc_final: 0.6135 (pt0) REVERT: A 223 ASP cc_start: 0.7940 (m-30) cc_final: 0.7560 (t70) REVERT: A 342 PHE cc_start: 0.7669 (m-80) cc_final: 0.7114 (m-80) REVERT: A 345 TYR cc_start: 0.8150 (m-10) cc_final: 0.7731 (m-80) REVERT: A 374 LEU cc_start: 0.7593 (OUTLIER) cc_final: 0.7350 (mm) REVERT: A 461 HIS cc_start: 0.7908 (OUTLIER) cc_final: 0.7237 (p90) REVERT: A 523 ASN cc_start: 0.8306 (t0) cc_final: 0.7630 (p0) REVERT: A 560 MET cc_start: 0.8533 (mmm) cc_final: 0.8167 (mmm) REVERT: A 566 ARG cc_start: 0.7970 (OUTLIER) cc_final: 0.7048 (mtp180) REVERT: A 598 GLN cc_start: 0.8375 (OUTLIER) cc_final: 0.8051 (tt0) REVERT: A 663 LYS cc_start: 0.8302 (mttp) cc_final: 0.7933 (mppt) REVERT: A 694 MET cc_start: 0.8362 (ttm) cc_final: 0.8098 (ttm) REVERT: A 1051 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8406 (tp) REVERT: A 1083 PHE cc_start: 0.6106 (t80) cc_final: 0.5719 (t80) REVERT: A 1085 ARG cc_start: 0.4877 (tpp80) cc_final: 0.4599 (ttt180) REVERT: A 1128 ARG cc_start: 0.8065 (ttp80) cc_final: 0.7688 (ttm-80) REVERT: A 1131 MET cc_start: 0.7610 (OUTLIER) cc_final: 0.6344 (mpp) REVERT: A 1157 MET cc_start: 0.8505 (tpp) cc_final: 0.8166 (tpt) REVERT: B 61 ASN cc_start: 0.6229 (m-40) cc_final: 0.5807 (m-40) REVERT: B 81 MET cc_start: 0.7740 (ptt) cc_final: 0.7392 (ptm) REVERT: B 96 TRP cc_start: 0.7613 (p-90) cc_final: 0.7072 (p-90) REVERT: B 129 MET cc_start: 0.7570 (mmt) cc_final: 0.7325 (mmp) REVERT: B 197 GLU cc_start: 0.6400 (tt0) cc_final: 0.6142 (pt0) REVERT: B 223 ASP cc_start: 0.7946 (m-30) cc_final: 0.7563 (t70) REVERT: B 313 THR cc_start: 0.8205 (m) cc_final: 0.8005 (m) REVERT: B 342 PHE cc_start: 0.7672 (m-80) cc_final: 0.7122 (m-80) REVERT: B 345 TYR cc_start: 0.8192 (m-10) cc_final: 0.7796 (m-80) REVERT: B 374 LEU cc_start: 0.7644 (OUTLIER) cc_final: 0.7442 (mm) REVERT: B 461 HIS cc_start: 0.7913 (OUTLIER) cc_final: 0.7233 (p90) REVERT: B 566 ARG cc_start: 0.7977 (OUTLIER) cc_final: 0.7044 (mtp180) REVERT: B 663 LYS cc_start: 0.8285 (mttp) cc_final: 0.7920 (mppt) REVERT: B 694 MET cc_start: 0.8385 (ttm) cc_final: 0.8122 (ttm) REVERT: B 1051 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8409 (tp) REVERT: B 1083 PHE cc_start: 0.6112 (t80) cc_final: 0.5723 (t80) REVERT: B 1085 ARG cc_start: 0.4887 (tpp80) cc_final: 0.4615 (ttt180) REVERT: B 1128 ARG cc_start: 0.8056 (ttp80) cc_final: 0.7686 (ttm-80) REVERT: B 1131 MET cc_start: 0.7629 (OUTLIER) cc_final: 0.6370 (mpp) REVERT: B 1157 MET cc_start: 0.8459 (tpp) cc_final: 0.8121 (tpt) REVERT: C 81 MET cc_start: 0.7750 (ptt) cc_final: 0.7398 (ptm) REVERT: C 96 TRP cc_start: 0.7594 (p-90) cc_final: 0.7033 (p-90) REVERT: C 197 GLU cc_start: 0.6338 (tt0) cc_final: 0.5677 (pp20) REVERT: C 223 ASP cc_start: 0.7926 (m-30) cc_final: 0.7495 (t70) REVERT: C 248 THR cc_start: 0.6954 (OUTLIER) cc_final: 0.6681 (t) REVERT: C 342 PHE cc_start: 0.7652 (m-80) cc_final: 0.7100 (m-80) REVERT: C 345 TYR cc_start: 0.8164 (m-10) cc_final: 0.7755 (m-80) REVERT: C 374 LEU cc_start: 0.7567 (OUTLIER) cc_final: 0.7301 (mm) REVERT: C 461 HIS cc_start: 0.7859 (OUTLIER) cc_final: 0.7236 (p90) REVERT: C 469 PHE cc_start: 0.7651 (OUTLIER) cc_final: 0.7439 (t80) REVERT: C 560 MET cc_start: 0.8542 (mmm) cc_final: 0.8176 (mmm) REVERT: C 566 ARG cc_start: 0.7975 (OUTLIER) cc_final: 0.7056 (mtp180) REVERT: C 663 LYS cc_start: 0.8290 (mttp) cc_final: 0.7919 (mppt) REVERT: C 694 MET cc_start: 0.8348 (ttm) cc_final: 0.8087 (ttm) REVERT: C 1051 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8399 (tp) REVERT: C 1083 PHE cc_start: 0.6099 (t80) cc_final: 0.5707 (t80) REVERT: C 1085 ARG cc_start: 0.4878 (tpp80) cc_final: 0.4608 (ttt180) REVERT: C 1128 ARG cc_start: 0.8063 (ttp80) cc_final: 0.7688 (ttm-80) REVERT: C 1131 MET cc_start: 0.7644 (OUTLIER) cc_final: 0.6383 (mpp) REVERT: C 1157 MET cc_start: 0.8506 (tpp) cc_final: 0.8153 (tpt) REVERT: D 81 MET cc_start: 0.7733 (ptt) cc_final: 0.7377 (ptm) REVERT: D 96 TRP cc_start: 0.7616 (p-90) cc_final: 0.7072 (p-90) REVERT: D 129 MET cc_start: 0.7689 (mmt) cc_final: 0.7440 (mmp) REVERT: D 197 GLU cc_start: 0.6366 (tt0) cc_final: 0.6105 (pt0) REVERT: D 223 ASP cc_start: 0.7937 (m-30) cc_final: 0.7560 (t70) REVERT: D 342 PHE cc_start: 0.7674 (m-80) cc_final: 0.7120 (m-80) REVERT: D 345 TYR cc_start: 0.8174 (m-10) cc_final: 0.7761 (m-80) REVERT: D 374 LEU cc_start: 0.7612 (OUTLIER) cc_final: 0.7357 (mm) REVERT: D 461 HIS cc_start: 0.7913 (OUTLIER) cc_final: 0.7235 (p90) REVERT: D 469 PHE cc_start: 0.7654 (OUTLIER) cc_final: 0.7439 (t80) REVERT: D 523 ASN cc_start: 0.8306 (t0) cc_final: 0.7634 (p0) REVERT: D 560 MET cc_start: 0.8529 (mmm) cc_final: 0.8163 (mmm) REVERT: D 566 ARG cc_start: 0.7979 (OUTLIER) cc_final: 0.7059 (mtp180) REVERT: D 663 LYS cc_start: 0.8308 (mttp) cc_final: 0.7940 (mppt) REVERT: D 694 MET cc_start: 0.8386 (ttm) cc_final: 0.8125 (ttm) REVERT: D 1051 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8404 (tp) REVERT: D 1083 PHE cc_start: 0.6151 (t80) cc_final: 0.5740 (t80) REVERT: D 1085 ARG cc_start: 0.4889 (tpp80) cc_final: 0.4618 (ttt180) REVERT: D 1128 ARG cc_start: 0.8061 (ttp80) cc_final: 0.7684 (ttm-80) REVERT: D 1131 MET cc_start: 0.7625 (OUTLIER) cc_final: 0.6360 (mpp) REVERT: D 1157 MET cc_start: 0.8501 (tpp) cc_final: 0.8154 (tpt) outliers start: 98 outliers final: 12 residues processed: 421 average time/residue: 0.6890 time to fit residues: 358.2207 Evaluate side-chains 364 residues out of total 4632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 328 time to evaluate : 1.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 461 HIS Chi-restraints excluded: chain A residue 566 ARG Chi-restraints excluded: chain A residue 598 GLN Chi-restraints excluded: chain A residue 907 VAL Chi-restraints excluded: chain A residue 1051 LEU Chi-restraints excluded: chain A residue 1115 LEU Chi-restraints excluded: chain A residue 1131 MET Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 461 HIS Chi-restraints excluded: chain B residue 566 ARG Chi-restraints excluded: chain B residue 907 VAL Chi-restraints excluded: chain B residue 1051 LEU Chi-restraints excluded: chain B residue 1115 LEU Chi-restraints excluded: chain B residue 1131 MET Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 374 LEU Chi-restraints excluded: chain C residue 461 HIS Chi-restraints excluded: chain C residue 469 PHE Chi-restraints excluded: chain C residue 566 ARG Chi-restraints excluded: chain C residue 907 VAL Chi-restraints excluded: chain C residue 1001 THR Chi-restraints excluded: chain C residue 1051 LEU Chi-restraints excluded: chain C residue 1115 LEU Chi-restraints excluded: chain C residue 1131 MET Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain D residue 461 HIS Chi-restraints excluded: chain D residue 469 PHE Chi-restraints excluded: chain D residue 566 ARG Chi-restraints excluded: chain D residue 907 VAL Chi-restraints excluded: chain D residue 1051 LEU Chi-restraints excluded: chain D residue 1115 LEU Chi-restraints excluded: chain D residue 1131 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 98 optimal weight: 5.9990 chunk 494 optimal weight: 1.9990 chunk 140 optimal weight: 10.0000 chunk 205 optimal weight: 4.9990 chunk 302 optimal weight: 7.9990 chunk 531 optimal weight: 9.9990 chunk 448 optimal weight: 1.9990 chunk 306 optimal weight: 10.0000 chunk 343 optimal weight: 1.9990 chunk 177 optimal weight: 8.9990 chunk 229 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 598 GLN A 992 ASN A1156 HIS B 440 HIS B 992 ASN B1156 HIS C 440 HIS C 992 ASN C1156 HIS D 440 HIS D 992 ASN D1045 GLN D1156 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.163568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.097001 restraints weight = 59607.089| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 2.10 r_work: 0.3053 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.3234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 40148 Z= 0.236 Angle : 0.600 9.090 54824 Z= 0.311 Chirality : 0.043 0.177 6428 Planarity : 0.004 0.045 7036 Dihedral : 5.114 58.066 6500 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.34 % Allowed : 12.50 % Favored : 84.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.46 (0.11), residues: 5372 helix: 1.82 (0.09), residues: 2972 sheet: -0.58 (0.25), residues: 372 loop : 0.09 (0.14), residues: 2028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 655 TYR 0.020 0.002 TYR B 979 PHE 0.019 0.002 PHE B 268 TRP 0.019 0.002 TRP C 726 HIS 0.005 0.002 HIS B 813 Details of bonding type rmsd covalent geometry : bond 0.00571 (40144) covalent geometry : angle 0.59978 (54816) SS BOND : bond 0.00186 ( 4) SS BOND : angle 0.82747 ( 8) hydrogen bonds : bond 0.05863 ( 2336) hydrogen bonds : angle 4.29092 ( 6852) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10744 Ramachandran restraints generated. 