Starting phenix.real_space_refine on Tue Jul 7 03:38:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8srf_40729/07_2026/8srf_40729.cif Found real_map, /net/cci-nas-00/data/ceres_data/8srf_40729/07_2026/8srf_40729.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8srf_40729/07_2026/8srf_40729.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8srf_40729/07_2026/8srf_40729.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8srf_40729/07_2026/8srf_40729.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8srf_40729/07_2026/8srf_40729.map" } resolution = 2.52 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= 0.097 sd= 1.424 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 16 5.49 5 Mg 21 5.21 5 S 244 5.16 5 C 27444 2.51 5 N 7328 2.21 5 O 7736 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 42789 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 10534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1377, 10534 Classifications: {'peptide': 1377} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 117} Link IDs: {'PTRANS': 56, 'TRANS': 1320} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 395 Unresolved non-hydrogen angles: 493 Unresolved non-hydrogen dihedrals: 323 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLU:plan': 17, 'ASP:plan': 17, 'GLN:plan1': 4, 'HIS:plan': 7, 'ASN:plan1': 7, 'TYR:plan': 1, 'ARG:plan': 7, 'PHE:plan': 4} Unresolved non-hydrogen planarities: 257 Chain: "B" Number of atoms: 10534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1377, 10534 Classifications: {'peptide': 1377} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 117} Link IDs: {'PTRANS': 56, 'TRANS': 1320} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 395 Unresolved non-hydrogen angles: 493 Unresolved non-hydrogen dihedrals: 323 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLU:plan': 17, 'ASP:plan': 17, 'GLN:plan1': 4, 'HIS:plan': 7, 'ASN:plan1': 7, 'TYR:plan': 1, 'ARG:plan': 7, 'PHE:plan': 4} Unresolved non-hydrogen planarities: 257 Chain: "C" Number of atoms: 10534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1377, 10534 Classifications: {'peptide': 1377} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 117} Link IDs: {'PTRANS': 56, 'TRANS': 1320} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 395 Unresolved non-hydrogen angles: 493 Unresolved non-hydrogen dihedrals: 323 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLU:plan': 17, 'ASP:plan': 17, 'GLN:plan1': 4, 'HIS:plan': 7, 'ASN:plan1': 7, 'TYR:plan': 1, 'ARG:plan': 7, 'PHE:plan': 4} Unresolved non-hydrogen planarities: 257 Chain: "D" Number of atoms: 10534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1377, 10534 Classifications: {'peptide': 1377} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 117} Link IDs: {'PTRANS': 56, 'TRANS': 1320} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 395 Unresolved non-hydrogen angles: 493 Unresolved non-hydrogen dihedrals: 323 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLU:plan': 17, 'ASP:plan': 17, 'GLN:plan1': 4, 'HIS:plan': 7, 'ASN:plan1': 7, 'TYR:plan': 1, 'ARG:plan': 7, 'PHE:plan': 4} Unresolved non-hydrogen planarities: 257 Chain: "A" Number of atoms: 163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 163 Unusual residues: {' MG': 6, 'AMP%rna3p': 1, 'APR': 1, 'CLR': 3, 'RP5': 1} Classifications: {'RNA_mixed': 1, 'undetermined': 11} Modifications used: {'rna3p': 1} Link IDs: {None: 11} Chain: "B" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 162 Unusual residues: {' MG': 5, 'AMP%rna3p': 1, 'APR': 1, 'CLR': 3, 'RP5': 1} Classifications: {'RNA_mixed': 1, 'undetermined': 10} Modifications used: {'rna3p': 1} Link IDs: {None: 10} Chain: "C" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 162 Unusual residues: {' MG': 5, 'AMP%rna3p': 1, 'APR': 1, 'CLR': 3, 'RP5': 1} Classifications: {'RNA_mixed': 1, 'undetermined': 10} Modifications used: {'rna3p': 1} Link IDs: {None: 10} Chain: "D" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 162 Unusual residues: {' MG': 5, 'AMP%rna3p': 1, 'APR': 1, 'CLR': 3, 'RP5': 1} Classifications: {'RNA_mixed': 1, 'undetermined': 10} Modifications used: {'rna3p': 1} Link IDs: {None: 10} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 9.04, per 1000 atoms: 0.21 Number of scatterers: 42789 At special positions: 0 Unit cell: (162.722, 162.722, 185.85, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 244 16.00 P 16 15.00 Mg 21 11.99 O 7736 8.00 N 7328 7.00 C 27444 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: 3.38 Conformation dependent library (CDL) restraints added in 2.0 seconds 10952 Ramachandran restraints generated. 5476 Oldfield, 0 Emsley, 5476 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10368 Finding SS restraints... Secondary structure from input PDB file: 236 helices and 36 sheets defined 60.1% alpha, 9.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.72 Creating SS restraints... Processing helix chain 'A' and resid 72 through 77 Processing helix chain 'A' and resid 118 through 135 removed outlier: 3.618A pdb=" N ALA A 122 " --> pdb=" O ASP A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 176 removed outlier: 3.575A pdb=" N GLU A 161 " --> pdb=" O PRO A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 203 removed outlier: 3.819A pdb=" N LYS A 201 " --> pdb=" O GLU A 197 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N THR A 202 " --> pdb=" O ALA A 198 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLN A 203 " --> pdb=" O LEU A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 227 removed outlier: 3.514A pdb=" N MET A 225 " --> pdb=" O GLY A 221 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N THR A 226 " --> pdb=" O GLY A 222 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ARG A 227 " --> pdb=" O ASP A 223 " (cutoff:3.500A) No H-bonds generated for '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: 3.505A pdb=" N LEU A 302 " --> pdb=" O GLY A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 336 Processing helix chain 'A' and resid 339 through 344 removed outlier: 3.602A pdb=" N PHE A 342 " --> pdb=" O LEU A 339 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N SER A 344 " --> pdb=" O ARG A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 359 Processing helix chain 'A' and resid 362 through 377 removed outlier: 3.655A pdb=" N VAL A 377 " --> pdb=" O ALA A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 406 Processing helix chain 'A' and resid 410 through 421 Processing helix chain 'A' and resid 423 through 437 removed outlier: 3.631A pdb=" N ALA A 427 " --> pdb=" O GLN A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 457 removed outlier: 3.608A pdb=" N CYS A 446 " --> pdb=" O GLU A 442 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N ASN A 448 " --> pdb=" O ALA A 444 " (cutoff:3.500A) removed outlier: 5.424A 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: 3.511A pdb=" N GLU A 475 " --> pdb=" O LYS A 472 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU A 476 " --> pdb=" O ILE A 473 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 472 through 476' Processing helix chain 'A' and resid 487 through 492 Processing helix chain 'A' and resid 494 through 509 removed outlier: 3.659A pdb=" N LEU A 498 " --> pdb=" O PRO A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 523 removed outlier: 3.674A pdb=" N ARG A 517 " --> pdb=" O SER A 513 " (cutoff:3.500A) removed outlier: 4.189A 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: 3.761A pdb=" N SER A 569 " --> pdb=" O ALA A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 586 removed outlier: 3.924A pdb=" N ILE A 580 " --> pdb=" O ASP A 577 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N SER A 583 " --> pdb=" O ILE A 580 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N LYS A 584 " --> pdb=" O TYR A 581 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N TYR A 585 " --> pdb=" O ASP A 582 " (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: 3.753A pdb=" N THR A 642 " --> pdb=" O GLU A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 643 through 647 removed outlier: 3.644A pdb=" N GLN A 647 " --> pdb=" O ARG A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 650 No H-bonds generated for 'chain 'A' and resid 648 through 650' Processing helix chain 'A' and resid 651 through 680 Processing helix chain 'A' and resid 680 through 689 Processing helix chain 'A' and resid 692 through 696 removed outlier: 3.625A pdb=" N PHE A 695 " --> pdb=" O ASN A 692 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASN A 696 " --> pdb=" O ASP A 693 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 692 through 696' Processing helix chain 'A' and resid 699 through 707 Processing helix chain 'A' and resid 709 through 714 Processing helix chain 'A' and resid 715 through 728 Processing helix chain 'A' and resid 735 through 745 Processing helix chain 'A' and resid 745 through 750 removed outlier: 3.776A pdb=" N LEU A 750 " --> pdb=" O PRO A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 788 through 800 removed outlier: 3.520A pdb=" N ARG A 792 " --> pdb=" O ALA A 788 " (cutoff:3.500A) removed outlier: 3.960A 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: 3.509A pdb=" N TYR A 863 " --> pdb=" O GLY A 859 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ASP A 866 " --> pdb=" O GLU A 862 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 889 removed outlier: 3.661A pdb=" N ARG A 870 " --> pdb=" O ASP A 866 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ASP A 889 " --> pdb=" O THR A 885 " (cutoff:3.500A) Processing helix chain 'A' and resid 892 through 914 removed outlier: 4.098A pdb=" N PHE A 905 " --> pdb=" O GLY A 901 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL A 908 " --> pdb=" O ALA A 904 " (cutoff:3.500A) Processing helix chain 'A' and resid 915 through 921 removed outlier: 3.998A pdb=" N LEU A 920 " --> pdb=" O TYR A 917 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 961 removed outlier: 3.667A pdb=" N LYS A 927 " --> pdb=" O ASN A 923 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N LYS A 936 " --> pdb=" O MET A 932 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ASP A 937 " --> pdb=" O GLU A 933 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ILE A 947 " --> pdb=" O PHE A 943 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N PHE A 948 " --> pdb=" O LEU A 944 " (cutoff:3.500A) Processing helix chain 'A' and resid 967 through 981 removed outlier: 3.645A pdb=" N PHE A 971 " --> pdb=" O SER A 967 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N ARG A 977 " --> pdb=" O GLY A 973 " (cutoff:3.500A) Proline residue: A 978 - end of helix Processing helix chain 'A' and resid 982 through 984 No H-bonds generated for 