5372 Oldfield, 0 Emsley, 5372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10744 Ramachandran restraints generated. 5372 Oldfield, 0 Emsley, 5372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 4632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 348 time to evaluate : 1.610 Fit side-chains REVERT: A 96 TRP cc_start: 0.7696 (p-90) cc_final: 0.7169 (p-90) REVERT: A 129 MET cc_start: 0.7721 (mmt) cc_final: 0.7398 (mmp) REVERT: A 197 GLU cc_start: 0.6781 (tt0) cc_final: 0.6086 (pp20) REVERT: A 223 ASP cc_start: 0.8041 (m-30) cc_final: 0.7449 (t0) REVERT: A 342 PHE cc_start: 0.7732 (m-80) cc_final: 0.7136 (m-80) REVERT: A 345 TYR cc_start: 0.8327 (m-10) cc_final: 0.7817 (m-80) REVERT: A 374 LEU cc_start: 0.7577 (OUTLIER) cc_final: 0.7301 (mm) REVERT: A 461 HIS cc_start: 0.7930 (OUTLIER) cc_final: 0.7258 (p90) REVERT: A 566 ARG cc_start: 0.8195 (OUTLIER) cc_final: 0.7288 (mtp180) REVERT: A 663 LYS cc_start: 0.8501 (mttp) cc_final: 0.8213 (mppt) REVERT: A 694 MET cc_start: 0.8496 (ttm) cc_final: 0.8259 (ttm) REVERT: A 805 ARG cc_start: 0.8675 (OUTLIER) cc_final: 0.8119 (mtp85) REVERT: A 865 SER cc_start: 0.8249 (m) cc_final: 0.8028 (p) REVERT: A 1083 PHE cc_start: 0.6203 (t80) cc_final: 0.5831 (t80) REVERT: A 1085 ARG cc_start: 0.5025 (tpp80) cc_final: 0.4755 (ttt180) REVERT: A 1131 MET cc_start: 0.8050 (OUTLIER) cc_final: 0.7580 (mmm) REVERT: A 1157 MET cc_start: 0.8542 (tpp) cc_final: 0.8309 (tpt) REVERT: A 1335 ARG cc_start: 0.6663 (OUTLIER) cc_final: 0.6432 (ptp90) REVERT: A 1493 TYR cc_start: 0.7117 (t80) cc_final: 0.6653 (t80) REVERT: B 61 ASN cc_start: 0.6305 (m-40) cc_final: 0.5928 (m-40) REVERT: B 96 TRP cc_start: 0.7709 (p-90) cc_final: 0.7173 (p-90) REVERT: B 129 MET cc_start: 0.7722 (mmt) cc_final: 0.7398 (mmp) REVERT: B 197 GLU cc_start: 0.6776 (tt0) cc_final: 0.6085 (pp20) REVERT: B 223 ASP cc_start: 0.8047 (m-30) cc_final: 0.7459 (t0) REVERT: B 345 TYR cc_start: 0.8345 (m-10) cc_final: 0.7715 (m-80) REVERT: B 374 LEU cc_start: 0.7543 (OUTLIER) cc_final: 0.7263 (mm) REVERT: B 461 HIS cc_start: 0.7951 (OUTLIER) cc_final: 0.7227 (p90) REVERT: B 566 ARG cc_start: 0.8204 (OUTLIER) cc_final: 0.7278 (mtp180) REVERT: B 663 LYS cc_start: 0.8491 (mttp) cc_final: 0.8205 (mppt) REVERT: B 694 MET cc_start: 0.8501 (ttm) cc_final: 0.8259 (ttm) REVERT: B 805 ARG cc_start: 0.8677 (OUTLIER) cc_final: 0.8151 (mtp85) REVERT: B 865 SER cc_start: 0.8249 (m) cc_final: 0.8026 (p) REVERT: B 1083 PHE cc_start: 0.6202 (t80) cc_final: 0.5829 (t80) REVERT: B 1085 ARG cc_start: 0.5019 (tpp80) cc_final: 0.4752 (ttt180) REVERT: B 1131 MET cc_start: 0.8052 (OUTLIER) cc_final: 0.7578 (mmm) REVERT: B 1157 MET cc_start: 0.8532 (tpp) cc_final: 0.8308 (tpt) REVERT: B 1335 ARG cc_start: 0.6691 (OUTLIER) cc_final: 0.6468 (ptp90) REVERT: B 1493 TYR cc_start: 0.7128 (t80) cc_final: 0.6667 (t80) REVERT: C 96 TRP cc_start: 0.7701 (p-90) cc_final: 0.7172 (p-90) REVERT: C 197 GLU cc_start: 0.6751 (tt0) cc_final: 0.6058 (pp20) REVERT: C 223 ASP cc_start: 0.8049 (m-30) cc_final: 0.7469 (t0) REVERT: C 342 PHE cc_start: 0.7702 (m-80) cc_final: 0.7109 (m-80) REVERT: C 345 TYR cc_start: 0.8323 (m-10) cc_final: 0.7836 (m-80) REVERT: C 374 LEU cc_start: 0.7569 (OUTLIER) cc_final: 0.7291 (mm) REVERT: C 461 HIS cc_start: 0.7906 (OUTLIER) cc_final: 0.7272 (p90) REVERT: C 566 ARG cc_start: 0.8203 (OUTLIER) cc_final: 0.7286 (mtp180) REVERT: C 663 LYS cc_start: 0.8487 (mttp) cc_final: 0.8197 (mppt) REVERT: C 694 MET cc_start: 0.8510 (ttm) cc_final: 0.8268 (ttm) REVERT: C 805 ARG cc_start: 0.8673 (OUTLIER) cc_final: 0.8131 (mtp85) REVERT: C 865 SER cc_start: 0.8235 (m) cc_final: 0.8010 (p) REVERT: C 1083 PHE cc_start: 0.6198 (t80) cc_final: 0.5827 (t80) REVERT: C 1085 ARG cc_start: 0.5016 (tpp80) cc_final: 0.4748 (ttt180) REVERT: C 1131 MET cc_start: 0.8057 (OUTLIER) cc_final: 0.7584 (mmm) REVERT: C 1157 MET cc_start: 0.8580 (tpp) cc_final: 0.8337 (tpt) REVERT: C 1335 ARG cc_start: 0.6672 (OUTLIER) cc_final: 0.6456 (ptp90) REVERT: C 1468 MET cc_start: 0.6178 (OUTLIER) cc_final: 0.5948 (ppp) REVERT: C 1493 TYR cc_start: 0.7036 (t80) cc_final: 0.6624 (t80) REVERT: D 96 TRP cc_start: 0.7701 (p-90) cc_final: 0.7148 (p-90) REVERT: D 129 MET cc_start: 0.7892 (mmt) cc_final: 0.7541 (mmp) REVERT: D 197 GLU cc_start: 0.6779 (tt0) cc_final: 0.6083 (pp20) REVERT: D 223 ASP cc_start: 0.8043 (m-30) cc_final: 0.7455 (t0) REVERT: D 342 PHE cc_start: 0.7723 (m-80) cc_final: 0.7130 (m-80) REVERT: D 345 TYR cc_start: 0.8328 (m-10) cc_final: 0.7824 (m-80) REVERT: D 374 LEU cc_start: 0.7578 (OUTLIER) cc_final: 0.7308 (mm) REVERT: D 461 HIS cc_start: 0.7917 (OUTLIER) cc_final: 0.7183 (p90) REVERT: D 566 ARG cc_start: 0.8193 (OUTLIER) cc_final: 0.7284 (mtp180) REVERT: D 663 LYS cc_start: 0.8499 (mttp) cc_final: 0.8208 (mppt) REVERT: D 694 MET cc_start: 0.8507 (ttm) cc_final: 0.8269 (ttm) REVERT: D 805 ARG cc_start: 0.8674 (OUTLIER) cc_final: 0.8128 (mtp85) REVERT: D 865 SER cc_start: 0.8242 (m) cc_final: 0.8016 (p) REVERT: D 1083 PHE cc_start: 0.6196 (t80) cc_final: 0.5827 (t80) REVERT: D 1085 ARG cc_start: 0.5019 (tpp80) cc_final: 0.4750 (ttt180) REVERT: D 1131 MET cc_start: 0.8061 (OUTLIER) cc_final: 0.7586 (mmm) REVERT: D 1149 MET cc_start: 0.8472 (OUTLIER) cc_final: 0.7990 (mtp) REVERT: D 1157 MET cc_start: 0.8566 (tpp) cc_final: 0.8284 (tpt) REVERT: D 1335 ARG cc_start: 0.6683 (OUTLIER) cc_final: 0.6467 (ptp90) REVERT: D 1468 MET cc_start: 0.6185 (OUTLIER) cc_final: 0.5949 (ppp) REVERT: D 1493 TYR cc_start: 0.7045 (t80) cc_final: 0.6664 (t80) outliers start: 116 outliers final: 39 residues processed: 414 average time/residue: 0.7309 time to fit residues: 369.5197 Evaluate side-chains 397 residues out of total 4632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 331 time to evaluate : 1.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 189 MET Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 461 HIS Chi-restraints excluded: chain A residue 566 ARG Chi-restraints excluded: chain A residue 805 ARG Chi-restraints excluded: chain A residue 875 MET Chi-restraints excluded: chain A residue 930 MET Chi-restraints excluded: chain A residue 1131 MET Chi-restraints excluded: chain A residue 1138 MET Chi-restraints excluded: chain A residue 1335 ARG Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 189 MET Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 461 HIS Chi-restraints excluded: chain B residue 566 ARG Chi-restraints excluded: chain B residue 805 ARG Chi-restraints excluded: chain B residue 875 MET Chi-restraints excluded: chain B residue 930 MET Chi-restraints excluded: chain B residue 1131 MET Chi-restraints excluded: chain B residue 1138 MET Chi-restraints excluded: chain B residue 1335 ARG Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 189 MET Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 313 THR Chi-restraints excluded: chain C residue 340 THR Chi-restraints excluded: chain C residue 372 SER Chi-restraints excluded: chain C residue 374 LEU Chi-restraints excluded: chain C residue 461 HIS Chi-restraints excluded: chain C residue 566 ARG Chi-restraints excluded: chain C residue 805 ARG Chi-restraints excluded: chain C residue 875 MET Chi-restraints excluded: chain C residue 930 MET Chi-restraints excluded: chain C residue 1131 MET Chi-restraints excluded: chain C residue 1138 MET Chi-restraints excluded: chain C residue 1150 MET Chi-restraints excluded: chain C residue 1335 ARG Chi-restraints excluded: chain C residue 1468 MET Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 189 MET Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 313 THR Chi-restraints excluded: chain D residue 340 THR Chi-restraints excluded: chain D residue 372 SER Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain D residue 461 HIS Chi-restraints excluded: chain D residue 566 ARG Chi-restraints excluded: chain D residue 805 ARG Chi-restraints excluded: chain D residue 875 MET Chi-restraints excluded: chain D residue 930 MET Chi-restraints excluded: chain D residue 1131 MET Chi-restraints excluded: chain D residue 1138 MET Chi-restraints excluded: chain D residue 1149 MET Chi-restraints excluded: chain D residue 1150 MET Chi-restraints excluded: chain D residue 1335 ARG Chi-restraints excluded: chain D residue 1468 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 263 optimal weight: 4.9990 chunk 182 optimal weight: 8.9990 chunk 472 optimal weight: 4.9990 chunk 318 optimal weight: 8.9990 chunk 448 optimal weight: 0.0030 chunk 381 optimal weight: 20.0000 chunk 146 optimal weight: 7.9990 chunk 242 optimal weight: 2.9990 chunk 489 optimal weight: 1.9990 chunk 123 optimal weight: 30.0000 chunk 81 optimal weight: 2.9990 overall best weight: 2.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 598 GLN B 598 GLN C 598 GLN D 598 GLN D1152 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.163542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.106906 restraints weight = 59582.157| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 2.48 r_work: 0.3039 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.3545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 40148 Z= 0.196 Angle : 0.535 6.938 54824 Z= 0.279 Chirality : 0.041 0.174 6428 Planarity : 0.004 0.039 7036 Dihedral : 4.956 56.621 6500 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.92 % Allowed : 12.70 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.45 (0.11), residues: 5372 helix: 1.83 (0.09), residues: 2976 sheet: -0.80 (0.27), residues: 324 loop : 0.07 (0.14), residues: 2072 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 655 TYR 0.017 0.002 TYR A 979 PHE 0.020 0.002 PHE D 268 TRP 0.017 0.002 TRP B 726 HIS 0.004 0.001 HIS B 813 Details of bonding type rmsd covalent geometry : bond 0.00463 (40144) covalent geometry : angle 0.53489 (54816) SS BOND : bond 0.00241 ( 4) SS BOND : angle 0.61147 ( 8) hydrogen bonds : bond 0.05223 ( 2336) hydrogen bonds : angle 4.19081 ( 6852) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10744 Ramachandran restraints generated. 5372 Oldfield, 0 Emsley, 5372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10744 Ramachandran restraints generated. 5372 Oldfield, 0 Emsley, 5372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 4632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 340 time to evaluate : 1.654 Fit side-chains REVERT: A 96 TRP cc_start: 0.7649 (p-90) cc_final: 0.7050 (p-90) REVERT: A 129 MET cc_start: 0.7724 (mmt) cc_final: 0.7459 (mmp) REVERT: A 159 ARG cc_start: 0.5548 (mtp85) cc_final: 0.4100 (pmt170) REVERT: A 197 GLU cc_start: 0.6750 (tt0) cc_final: 0.6011 (pp20) REVERT: A 374 LEU cc_start: 0.7604 (OUTLIER) cc_final: 0.7395 (mm) REVERT: A 461 HIS cc_start: 0.7875 (OUTLIER) cc_final: 0.7157 (p90) REVERT: A 469 PHE cc_start: 0.7375 (OUTLIER) cc_final: 0.7114 (t80) REVERT: A 566 ARG cc_start: 0.8132 (OUTLIER) cc_final: 0.7148 (mtp180) REVERT: A 663 LYS cc_start: 0.8465 (mttp) cc_final: 0.8073 (mppt) REVERT: A 694 MET cc_start: 0.8349 (ttm) cc_final: 0.8086 (ttm) REVERT: A 865 SER cc_start: 0.8248 (m) cc_final: 0.7994 (p) REVERT: A 1038 ASN cc_start: 0.9079 (OUTLIER) cc_final: 0.8692 (m110) REVERT: A 1085 ARG cc_start: 0.4875 (tpp80) cc_final: 0.4643 (ttt180) REVERT: A 1131 MET cc_start: 0.7909 (OUTLIER) cc_final: 0.6575 (mpp) REVERT: A 1157 MET cc_start: 0.8486 (tpp) cc_final: 0.8273 (tpt) REVERT: A 1335 ARG cc_start: 0.6769 (OUTLIER) cc_final: 0.6480 (ptp90) REVERT: A 1493 TYR cc_start: 0.6945 (t80) cc_final: 0.6633 (t80) REVERT: B 61 ASN cc_start: 0.6400 (m-40) cc_final: 0.6026 (m-40) REVERT: B 96 TRP cc_start: 0.7643 (p-90) cc_final: 0.7043 (p-90) REVERT: B 129 MET cc_start: 0.7671 (mmt) cc_final: 0.7416 (mmp) REVERT: B 159 ARG cc_start: 0.5560 (mtp85) cc_final: 0.4114 (pmt170) REVERT: B 197 GLU cc_start: 0.6830 (tt0) cc_final: 0.6085 (pp20) REVERT: B 374 LEU cc_start: 0.7631 (OUTLIER) cc_final: 0.7398 (mm) REVERT: B 461 HIS cc_start: 0.7842 (OUTLIER) cc_final: 0.7055 (p90) REVERT: B 469 PHE cc_start: 0.7362 (OUTLIER) cc_final: 0.7094 (t80) REVERT: B 566 ARG cc_start: 0.8132 (OUTLIER) cc_final: 0.7140 (mtp180) REVERT: B 663 LYS cc_start: 0.8458 (mttp) cc_final: 0.8072 (mppt) REVERT: B 694 MET cc_start: 0.8349 (ttm) cc_final: 0.8086 (ttm) REVERT: B 865 SER cc_start: 0.8251 (m) cc_final: 0.7996 (p) REVERT: B 1038 ASN cc_start: 0.9076 (OUTLIER) cc_final: 0.8683 (m110) REVERT: B 1085 ARG cc_start: 0.4861 (tpp80) cc_final: 0.4631 (ttt180) REVERT: B 1131 MET cc_start: 0.7923 (OUTLIER) cc_final: 0.6578 (mpp) REVERT: B 1335 ARG cc_start: 0.6783 (OUTLIER) cc_final: 0.6504 (ptp90) REVERT: B 1493 TYR cc_start: 0.6963 (t80) cc_final: 0.6654 (t80) REVERT: C 96 TRP cc_start: 0.7652 (p-90) cc_final: 0.7052 (p-90) REVERT: C 159 ARG cc_start: 0.5494 (mtp85) cc_final: 0.4085 (pmt170) REVERT: C 197 GLU cc_start: 0.6732 (tt0) cc_final: 0.6003 (pp20) REVERT: C 223 ASP cc_start: 0.8222 (m-30) cc_final: 0.7497 (t0) REVERT: C 374 LEU cc_start: 0.7619 (OUTLIER) cc_final: 0.7401 (mm) REVERT: C 461 HIS cc_start: 0.7801 (OUTLIER) cc_final: 0.7105 (p90) REVERT: C 469 PHE cc_start: 0.7380 (OUTLIER) cc_final: 0.7102 (t80) REVERT: C 566 ARG cc_start: 0.8125 (OUTLIER) cc_final: 0.7141 (mtp180) REVERT: C 663 LYS cc_start: 0.8447 (mttp) cc_final: 0.8070 (mppt) REVERT: C 694 MET cc_start: 0.8336 (ttm) cc_final: 0.8077 (ttm) REVERT: C 865 SER cc_start: 0.8234 (m) cc_final: 0.7975 (p) REVERT: C 1038 ASN cc_start: 0.9083 (OUTLIER) cc_final: 0.8703 (m110) REVERT: C 1085 ARG cc_start: 0.4858 (tpp80) cc_final: 0.4629 (ttt180) REVERT: C 1131 MET cc_start: 0.7904 (OUTLIER) cc_final: 0.6572 (mpp) REVERT: C 1493 TYR cc_start: 0.6935 (t80) cc_final: 0.6678 (t80) REVERT: D 96 TRP cc_start: 0.7643 (p-90) cc_final: 0.7035 (p-90) REVERT: D 129 MET cc_start: 0.7855 (mmt) cc_final: 0.7570 (mmp) REVERT: D 159 ARG cc_start: 0.5520 (mtp85) cc_final: 0.4104 (pmt170) REVERT: D 197 GLU cc_start: 0.6751 (tt0) cc_final: 0.6008 (pp20) REVERT: D 330 TYR cc_start: 0.8009 (t80) cc_final: 0.7801 (t80) REVERT: D 374 LEU cc_start: 0.7610 (OUTLIER) cc_final: 0.7398 (mm) REVERT: D 461 HIS cc_start: 0.7843 (OUTLIER) cc_final: 0.7056 (p90) REVERT: D 469 PHE cc_start: 0.7369 (OUTLIER) cc_final: 0.7093 (t80) REVERT: D 566 ARG cc_start: 0.8126 (OUTLIER) cc_final: 0.7142 (mtp180) REVERT: D 663 LYS cc_start: 0.8407 (mttp) cc_final: 0.8031 (mppt) REVERT: D 694 MET cc_start: 0.8349 (ttm) cc_final: 0.8088 (ttm) REVERT: D 865 SER cc_start: 0.8239 (m) cc_final: 0.7982 (p) REVERT: D 1038 ASN cc_start: 0.9074 (OUTLIER) cc_final: 0.8682 (m110) REVERT: D 1085 ARG cc_start: 0.4855 (tpp80) cc_final: 0.4624 (ttt180) REVERT: D 1131 MET cc_start: 0.7936 (OUTLIER) cc_final: 0.6581 (mpp) REVERT: D 1149 MET cc_start: 0.8469 (OUTLIER) cc_final: 0.8006 (mtp) REVERT: D 1335 ARG cc_start: 0.6751 (OUTLIER) cc_final: 0.6531 (ptp90) REVERT: D 1493 TYR cc_start: 0.6945 (t80) cc_final: 0.6628 (t80) outliers start: 136 outliers final: 44 residues processed: 428 average time/residue: 0.7359 time to fit residues: 384.5816 Evaluate side-chains 389 residues out of total 4632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 317 time to evaluate : 1.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 189 MET Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 461 HIS Chi-restraints excluded: chain A residue 469 PHE Chi-restraints excluded: chain A residue 566 ARG Chi-restraints excluded: chain A residue 805 ARG Chi-restraints excluded: chain A residue 875 MET Chi-restraints excluded: chain A residue 907 VAL Chi-restraints excluded: chain A residue 1038 ASN Chi-restraints excluded: chain A residue 1115 LEU Chi-restraints excluded: chain A residue 1131 MET Chi-restraints excluded: chain A residue 1138 MET Chi-restraints excluded: chain A residue 1150 MET Chi-restraints excluded: chain A residue 1335 ARG Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 189 MET Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 461 HIS Chi-restraints excluded: chain B residue 469 PHE Chi-restraints excluded: chain B residue 566 ARG Chi-restraints excluded: chain B residue 805 ARG Chi-restraints excluded: chain B residue 875 MET Chi-restraints excluded: chain B residue 907 VAL Chi-restraints excluded: chain B residue 1038 ASN Chi-restraints excluded: chain B residue 1115 LEU Chi-restraints excluded: chain B residue 1131 MET Chi-restraints excluded: chain B residue 1138 MET Chi-restraints excluded: chain B residue 1150 MET Chi-restraints excluded: chain B residue 1335 ARG Chi-restraints excluded: chain B residue 1355 PHE Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 189 MET Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain C residue 313 THR Chi-restraints excluded: chain C residue 372 SER Chi-restraints excluded: chain C residue 374 LEU Chi-restraints excluded: chain C residue 461 HIS Chi-restraints excluded: chain C residue 469 PHE Chi-restraints excluded: chain C residue 566 ARG Chi-restraints excluded: chain C residue 805 ARG Chi-restraints excluded: chain C residue 875 MET Chi-restraints excluded: chain C residue 907 VAL Chi-restraints excluded: chain C residue 1038 ASN Chi-restraints excluded: chain C residue 1115 LEU Chi-restraints excluded: chain C residue 1131 MET Chi-restraints excluded: chain C residue 1138 MET Chi-restraints excluded: chain C residue 1150 MET Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 189 MET Chi-restraints excluded: chain D residue 293 ILE Chi-restraints excluded: chain D residue 313 THR Chi-restraints excluded: chain D residue 372 SER Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain D residue 461 HIS Chi-restraints excluded: chain D residue 469 PHE Chi-restraints excluded: chain D residue 566 ARG Chi-restraints