'chain 'A' and resid 982 through 984' Processing helix chain 'A' and resid 987 through 995 Processing helix chain 'A' and resid 1010 through 1012 No H-bonds generated for 'chain 'A' and resid 1010 through 1012' Processing helix chain 'A' and resid 1013 through 1026 removed outlier: 3.820A pdb=" N LEU A1023 " --> pdb=" O ALA A1019 " (cutoff:3.500A) Processing helix chain 'A' and resid 1028 through 1066 removed outlier: 5.748A pdb=" N GLU A1046 " --> pdb=" O MET A1042 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N ALA A1047 " --> pdb=" O LYS A1043 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N TYR A1057 " --> pdb=" O ARG A1053 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ASP A1065 " --> pdb=" O ALA A1061 " (cutoff:3.500A) Processing helix chain 'A' and resid 1073 through 1090 removed outlier: 4.113A 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 1169 Processing helix chain 'A' and resid 1202 through 1206 Processing helix chain 'A' and resid 1255 through 1260 Processing helix chain 'A' and resid 1378 through 1391 Processing helix chain 'A' and resid 1404 through 1413 removed outlier: 3.682A pdb=" N SER A1408 " --> pdb=" O GLU A1404 " (cutoff:3.500A) Processing helix chain 'A' and resid 1447 through 1452 removed outlier: 3.707A pdb=" N ARG A1452 " --> pdb=" O ARG A1448 " (cutoff:3.500A) Processing helix chain 'A' and resid 1478 through 1491 Processing helix chain 'B' and resid 72 through 77 Processing helix chain 'B' and resid 118 through 135 removed outlier: 3.618A pdb=" N ALA B 122 " --> pdb=" O ASP B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 176 removed outlier: 3.575A pdb=" N GLU B 161 " --> pdb=" O PRO B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 203 removed outlier: 3.819A pdb=" N LYS B 201 " --> pdb=" O GLU B 197 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N THR B 202 " --> pdb=" O ALA B 198 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLN B 203 " --> pdb=" O LEU B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 227 removed outlier: 3.514A pdb=" N MET B 225 " --> pdb=" O GLY B 221 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N THR B 226 " --> pdb=" O GLY B 222 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ARG B 227 " --> pdb=" O ASP B 223 " (cutoff:3.500A) No H-bonds generated for '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: 3.505A pdb=" N LEU B 302 " --> pdb=" O GLY B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 336 Processing helix chain 'B' and resid 339 through 344 removed outlier: 3.602A pdb=" N PHE B 342 " --> pdb=" O LEU B 339 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N SER B 344 " --> pdb=" O ARG B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 359 Processing helix chain 'B' and resid 362 through 377 removed outlier: 3.655A pdb=" N VAL B 377 " --> pdb=" O ALA B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 406 Processing helix chain 'B' and resid 410 through 421 Processing helix chain 'B' and resid 423 through 437 removed outlier: 3.631A pdb=" N ALA B 427 " --> pdb=" O GLN B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 457 removed outlier: 3.608A pdb=" N CYS B 446 " --> pdb=" O GLU B 442 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N ASN B 448 " --> pdb=" O ALA B 444 " (cutoff:3.500A) removed outlier: 5.424A 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: 3.511A pdb=" N GLU B 475 " --> pdb=" O LYS B 472 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU B 476 " --> pdb=" O ILE B 473 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 472 through 476' Processing helix chain 'B' and resid 487 through 492 Processing helix chain 'B' and resid 494 through 509 removed outlier: 3.659A pdb=" N LEU B 498 " --> pdb=" O PRO B 494 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 523 removed outlier: 3.674A pdb=" N ARG B 517 " --> pdb=" O SER B 513 " (cutoff:3.500A) removed outlier: 4.189A 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: 3.761A pdb=" N SER B 569 " --> pdb=" O ALA B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 577 through 586 removed outlier: 3.924A pdb=" N ILE B 580 " --> pdb=" O ASP B 577 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N SER B 583 " --> pdb=" O ILE B 580 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N LYS B 584 " --> pdb=" O TYR B 581 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TYR B 585 " --> pdb=" O ASP B 582 " (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: 3.753A pdb=" N THR B 642 " --> pdb=" O GLU B 638 " (cutoff:3.500A) Processing helix chain 'B' and resid 643 through 647 removed outlier: 3.645A pdb=" N GLN B 647 " --> pdb=" O ARG B 644 " (cutoff:3.500A) Processing helix chain 'B' and resid 648 through 650 No H-bonds generated for 'chain 'B' and resid 648 through 650' Processing helix chain 'B' and resid 651 through 680 Processing helix chain 'B' and resid 680 through 689 Processing helix chain 'B' and resid 692 through 696 removed outlier: 3.625A pdb=" N PHE B 695 " --> pdb=" O ASN B 692 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASN B 696 " --> pdb=" O ASP B 693 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 692 through 696' Processing helix chain 'B' and resid 699 through 707 Processing helix chain 'B' and resid 709 through 714 Processing helix chain 'B' and resid 715 through 728 Processing helix chain 'B' and resid 735 through 745 Processing helix chain 'B' and resid 745 through 750 removed outlier: 3.776A pdb=" N LEU B 750 " --> pdb=" O PRO B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 788 through 800 removed outlier: 3.520A pdb=" N ARG B 792 " --> pdb=" O ALA B 788 " (cutoff:3.500A) removed outlier: 3.960A 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: 3.509A pdb=" N TYR B 863 " --> pdb=" O GLY B 859 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ASP B 866 " --> pdb=" O GLU B 862 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 889 removed outlier: 3.661A pdb=" N ARG B 870 " --> pdb=" O ASP B 866 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ASP B 889 " --> pdb=" O THR B 885 " (cutoff:3.500A) Processing helix chain 'B' and resid 892 through 914 removed outlier: 4.098A pdb=" N PHE B 905 " --> pdb=" O GLY B 901 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL B 908 " --> pdb=" O ALA B 904 " (cutoff:3.500A) Processing helix chain 'B' and resid 915 through 921 removed outlier: 3.998A pdb=" N LEU B 920 " --> pdb=" O TYR B 917 " (cutoff:3.500A) Processing helix chain 'B' and resid 923 through 961 removed outlier: 3.667A pdb=" N LYS B 927 " --> pdb=" O ASN B 923 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N LYS B 936 " --> pdb=" O MET B 932 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ASP B 937 " --> pdb=" O GLU B 933 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ILE B 947 " --> pdb=" O PHE B 943 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N PHE B 948 " --> pdb=" O LEU B 944 " (cutoff:3.500A) Processing helix chain 'B' and resid 967 through 981 removed outlier: 3.644A pdb=" N PHE B 971 " --> pdb=" O SER B 967 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N ARG B 977 " --> pdb=" O GLY B 973 " (cutoff:3.500A) Proline residue: B 978 - end of helix Processing helix chain 'B' and resid 982 through 984 No H-bonds generated for 'chain 'B' and resid 982 through 984' Processing helix chain 'B' and resid 987 through 995 Processing helix chain 'B' and resid 1010 through 1012 No H-bonds generated for 'chain 'B' and resid 1010 through 1012' Processing helix chain 'B' and resid 1013 through 1026 removed outlier: 3.820A pdb=" N LEU B1023 " --> pdb=" O ALA B1019 " (cutoff:3.500A) Processing helix chain 'B' and resid 1028 through 1066 removed outlier: 5.748A pdb=" N GLU B1046 " --> pdb=" O MET B1042 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N ALA B1047 " --> pdb=" O LYS B1043 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N TYR B1057 " --> pdb=" O ARG B1053 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ASP B1065 " --> pdb=" O ALA B1061 " (cutoff:3.500A) Processing helix chain 'B' and resid 1073 through 1090 removed outlier: 4.113A 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 1169 Processing helix chain 'B' and resid 1202 through 1206 Processing helix chain 'B' and resid 1255 through 1260 Processing helix chain 'B' and resid 1378 through 1391 Processing helix chain 'B' and resid 1404 through 1413 removed outlier: 3.682A pdb=" N SER B1408 " --> pdb=" O GLU B1404 " (cutoff:3.500A) Processing helix chain 'B' and resid 1447 through 1452 removed outlier: 3.708A pdb=" N ARG B1452 " --> pdb=" O ARG B1448 " (cutoff:3.500A) Processing helix chain 'B' and resid 1478 through 1491 Processing helix chain 'C' and resid 72 through 77 Processing helix chain 'C' and resid 118 through 135 removed outlier: 3.618A pdb=" N ALA C 122 " --> pdb=" O ASP C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 176 removed outlier: 3.575A pdb=" N GLU C 161 " --> pdb=" O PRO C 157 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 203 removed outlier: 3.819A pdb=" N LYS C 201 " --> pdb=" O GLU C 197 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N THR C 202 " --> pdb=" O ALA C 198 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLN C 203 " --> pdb=" O LEU C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 227 removed outlier: 3.514A pdb=" N MET C 225 " --> pdb=" O GLY C 221 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N THR C 226 " --> pdb=" O GLY C 222 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ARG C 227 " --> pdb=" O ASP C 223 " (cutoff:3.500A) No H-bonds generated for '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: 3.505A pdb=" N LEU C 302 " --> pdb=" O GLY C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 336 Processing helix chain 'C' and resid 339 through 344 removed outlier: 3.602A pdb=" N PHE C 342 " --> pdb=" O LEU C 339 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N SER C 344 " --> pdb=" O ARG C 341 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 359 Processing helix chain 'C' and resid 362 through 377 removed outlier: 3.655A pdb=" N VAL C 377 " --> pdb=" O ALA C 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 395 through 406 Processing helix chain 'C' and resid 410 through 421 Processing helix chain 'C' and resid 423 through 437 removed outlier: 3.631A pdb=" N ALA C 427 " --> pdb=" O GLN C 423 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 457 removed outlier: 3.608A pdb=" N CYS C 446 " --> pdb=" O GLU C 442 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N ASN C 448 " --> pdb=" O ALA C 444 " (cutoff:3.500A) removed outlier: 5.424A 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: 3.511A pdb=" N GLU C 475 " --> pdb=" O LYS C 472 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU C 476 " --> pdb=" O ILE C 473 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 472 through 476' Processing helix chain 'C' and resid 487 through 492 Processing helix chain 'C' and resid 494 through 509 removed outlier: 3.659A pdb=" N LEU C 498 " --> pdb=" O PRO C 494 " (cutoff:3.500A) Processing helix chain 'C' and resid 513 through 523 removed outlier: 3.674A pdb=" N ARG C 517 " --> pdb=" O SER C 513 " (cutoff:3.500A) removed outlier: 4.189A 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: 3.761A pdb=" N SER C 569 " --> pdb=" O ALA C 565 " (cutoff:3.500A) Processing helix chain 'C' and resid 577 through 586 removed outlier: 3.923A pdb=" N ILE C 580 " --> pdb=" O ASP C 577 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N SER C 583 " --> pdb=" O ILE C 580 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N LYS C 584 " --> pdb=" O TYR C 581 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N TYR C 585 " --> pdb=" O ASP C 582 " (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: 3.753A pdb=" N THR C 642 " --> pdb=" O GLU C 638 " (cutoff:3.500A) Processing helix chain 'C' and resid 643 through 647 removed outlier: 3.644A pdb=" N GLN C 647 " --> pdb=" O ARG C 644 " (cutoff:3.500A) Processing helix chain 'C' and resid 648 through 650 No H-bonds generated for 'chain 'C' and resid 648 through 650' Processing helix chain 'C' and resid 651 through 680 Processing helix chain 'C' and resid 680 through 689 Processing helix chain 'C' and resid 692 through 696 removed outlier: 3.624A pdb=" N PHE C 695 " --> pdb=" O ASN C 692 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASN C 696 " --> pdb=" O ASP C 693 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 692 through 696' Processing helix chain 'C' and resid 699 through 707 Processing helix chain 'C' and resid 709 through 714 Processing helix chain 'C' and resid 715 through 728 Processing helix chain 'C' and resid 735 through 745 Processing helix chain 'C' and resid 745 through 750 removed outlier: 3.776A pdb=" N LEU C 750 " --> pdb=" O PRO C 746 " (cutoff:3.500A) Processing helix chain 'C' and resid 788 through 800 removed outlier: 3.520A pdb=" N ARG C 792 " --> pdb=" O ALA C 788 " (cutoff:3.500A) removed outlier: 3.960A 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: 3.509A pdb=" N TYR C 863 " --> pdb=" O GLY C 859 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ASP C 866 " --> pdb=" O GLU C 862 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 889 removed outlier: 3.661A pdb=" N ARG C 870 " --> pdb=" O ASP C 866 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ASP C 889 " --> pdb=" O THR C 885 " (cutoff:3.500A) Processing helix chain 'C' and resid 892 through 914 removed outlier: 4.098A pdb=" N PHE C 905 " --> pdb=" O GLY C 901 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL C 908 " --> pdb=" O ALA C 904 " (cutoff:3.500A) Processing helix chain 'C' and resid 915 through 921 removed outlier: 3.998A pdb=" N LEU C 920 " --> pdb=" O TYR C 917 " (cutoff:3.500A) Processing helix chain 'C' and resid 923 through 961 removed outlier: 3.667A pdb=" N LYS C 927 " --> pdb=" O ASN C 923 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N LYS C 936 " --> pdb=" O MET C 932 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ASP C 937 " --> pdb=" O GLU C 933 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ILE C 947 " --> pdb=" O PHE C 943 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N PHE C 948 " --> pdb=" O LEU C 944 " (cutoff:3.500A) Processing helix chain 'C' and resid 967 through 981 removed outlier: 3.644A pdb=" N PHE C 971 " --> pdb=" O SER C 967 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N ARG C 977 " --> pdb=" O GLY C 973 " (cutoff:3.500A) Proline residue: C 978 - end of helix Processing helix chain 'C' and resid 982 through 984 No H-bonds generated for 'chain 'C' and resid 982 through 984' Processing helix chain 'C' and resid 987 through 995 Processing helix chain 'C' and resid 1010 through 1012 No H-bonds generated for 'chain 'C' and resid 1010 through 1012' Processing helix chain 'C' and resid 1013 through 1026 removed outlier: 3.820A pdb=" N LEU C1023 " --> pdb=" O ALA C1019 " (cutoff:3.500A) Processing helix chain 'C' and resid 1028 through 1066 removed outlier: 5.748A pdb=" N GLU C1046 " --> pdb=" O MET C1042 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N ALA C1047 " --> pdb=" O LYS C1043 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N TYR C1057 " --> pdb=" O ARG C1053 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ASP C1065 " --> pdb=" O ALA C1061 " (cutoff:3.500A) Processing helix chain 'C' and resid 1073 through 1090 removed outlier: 4.113A 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 1169 Processing helix chain 'C' and resid 1202 through 1206 Processing helix chain 'C' and resid 1255 through 1260 Processing helix chain 'C' and resid 1378 through 1391 Processing helix chain 'C' and resid 1404 through 1413 removed outlier: 3.682A pdb=" N SER C1408 " --> pdb=" O GLU C1404 " (cutoff:3.500A) Processing helix chain 'C' and resid 1447 through 1452 removed outlier: 3.707A pdb=" N ARG C1452 " --> pdb=" O ARG C1448 " (cutoff:3.500A) Processing helix chain 'C' and resid 1478 through 1491 Processing helix chain 'D' and resid 72 through 77 Processing helix chain 'D' and resid 118 through 135 removed outlier: 3.618A pdb=" N ALA D 122 " --> pdb=" O ASP D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 176 removed outlier: 3.574A pdb=" N GLU D 161 " --> pdb=" O PRO D 157 " (cutoff:3.500A) Processing helix chain 'D' and resid 186 through 203 removed outlier: 3.819A pdb=" N LYS D 201 " --> pdb=" O GLU D 197 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N THR D 202 " --> pdb=" O ALA D 198 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLN D 203 " --> pdb=" O LEU D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 227 removed outlier: 3.514A pdb=" N MET D 225 " --> pdb=" O GLY D 221 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N THR D 226 " --> pdb=" O GLY D 222 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ARG D 227 " --> pdb=" O ASP D 223 " (cutoff:3.500A) No H-bonds generated for '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: 3.505A pdb=" N LEU D 302 " --> pdb=" O GLY D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 336 Processing helix chain 'D' and resid 339 through 344 removed outlier: 3.602A pdb=" N PHE D 342 " --> pdb=" O LEU D 339 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N SER D 344 " --> pdb=" O ARG D 341 " (cutoff:3.500A) Processing helix chain 'D' and resid 346 through 359 Processing helix chain 'D' and resid 362 through 377 removed outlier: 3.654A pdb=" N VAL D 377 " --> pdb=" O ALA D 373 " (cutoff:3.500A) Processing helix chain 'D' and resid 395 through 406 Processing helix chain 'D' and resid 410 through 421 Processing helix chain 'D' and resid 423 through 437 removed outlier: 3.631A pdb=" N ALA D 427 " --> pdb=" O GLN D 423 " (cutoff:3.500A) Processing helix chain 'D' and resid 439 through 457 removed outlier: 3.608A pdb=" N CYS D 446 " --> pdb=" O GLU D 442 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N ASN D 448 " --> pdb=" O ALA D 444 " (cutoff:3.500A) removed outlier: 5.423A 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: 3.511A pdb=" N GLU D 475 " --> pdb=" O LYS D 472 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU D 476 " --> pdb=" O ILE D 473 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 472 through 476' Processing helix chain 'D' and resid 487 through 492 Processing helix chain 'D' and resid 494 through 509 removed outlier: 3.659A pdb=" N LEU D 498 " --> pdb=" O PRO D 494 " (cutoff:3.500A) Processing helix chain 'D' and resid 513 through 523 removed outlier: 3.675A pdb=" N ARG D 517 " --> pdb=" O SER D 513 " (cutoff:3.500A) removed outlier: 4.188A 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: 3.761A pdb=" N SER D 569 " --> pdb=" O ALA D 565 " (cutoff:3.500A) Processing helix chain 'D' and resid 577 through 586 removed outlier: 3.924A pdb=" N ILE D 580 " --> pdb=" O ASP D 577 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N SER D 583 " --> pdb=" O ILE D 580 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N LYS D 584 " --> pdb=" O TYR D 581 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N TYR D 585 " --> pdb=" O ASP D 582 " (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: 3.753A pdb=" N THR D 642 " --> pdb=" O GLU D 638 " (cutoff:3.500A) Processing helix chain 'D' and resid 643 through 647 removed outlier: 3.644A pdb=" N GLN D 647 " --> pdb=" O ARG D 644 " (cutoff:3.500A) Processing helix chain 'D' and resid 648 through 650 No H-bonds generated for 'chain 'D' and resid 648 through 650' Processing helix chain 'D' and resid 651 through 680 Processing helix chain 'D' and resid 680 through 689 Processing helix chain 'D' and resid 692 through 696 removed outlier: 3.625A pdb=" N PHE D 695 " --> pdb=" O ASN D 692 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASN D 696 " --> pdb=" O ASP D 693 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 692 through 696' Processing helix chain 'D' and resid 699 through 707 Processing helix chain 'D' and resid 709 through 714 Processing helix chain 'D' and resid 715 through 728 Processing helix chain 'D' and resid 735 through 745 Processing helix chain 'D' and resid 745 through 750 removed outlier: 3.776A pdb=" N LEU D 750 " --> pdb=" O PRO D 746 " (cutoff:3.500A) Processing helix chain 'D' and resid 788 through 800 removed outlier: 3.520A pdb=" N ARG D 792 " --> pdb=" O ALA D 788 " (cutoff:3.500A) removed outlier: 3.960A 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: 3.509A pdb=" N TYR D 863 " --> pdb=" O GLY D 859 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ASP D 866 " --> pdb=" O GLU D 862 " (cutoff:3.500A) Processing helix chain 'D' and resid 866 through 889 removed outlier: 3.661A pdb=" N ARG D 870 " --> pdb=" O ASP D 866 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ASP D 889 " --> pdb=" O THR D 885 " (cutoff:3.500A) Processing helix chain 'D' and resid 892 through 914 removed outlier: 4.098A pdb=" N PHE D 905 " --> pdb=" O GLY D 901 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL D 908 " --> pdb=" O ALA D 904 " (cutoff:3.500A) Processing helix chain 'D' and resid 915 through 921 removed outlier: 3.998A pdb=" N LEU D 920 " --> pdb=" O TYR D 917 " (cutoff:3.500A) Processing helix chain 'D' and resid 923 through 961 removed outlier: 3.667A pdb=" N LYS D 927 " --> pdb=" O ASN D 923 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N LYS D 936 " --> pdb=" O MET D 932 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ASP D 937 " --> pdb=" O GLU D 933 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ILE D 947 " --> pdb=" O PHE D 943 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N PHE D 948 " --> pdb=" O LEU D 944 " (cutoff:3.500A) Processing helix chain 'D' and resid 967 through 981 removed outlier: 3.645A pdb=" N PHE D 971 " --> pdb=" O SER D 967 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N ARG D 977 " --> pdb=" O GLY D 973 " (cutoff:3.500A) Proline residue: D 978 - end of helix Processing helix chain 'D' and resid 982 through 984 No H-bonds generated for 'chain 'D' and resid 982 through 984' Processing helix chain 'D' and resid 987 through 995 Processing helix chain 'D' and resid 1010 through 1012 No H-bonds generated for 'chain 'D' and resid 1010 through 1012' Processing helix chain 'D' and resid 1013 through 1026 removed outlier: 3.820A pdb=" N LEU D1023 " --> pdb=" O ALA D1019 " (cutoff:3.500A) Processing helix chain 'D' and resid 1028 through 1066 removed outlier: 5.748A pdb=" N GLU D1046 " --> pdb=" O MET D1042 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N ALA D1047 " --> pdb=" O LYS D1043 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N TYR D1057 " --> pdb=" O ARG D1053 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ASP D1065 " --> pdb=" O ALA D1061 " (cutoff:3.500A) Processing helix chain 'D' and resid 1073 through 1090 removed outlier: 4.112A 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 1169 Processing helix chain 'D' and resid 1202 through 1206 Processing helix chain 'D' and resid 1255 through 1260 Processing helix chain 'D' and resid 1378 through 1391 Processing helix chain 'D' and resid 1404 through 1413 removed outlier: 3.682A pdb=" N SER D1408 " --> pdb=" O GLU D1404 " (cutoff:3.500A) Processing helix chain 'D' and resid 1447 through 1452 removed outlier: 3.707A pdb=" N ARG D1452 " --> pdb=" O ARG D1448 " (cutoff:3.500A) Processing helix chain 'D' and resid 1478 through 1491 Processing sheet with id=AA1, first strand: chain 'A' and resid 56 through 60 Processing sheet with id=AA2, first strand: chain 'A' and resid 80 through 81 Processing sheet with id=AA3, first strand: chain 'A' and resid 231 through 236 removed outlier: 8.219A pdb=" N TRP A 96 " --> pdb=" O PRO A 231 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N ILE A 233 " --> pdb=" O TRP A 96 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N THR A 98 " --> pdb=" O ILE A 233 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N LEU A 259 " --> pdb=" O PRO A 109 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N LEU A 111 " --> pdb=" O LEU A 259 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N ASP A 261 " --> pdb=" O LEU A 111 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N LEU A 113 " --> pdb=" O ASP A 261 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N VAL A 179 " --> pdb=" O ILE A 211 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N ILE A 213 " --> pdb=" O VAL A 179 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N THR A 181 " --> pdb=" O ILE A 213 " (cutoff:3.500A) removed outlier: 8.745A pdb=" N THR A 215 " --> pdb=" O THR A 181 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ILE A 144 " --> pdb=" O VAL A 291 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N ILE A 293 " --> pdb=" O ILE A 144 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N SER A 146 " --> pdb=" O ILE A 293 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N VAL A 295 " --> pdb=" O SER A 146 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N THR A 148 " --> pdb=" O VAL A 295 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1251 through 1254 removed outlier: 6.034A pdb=" N VAL A1251 " --> pdb=" O THR A1315 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N ARG A1317 " --> pdb=" O VAL A1251 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N TYR A1253 " --> pdb=" O ARG A1317 " (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: 4.366A 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: 5.602A pdb=" N VAL A1333 " --> pdb=" O VAL A1356 " (cutoff:3.500A) removed outlier: 8.273A pdb=" N ILE A1358 " --> pdb=" O THR A1331 " (cutoff:3.500A) removed outlier: 11.587A pdb=" N THR A1331 " --> pdb=" O ILE A1358 " (cutoff:3.500A) removed outlier: 13.677A pdb=" N ARG A1360 " --> pdb=" O ALA A1329 " (cutoff:3.500A) removed outlier: 17.411A pdb=" N ALA A1329 " --> pdb=" O ARG A1360 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N TRP A1336 " --> pdb=" O ASP A1444 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ALA A1420 " --> pdb=" O CYS A1439 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ASN A1441 " --> pdb=" O ILE A1418 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N ILE A1418 " --> pdb=" O ASN A1441 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N HIS A1443 " --> pdb=" O GLY A1416 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N GLY A1416 " --> pdb=" O HIS A1443 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1370 through 1372 removed outlier: 17.411A pdb=" N ALA A1329 " --> pdb=" O ARG A1360 " (cutoff:3.500A) removed outlier: 13.677A pdb=" N ARG A1360 " --> pdb=" O ALA A1329 " (cutoff:3.500A) removed outlier: 11.587A pdb=" N THR A1331 " --> pdb=" O ILE A1358 " (cutoff:3.500A) removed outlier: 8.273A pdb=" N ILE A1358 " --> pdb=" O THR A1331 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N VAL A1333 " --> pdb=" O VAL A1356 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N LEU A1353 " --> pdb=" O MET A1468 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N MET A1468 " --> pdb=" O LEU A1353 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N PHE A1355 " --> pdb=" O TRP A1466 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N TRP A1466 " --> pdb=" O PHE A1355 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ALA A1357 " --> pdb=" O ALA A1464 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ALA A1464 " --> pdb=" O ALA A1357 " (cutoff:3.500A) removed outlier: 6.445A 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 231 through 236 removed outlier: 8.219A pdb=" N TRP B 96 " --> pdb=" O PRO B 231 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N ILE B 233 " --> pdb=" O TRP B 96 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N THR B 98 " --> pdb=" O ILE B 233 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N LEU B 259 " --> pdb=" O PRO B 109 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N LEU B 111 " --> pdb=" O LEU B 259 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N ASP B 261 " --> pdb=" O LEU B 111 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N LEU B 113 " --> pdb=" O ASP B 261 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N VAL B 179 " --> pdb=" O ILE B 211 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N ILE B 213 " --> pdb=" O VAL B 179 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N THR B 181 " --> pdb=" O ILE B 213 " (cutoff:3.500A) removed outlier: 8.745A pdb=" N THR B 215 " --> pdb=" O THR B 181 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ILE B 144 " --> pdb=" O VAL B 291 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N ILE B 293 " --> pdb=" O ILE B 144 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N SER B 146 " --> pdb=" O ILE B 293 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N VAL B 295 " --> pdb=" O SER B 146 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N THR B 148 " --> pdb=" O VAL B 295 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 1251 through 1254 removed outlier: 6.034A pdb=" N VAL B1251 " --> pdb=" O THR B1315 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N ARG B1317 " --> pdb=" O VAL B1251 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N TYR B1253 " --> pdb=" O ARG B1317 " (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: 4.366A 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: 5.602A pdb=" N VAL B1333 " --> pdb=" O VAL B1356 " (cutoff:3.500A) removed outlier: 8.272A pdb=" N ILE B1358 " --> pdb=" O THR B1331 " (cutoff:3.500A) removed outlier: 11.587A pdb=" N THR B1331 " --> pdb=" O ILE B1358 " (cutoff:3.500A) removed outlier: 13.676A pdb=" N ARG B1360 " --> pdb=" O ALA B1329 " (cutoff:3.500A) removed outlier: 17.411A pdb=" N ALA B1329 " --> pdb=" O ARG B1360 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N TRP B1336 " --> pdb=" O ASP B1444 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ALA B1420 " --> pdb=" O CYS B1439 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ASN B1441 " --> pdb=" O ILE B1418 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N ILE B1418 " --> pdb=" O ASN B1441 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N HIS B1443 " --> pdb=" O GLY B1416 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N GLY B1416 " --> pdb=" O HIS B1443 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 1370 through 1372 removed outlier: 17.411A pdb=" N ALA B1329 " --> pdb=" O ARG B1360 " (cutoff:3.500A) removed outlier: 13.676A pdb=" N ARG B1360 " --> pdb=" O ALA B1329 " (cutoff:3.500A) removed outlier: 11.587A pdb=" N THR B1331 " --> pdb=" O ILE B1358 " (cutoff:3.500A) removed outlier: 8.272A pdb=" N ILE B1358 " --> pdb=" O THR B1331 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N VAL B1333 " --> pdb=" O VAL B1356 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N LEU B1353 " --> pdb=" O MET B1468 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N MET B1468 " --> pdb=" O LEU B1353 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N PHE B1355 " --> pdb=" O TRP B1466 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N TRP B1466 " --> pdb=" O PHE B1355 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ALA B1357 " --> pdb=" O ALA B1464 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ALA B1464 " --> pdb=" O ALA B1357 " (cutoff:3.500A) removed outlier: 6.445A 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 231 through 236 removed outlier: 8.219A pdb=" N TRP C 96 " --> pdb=" O PRO C 231 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N ILE C 233 " --> pdb=" O TRP C 96 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N THR C 98 " --> pdb=" O ILE C 233 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N LEU C 259 " --> pdb=" O PRO C 109 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N LEU C 111 " --> pdb=" O LEU C 259 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N ASP C 261 " --> pdb=" O LEU C 111 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N LEU C 113 " --> pdb=" O ASP C 261 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N VAL C 179 " --> pdb=" O ILE C 211 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N ILE C 213 " --> pdb=" O VAL C 179 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N THR C 181 " --> pdb=" O ILE C 213 " (cutoff:3.500A) removed outlier: 8.745A pdb=" N THR C 215 " --> pdb=" O THR C 181 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ILE