excluded: chain D residue 805 ARG Chi-restraints excluded: chain D residue 875 MET Chi-restraints excluded: chain D residue 907 VAL Chi-restraints excluded: chain D residue 1038 ASN Chi-restraints excluded: chain D residue 1131 MET Chi-restraints excluded: chain D residue 1138 MET Chi-restraints excluded: chain D residue 1149 MET Chi-restraints excluded: chain D residue 1335 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 156 optimal weight: 5.9990 chunk 83 optimal weight: 0.6980 chunk 164 optimal weight: 0.8980 chunk 174 optimal weight: 0.9980 chunk 414 optimal weight: 0.0980 chunk 76 optimal weight: 0.9990 chunk 503 optimal weight: 3.9990 chunk 239 optimal weight: 2.9990 chunk 478 optimal weight: 0.8980 chunk 22 optimal weight: 9.9990 chunk 280 optimal weight: 10.0000 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 598 GLN A 702 ASN B 598 GLN C 598 GLN D 598 GLN D 702 ASN D1152 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.165135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.099665 restraints weight = 60017.854| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 2.09 r_work: 0.3091 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.3601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 40148 Z= 0.104 Angle : 0.462 7.355 54824 Z= 0.238 Chirality : 0.037 0.138 6428 Planarity : 0.003 0.039 7036 Dihedral : 4.715 56.414 6500 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 3.02 % Allowed : 14.57 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.78 (0.12), residues: 5372 helix: 2.18 (0.10), residues: 2980 sheet: -0.74 (0.28), residues: 324 loop : 0.09 (0.14), residues: 2068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 517 TYR 0.016 0.001 TYR B 345 PHE 0.015 0.001 PHE D 268 TRP 0.015 0.001 TRP C1052 HIS 0.003 0.001 HIS A 813 Details of bonding type rmsd covalent geometry : bond 0.00222 (40144) covalent geometry : angle 0.46167 (54816) SS BOND : bond 0.00073 ( 4) SS BOND : angle 0.42611 ( 8) hydrogen bonds : bond 0.04004 ( 2336) hydrogen bonds : angle 3.97115 ( 6852) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10744 Ramachandran restraints generated. 5372 Oldfield, 0 Emsley, 5372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10744 Ramachandran restraints generated. 5372 Oldfield, 0 Emsley, 5372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 4632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 329 time to evaluate : 1.690 Fit side-chains revert: symmetry clash REVERT: A 96 TRP cc_start: 0.7546 (p-90) cc_final: 0.7082 (p-90) REVERT: A 129 MET cc_start: 0.7687 (mmt) cc_final: 0.7440 (mmp) REVERT: A 159 ARG cc_start: 0.5577 (mtp85) cc_final: 0.4138 (pmt170) REVERT: A 197 GLU cc_start: 0.6723 (tt0) cc_final: 0.5992 (pp20) REVERT: A 342 PHE cc_start: 0.7570 (m-80) cc_final: 0.7207 (m-80) REVERT: A 345 TYR cc_start: 0.8263 (m-10) cc_final: 0.7926 (m-80) REVERT: A 374 LEU cc_start: 0.7618 (OUTLIER) cc_final: 0.7385 (mm) REVERT: A 461 HIS cc_start: 0.7894 (OUTLIER) cc_final: 0.7178 (p90) REVERT: A 469 PHE cc_start: 0.7400 (OUTLIER) cc_final: 0.7110 (t80) REVERT: A 566 ARG cc_start: 0.8052 (OUTLIER) cc_final: 0.7085 (mtp180) REVERT: A 663 LYS cc_start: 0.8378 (mttp) cc_final: 0.8029 (mppt) REVERT: A 694 MET cc_start: 0.8261 (ttm) cc_final: 0.8040 (ttm) REVERT: A 865 SER cc_start: 0.8232 (m) cc_final: 0.7974 (p) REVERT: A 934 MET cc_start: 0.8538 (OUTLIER) cc_final: 0.8209 (mtp) REVERT: A 1038 ASN cc_start: 0.8961 (OUTLIER) cc_final: 0.8494 (m110) REVERT: A 1085 ARG cc_start: 0.4882 (tpp80) cc_final: 0.4653 (ttt180) REVERT: A 1131 MET cc_start: 0.7744 (OUTLIER) cc_final: 0.6439 (mpp) REVERT: A 1157 MET cc_start: 0.8557 (tpp) cc_final: 0.8139 (tpt) REVERT: A 1335 ARG cc_start: 0.6529 (OUTLIER) cc_final: 0.6254 (ptp90) REVERT: A 1493 TYR cc_start: 0.7056 (t80) cc_final: 0.6781 (t80) REVERT: B 61 ASN cc_start: 0.6429 (m-40) cc_final: 0.6093 (m-40) REVERT: B 96 TRP cc_start: 0.7547 (p-90) cc_final: 0.7075 (p-90) REVERT: B 129 MET cc_start: 0.7625 (mmt) cc_final: 0.7370 (mmp) REVERT: B 159 ARG cc_start: 0.5588 (mtp85) cc_final: 0.4151 (pmt170) REVERT: B 197 GLU cc_start: 0.6733 (tt0) cc_final: 0.6002 (pp20) REVERT: B 342 PHE cc_start: 0.7343 (m-80) cc_final: 0.6997 (m-80) REVERT: B 345 TYR cc_start: 0.8317 (m-10) cc_final: 0.8014 (m-80) REVERT: B 461 HIS cc_start: 0.7918 (OUTLIER) cc_final: 0.7198 (p90) REVERT: B 469 PHE cc_start: 0.7392 (OUTLIER) cc_final: 0.7107 (t80) REVERT: B 566 ARG cc_start: 0.8052 (OUTLIER) cc_final: 0.7077 (mtp180) REVERT: B 663 LYS cc_start: 0.8374 (mttp) cc_final: 0.8028 (mppt) REVERT: B 694 MET cc_start: 0.8269 (ttm) cc_final: 0.8043 (ttm) REVERT: B 865 SER cc_start: 0.8112 (m) cc_final: 0.7884 (p) REVERT: B 934 MET cc_start: 0.8543 (OUTLIER) cc_final: 0.8219 (mtp) REVERT: B 1038 ASN cc_start: 0.8967 (OUTLIER) cc_final: 0.8507 (m110) REVERT: B 1085 ARG cc_start: 0.4882 (tpp80) cc_final: 0.4655 (ttt180) REVERT: B 1131 MET cc_start: 0.7734 (OUTLIER) cc_final: 0.6431 (mpp) REVERT: B 1493 TYR cc_start: 0.7061 (t80) cc_final: 0.6781 (t80) REVERT: C 81 MET cc_start: 0.7563 (ptt) cc_final: 0.7356 (ptp) REVERT: C 96 TRP cc_start: 0.7605 (p-90) cc_final: 0.7132 (p-90) REVERT: C 159 ARG cc_start: 0.5527 (mtp85) cc_final: 0.4116 (pmt170) REVERT: C 197 GLU cc_start: 0.6701 (tt0) cc_final: 0.5982 (pp20) REVERT: C 342 PHE cc_start: 0.7546 (m-80) cc_final: 0.7181 (m-80) REVERT: C 345 TYR cc_start: 0.8251 (m-10) cc_final: 0.7925 (m-80) REVERT: C 374 LEU cc_start: 0.7606 (OUTLIER) cc_final: 0.7356 (mm) REVERT: C 461 HIS cc_start: 0.7834 (OUTLIER) cc_final: 0.7146 (p90) REVERT: C 469 PHE cc_start: 0.7349 (OUTLIER) cc_final: 0.7097 (t80) REVERT: C 566 ARG cc_start: 0.8033 (OUTLIER) cc_final: 0.7064 (mtp180) REVERT: C 663 LYS cc_start: 0.8366 (mttp) cc_final: 0.8028 (mppt) REVERT: C 694 MET cc_start: 0.8257 (ttm) cc_final: 0.8029 (ttm) REVERT: C 865 SER cc_start: 0.8150 (m) cc_final: 0.7927 (p) REVERT: C 934 MET cc_start: 0.8538 (OUTLIER) cc_final: 0.8215 (mtp) REVERT: C 1038 ASN cc_start: 0.8961 (OUTLIER) cc_final: 0.8495 (m110) REVERT: C 1131 MET cc_start: 0.7755 (OUTLIER) cc_final: 0.6453 (mpp) REVERT: C 1160 PHE cc_start: 0.7246 (OUTLIER) cc_final: 0.6929 (t80) REVERT: C 1493 TYR cc_start: 0.7038 (t80) cc_final: 0.6789 (t80) REVERT: D 96 TRP cc_start: 0.7592 (p-90) cc_final: 0.7100 (p-90) REVERT: D 129 MET cc_start: 0.7803 (mmt) cc_final: 0.7513 (mmp) REVERT: D 159 ARG cc_start: 0.5549 (mtp85) cc_final: 0.4132 (pmt170) REVERT: D 197 GLU cc_start: 0.6715 (tt0) cc_final: 0.5986 (pp20) REVERT: D 342 PHE cc_start: 0.7565 (m-80) cc_final: 0.7193 (m-80) REVERT: D 345 TYR cc_start: 0.8256 (m-10) cc_final: 0.7899 (m-80) REVERT: D 374 LEU cc_start: 0.7625 (OUTLIER) cc_final: 0.7355 (mm) REVERT: D 461 HIS cc_start: 0.7919 (OUTLIER) cc_final: 0.7135 (p90) REVERT: D 469 PHE cc_start: 0.7336 (OUTLIER) cc_final: 0.7085 (t80) REVERT: D 566 ARG cc_start: 0.8059 (OUTLIER) cc_final: 0.7096 (mtp180) REVERT: D 663 LYS cc_start: 0.8382 (mttp) cc_final: 0.8034 (mppt) REVERT: D 694 MET cc_start: 0.8275 (ttm) cc_final: 0.8045 (ttm) REVERT: D 865 SER cc_start: 0.8152 (m) cc_final: 0.7929 (p) REVERT: D 934 MET cc_start: 0.8539 (OUTLIER) cc_final: 0.8206 (mtp) REVERT: D 1038 ASN cc_start: 0.8953 (OUTLIER) cc_final: 0.8487 (m110) REVERT: D 1085 ARG cc_start: 0.4862 (tpp80) cc_final: 0.4633 (ttt180) REVERT: D 1131 MET cc_start: 0.7734 (OUTLIER) cc_final: 0.6428 (mpp) REVERT: D 1149 MET cc_start: 0.8477 (OUTLIER) cc_final: 0.7998 (mtp) REVERT: D 1160 PHE cc_start: 0.7210 (OUTLIER) cc_final: 0.6907 (t80) REVERT: D 1493 TYR cc_start: 0.7055 (t80) cc_final: 0.6811 (t80) outliers start: 105 outliers final: 37 residues processed: 406 average time/residue: 0.7223 time to fit residues: 358.6134 Evaluate side-chains 391 residues out of total 4632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 323 time to evaluate : 1.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 189 MET Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 461 HIS Chi-restraints excluded: chain A residue 469 PHE Chi-restraints excluded: chain A residue 566 ARG Chi-restraints excluded: chain A residue 875 MET Chi-restraints excluded: chain A residue 907 VAL Chi-restraints excluded: chain A residue 934 MET Chi-restraints excluded: chain A residue 1011 VAL Chi-restraints excluded: chain A residue 1038 ASN Chi-restraints excluded: chain A residue 1131 MET Chi-restraints excluded: chain A residue 1138 MET Chi-restraints excluded: chain A residue 1333 VAL Chi-restraints excluded: chain A residue 1335 ARG Chi-restraints excluded: chain A residue 1355 PHE Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 189 MET Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 461 HIS Chi-restraints excluded: chain B residue 469 PHE Chi-restraints excluded: chain B residue 566 ARG Chi-restraints excluded: chain B residue 875 MET Chi-restraints excluded: chain B residue 907 VAL Chi-restraints excluded: chain B residue 934 MET Chi-restraints excluded: chain B residue 1011 VAL Chi-restraints excluded: chain B residue 1038 ASN Chi-restraints excluded: chain B residue 1131 MET Chi-restraints excluded: chain B residue 1138 MET Chi-restraints excluded: chain B residue 1333 VAL Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 189 MET Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 372 SER Chi-restraints excluded: chain C residue 374 LEU Chi-restraints excluded: chain C residue 419 MET Chi-restraints excluded: chain C residue 461 HIS Chi-restraints excluded: chain C residue 469 PHE Chi-restraints excluded: chain C residue 566 ARG Chi-restraints excluded: chain C residue 875 MET Chi-restraints excluded: chain C residue 907 VAL Chi-restraints excluded: chain C residue 934 MET Chi-restraints excluded: chain C residue 1011 VAL Chi-restraints excluded: chain C residue 1038 ASN Chi-restraints excluded: chain C residue 1131 MET Chi-restraints excluded: chain C residue 1138 MET Chi-restraints excluded: chain C residue 1160 PHE Chi-restraints excluded: chain C residue 1335 ARG Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 189 MET Chi-restraints excluded: chain D residue 372 SER Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain D residue 461 HIS Chi-restraints excluded: chain D residue 469 PHE Chi-restraints excluded: chain D residue 566 ARG Chi-restraints excluded: chain D residue 875 MET Chi-restraints excluded: chain D residue 907 VAL Chi-restraints excluded: chain D residue 934 MET Chi-restraints excluded: chain D residue 1011 VAL Chi-restraints excluded: chain D residue 1038 ASN Chi-restraints excluded: chain D residue 1131 MET Chi-restraints excluded: chain D residue 1138 MET Chi-restraints excluded: chain D residue 1149 MET Chi-restraints excluded: chain D residue 1160 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 452 optimal weight: 10.0000 chunk 69 optimal weight: 8.9990 chunk 441 optimal weight: 10.0000 chunk 145 optimal weight: 7.9990 chunk 99 optimal weight: 9.9990 chunk 531 optimal weight: 30.0000 chunk 104 optimal weight: 2.9990 chunk 396 optimal weight: 30.0000 chunk 252 optimal weight: 30.0000 chunk 48 optimal weight: 9.9990 chunk 533 optimal weight: 20.0000 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 ASN A 702 ASN A1443 HIS B 255 ASN B1443 HIS C 255 ASN C1443 HIS D 255 ASN D 702 ASN D1443 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.159419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.100528 restraints weight = 59952.757| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 2.68 r_work: 0.2959 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2824 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.4419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.128 40148 Z= 0.553 Angle : 0.890 10.351 54824 Z= 0.465 Chirality : 0.057 0.285 6428 Planarity : 0.007 0.064 7036 Dihedral : 5.859 53.499 6500 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 3.97 % Allowed : 14.17 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.01 (0.11), residues: 5372 helix: 0.63 (0.09), residues: 2992 sheet: -1.35 (0.23), residues: 416 loop : -0.48 (0.14), residues: 1964 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.002 ARG C 655 TYR 0.028 0.004 TYR D 979 PHE 0.034 0.004 PHE A1355 TRP 0.025 0.004 TRP D 726 HIS 0.012 0.003 HIS D 813 Details of bonding type rmsd covalent geometry : bond 0.01333 (40144) covalent geometry : angle 0.89011 (54816) SS BOND : bond 0.00671 ( 4) SS BOND : angle 1.31237 ( 8) hydrogen bonds : bond 0.08270 ( 2336) hydrogen bonds : angle 4.97696 ( 6852) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10744 Ramachandran restraints generated. 5372 Oldfield, 0 Emsley, 5372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10744 Ramachandran restraints generated. 5372 Oldfield, 0 Emsley, 5372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 4632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 348 time to evaluate : 1.522 Fit side-chains revert: symmetry clash REVERT: A 129 MET cc_start: 0.7832 (mmt) cc_final: 0.7565 (mmp) REVERT: A 159 ARG cc_start: 0.5881 (mtp85) cc_final: 0.4266 (pmt170) REVERT: A 374 LEU cc_start: 0.7778 (OUTLIER) cc_final: 0.7542 (mm) REVERT: A 449 ASP cc_start: 0.8131 (OUTLIER) cc_final: 0.7899 (m-30) REVERT: A 566 ARG cc_start: 0.8255 (OUTLIER) cc_final: 0.7396 (mtp180) REVERT: A 663 LYS cc_start: 0.8543 (mttp) cc_final: 0.8243 (mppt) REVERT: A 865 SER cc_start: 0.8311 (m) cc_final: 0.8084 (p) REVERT: A 933 GLU cc_start: 0.8705 (mm-30) cc_final: 0.8395 (mm-30) REVERT: A 1011 VAL cc_start: 0.9393 (OUTLIER) cc_final: 0.9190 (p) REVERT: A 1038 ASN cc_start: 0.9057 (OUTLIER) cc_final: 0.8831 (m110) REVERT: A 1085 ARG cc_start: 0.4942 (tpp80) cc_final: 0.4723 (ttt180) REVERT: A 1131 MET cc_start: 0.8231 (OUTLIER) cc_final: 0.7833 (mmm) REVERT: A 1335 ARG cc_start: 0.6732 (OUTLIER) cc_final: 0.6460 (ptt-90) REVERT: B 129 MET cc_start: 0.7822 (mmt) cc_final: 0.7556 (mmp) REVERT: B 159 ARG cc_start: 0.5886 (mtp85) cc_final: 0.4286 (pmt170) REVERT: B 374 LEU cc_start: 0.7786 (OUTLIER) cc_final: 0.7489 (mm) REVERT: B 566 ARG cc_start: 0.8250 (OUTLIER) cc_final: 0.7378 (mtp180) REVERT: B 598 GLN cc_start: 0.8608 (OUTLIER) cc_final: 0.8317 (tt0) REVERT: B 663 LYS cc_start: 0.8549 (mttp) cc_final: 0.8252 (mppt) REVERT: B 865 SER cc_start: 0.8309 (m) cc_final: 0.8085 (p) REVERT: B 933 GLU cc_start: 0.8726 (mm-30) cc_final: 0.8415 (mm-30) REVERT: B 1011 VAL cc_start: 0.9389 (OUTLIER) cc_final: 0.9188 (p) REVERT: B 1038 ASN cc_start: 0.9052 (OUTLIER) cc_final: 0.8824 (m110) REVERT: B 1085 ARG cc_start: 0.4935 (tpp80) cc_final: 0.4718 (ttt180) REVERT: B 1131 MET cc_start: 0.8218 (OUTLIER) cc_final: 0.7775 (mmm) REVERT: B 1157 MET cc_start: 0.8389 (OUTLIER) cc_final: 0.7848 (mmm) REVERT: B 1335 ARG cc_start: 0.6712 (OUTLIER) cc_final: 0.6433 (ptt-90) REVERT: B 1463 HIS cc_start: 0.5251 (m-70) cc_final: 0.4995 (m-70) REVERT: C 159 ARG cc_start: 0.5786 (mtp85) cc_final: 0.4260 (pmt170) REVERT: C 197 GLU cc_start: 0.6828 (tt0) cc_final: 0.6067 (tp30) REVERT: C 374 LEU cc_start: 0.7761 (OUTLIER) cc_final: 0.7439 (mm) REVERT: C 449 ASP cc_start: 0.8091 (OUTLIER) cc_final: 0.7862 (m-30) REVERT: C 566 ARG cc_start: 0.8247 (OUTLIER) cc_final: 0.7390 (mtp180) REVERT: C 663 LYS cc_start: 0.8553 (mttp) cc_final: 0.8258 (mppt) REVERT: C 865 SER cc_start: 0.8305 (m) cc_final: 0.8074 (p) REVERT: C 933 GLU cc_start: 0.8733 (mm-30) cc_final: 0.8422 (mm-30) REVERT: C 1038 ASN cc_start: 0.9051 (OUTLIER) cc_final: 0.8823 (m110) REVERT: C 1131 MET cc_start: 0.8231 (OUTLIER) cc_final: 0.7833 (mmm) REVERT: C 1157 MET cc_start: 0.8082 (tpt) cc_final: 0.7829 (mmm) REVERT: C 1335 ARG cc_start: 0.6798 (OUTLIER) cc_final: 0.6385 (ptp90) REVERT: C 1463 HIS cc_start: 0.5108 (m-70) cc_final: 0.4826 (m-70) REVERT: D 129 MET cc_start: 0.7975 (mmt) cc_final: 0.7679 (mmp) REVERT: D 159 ARG cc_start: 0.5868 (mtp85) cc_final: 0.4265 (pmt170) REVERT: D 374 LEU cc_start: 0.7784 (OUTLIER) cc_final: 0.7470 (mm) REVERT: D 449 ASP cc_start: 0.8095 (OUTLIER) cc_final: 0.7866 (m-30) REVERT: D 566 ARG cc_start: 0.8250 (OUTLIER) cc_final: 0.7394 (mtp180) REVERT: D 663 LYS cc_start: 0.8552 (mttp) cc_final: 0.8256 (mppt) REVERT: D 865 SER cc_start: 0.8310 (m) cc_final: 0.8077 (p) REVERT: D 933 GLU cc_start: 0.8770 (mm-30) cc_final: 0.8468 (mm-30) REVERT: D 1011 VAL cc_start: 0.9391 (OUTLIER) cc_final: 0.9188 (p) REVERT: D 1038 ASN cc_start: 0.9056 (OUTLIER) cc_final: 0.8829 (m110) REVERT: D 1085 ARG cc_start: 0.4949 (tpp80) cc_final: 0.4730 (ttt180) REVERT: D 1131 MET cc_start: 0.8236 (OUTLIER) cc_final: 0.7800 (mmm) REVERT: D 1157 MET cc_start: 0.8370 (tpp) cc_final: 0.7821 (mmm) REVERT: D 1463 HIS cc_start: 0.5106 (m-70) cc_final: 0.4834 (m-70) REVERT: D 1465 ARG cc_start: 0.4494 (pmt170) cc_final: 0.4267 (pmt170) outliers start: 138 outliers final: 55 residues processed: 441 average time/residue: 0.6965 time to fit residues: 378.1338 Evaluate side-chains 411 residues out of total 4632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 329 time to evaluate : 1.