C 144 " --> pdb=" O VAL C 291 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N ILE C 293 " --> pdb=" O ILE C 144 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N SER C 146 " --> pdb=" O ILE C 293 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N VAL C 295 " --> pdb=" O SER C 146 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N THR C 148 " --> pdb=" O VAL C 295 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 1251 through 1254 removed outlier: 6.034A pdb=" N VAL C1251 " --> pdb=" O THR C1315 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N ARG C1317 " --> pdb=" O VAL C1251 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N TYR C1253 " --> pdb=" O ARG C1317 " (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: 4.366A 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: 5.602A pdb=" N VAL C1333 " --> pdb=" O VAL C1356 " (cutoff:3.500A) removed outlier: 8.273A pdb=" N ILE C1358 " --> pdb=" O THR C1331 " (cutoff:3.500A) removed outlier: 11.587A pdb=" N THR C1331 " --> pdb=" O ILE C1358 " (cutoff:3.500A) removed outlier: 13.676A pdb=" N ARG C1360 " --> pdb=" O ALA C1329 " (cutoff:3.500A) removed outlier: 17.411A pdb=" N ALA C1329 " --> pdb=" O ARG C1360 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N TRP C1336 " --> pdb=" O ASP C1444 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ALA C1420 " --> pdb=" O CYS C1439 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ASN C1441 " --> pdb=" O ILE C1418 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N ILE C1418 " --> pdb=" O ASN C1441 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N HIS C1443 " --> pdb=" O GLY C1416 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N GLY C1416 " --> pdb=" O HIS C1443 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 1370 through 1372 removed outlier: 17.411A pdb=" N ALA C1329 " --> pdb=" O ARG C1360 " (cutoff:3.500A) removed outlier: 13.676A pdb=" N ARG C1360 " --> pdb=" O ALA C1329 " (cutoff:3.500A) removed outlier: 11.587A pdb=" N THR C1331 " --> pdb=" O ILE C1358 " (cutoff:3.500A) removed outlier: 8.273A pdb=" N ILE C1358 " --> pdb=" O THR C1331 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N VAL C1333 " --> pdb=" O VAL C1356 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N LEU C1353 " --> pdb=" O MET C1468 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N MET C1468 " --> pdb=" O LEU C1353 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N PHE C1355 " --> pdb=" O TRP C1466 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N TRP C1466 " --> pdb=" O PHE C1355 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ALA C1357 " --> pdb=" O ALA C1464 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ALA C1464 " --> pdb=" O ALA C1357 " (cutoff:3.500A) removed outlier: 6.445A 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 231 through 236 removed outlier: 8.219A pdb=" N TRP D 96 " --> pdb=" O PRO D 231 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N ILE D 233 " --> pdb=" O TRP D 96 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N THR D 98 " --> pdb=" O ILE D 233 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N LEU D 259 " --> pdb=" O PRO D 109 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N LEU D 111 " --> pdb=" O LEU D 259 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N ASP D 261 " --> pdb=" O LEU D 111 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N LEU D 113 " --> pdb=" O ASP D 261 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N VAL D 179 " --> pdb=" O ILE D 211 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N ILE D 213 " --> pdb=" O VAL D 179 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N THR D 181 " --> pdb=" O ILE D 213 " (cutoff:3.500A) removed outlier: 8.746A pdb=" N THR D 215 " --> pdb=" O THR D 181 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ILE D 144 " --> pdb=" O VAL D 291 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N ILE D 293 " --> pdb=" O ILE D 144 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N SER D 146 " --> pdb=" O ILE D 293 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N VAL D 295 " --> pdb=" O SER D 146 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N THR D 148 " --> pdb=" O VAL D 295 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 1251 through 1254 removed outlier: 6.034A pdb=" N VAL D1251 " --> pdb=" O THR D1315 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N ARG D1317 " --> pdb=" O VAL D1251 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N TYR D1253 " --> pdb=" O ARG D1317 " (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: 4.366A 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: 5.602A pdb=" N VAL D1333 " --> pdb=" O VAL D1356 " (cutoff:3.500A) removed outlier: 8.272A pdb=" N ILE D1358 " --> pdb=" O THR D1331 " (cutoff:3.500A) removed outlier: 11.588A pdb=" N THR D1331 " --> pdb=" O ILE D1358 " (cutoff:3.500A) removed outlier: 13.677A pdb=" N ARG D1360 " --> pdb=" O ALA D1329 " (cutoff:3.500A) removed outlier: 17.412A pdb=" N ALA D1329 " --> pdb=" O ARG D1360 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N TRP D1336 " --> pdb=" O ASP D1444 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ALA D1420 " --> pdb=" O CYS D1439 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ASN D1441 " --> pdb=" O ILE D1418 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N ILE D1418 " --> pdb=" O ASN D1441 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N HIS D1443 " --> pdb=" O GLY D1416 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N GLY D1416 " --> pdb=" O HIS D1443 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 1370 through 1372 removed outlier: 17.412A pdb=" N ALA D1329 " --> pdb=" O ARG D1360 " (cutoff:3.500A) removed outlier: 13.677A pdb=" N ARG D1360 " --> pdb=" O ALA D1329 " (cutoff:3.500A) removed outlier: 11.588A pdb=" N THR D1331 " --> pdb=" O ILE D1358 " (cutoff:3.500A) removed outlier: 8.272A pdb=" N ILE D1358 " --> pdb=" O THR D1331 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N VAL D1333 " --> pdb=" O VAL D1356 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N LEU D1353 " --> pdb=" O MET D1468 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N MET D1468 " --> pdb=" O LEU D1353 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N PHE D1355 " --> pdb=" O TRP D1466 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N TRP D1466 " --> pdb=" O PHE D1355 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ALA D1357 " --> pdb=" O ALA D1464 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ALA D1464 " --> pdb=" O ALA D1357 " (cutoff:3.500A) removed outlier: 6.445A 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 2408 hydrogen bonds defined for protein. 7032 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 11.17 Time building geometry restraints manager: 4.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 6920 1.31 - 1.44: 11720 1.44 - 1.56: 24628 1.56 - 1.69: 68 1.69 - 1.82: 436 Bond restraints: 43772 Sorted by residual: bond pdb=" C2 RP5 A1501 " pdb=" C3 RP5 A1501 " ideal model delta sigma weight residual 1.525 1.237 0.288 2.00e-02 2.50e+03 2.08e+02 bond pdb=" C2 RP5 D6003 " pdb=" C3 RP5 D6003 " ideal model delta sigma weight residual 1.525 1.237 0.288 2.00e-02 2.50e+03 2.08e+02 bond pdb=" C2 RP5 B1501 " pdb=" C3 RP5 B1501 " ideal model delta sigma weight residual 1.525 1.237 0.288 2.00e-02 2.50e+03 2.08e+02 bond pdb=" C2 RP5 C1501 " pdb=" C3 RP5 C1501 " ideal model delta sigma weight residual 1.525 1.237 0.288 2.00e-02 2.50e+03 2.08e+02 bond pdb=" C4 AMP D6004 " pdb=" C5 AMP D6004 " ideal model delta sigma weight residual 1.490 1.345 0.145 2.00e-02 2.50e+03 5.25e+01 ... (remaining 43767 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.97: 54435 2.97 - 5.94: 4430 5.94 - 8.91: 583 8.91 - 11.88: 84 11.88 - 14.85: 16 Bond angle restraints: 59548 Sorted by residual: angle pdb=" N GLU D1404 " pdb=" CA GLU D1404 " pdb=" C GLU D1404 " ideal model delta sigma weight residual 114.04 100.24 13.80 1.24e+00 6.50e-01 1.24e+02 angle pdb=" N GLU C1404 " pdb=" CA GLU C1404 " pdb=" C GLU C1404 " ideal model delta sigma weight residual 114.04 100.24 13.80 1.24e+00 6.50e-01 1.24e+02 angle pdb=" N GLU A1404 " pdb=" CA GLU A1404 " pdb=" C GLU A1404 " ideal model delta sigma weight residual 114.04 100.24 13.80 1.24e+00 6.50e-01 1.24e+02 angle pdb=" N GLU B1404 " pdb=" CA GLU B1404 " pdb=" C GLU B1404 " ideal model delta sigma weight residual 114.04 100.28 13.76 1.24e+00 6.50e-01 1.23e+02 angle pdb=" N THR D 340 " pdb=" CA THR D 340 " pdb=" C THR D 340 " ideal model delta sigma weight residual 111.82 120.59 -8.77 1.16e+00 7.43e-01 5.72e+01 ... (remaining 59543 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.28: 25020 21.28 - 42.55: 1476 42.55 - 63.83: 176 63.83 - 85.11: 80 85.11 - 106.39: 8 Dihedral angle restraints: 26760 sinusoidal: 10748 harmonic: 16012 Sorted by residual: dihedral pdb=" C2' AMP B1502 " pdb=" C1' AMP B1502 " pdb=" N9 AMP B1502 " pdb=" C4 AMP B1502 " ideal model delta sinusoidal sigma weight residual 91.55 -14.83 106.39 1 2.00e+01 2.50e-03 3.08e+01 dihedral pdb=" C2' AMP A1502 " pdb=" C1' AMP A1502 " pdb=" N9 AMP A1502 " pdb=" C4 AMP A1502 " ideal model delta sinusoidal sigma weight residual 91.55 -14.83 106.39 1 2.00e+01 2.50e-03 3.08e+01 dihedral pdb=" C2' AMP C1502 " pdb=" C1' AMP C1502 " pdb=" N9 AMP C1502 " pdb=" C4 AMP C1502 " ideal model delta sinusoidal sigma weight residual 91.55 -14.83 106.39 1 2.00e+01 2.50e-03 3.08e+01 ... (remaining 26757 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 5386 0.099 - 0.199: 1103 0.199 - 0.298: 199 0.298 - 0.398: 60 0.398 - 0.497: 20 Chirality restraints: 6768 Sorted by residual: chirality pdb=" CA ASN C 153 " pdb=" N ASN C 153 " pdb=" C ASN C 153 " pdb=" CB ASN C 153 " both_signs ideal model delta sigma weight residual False 2.51 3.01 -0.50 2.00e-01 2.50e+01 6.18e+00 chirality pdb=" CA ASN A 153 " pdb=" N ASN A 153 " pdb=" C ASN A 153 " pdb=" CB ASN A 153 " both_signs ideal model delta sigma weight residual False 2.51 3.01 -0.50 2.00e-01 2.50e+01 6.17e+00 chirality pdb=" CA ASN B 153 " pdb=" N ASN B 153 " pdb=" C ASN B 153 " pdb=" CB ASN B 153 " both_signs ideal model delta sigma weight residual False 2.51 3.01 -0.50 2.00e-01 2.50e+01 6.17e+00 ... (remaining 6765 not shown) Planarity restraints: 7544 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 59 " -0.025 2.00e-02 2.50e+03 5.00e-02 2.50e+01 pdb=" C ILE A 59 " 0.087 2.00e-02 2.50e+03 pdb=" O ILE A 59 " -0.033 2.00e-02 2.50e+03 pdb=" N GLU A 60 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 59 " -0.025 2.00e-02 2.50e+03 5.00e-02 2.50e+01 pdb=" C ILE B 59 " 0.087 2.00e-02 2.50e+03 pdb=" O ILE B 59 " -0.033 2.00e-02 2.50e+03 pdb=" N GLU B 60 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE C 59 " -0.025 2.00e-02 2.50e+03 5.00e-02 2.50e+01 pdb=" C ILE C 59 " 0.087 2.00e-02 2.50e+03 pdb=" O ILE C 59 " -0.033 2.00e-02 2.50e+03 pdb=" N GLU C 60 " -0.029 2.00e-02 2.50e+03 ... (remaining 7541 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 620 2.68 - 3.23: 36561 3.23 - 3.79: 67163 3.79 - 4.34: 89698 4.34 - 4.90: 149730 Nonbonded interactions: 343772 Sorted by model distance: nonbonded pdb=" OE2 GLU C1390 " pdb="MG MG C1506 " model vdw 2.119 2.170 nonbonded pdb=" OE2 GLU B1390 " pdb="MG MG B1506 " model vdw 2.119 2.170 nonbonded pdb=" OE2 GLU A1390 " pdb="MG MG A1506 " model vdw 2.119 2.170 nonbonded pdb=" OE2 GLU D1390 " pdb="MG MG D6008 " model vdw 2.119 2.170 nonbonded pdb=" O1X RP5 D6003 " pdb="MG MG D6008 " model vdw 2.123 2.170 ... (remaining 343767 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 51 through 1494 or resid 1506 through 1508 or resid 1511)) \ selection = (chain 'B' and (resid 51 through 1494 or resid 1506 through 1508 or resid 1511)) \ selection = (chain 'C' and (resid 51 through 1494 or resid 1506 through 1508 or resid 1511)) \ selection = (chain 'D' and (resid 51 through 1494 or resid 6006 through 6008 or resid 6011)) \ } 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: 5.