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 189 MET Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 449 ASP Chi-restraints excluded: chain A residue 566 ARG Chi-restraints excluded: chain A residue 875 MET Chi-restraints excluded: chain A residue 907 VAL Chi-restraints excluded: chain A residue 1011 VAL Chi-restraints excluded: chain A residue 1038 ASN Chi-restraints excluded: chain A residue 1131 MET Chi-restraints excluded: chain A residue 1138 MET Chi-restraints excluded: chain A residue 1150 MET Chi-restraints excluded: chain A residue 1333 VAL Chi-restraints excluded: chain A residue 1335 ARG Chi-restraints excluded: chain A residue 1468 MET Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 189 MET Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 374 LEU Chi-restraints excluded: chain B residue 461 HIS Chi-restraints excluded: chain B residue 566 ARG Chi-restraints excluded: chain B residue 598 GLN Chi-restraints excluded: chain B residue 875 MET Chi-restraints excluded: chain B residue 907 VAL Chi-restraints excluded: chain B residue 1011 VAL Chi-restraints excluded: chain B residue 1038 ASN Chi-restraints excluded: chain B residue 1131 MET Chi-restraints excluded: chain B residue 1138 MET Chi-restraints excluded: chain B residue 1150 MET Chi-restraints excluded: chain B residue 1157 MET Chi-restraints excluded: chain B residue 1333 VAL Chi-restraints excluded: chain B residue 1335 ARG Chi-restraints excluded: chain B residue 1468 MET Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 189 MET Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain C residue 313 THR Chi-restraints excluded: chain C residue 372 SER Chi-restraints excluded: chain C residue 374 LEU Chi-restraints excluded: chain C residue 449 ASP Chi-restraints excluded: chain C residue 461 HIS Chi-restraints excluded: chain C residue 566 ARG Chi-restraints excluded: chain C residue 875 MET Chi-restraints excluded: chain C residue 907 VAL Chi-restraints excluded: chain C residue 1038 ASN Chi-restraints excluded: chain C residue 1131 MET Chi-restraints excluded: chain C residue 1138 MET Chi-restraints excluded: chain C residue 1147 MET Chi-restraints excluded: chain C residue 1150 MET Chi-restraints excluded: chain C residue 1333 VAL Chi-restraints excluded: chain C residue 1335 ARG Chi-restraints excluded: chain C residue 1468 MET Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 189 MET Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 293 ILE Chi-restraints excluded: chain D residue 313 THR Chi-restraints excluded: chain D residue 370 LEU Chi-restraints excluded: chain D residue 372 SER Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain D residue 449 ASP Chi-restraints excluded: chain D residue 566 ARG Chi-restraints excluded: chain D residue 875 MET Chi-restraints excluded: chain D residue 907 VAL Chi-restraints excluded: chain D residue 1011 VAL Chi-restraints excluded: chain D residue 1038 ASN Chi-restraints excluded: chain D residue 1131 MET Chi-restraints excluded: chain D residue 1138 MET Chi-restraints excluded: chain D residue 1150 MET Chi-restraints excluded: chain D residue 1333 VAL Chi-restraints excluded: chain D residue 1335 ARG Chi-restraints excluded: chain D residue 1468 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 509 optimal weight: 1.9990 chunk 454 optimal weight: 1.9990 chunk 154 optimal weight: 7.9990 chunk 237 optimal weight: 0.6980 chunk 437 optimal weight: 6.9990 chunk 429 optimal weight: 1.9990 chunk 446 optimal weight: 0.8980 chunk 84 optimal weight: 0.9980 chunk 5 optimal weight: 5.9990 chunk 171 optimal weight: 3.9990 chunk 230 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 598 GLN A 702 ASN A1443 HIS B 598 GLN B1443 HIS C 598 GLN C1443 HIS D 598 GLN D 702 ASN D1443 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.163563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.105687 restraints weight = 59442.264| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 2.74 r_work: 0.3043 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2909 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.4286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 40148 Z= 0.135 Angle : 0.523 8.013 54824 Z= 0.272 Chirality : 0.039 0.181 6428 Planarity : 0.004 0.043 7036 Dihedral : 5.068 56.572 6500 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.76 % Allowed : 15.78 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.09 (0.11), residues: 5372 helix: 1.62 (0.09), residues: 2976 sheet: -1.40 (0.24), residues: 392 loop : -0.08 (0.14), residues: 2004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 977 TYR 0.031 0.002 TYR D 345 PHE 0.044 0.001 PHE D1355 TRP 0.020 0.001 TRP D 726 HIS 0.004 0.001 HIS B 813 Details of bonding type rmsd covalent geometry : bond 0.00302 (40144) covalent geometry : angle 0.52256 (54816) SS BOND : bond 0.00251 ( 4) SS BOND : angle 0.63663 ( 8) hydrogen bonds : bond 0.04852 ( 2336) hydrogen bonds : angle 4.33961 ( 6852) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10744 Ramachandran restraints generated. 5372 Oldfield, 0 Emsley, 5372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10744 Ramachandran restraints generated. 5372 Oldfield, 0 Emsley, 5372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 4632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 338 time to evaluate : 1.694 Fit side-chains REVERT: A 132 GLN cc_start: 0.5612 (OUTLIER) cc_final: 0.5390 (tm130) REVERT: A 159 ARG cc_start: 0.5803 (mtp85) cc_final: 0.4355 (pmt170) REVERT: A 197 GLU cc_start: 0.6564 (tt0) cc_final: 0.6182 (mt-10) REVERT: A 199 LEU cc_start: 0.7269 (tp) cc_final: 0.7036 (mt) REVERT: A 374 LEU cc_start: 0.7493 (mm) cc_final: 0.7249 (mm) REVERT: A 566 ARG cc_start: 0.8138 (OUTLIER) cc_final: 0.7197 (mtp180) REVERT: A 663 LYS cc_start: 0.8486 (mttp) cc_final: 0.8174 (mppt) REVERT: A 933 GLU cc_start: 0.8647 (mm-30) cc_final: 0.8335 (mm-30) REVERT: A 1085 ARG cc_start: 0.4711 (tpp80) cc_final: 0.4510 (ttm170) REVERT: A 1131 MET cc_start: 0.8020 (OUTLIER) cc_final: 0.7517 (mmm) REVERT: A 1335 ARG cc_start: 0.6668 (OUTLIER) cc_final: 0.6397 (ptt-90) REVERT: B 61 ASN cc_start: 0.6612 (m-40) cc_final: 0.6292 (m-40) REVERT: B 132 GLN cc_start: 0.5613 (OUTLIER) cc_final: 0.5390 (tm130) REVERT: B 159 ARG cc_start: 0.5804 (mtp85) cc_final: 0.4368 (pmt170) REVERT: B 197 GLU cc_start: 0.6586 (tt0) cc_final: 0.6212 (mt-10) REVERT: B 199 LEU cc_start: 0.7290 (tp) cc_final: 0.7054 (mt) REVERT: B 566 ARG cc_start: 0.8142 (OUTLIER) cc_final: 0.7161 (mtp180) REVERT: B 663 LYS cc_start: 0.8480 (mttp) cc_final: 0.8171 (mppt) REVERT: B 933 GLU cc_start: 0.8668 (mm-30) cc_final: 0.8353 (mm-30) REVERT: B 1131 MET cc_start: 0.8012 (OUTLIER) cc_final: 0.7489 (mmm) REVERT: B 1157 MET cc_start: 0.8368 (tpt) cc_final: 0.7766 (mmm) REVERT: B 1335 ARG cc_start: 0.6692 (OUTLIER) cc_final: 0.6402 (ptt-90) REVERT: B 1463 HIS cc_start: 0.5235 (m-70) cc_final: 0.4951 (m170) REVERT: C 159 ARG cc_start: 0.5790 (mtp85) cc_final: 0.4330 (pmt170) REVERT: C 197 GLU cc_start: 0.6774 (tt0) cc_final: 0.5948 (tp30) REVERT: C 199 LEU cc_start: 0.7273 (tp) cc_final: 0.7028 (mt) REVERT: C 566 ARG cc_start: 0.8119 (OUTLIER) cc_final: 0.7173 (mtp180) REVERT: C 663 LYS cc_start: 0.8485 (mttp) cc_final: 0.8166 (mppt) REVERT: C 933 GLU cc_start: 0.8645 (mm-30) cc_final: 0.8335 (mm-30) REVERT: C 1131 MET cc_start: 0.8030 (OUTLIER) cc_final: 0.7526 (mmm) REVERT: C 1335 ARG cc_start: 0.6837 (OUTLIER) cc_final: 0.6581 (ptt-90) REVERT: D 129 MET cc_start: 0.7895 (mmt) cc_final: 0.7615 (mmp) REVERT: D 159 ARG cc_start: 0.5799 (mtp85) cc_final: 0.4351 (pmt170) REVERT: D 197 GLU cc_start: 0.6585 (tt0) cc_final: 0.6211 (mt-10) REVERT: D 199 LEU cc_start: 0.7273 (tp) cc_final: 0.7037 (mt) REVERT: D 566 ARG cc_start: 0.8127 (OUTLIER) cc_final: 0.7183 (mtp180) REVERT: D 663 LYS cc_start: 0.8492 (mttp) cc_final: 0.8179 (mppt) REVERT: D 933 GLU cc_start: 0.8610 (mm-30) cc_final: 0.8295 (mm-30) REVERT: D 1131 MET cc_start: 0.8015 (OUTLIER) cc_final: 0.7497 (mmm) REVERT: D 1157 MET cc_start: 0.8521 (tpp) cc_final: 0.8046 (mmm) outliers start: 96 outliers final: 39 residues processed: 401 average time/residue: 0.7435 time to fit residues: 362.9932 Evaluate side-chains 381 residues out of total 4632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 329 time to evaluate : 1.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 GLN Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 189 MET Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 566 ARG Chi-restraints excluded: chain A residue 875 MET Chi-restraints excluded: chain A residue 907 VAL Chi-restraints excluded: chain A residue 1011 VAL Chi-restraints excluded: chain A residue 1131 MET Chi-restraints excluded: chain A residue 1138 MET Chi-restraints excluded: chain A residue 1335 ARG Chi-restraints excluded: chain A residue 1345 LEU Chi-restraints excluded: chain A residue 1468 MET Chi-restraints excluded: chain B residue 132 GLN Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 189 MET Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 566 ARG Chi-restraints excluded: chain B residue 875 MET Chi-restraints excluded: chain B residue 907 VAL Chi-restraints excluded: chain B residue 1011 VAL Chi-restraints excluded: chain B residue 1131 MET Chi-restraints excluded: chain B residue 1138 MET Chi-restraints excluded: chain B residue 1333 VAL Chi-restraints excluded: chain B residue 1335 ARG Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 189 MET Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 372 SER Chi-restraints excluded: chain C residue 566 ARG Chi-restraints excluded: chain C residue 875 MET Chi-restraints excluded: chain C residue 907 VAL Chi-restraints excluded: chain C residue 1131 MET Chi-restraints excluded: chain C residue 1138 MET Chi-restraints excluded: chain C residue 1335 ARG Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 189 MET Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 372 SER Chi-restraints excluded: chain D residue 566 ARG Chi-restraints excluded: chain D residue 875 MET Chi-restraints excluded: chain D residue 907 VAL Chi-restraints excluded: chain D residue 1011 VAL Chi-restraints excluded: chain D residue 1131 MET Chi-restraints excluded: chain D residue 1138 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 508 optimal weight: 1.9990 chunk 409 optimal weight: 20.0000 chunk 140 optimal weight: 10.0000 chunk 124 optimal weight: 8.9990 chunk 128 optimal weight: 5.9990 chunk 510 optimal weight: 0.8980 chunk 244 optimal weight: 30.0000 chunk 390 optimal weight: 0.5980 chunk 533 optimal weight: 7.9990 chunk 501 optimal weight: 0.7980 chunk 373 optimal weight: 0.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 598 GLN A 660 HIS A1463 HIS B 598 GLN B 660 HIS B 702 ASN B1443 HIS C 598 GLN C 660 HIS C 702 ASN C1443 HIS D 598 GLN D 660 HIS D1152 GLN D1443 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.164492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.106810 restraints weight = 59838.732| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 2.62 r_work: 0.3029 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2889 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.4296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 40148 Z= 0.121 Angle : 0.488 7.638 54824 Z= 0.252 Chirality : 0.038 0.153 6428 Planarity : 0.004 0.044 7036 Dihedral : 4.757 58.295 6500 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.07 % Allowed : 16.68 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.59 (0.12), residues: 5372 helix: 2.08 (0.09), residues: 2972 sheet: -1.30 (0.24), residues: 388 loop : 0.08 (0.14), residues: 2012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 517 TYR 0.021 0.002 TYR B 345 PHE 0.043 0.001 PHE B1355 TRP 0.018 0.001 TRP C 726 HIS 0.008 0.001 HIS A1463 Details of bonding type rmsd covalent geometry : bond 0.00277 (40144) covalent geometry : angle 0.48793 (54816) SS BOND : bond 0.00086 ( 4) SS BOND : angle 0.58136 ( 8) hydrogen bonds : bond 0.04199 ( 2336) hydrogen bonds : angle 4.10345 ( 6852) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10744 Ramachandran restraints generated. 5372 Oldfield, 0 Emsley, 5372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10744 Ramachandran restraints generated. 5372 Oldfield, 0 Emsley, 5372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 4632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 328 time to evaluate : 1.675 Fit side-chains REVERT: A 132 GLN cc_start: 0.5683 (OUTLIER) cc_final: 0.5466 (tm130) REVERT: A 159 ARG cc_start: 0.5840 (mtp85) cc_final: 0.4311 (pmt170) REVERT: A 197 GLU cc_start: 0.6579 (tt0) cc_final: 0.6178 (mt-10) REVERT: A 507 GLU cc_start: 0.8171 (tp30) cc_final: 0.7962 (mm-30) REVERT: A 566 ARG cc_start: 0.8125 (OUTLIER) cc_final: 0.7152 (mtp180) REVERT: A 663 LYS cc_start: 0.8463 (mttp) cc_final: 0.8135 (mppt) REVERT: A 933 GLU cc_start: 0.8748 (mm-30) cc_final: 0.8429 (mm-30) REVERT: A 1085 ARG cc_start: 0.4796 (tpp80) cc_final: 0.4564 (ttm170) REVERT: A 1131 MET cc_start: 0.7810 (OUTLIER) cc_final: 0.7402 (mmt) REVERT: A 1157 MET cc_start: 0.8241 (mmm) cc_final: 0.7860 (mmm) REVERT: A 1335 ARG cc_start: 0.6719 (OUTLIER) cc_final: 0.6476 (ptp90) REVERT: B 61 ASN cc_start: 0.6616 (m-40) cc_final: 0.6281 (m-40) REVERT: B 132 GLN cc_start: 0.5722 (OUTLIER) cc_final: 0.5509 (tm130) REVERT: B 159 ARG cc_start: 0.5857 (mtp85) cc_final: 0.4343 (pmt170) REVERT: B 197 GLU cc_start: 0.6598 (tt0) cc_final: 0.6196 (mt-10) REVERT: B 507 GLU cc_start: 0.8181 (tp30) cc_final: 0.7964 (mm-30) REVERT: B 566 ARG cc_start: 0.8121 (OUTLIER) cc_final: 0.7156 (mtp180) REVERT: B 663 LYS cc_start: 0.8494 (mttp) cc_final: 0.8142 (mppt) REVERT: B 933 GLU cc_start: 0.8757 (mm-30) cc_final: 0.8434 (mm-30) REVERT: B 1131 MET cc_start: 0.7793 (OUTLIER) cc_final: 0.6504 (mpp) REVERT: B 1335 ARG cc_start: 0.6664 (OUTLIER) cc_final: 0.6433 (ptp90) REVERT: B 1355 PHE cc_start: 0.6824 (p90) cc_final: 0.6363 (p90) REVERT: C 159 ARG cc_start: 0.5814 (mtp85) cc_final: 0.4283 (pmt170) REVERT: C 197 GLU cc_start: 0.6770 (tt0) cc_final: 0.5924 (tp30) REVERT: C 374 LEU cc_start: 0.7498 (mm) cc_final: 0.7224 (mm) REVERT: C 455 MET cc_start: 0.8507 (mtt) cc_final: 0.8262 (mtm) REVERT: C 507 GLU cc_start: 0.8191 (tp30) cc_final: 0.7985 (mm-30) REVERT: C 566 ARG cc_start: 0.8115 (OUTLIER) cc_final: 0.7135 (mtp180) REVERT: C 663 LYS cc_start: 0.8458 (mttp) cc_final: 0.8129 (mppt) REVERT: C 933 GLU cc_start: 0.8754 (mm-30) cc_final: 0.8436 (mm-30) REVERT: C 1131 MET cc_start: 0.7826 (OUTLIER) cc_final: 0.7416 (mmt) REVERT: C 1493 TYR cc_start: 0.7032 (t80) cc_final: 0.6760 (t80) REVERT: D 129 MET cc_start: 0.7859 (mmt) cc_final: 0.7635 (mmp) REVERT: D 159 ARG cc_start: 0.5829 (mtp85) cc_final: 0.4301 (pmt170) REVERT: D 197 GLU cc_start: 0.6593 (tt0) cc_final: 0.6193 (mt-10) REVERT: D 374 LEU cc_start: 0.7505 (mm) cc_final: 0.7244 (mm) REVERT: D 566 ARG cc_start: 0.8126 (OUTLIER) cc_final: 0.7149 (mtp180) REVERT: D 663 LYS cc_start: 0.8498 (mttp) cc_final: 0.8142 (mppt) REVERT: D 933 GLU cc_start: 0.8720 (mm-30) cc_final: 0.8397 (mm-30) REVERT: D 1131 MET cc_start: 0.7791 (OUTLIER) cc_final: 0.6501 (mpp) REVERT: D 1157 MET cc_start: 0.8521 (tpp) cc_final: 0.7956 (mmm) outliers start: 72 outliers final: 42 residues processed: 372 average time/residue: 0.7769 time to fit residues: 350.2907 Evaluate side-chains 379 residues out of total 4632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 325 time to evaluate : 1.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 GLN Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 189 MET Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 566 ARG Chi-restraints excluded: chain A residue 875 MET Chi-restraints excluded: chain A residue 907 VAL Chi-restraints excluded: chain A residue 1011 VAL Chi-restraints excluded: chain A residue 1131 MET Chi-restraints excluded: chain A residue 1138 MET Chi-restraints excluded: chain A residue 1335 ARG Chi-restraints excluded: chain A residue 1468 MET Chi-restraints excluded: chain B residue 132 GLN Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 189 MET Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 566 ARG Chi-restraints excluded: chain B residue 875 MET Chi-restraints excluded: chain B residue 907 VAL Chi-restraints excluded: chain B residue 1011 VAL Chi-restraints excluded: chain B residue 1131 MET Chi-restraints excluded: chain B residue 1138 MET Chi-restraints excluded: chain B residue 1333 VAL Chi-restraints excluded: chain B residue 1335 ARG Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 189 MET Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 372 SER Chi-restraints excluded: chain C residue 566 ARG Chi-restraints excluded: chain C residue 574 VAL Chi-restraints excluded: chain C residue 875 MET Chi-restraints excluded: chain C residue 907 VAL Chi-restraints excluded: chain C residue 1131 MET Chi-restraints excluded: chain C residue 1138 MET Chi-restraints excluded: chain C residue 1468 MET Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 189 MET Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 372 SER Chi-restraints excluded: chain D residue 566 ARG Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 875 MET Chi-restraints excluded: chain D residue 907 VAL Chi-restraints excluded: chain D residue 1011 VAL Chi-restraints excluded: chain D residue 1131 MET Chi-restraints excluded: chain D residue 1138 MET Chi-restraints excluded: chain D residue 1468 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 103 optimal weight: 0.5980 chunk 144 optimal weight: 7.9990 chunk 470 optimal weight: 5.9990 chunk 179 optimal weight: 0.8980 chunk 499 optimal weight: 1.9990 chunk 332 optimal weight: 4.9990 chunk 457 optimal weight: 2.9990 chunk 129 optimal weight: 2.9990 chunk 253 optimal weight: 40.0000 chunk 42 optimal weight: 4.9990 chunk 397 optimal weight: 6.