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.830 Check model and map are aligned: 0.130 Set scattering table: 0.110 Process input model: 40.980 Find NCS groups from input model: 1.470 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 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 : 0.012 0.288 43776 Z= 0.692 Angle : 1.731 14.854 59556 Z= 1.089 Chirality : 0.090 0.497 6768 Planarity : 0.011 0.059 7544 Dihedral : 13.758 106.387 16380 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 0.47 % Allowed : 1.13 % Favored : 98.39 % Cbeta Deviations : 0.62 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.11), residues: 5476 helix: 1.13 (0.09), residues: 2960 sheet: -0.87 (0.22), residues: 424 loop : -0.50 (0.14), residues: 2092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG A 112 TYR 0.052 0.006 TYR D 466 PHE 0.067 0.006 PHE A 695 TRP 0.032 0.003 TRP D 726 HIS 0.012 0.002 HIS A 82 Details of bonding type rmsd/Z covalent geometry : bond 0.01232 / 0.69 (43772) covalent geometry : angle 1.73142 / 1.09 (59548) SS BOND : bond 0.00171 / 0.09 ( 4) SS BOND : angle 2.19525 / 1.27 ( 8) hydrogen bonds : bond 0.16781 / 11.37 ( 2396) hydrogen bonds : angle 7.05502 / 5.11 ( 7032) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10952 Ramachandran restraints generated. 5476 Oldfield, 0 Emsley, 5476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10952 Ramachandran restraints generated. 5476 Oldfield, 0 Emsley, 5476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 968 residues out of total 4700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 948 time to evaluate : 1.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 GLU cc_start: 0.6886 (mm-30) cc_final: 0.6622 (mm-30) REVERT: A 121 ASP cc_start: 0.6074 (m-30) cc_final: 0.5824 (m-30) REVERT: A 166 LYS cc_start: 0.6597 (tttm) cc_final: 0.5984 (mtmm) REVERT: A 176 ASN cc_start: 0.8067 (m-40) cc_final: 0.7796 (m-40) REVERT: A 196 MET cc_start: 0.6913 (mmm) cc_final: 0.6672 (mmp) REVERT: A 200 SER cc_start: 0.7196 (p) cc_final: 0.6875 (p) REVERT: A 201 LYS cc_start: 0.6783 (mttt) cc_final: 0.6334 (pttm) REVERT: A 240 HIS cc_start: 0.6892 (m-70) cc_final: 0.6686 (m-70) REVERT: A 341 ARG cc_start: 0.7668 (mtm-85) cc_final: 0.7290 (mtm110) REVERT: A 416 LYS cc_start: 0.6494 (mttp) cc_final: 0.5988 (tttp) REVERT: A 422 ASP cc_start: 0.6980 (t0) cc_final: 0.6649 (t0) REVERT: A 455 MET cc_start: 0.6563 (mtm) cc_final: 0.6336 (mtt) REVERT: A 461 HIS cc_start: 0.6328 (m-70) cc_final: 0.5305 (p-80) REVERT: A 502 GLU cc_start: 0.6597 (tt0) cc_final: 0.5890 (tm-30) REVERT: A 553 ARG cc_start: 0.6980 (mmm-85) cc_final: 0.6712 (mtp180) REVERT: A 559 ARG cc_start: 0.6189 (ttt180) cc_final: 0.5904 (tmt90) REVERT: A 560 MET cc_start: 0.5872 (mmm) cc_final: 0.5626 (mmm) REVERT: A 614 ARG cc_start: 0.6113 (mtt180) cc_final: 0.5714 (mpp-170) REVERT: A 624 ASP cc_start: 0.7116 (p0) cc_final: 0.6574 (p0) REVERT: A 638 GLU cc_start: 0.6380 (mt-10) cc_final: 0.5643 (tm-30) REVERT: A 663 LYS cc_start: 0.7365 (mttt) cc_final: 0.7145 (mttt) REVERT: A 666 GLU cc_start: 0.6260 (tt0) cc_final: 0.5587 (tt0) REVERT: A 667 GLU cc_start: 0.5960 (tp30) cc_final: 0.5615 (tt0) REVERT: A 683 MET cc_start: 0.7612 (tpp) cc_final: 0.7284 (tpp) REVERT: A 686 GLU cc_start: 0.6692 (tt0) cc_final: 0.6106 (tp30) REVERT: A 691 LYS cc_start: 0.7522 (mttt) cc_final: 0.7279 (mttt) REVERT: A 699 ASN cc_start: 0.6688 (p0) cc_final: 0.5867 (p0) REVERT: A 702 ASN cc_start: 0.7309 (m-40) cc_final: 0.6691 (m110) REVERT: A 729 HIS cc_start: 0.6164 (m90) cc_final: 0.5761 (m170) REVERT: A 797 LYS cc_start: 0.6081 (mttt) cc_final: 0.5794 (mtmt) REVERT: A 829 GLU cc_start: 0.7300 (mt-10) cc_final: 0.6392 (mm-30) REVERT: A 862 GLU cc_start: 0.6337 (tt0) cc_final: 0.6081 (tm-30) REVERT: A 870 ARG cc_start: 0.7276 (mtt180) cc_final: 0.6984 (mtt180) REVERT: A 915 MET cc_start: 0.8432 (mtm) cc_final: 0.8058 (mtt) REVERT: A 930 MET cc_start: 0.6333 (OUTLIER) cc_final: 0.5130 (tpp) REVERT: A 932 MET cc_start: 0.6078 (mpp) cc_final: 0.5668 (mmm) REVERT: A 935 MET cc_start: 0.7025 (mmt) cc_final: 0.6578 (mmm) REVERT: A 971 PHE cc_start: 0.7861 (t80) cc_final: 0.7645 (t80) REVERT: A 994 GLU cc_start: 0.6277 (mt-10) cc_final: 0.6047 (mt-10) REVERT: A 1013 MET cc_start: 0.8091 (mtm) cc_final: 0.7852 (mtm) REVERT: A 1042 MET cc_start: 0.7368 (mtm) cc_final: 0.6466 (mmt) REVERT: A 1059 LEU cc_start: 0.6678 (mt) cc_final: 0.6284 (mm) REVERT: A 1081 MET cc_start: 0.6370 (mtm) cc_final: 0.6101 (mtm) REVERT: A 1119 LYS cc_start: 0.6145 (mtpt) cc_final: 0.5612 (ttpp) REVERT: A 1123 ARG cc_start: 0.5913 (ttp80) cc_final: 0.5356 (ttt-90) REVERT: A 1125 GLU cc_start: 0.5540 (mm-30) cc_final: 0.5070 (mp0) REVERT: A 1126 ARG cc_start: 0.5982 (ttm110) cc_final: 0.5528 (ttm170) REVERT: A 1129 GLN cc_start: 0.5711 (mm110) cc_final: 0.4909 (mt0) REVERT: A 1130 GLU cc_start: 0.6556 (mt-10) cc_final: 0.5675 (mm-30) REVERT: A 1131 MET cc_start: 0.6125 (mmp) cc_final: 0.5902 (mmp) REVERT: A 1249 ASP cc_start: 0.7977 (t0) cc_final: 0.7760 (p0) REVERT: A 1378 ASP cc_start: 0.7476 (t0) cc_final: 0.7146 (t70) REVERT: A 1407 ASP cc_start: 0.8228 (t0) cc_final: 0.7803 (m-30) REVERT: A 1444 ASP cc_start: 0.8161 (t0) cc_final: 0.7920 (t0) REVERT: A 1454 LYS cc_start: 0.8138 (mttm) cc_final: 0.7883 (mttm) REVERT: B 120 GLU cc_start: 0.6888 (mm-30) cc_final: 0.6617 (mm-30) REVERT: B 121 ASP cc_start: 0.6078 (m-30) cc_final: 0.5831 (m-30) REVERT: B 166 LYS cc_start: 0.6604 (tttm) cc_final: 0.5990 (mtmm) REVERT: B 176 ASN cc_start: 0.8071 (m-40) cc_final: 0.7800 (m-40) REVERT: B 196 MET cc_start: 0.6919 (mmm) cc_final: 0.6677 (mmp) REVERT: B 200 SER cc_start: 0.7196 (p) cc_final: 0.6875 (p) REVERT: B 201 LYS cc_start: 0.6787 (mttt) cc_final: 0.6340 (pttm) REVERT: B 341 ARG cc_start: 0.7677 (mtm-85) cc_final: 0.7298 (mtm110) REVERT: B 416 LYS cc_start: 0.6495 (mttp) cc_final: 0.5989 (tttp) REVERT: B 422 ASP cc_start: 0.6982 (t0) cc_final: 0.6655 (t0) REVERT: B 455 MET cc_start: 0.6565 (mtm) cc_final: 0.6335 (mtt) REVERT: B 461 HIS cc_start: 0.6330 (m-70) cc_final: 0.5310 (p-80) REVERT: B 502 GLU cc_start: 0.6595 (tt0) cc_final: 0.5887 (tm-30) REVERT: B 553 ARG cc_start: 0.6975 (mmm-85) cc_final: 0.6707 (mtp180) REVERT: B 559 ARG cc_start: 0.6169 (ttt180) cc_final: 0.5870 (tmt90) REVERT: B 560 MET cc_start: 0.5951 (mmm) cc_final: 0.5699 (mmm) REVERT: B 614 ARG cc_start: 0.6112 (mtt180) cc_final: 0.5713 (mpp-170) REVERT: B 624 ASP cc_start: 0.7113 (p0) cc_final: 0.6570 (p0) REVERT: B 638 GLU cc_start: 0.6369 (mt-10) cc_final: 0.5672 (tm-30) REVERT: B 663 LYS cc_start: 0.7365 (mttt) cc_final: 0.7145 (mttt) REVERT: B 666 GLU cc_start: 0.6229 (tt0) cc_final: 0.5554 (tt0) REVERT: B 667 GLU cc_start: 0.5962 (tp30) cc_final: 0.5616 (tt0) REVERT: B 683 MET cc_start: 0.7616 (tpp) cc_final: 0.7305 (tpp) REVERT: B 686 GLU cc_start: 0.6692 (tt0) cc_final: 0.6107 (tp30) REVERT: B 691 LYS cc_start: 0.7520 (mttt) cc_final: 0.7276 (mttt) REVERT: B 699 ASN cc_start: 0.6690 (p0) cc_final: 0.5846 (p0) REVERT: B 702 ASN cc_start: 0.7310 (m-40) cc_final: 0.6676 (m110) REVERT: B 729 HIS cc_start: 0.6145 (m90) cc_final: 0.5757 (m170) REVERT: B 797 LYS cc_start: 0.6081 (mttt) cc_final: 0.5794 (mtmt) REVERT: B 829 GLU cc_start: 0.7301 (mt-10) cc_final: 0.6389 (mm-30) REVERT: B 862 GLU cc_start: 0.6339 (tt0) cc_final: 0.6082 (tm-30) REVERT: B 870 ARG cc_start: 0.7276 (mtt180) cc_final: 0.6984 (mtt180) REVERT: B 915 MET cc_start: 0.8431 (mtm) cc_final: 0.8058 (mtt) REVERT: B 930 MET cc_start: 0.6328 (OUTLIER) cc_final: 0.5113 (tpp) REVERT: B 932 MET cc_start: 0.6076 (mpp) cc_final: 0.5670 (mmm) REVERT: B 935 MET cc_start: 0.7023 (mmt) cc_final: 0.6576 (mmm) REVERT: B 971 PHE cc_start: 0.7862 (t80) cc_final: 0.7647 (t80) REVERT: B 994 GLU cc_start: 0.6280 (mt-10) cc_final: 0.6051 (mt-10) REVERT: B 1013 MET cc_start: 0.8092 (mtm) cc_final: 0.7852 (mtm) REVERT: B 1042 MET cc_start: 0.7364 (mtm) cc_final: 0.6467 (mmt) REVERT: B 1059 LEU cc_start: 0.6680 (mt) cc_final: 0.6285 (mm) REVERT: B 1081 MET cc_start: 0.6370 (mtm) cc_final: 0.6103 (mtm) REVERT: B 1119 LYS cc_start: 0.6146 (mtpt) cc_final: 0.5602 (ttpp) REVERT: B 1123 ARG cc_start: 0.5914 (ttp80) cc_final: 0.5355 (ttt-90) REVERT: B 1125 GLU cc_start: 0.5541 (mm-30) cc_final: 0.5072 (mp0) REVERT: B 1126 ARG cc_start: 0.5984 (ttm110) cc_final: 0.5530 (ttm170) REVERT: B 1129 GLN cc_start: 0.5712 (mm110) cc_final: 0.4911 (mt0) REVERT: B 1130 GLU cc_start: 0.6556 (mt-10) cc_final: 0.5676 (mm-30) REVERT: B 1131 MET cc_start: 0.6123 (mmp) cc_final: 0.5900 (mmp) REVERT: B 1145 GLN cc_start: 0.7144 (tt0) cc_final: 0.6796 (tt0) REVERT: B 1249 ASP cc_start: 0.7981 (t0) cc_final: 0.7763 (p0) REVERT: B 1378 ASP cc_start: 0.7478 (t0) cc_final: 0.7147 (t70) REVERT: B 1407 ASP cc_start: 0.8227 (t0) cc_final: 0.7804 (m-30) REVERT: B 1444 ASP cc_start: 0.8153 (t0) cc_final: 0.7912 (t0) REVERT: B 1454 LYS cc_start: 0.8159 (mttm) cc_final: 0.7897 (mttm) REVERT: C 120 GLU cc_start: 0.6890 (mm-30) cc_final: 0.6618 (mm-30) REVERT: C 121 ASP cc_start: 0.6078 (m-30) cc_final: 0.5831 (m-30) REVERT: C 166 LYS cc_start: 0.6602 (tttm) cc_final: 0.5988 (mtmm) REVERT: C 176 ASN cc_start: 0.8071 (m-40) cc_final: 0.7799 (m-40) REVERT: C 196 MET cc_start: 0.6918 (mmm) cc_final: 0.6676 (mmp) REVERT: C 200 SER cc_start: 0.7196 (p) cc_final: 0.6876 (p) REVERT: C 201 LYS cc_start: 0.6784 (mttt) cc_final: 0.6336 (pttm) REVERT: C 341 ARG cc_start: 0.7624 (mtm-85) cc_final: 0.7252 (mtm110) REVERT: C 416 LYS cc_start: 0.6495 (mttp) cc_final: 0.5990 (tttp) REVERT: C 422 ASP cc_start: 0.6981 (t0) cc_final: 0.6654 (t0) REVERT: C 455 MET cc_start: 0.6564 (mtm) cc_final: 0.6336 (mtt) REVERT: C 461 HIS cc_start: 0.6332 (m-70) cc_final: 0.5311 (p-80) REVERT: C 502 GLU cc_start: 0.6595 (tt0) cc_final: 0.5888 (tm-30) REVERT: C 553 ARG cc_start: 0.6975 (mmm-85) cc_final: 0.6708 (mtp180) REVERT: C 559 ARG cc_start: 0.6170 (ttt180) cc_final: 0.5870 (tmt90) REVERT: C 560 MET cc_start: 0.5950 (mmm) cc_final: 0.5698 (mmm) REVERT: C 614 ARG cc_start: 0.6113 (mtt180) cc_final: 0.5714 (mpp-170) REVERT: C 624 ASP cc_start: 0.7113 (p0) cc_final: 0.6570 (p0) REVERT: C 638 GLU cc_start: 0.6391 (mt-10) cc_final: 0.5693 (tm-30) REVERT: C 663 LYS cc_start: 0.7365 (mttt) cc_final: 0.7145 (mttt) REVERT: C 666 GLU cc_start: 0.6257 (tt0) cc_final: 0.5584 (tt0) REVERT: C 667 GLU cc_start: 0.5963 (tp30) cc_final: 0.5616 (tt0) REVERT: C 683 MET cc_start: 0.7615 (tpp) cc_final: 0.7305 (tpp) REVERT: C 686 GLU cc_start: 0.6690 (tt0) cc_final: 0.6106 (tp30) REVERT: C 691 LYS cc_start: 0.7520 (mttt) cc_final: 0.7276 (mttt) REVERT: C 699 ASN cc_start: 0.6690 (p0) cc_final: 0.5845 (p0) REVERT: C 702 ASN cc_start: 0.7309 (m-40) cc_final: 0.6675 (m110) REVERT: C 729 HIS cc_start: 0.6145 (m90) cc_final: 0.5756 (m170) REVERT: C 797 LYS cc_start: 0.6082 (mttt) cc_final: 0.5795 (mtmt) REVERT: C 829 GLU cc_start: 0.7300 (mt-10) cc_final: 0.6390 (mm-30) REVERT: C 862 GLU cc_start: 0.6341 (tt0) cc_final: 0.6084 (tm-30) REVERT: C 870 ARG cc_start: 0.7277 (mtt180) cc_final: 0.6985 (mtt180) REVERT: C 915 MET cc_start: 0.8430 (mtm) cc_final: 0.8057 (mtt) REVERT: C 930 MET cc_start: 0.6329 (OUTLIER) cc_final: 0.5115 (tpp) REVERT: C 932 MET cc_start: 0.6078 (mpp) cc_final: 0.5671 (mmm) REVERT: C 935 MET cc_start: 0.7009 (mmt) cc_final: 0.6564 (mmm) REVERT: C 971 PHE cc_start: 0.7862 (t80) cc_final: 0.7647 (t80) REVERT: C 994 GLU cc_start: 0.6278 (mt-10) cc_final: 0.6050 (mt-10) REVERT: C 1013 MET cc_start: 0.8092 (mtm) cc_final: 0.7853 (mtm) REVERT: C 1042 MET cc_start: 0.7364 (mtm) cc_final: 0.6467 (mmt) REVERT: C 1059 LEU cc_start: 0.6680 (mt) cc_final: 0.6285 (mm) REVERT: C 1081 MET cc_start: 0.6371 (mtm) cc_final: 0.6103 (mtm) REVERT: C 1119 LYS cc_start: 0.6145 (mtpt) cc_final: 0.5601 (ttpp) REVERT: C 1123 ARG cc_start: 0.5913 (ttp80) cc_final: 0.5355 (ttt-90) REVERT: C 1125 GLU cc_start: 0.5541 (mm-30) cc_final: 0.5072 (mp0) REVERT: C 1126 ARG cc_start: 0.5984 (ttm110) cc_final: 0.5530 (ttm170) REVERT: C 1129 GLN cc_start: 0.5713 (mm110) cc_final: 0.4911 (mt0) REVERT: C 1130 GLU cc_start: 0.6556 (mt-10) cc_final: 0.5675 (mm-30) REVERT: C 1131 MET cc_start: 0.6124 (mmp) cc_final: 0.5901 (mmp) REVERT: C 1249 ASP cc_start: 0.7982 (t0) cc_final: 0.7764 (p0) REVERT: C 1378 ASP cc_start: 0.7478 (t0) cc_final: 0.7147 (t70) REVERT: C 1407 ASP cc_start: 0.8225 (t0) cc_final: 0.7803 (m-30) REVERT: C 1444 ASP cc_start: 0.8153 (t0) cc_final: 0.7911 (t0) REVERT: C 1454 LYS cc_start: 0.8159 (mttm) cc_final: 0.7896 (mttm) REVERT: D 120 GLU cc_start: 0.6894 (mm-30) cc_final: 0.6628 (mm-30) REVERT: D 121 ASP cc_start: 0.6085 (m-30) cc_final: 0.5838 (m-30) REVERT: D 166 LYS cc_start: 0.6591 (tttm) cc_final: 0.5962 (mtmm) REVERT: D 176 ASN cc_start: 0.8074 (m-40) cc_final: 0.7805 (m-40) REVERT: D 196 MET cc_start: 0.6868 (mmm) cc_final: 0.6632 (mmp) REVERT: D 200 SER cc_start: 0.7197 (p) cc_final: 0.6878 (p) REVERT: D 201 LYS cc_start: 0.6788 (mttt) cc_final: 0.6341 (pttm) REVERT: D 341 ARG cc_start: 0.7622 (mtm-85) cc_final: 0.7257 (mtm110) REVERT: D 416 LYS cc_start: 0.6495 (mttp) cc_final: 0.5989 (tttp) REVERT: D 422 ASP cc_start: 0.6988 (t0) cc_final: 0.6660 (t0) REVERT: D 455 MET cc_start: 0.6564 (mtm) cc_final: 0.6339 (mtt) REVERT: D 461 HIS cc_start: 0.6332 (m-70) cc_final: 0.5312 (p-80) REVERT: D 502 GLU cc_start: 0.6596 (tt0) cc_final: 0.5885 (tm-30) REVERT: D 553 ARG cc_start: 0.6975 (mmm-85) cc_final: 0.6709 (mtp180) REVERT: D 559 ARG cc_start: 0.6170 (ttt180) cc_final: 0.5870 (tmt90) REVERT: D 560 MET cc_start: 0.5953 (mmm) cc_final: 0.5702 (mmm) REVERT: D 614 ARG cc_start: 0.6115 (mtt180) cc_final: 0.5718 (mpp-170) REVERT: D 624 ASP cc_start: 0.7115 (p0) cc_final: 0.6604 (p0) REVERT: D 638 GLU cc_start: 0.6363 (mt-10) cc_final: 0.5651 (tm-30) REVERT: D 663 LYS cc_start: 0.7365 (mttt) cc_final: 0.7145 (mttt) REVERT: D 666 GLU cc_start: 0.6223 (tt0) cc_final: 0.5549 (tt0) REVERT: D 667 GLU cc_start: 0.5964 (tp30) cc_final: 0.5618 (tt0) REVERT: D 683 MET cc_start: 0.7617 (tpp) cc_final: 0.7303 (tpp) REVERT: D 686 GLU cc_start: 0.6690 (tt0) cc_final: 0.6107 (tp30) REVERT: D 691 LYS cc_start: 0.7490 (mttt) cc_final: 0.7242 (mttt) REVERT: D 699 ASN cc_start: 0.6692 (p0) cc_final: 0.5845 (p0) REVERT: D 702 ASN cc_start: 0.7308 (m-40) cc_final: 0.6675 (m110) REVERT: D 729 HIS cc_start: 0.6143 (m90) cc_final: 0.5758 (m170) REVERT: D 797 LYS cc_start: 0.6097 (mttt) cc_final: 0.5802 (mtmt) REVERT: D 829 GLU cc_start: 0.7283 (mt-10) cc_final: 0.6375 (mm-30) REVERT: D 862 GLU cc_start: 0.6343 (tt0) cc_final: 0.6085 (tm-30) REVERT: D 870 ARG cc_start: 0.7278 (mtt180) cc_final: 0.6986 (mtt180) REVERT: D 915 MET cc_start: 0.8430 (mtm) cc_final: 0.8057 (mtt) REVERT: D 930 MET cc_start: 0.6329 (OUTLIER) cc_final: 0.5079 (tpp) REVERT: D 932 MET cc_start: 0.6077 (mpp) cc_final: 0.5667 (mmm) REVERT: D 935 MET cc_start: 0.7008 (mmt) cc_final: 0.6564 (mmm) REVERT: D 971 PHE cc_start: 0.7860 (t80) cc_final: 0.7644 (t80) REVERT: D 994 GLU cc_start: 0.6279 (mt-10) cc_final: 0.6048 (mt-10) REVERT: D 1013 MET cc_start: 0.8092 (mtm) cc_final: 0.7852 (mtm) REVERT: D 1042 MET cc_start: 0.7367 (mtm) cc_final: 0.6464 (mmt) REVERT: D 1059 LEU cc_start: 0.6681 (mt) cc_final: 0.6282 (mm) REVERT: D 1081 MET cc_start: 0.6370 (mtm) cc_final: 0.6106 (mtm) REVERT: D 1119 LYS cc_start: 0.6148 (mtpt) cc_final: 0.5602 (ttpp) REVERT: D 1123 ARG cc_start: 0.5916 (ttp80) cc_final: 0.5355 (ttt-90) REVERT: D 1125 GLU cc_start: 0.5519 (mm-30) cc_final: 0.5052 (mp0) REVERT: D 1126 ARG cc_start: 0.5985 (ttm110) cc_final: 0.5532 (ttm170) REVERT: D 1129 GLN cc_start: 0.5713 (mm110) cc_final: 0.4913 (mt0) REVERT: D 1130 GLU cc_start: 0.6557 (mt-10) cc_final: 0.5676 (mm-30) REVERT: D 1131 MET cc_start: 0.6119 (mmp) cc_final: 0.5907 (mmp) REVERT: D 1145 GLN cc_start: 0.7142 (tt0) cc_final: 0.6794 (tt0) REVERT: D 1249 ASP cc_start: 0.7991 (t0) cc_final: 0.7762 (p0) REVERT: D 1378 ASP cc_start: 0.7483 (t0) cc_final: 0.7149 (t70) REVERT: D 1407 ASP cc_start: 0.8234 (t0) cc_final: 0.7792 (m-30) REVERT: D 1444 ASP cc_start: 0.8130 (t0) cc_final: 0.7880 (t0) REVERT: D 1454 LYS cc_start: 0.8161 (mttm) cc_final: 0.7901 (mttm) outliers start: 20 outliers final: 0 residues processed: 960 average time/residue: 0.7923 time to fit residues: 924.4352 Evaluate side-chains 632 residues out of total 4700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 628 time to evaluate : 1.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 930 MET Chi-restraints excluded: chain B residue 930 MET Chi-restraints excluded: chain C residue 930 MET Chi-restraints excluded: chain D residue 930 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 548 random chunks: chunk 394 optimal weight: 0.5980 chunk 430 optimal weight: 4.9990 chunk 41 optimal weight: 0.9990 chunk 265 optimal weight: 0.9990 chunk 523 optimal weight: 4.9990 chunk 497 optimal weight: 5.9990 chunk 414 optimal weight: 5.9990 chunk 310 optimal weight: 5.9990 chunk 488 optimal weight: 0.9980 chunk 366 optimal weight: 0.8980 chunk 223 optimal weight: 4.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 592 GLN A 659 GLN A 682 HIS A1101 GLN A1145 GLN A1166 GLN A1292 HIS A1307 ASN B 592 GLN B 659 GLN B 682 HIS B1101 GLN B1166 GLN B1292 HIS B1307 ASN C 592 GLN C 659 GLN C 682 HIS C1101 GLN C1145 GLN C1166 GLN C1292 HIS C1307 ASN D 82 HIS D 307 GLN D 592 GLN D 659 GLN D 682 HIS D1101 GLN D1166 GLN D1292 HIS D1307 ASN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.168444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.124559 restraints weight = 54367.944| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 2.23 r_work: 0.3289 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 43776 Z= 0.149 Angle : 0.570 7.420 59556 Z= 0.296 Chirality : 0.040 0.144 6768 Planarity : 0.004 0.049 7544 Dihedral : 8.629 97.713 7028 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.26 % Favored : 97.66 % Rotamer: Outliers : 1.80 % Allowed : 7.40 % Favored : 90.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.29 (0.11), residues: 5476 helix: 1.93 (0.09), residues: 3020 sheet: -0.66 (0.21), residues: 448 loop : -0.41 (0.14), residues: 2008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 174 TYR 0.019 0.002 TYR A 138 PHE 0.020 0.002 PHE C 274 TRP 0.011 0.001 TRP D 726 HIS 0.010 0.001 HIS B 682 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.15 (43772) covalent geometry : angle 0.56971 / 0.30 (59548) SS BOND : bond 0.00114 / 0.06 ( 4) SS BOND : angle 0.33211 / 0.20 ( 8) hydrogen bonds : bond 0.04503 / 2.99 ( 2396) hydrogen bonds : angle 4.09111 / 2.97 ( 7032) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10952 Ramachandran restraints generated. 5476 Oldfield, 0 Emsley, 5476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10952 Ramachandran restraints generated. 5476 Oldfield, 0 Emsley, 5476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 758 residues out of total 4700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 682 time to evaluate : 1.