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 598 GLN B 598 GLN C 598 GLN C1443 HIS D 598 GLN D1152 GLN D1443 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.163319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.105767 restraints weight = 59335.041| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 2.73 r_work: 0.3036 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2904 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.4383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 40148 Z= 0.162 Angle : 0.528 10.284 54824 Z= 0.272 Chirality : 0.039 0.184 6428 Planarity : 0.004 0.043 7036 Dihedral : 4.820 54.017 6500 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.28 % Allowed : 17.17 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.51 (0.11), residues: 5372 helix: 1.97 (0.09), residues: 3000 sheet: -1.38 (0.25), residues: 336 loop : 0.04 (0.14), residues: 2036 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 655 TYR 0.040 0.002 TYR B 345 PHE 0.049 0.002 PHE C1355 TRP 0.030 0.002 TRP C 96 HIS 0.004 0.001 HIS B 813 Details of bonding type rmsd covalent geometry : bond 0.00385 (40144) covalent geometry : angle 0.52793 (54816) SS BOND : bond 0.00144 ( 4) SS BOND : angle 0.61396 ( 8) hydrogen bonds : bond 0.04829 ( 2336) hydrogen bonds : angle 4.16568 ( 6852) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10744 Ramachandran restraints generated. 5372 Oldfield, 0 Emsley, 5372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10744 Ramachandran restraints generated. 5372 Oldfield, 0 Emsley, 5372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 4632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 335 time to evaluate : 1.641 Fit side-chains REVERT: A 132 GLN cc_start: 0.5682 (OUTLIER) cc_final: 0.5447 (tm130) REVERT: A 159 ARG cc_start: 0.5886 (mtp85) cc_final: 0.4373 (pmt170) REVERT: A 197 GLU cc_start: 0.6570 (tt0) cc_final: 0.6194 (mt-10) REVERT: A 345 TYR cc_start: 0.8413 (m-80) cc_final: 0.8125 (m-80) REVERT: A 507 GLU cc_start: 0.8169 (tp30) cc_final: 0.7944 (mm-30) REVERT: A 566 ARG cc_start: 0.8140 (OUTLIER) cc_final: 0.7193 (mtp180) REVERT: A 663 LYS cc_start: 0.8466 (mttp) cc_final: 0.8136 (mppt) REVERT: A 933 GLU cc_start: 0.8666 (mm-30) cc_final: 0.8347 (mm-30) REVERT: A 1131 MET cc_start: 0.7795 (OUTLIER) cc_final: 0.6516 (mpp) REVERT: A 1157 MET cc_start: 0.8175 (mmm) cc_final: 0.7962 (mmt) REVERT: A 1335 ARG cc_start: 0.6656 (OUTLIER) cc_final: 0.6413 (ptp90) REVERT: B 61 ASN cc_start: 0.6616 (m-40) cc_final: 0.6282 (m-40) REVERT: B 71 GLU cc_start: 0.7223 (OUTLIER) cc_final: 0.7009 (pt0) REVERT: B 132 GLN cc_start: 0.5687 (OUTLIER) cc_final: 0.5449 (tm130) REVERT: B 159 ARG cc_start: 0.5890 (mtp85) cc_final: 0.4426 (pmt170) REVERT: B 197 GLU cc_start: 0.6586 (tt0) cc_final: 0.6209 (mt-10) REVERT: B 507 GLU cc_start: 0.8206 (tp30) cc_final: 0.7961 (mm-30) REVERT: B 566 ARG cc_start: 0.8139 (OUTLIER) cc_final: 0.7154 (mtp180) REVERT: B 663 LYS cc_start: 0.8435 (mttp) cc_final: 0.8108 (mppt) REVERT: B 933 GLU cc_start: 0.8620 (mm-30) cc_final: 0.8281 (mm-30) REVERT: B 1131 MET cc_start: 0.7805 (OUTLIER) cc_final: 0.6532 (mpp) REVERT: B 1335 ARG cc_start: 0.6778 (OUTLIER) cc_final: 0.6538 (ptp90) REVERT: C 96 TRP cc_start: 0.7623 (p-90) cc_final: 0.7164 (p-90) REVERT: C 159 ARG cc_start: 0.5851 (mtp85) cc_final: 0.4329 (pmt170) REVERT: C 197 GLU cc_start: 0.6778 (tt0) cc_final: 0.5957 (tp30) REVERT: C 345 TYR cc_start: 0.8407 (m-80) cc_final: 0.7868 (m-80) REVERT: C 566 ARG cc_start: 0.8133 (OUTLIER) cc_final: 0.7178 (mtp180) REVERT: C 663 LYS cc_start: 0.8453 (mttp) cc_final: 0.8131 (mppt) REVERT: C 933 GLU cc_start: 0.8666 (mm-30) cc_final: 0.8348 (mm-30) REVERT: C 1131 MET cc_start: 0.7816 (OUTLIER) cc_final: 0.6551 (mpp) REVERT: C 1355 PHE cc_start: 0.7032 (p90) cc_final: 0.6536 (p90) REVERT: C 1493 TYR cc_start: 0.7122 (t80) cc_final: 0.6884 (t80) REVERT: D 96 TRP cc_start: 0.7612 (p-90) cc_final: 0.7134 (p-90) REVERT: D 129 MET cc_start: 0.7813 (mmt) cc_final: 0.7597 (mmp) REVERT: D 159 ARG cc_start: 0.5878 (mtp85) cc_final: 0.4365 (pmt170) REVERT: D 197 GLU cc_start: 0.6579 (tt0) cc_final: 0.6204 (mt-10) REVERT: D 566 ARG cc_start: 0.8141 (OUTLIER) cc_final: 0.7188 (mtp180) REVERT: D 663 LYS cc_start: 0.8449 (mttp) cc_final: 0.8128 (mppt) REVERT: D 933 GLU cc_start: 0.8655 (mm-30) cc_final: 0.8338 (mm-30) REVERT: D 1131 MET cc_start: 0.7805 (OUTLIER) cc_final: 0.6531 (mpp) REVERT: D 1157 MET cc_start: 0.8503 (tpp) cc_final: 0.7855 (mmm) REVERT: D 1355 PHE cc_start: 0.6962 (p90) cc_final: 0.6418 (p90) REVERT: D 1493 TYR cc_start: 0.7182 (t80) cc_final: 0.6940 (t80) outliers start: 79 outliers final: 49 residues processed: 385 average time/residue: 0.7676 time to fit residues: 357.9499 Evaluate side-chains 390 residues out of total 4632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 328 time to evaluate : 1.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 GLN Chi-restraints excluded: chain A residue 162 THR Chi-restraints excluded: chain A residue 189 MET Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 566 ARG Chi-restraints excluded: chain A residue 875 MET Chi-restraints excluded: chain A residue 907 VAL Chi-restraints excluded: chain A residue 920 LEU Chi-restraints excluded: chain A residue 1011 VAL Chi-restraints excluded: chain A residue 1131 MET Chi-restraints excluded: chain A residue 1138 MET Chi-restraints excluded: chain A residue 1335 ARG Chi-restraints excluded: chain A residue 1345 LEU Chi-restraints excluded: chain A residue 1468 MET Chi-restraints excluded: chain B residue 71 GLU Chi-restraints excluded: chain B residue 132 GLN Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 189 MET Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 566 ARG Chi-restraints excluded: chain B residue 875 MET Chi-restraints excluded: chain B residue 907 VAL Chi-restraints excluded: chain B residue 920 LEU Chi-restraints excluded: chain B residue 1011 VAL Chi-restraints excluded: chain B residue 1131 MET Chi-restraints excluded: chain B residue 1138 MET Chi-restraints excluded: chain B residue 1333 VAL Chi-restraints excluded: chain B residue 1335 ARG Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 189 MET Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 256 LEU Chi-restraints excluded: chain C residue 372 SER Chi-restraints excluded: chain C residue 566 ARG Chi-restraints excluded: chain C residue 574 VAL Chi-restraints excluded: chain C residue 875 MET Chi-restraints excluded: chain C residue 907 VAL Chi-restraints excluded: chain C residue 920 LEU Chi-restraints excluded: chain C residue 1131 MET Chi-restraints excluded: chain C residue 1138 MET Chi-restraints excluded: chain C residue 1333 VAL Chi-restraints excluded: chain C residue 1468 MET Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 189 MET Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 372 SER Chi-restraints excluded: chain D residue 566 ARG Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 875 MET Chi-restraints excluded: chain D residue 907 VAL Chi-restraints excluded: chain D residue 920 LEU Chi-restraints excluded: chain D residue 1011 VAL Chi-restraints excluded: chain D residue 1131 MET Chi-restraints excluded: chain D residue 1138 MET Chi-restraints excluded: chain D residue 1333 VAL Chi-restraints excluded: chain D residue 1468 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 296 optimal weight: 0.9990 chunk 118 optimal weight: 40.0000 chunk 94 optimal weight: 0.7980 chunk 46 optimal weight: 6.9990 chunk 448 optimal weight: 4.9990 chunk 270 optimal weight: 30.0000 chunk 463 optimal weight: 6.9990 chunk 292 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 470 optimal weight: 4.9990 chunk 455 optimal weight: 0.7980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 598 GLN B 598 GLN C 598 GLN C1443 HIS D 598 GLN D1152 GLN D1443 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.163933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.105735 restraints weight = 59786.753| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 2.60 r_work: 0.3022 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2882 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.4422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 40148 Z= 0.138 Angle : 0.505 9.410 54824 Z= 0.259 Chirality : 0.038 0.164 6428 Planarity : 0.004 0.043 7036 Dihedral : 4.756 55.927 6500 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.39 % Allowed : 17.05 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.56 (0.12), residues: 5372 helix: 2.03 (0.09), residues: 3004 sheet: -1.37 (0.25), residues: 336 loop : 0.03 (0.14), residues: 2032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 69 TYR 0.020 0.002 TYR B 330 PHE 0.042 0.002 PHE C1355 TRP 0.022 0.002 TRP C 96 HIS 0.004 0.001 HIS D 813 Details of bonding type rmsd covalent geometry : bond 0.00324 (40144) covalent geometry : angle 0.50515 (54816) SS BOND : bond 0.00125 ( 4) SS BOND : angle 0.58713 ( 8) hydrogen bonds : bond 0.04481 ( 2336) hydrogen bonds : angle 4.10741 ( 6852) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 21540.43 seconds wall clock time: 365 minutes 52.43 seconds (21952.43 seconds total)