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 MET cc_start: 0.6862 (OUTLIER) cc_final: 0.5538 (pmm) REVERT: A 129 MET cc_start: 0.6860 (mtm) cc_final: 0.6542 (mtt) REVERT: A 166 LYS cc_start: 0.7295 (tttm) cc_final: 0.6872 (ttmm) REVERT: A 196 MET cc_start: 0.7974 (mmm) cc_final: 0.7760 (mmp) REVERT: A 356 GLN cc_start: 0.7956 (tt0) cc_final: 0.7750 (tm-30) REVERT: A 416 LYS cc_start: 0.7257 (mttp) cc_final: 0.6553 (tttp) REVERT: A 455 MET cc_start: 0.7604 (mtm) cc_final: 0.7221 (mtt) REVERT: A 456 MET cc_start: 0.6052 (mtp) cc_final: 0.5623 (mmm) REVERT: A 461 HIS cc_start: 0.6582 (m-70) cc_final: 0.5733 (p-80) REVERT: A 502 GLU cc_start: 0.7175 (tt0) cc_final: 0.5947 (tm-30) REVERT: A 553 ARG cc_start: 0.7465 (mmm-85) cc_final: 0.7154 (mtp180) REVERT: A 595 ARG cc_start: 0.7189 (mtm-85) cc_final: 0.6414 (mtp85) REVERT: A 614 ARG cc_start: 0.7401 (mtt180) cc_final: 0.6788 (mpp-170) REVERT: A 624 ASP cc_start: 0.7310 (p0) cc_final: 0.7031 (p0) REVERT: A 638 GLU cc_start: 0.6674 (mt-10) cc_final: 0.6400 (tm-30) REVERT: A 666 GLU cc_start: 0.7317 (tt0) cc_final: 0.6891 (tt0) REVERT: A 667 GLU cc_start: 0.7566 (tp30) cc_final: 0.7310 (mt-10) REVERT: A 683 MET cc_start: 0.8578 (tpp) cc_final: 0.8363 (tpt) REVERT: A 686 GLU cc_start: 0.7794 (tt0) cc_final: 0.7253 (tp30) REVERT: A 702 ASN cc_start: 0.8021 (m-40) cc_final: 0.7421 (m-40) REVERT: A 729 HIS cc_start: 0.6737 (m90) cc_final: 0.6345 (m170) REVERT: A 797 LYS cc_start: 0.6734 (mttt) cc_final: 0.6509 (mtmt) REVERT: A 829 GLU cc_start: 0.7964 (mt-10) cc_final: 0.7301 (mm-30) REVERT: A 862 GLU cc_start: 0.6877 (tt0) cc_final: 0.6555 (mt-10) REVERT: A 915 MET cc_start: 0.8982 (mtm) cc_final: 0.8677 (mtt) REVERT: A 1042 MET cc_start: 0.8766 (mtm) cc_final: 0.8130 (mmt) REVERT: A 1059 LEU cc_start: 0.7986 (mt) cc_final: 0.7638 (mm) REVERT: A 1081 MET cc_start: 0.7015 (mtm) cc_final: 0.6747 (mtm) REVERT: A 1108 LYS cc_start: 0.7257 (ttpp) cc_final: 0.6929 (ttmm) REVERT: A 1119 LYS cc_start: 0.7221 (mtpt) cc_final: 0.6809 (ttpp) REVERT: A 1122 ARG cc_start: 0.6961 (mtm-85) cc_final: 0.6710 (mtp180) REVERT: A 1123 ARG cc_start: 0.7042 (ttp80) cc_final: 0.6472 (ttt-90) REVERT: A 1126 ARG cc_start: 0.6756 (ttm170) cc_final: 0.6320 (ttm170) REVERT: A 1130 GLU cc_start: 0.7227 (mt-10) cc_final: 0.6617 (mp0) REVERT: A 1131 MET cc_start: 0.7187 (mmp) cc_final: 0.6681 (mtt) REVERT: A 1346 GLU cc_start: 0.8439 (tt0) cc_final: 0.8134 (tp30) REVERT: A 1452 ARG cc_start: 0.8437 (OUTLIER) cc_final: 0.7899 (ttp80) REVERT: B 70 MET cc_start: 0.6872 (OUTLIER) cc_final: 0.5540 (pmm) REVERT: B 129 MET cc_start: 0.6860 (mtm) cc_final: 0.6544 (mtt) REVERT: B 166 LYS cc_start: 0.7308 (tttm) cc_final: 0.6887 (ttmm) REVERT: B 196 MET cc_start: 0.7978 (mmm) cc_final: 0.7764 (mmp) REVERT: B 356 GLN cc_start: 0.7946 (tt0) cc_final: 0.7739 (tm-30) REVERT: B 416 LYS cc_start: 0.7246 (mttp) cc_final: 0.6539 (tttp) REVERT: B 455 MET cc_start: 0.7589 (mtm) cc_final: 0.7201 (mtt) REVERT: B 456 MET cc_start: 0.6027 (mtp) cc_final: 0.5602 (mmm) REVERT: B 461 HIS cc_start: 0.6573 (m-70) cc_final: 0.5722 (p-80) REVERT: B 502 GLU cc_start: 0.7175 (tt0) cc_final: 0.5952 (tm-30) REVERT: B 553 ARG cc_start: 0.7473 (mmm-85) cc_final: 0.7152 (mtp180) REVERT: B 595 ARG cc_start: 0.7183 (mtm-85) cc_final: 0.6413 (mtp85) REVERT: B 614 ARG cc_start: 0.7396 (mtt180) cc_final: 0.6800 (mpp-170) REVERT: B 624 ASP cc_start: 0.7310 (p0) cc_final: 0.7034 (p0) REVERT: B 638 GLU cc_start: 0.6692 (mt-10) cc_final: 0.6473 (tm-30) REVERT: B 666 GLU cc_start: 0.7322 (tt0) cc_final: 0.6895 (tt0) REVERT: B 667 GLU cc_start: 0.7583 (tp30) cc_final: 0.7314 (mt-10) REVERT: B 683 MET cc_start: 0.8574 (tpp) cc_final: 0.8356 (tpt) REVERT: B 686 GLU cc_start: 0.7794 (tt0) cc_final: 0.7246 (tp30) REVERT: B 702 ASN cc_start: 0.7989 (m-40) cc_final: 0.7388 (m-40) REVERT: B 729 HIS cc_start: 0.6733 (m90) cc_final: 0.6340 (m170) REVERT: B 797 LYS cc_start: 0.6780 (mttt) cc_final: 0.6542 (mtmt) REVERT: B 829 GLU cc_start: 0.7958 (mt-10) cc_final: 0.7297 (mm-30) REVERT: B 862 GLU cc_start: 0.6876 (tt0) cc_final: 0.6555 (mt-10) REVERT: B 915 MET cc_start: 0.8986 (mtm) cc_final: 0.8683 (mtt) REVERT: B 1042 MET cc_start: 0.8782 (mtm) cc_final: 0.8147 (mmt) REVERT: B 1059 LEU cc_start: 0.7986 (mt) cc_final: 0.7634 (mm) REVERT: B 1081 MET cc_start: 0.7022 (mtm) cc_final: 0.6751 (mtm) REVERT: B 1108 LYS cc_start: 0.7253 (ttpp) cc_final: 0.6926 (ttmm) REVERT: B 1119 LYS cc_start: 0.7275 (mtpt) cc_final: 0.6939 (ttpp) REVERT: B 1123 ARG cc_start: 0.7065 (ttp80) cc_final: 0.6492 (ttt-90) REVERT: B 1126 ARG cc_start: 0.6770 (ttm170) cc_final: 0.6331 (ttm170) REVERT: B 1130 GLU cc_start: 0.7246 (mt-10) cc_final: 0.6636 (mp0) REVERT: B 1131 MET cc_start: 0.7208 (mmp) cc_final: 0.6705 (mtt) REVERT: B 1346 GLU cc_start: 0.8446 (tt0) cc_final: 0.8147 (tp30) REVERT: B 1452 ARG cc_start: 0.8429 (OUTLIER) cc_final: 0.7887 (ttp80) REVERT: C 70 MET cc_start: 0.6875 (OUTLIER) cc_final: 0.5551 (pmm) REVERT: C 129 MET cc_start: 0.6866 (mtm) cc_final: 0.6550 (mtt) REVERT: C 166 LYS cc_start: 0.7315 (tttm) cc_final: 0.6894 (ttmm) REVERT: C 196 MET cc_start: 0.7977 (mmm) cc_final: 0.7761 (mmp) REVERT: C 356 GLN cc_start: 0.7936 (tt0) cc_final: 0.7732 (tm-30) REVERT: C 416 LYS cc_start: 0.7244 (mttp) cc_final: 0.6539 (tttp) REVERT: C 455 MET cc_start: 0.7586 (mtm) cc_final: 0.7200 (mtt) REVERT: C 456 MET cc_start: 0.6025 (mtp) cc_final: 0.5597 (mmm) REVERT: C 461 HIS cc_start: 0.6566 (m-70) cc_final: 0.5716 (p-80) REVERT: C 502 GLU cc_start: 0.7176 (tt0) cc_final: 0.5958 (tm-30) REVERT: C 553 ARG cc_start: 0.7476 (mmm-85) cc_final: 0.7158 (mtp180) REVERT: C 595 ARG cc_start: 0.7194 (mtm-85) cc_final: 0.6427 (mtp85) REVERT: C 614 ARG cc_start: 0.7400 (mtt180) cc_final: 0.6793 (mpp-170) REVERT: C 624 ASP cc_start: 0.7320 (p0) cc_final: 0.7044 (p0) REVERT: C 638 GLU cc_start: 0.6681 (mt-10) cc_final: 0.6409 (tm-30) REVERT: C 666 GLU cc_start: 0.7320 (tt0) cc_final: 0.6890 (tt0) REVERT: C 667 GLU cc_start: 0.7588 (tp30) cc_final: 0.7319 (mt-10) REVERT: C 683 MET cc_start: 0.8575 (tpp) cc_final: 0.8356 (tpt) REVERT: C 686 GLU cc_start: 0.7805 (tt0) cc_final: 0.7255 (tp30) REVERT: C 702 ASN cc_start: 0.8028 (m-40) cc_final: 0.7439 (m-40) REVERT: C 729 HIS cc_start: 0.6734 (m90) cc_final: 0.6342 (m170) REVERT: C 797 LYS cc_start: 0.6776 (mttt) cc_final: 0.6538 (mtmt) REVERT: C 829 GLU cc_start: 0.7952 (mt-10) cc_final: 0.7292 (mm-30) REVERT: C 862 GLU cc_start: 0.6873 (tt0) cc_final: 0.6554 (mt-10) REVERT: C 915 MET cc_start: 0.8988 (mtm) cc_final: 0.8685 (mtt) REVERT: C 1042 MET cc_start: 0.8783 (mtm) cc_final: 0.8147 (mmt) REVERT: C 1059 LEU cc_start: 0.7980 (mt) cc_final: 0.7630 (mm) REVERT: C 1081 MET cc_start: 0.7037 (mtm) cc_final: 0.6766 (mtm) REVERT: C 1108 LYS cc_start: 0.7239 (ttpp) cc_final: 0.6914 (ttmm) REVERT: C 1119 LYS cc_start: 0.7259 (mtpt) cc_final: 0.6928 (ttpp) REVERT: C 1123 ARG cc_start: 0.7038 (ttp80) cc_final: 0.6463 (ttt-90) REVERT: C 1126 ARG cc_start: 0.6760 (ttm170) cc_final: 0.6326 (ttm170) REVERT: C 1130 GLU cc_start: 0.7236 (mt-10) cc_final: 0.6627 (mp0) REVERT: C 1131 MET cc_start: 0.7211 (mmp) cc_final: 0.6705 (mtt) REVERT: C 1346 GLU cc_start: 0.8459 (tt0) cc_final: 0.8159 (tp30) REVERT: C 1452 ARG cc_start: 0.8433 (OUTLIER) cc_final: 0.7891 (ttp80) REVERT: D 70 MET cc_start: 0.6851 (OUTLIER) cc_final: 0.5449 (pmm) REVERT: D 129 MET cc_start: 0.6903 (mtm) cc_final: 0.6600 (mtt) REVERT: D 166 LYS cc_start: 0.7317 (tttm) cc_final: 0.6894 (ttmm) REVERT: D 196 MET cc_start: 0.7985 (mmm) cc_final: 0.7771 (mmp) REVERT: D 416 LYS cc_start: 0.7258 (mttp) cc_final: 0.6554 (tttp) REVERT: D 455 MET cc_start: 0.7611 (mtm) cc_final: 0.7231 (mtt) REVERT: D 456 MET cc_start: 0.6056 (mtp) cc_final: 0.5589 (mmm) REVERT: D 461 HIS cc_start: 0.6598 (m-70) cc_final: 0.5749 (p-80) REVERT: D 553 ARG cc_start: 0.7468 (mmm-85) cc_final: 0.7153 (mtp180) REVERT: D 595 ARG cc_start: 0.7203 (mtm-85) cc_final: 0.6434 (mtp85) REVERT: D 614 ARG cc_start: 0.7393 (mtt180) cc_final: 0.6794 (mpp-170) REVERT: D 624 ASP cc_start: 0.7279 (p0) cc_final: 0.7004 (p0) REVERT: D 638 GLU cc_start: 0.6698 (mt-10) cc_final: 0.6422 (tm-30) REVERT: D 666 GLU cc_start: 0.7333 (tt0) cc_final: 0.6917 (tt0) REVERT: D 667 GLU cc_start: 0.7585 (tp30) cc_final: 0.7320 (mt-10) REVERT: D 683 MET cc_start: 0.8581 (tpp) cc_final: 0.8360 (tpt) REVERT: D 686 GLU cc_start: 0.7818 (tt0) cc_final: 0.7277 (tp30) REVERT: D 702 ASN cc_start: 0.8041 (m-40) cc_final: 0.7454 (m-40) REVERT: D 729 HIS cc_start: 0.6727 (m90) cc_final: 0.6338 (m170) REVERT: D 797 LYS cc_start: 0.6786 (mttt) cc_final: 0.6548 (mtmt) REVERT: D 829 GLU cc_start: 0.7967 (mt-10) cc_final: 0.7297 (mm-30) REVERT: D 862 GLU cc_start: 0.6887 (tt0) cc_final: 0.6568 (mt-10) REVERT: D 915 MET cc_start: 0.8985 (mtm) cc_final: 0.8682 (mtt) REVERT: D 1042 MET cc_start: 0.8780 (mtm) cc_final: 0.8148 (mmt) REVERT: D 1059 LEU cc_start: 0.7995 (mt) cc_final: 0.7643 (mm) REVERT: D 1081 MET cc_start: 0.7048 (mtm) cc_final: 0.6777 (mtm) REVERT: D 1108 LYS cc_start: 0.7264 (ttpp) cc_final: 0.6934 (ttmm) REVERT: D 1119 LYS cc_start: 0.7280 (mtpt) cc_final: 0.6923 (ttpp) REVERT: D 1123 ARG cc_start: 0.7068 (ttp80) cc_final: 0.6496 (ttt-90) REVERT: D 1126 ARG cc_start: 0.6765 (ttm170) cc_final: 0.6330 (ttm170) REVERT: D 1130 GLU cc_start: 0.7242 (mt-10) cc_final: 0.6633 (mp0) REVERT: D 1131 MET cc_start: 0.7215 (mmp) cc_final: 0.6704 (mtt) REVERT: D 1346 GLU cc_start: 0.8471 (tt0) cc_final: 0.8119 (tp30) REVERT: D 1452 ARG cc_start: 0.8441 (OUTLIER) cc_final: 0.7905 (ttp80) outliers start: 76 outliers final: 12 residues processed: 722 average time/residue: 0.8836 time to fit residues: 760.1227 Evaluate side-chains 586 residues out of total 4700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 566 time to evaluate : 1.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 MET Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 271 GLU Chi-restraints excluded: chain A residue 311 GLN Chi-restraints excluded: chain A residue 1452 ARG Chi-restraints excluded: chain B residue 70 MET Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 271 GLU Chi-restraints excluded: chain B residue 311 GLN Chi-restraints excluded: chain B residue 1452 ARG Chi-restraints excluded: chain C residue 70 MET Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 271 GLU Chi-restraints excluded: chain C residue 311 GLN Chi-restraints excluded: chain C residue 1452 ARG Chi-restraints excluded: chain D residue 70 MET Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 271 GLU Chi-restraints excluded: chain D residue 311 GLN Chi-restraints excluded: chain D residue 1452 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 548 random chunks: chunk 454 optimal weight: 20.0000 chunk 352 optimal weight: 3.9990 chunk 438 optimal weight: 0.9990 chunk 490 optimal weight: 4.9990 chunk 297 optimal weight: 0.9990 chunk 147 optimal weight: 0.0270 chunk 296 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 332 optimal weight: 7.9990 chunk 407 optimal weight: 0.0870 chunk 136 optimal weight: 0.9990 overall best weight: 0.6222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 365 GLN A 696 ASN A1282 ASN B 365 GLN B 696 ASN B1282 ASN C 365 GLN C 696 ASN C1282 ASN D 365 GLN D 660 HIS D 696 ASN D1282 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.166514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.122556 restraints weight = 53923.566| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 2.01 r_work: 0.3293 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3161 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.2935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 43776 Z= 0.116 Angle : 0.511 6.837 59556 Z= 0.263 Chirality : 0.038 0.143 6768 Planarity : 0.004 0.049 7544 Dihedral : 7.687 91.965 7016 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.80 % Allowed : 9.59 % Favored : 88.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.60 (0.11), residues: 5476 helix: 2.22 (0.09), residues: 2984 sheet: -0.59 (0.21), residues: 456 loop : -0.27 (0.14), residues: 2036 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B1107 TYR 0.012 0.001 TYR B 138 PHE 0.012 0.001 PHE B 879 TRP 0.010 0.001 TRP A1366 HIS 0.003 0.001 HIS C 813 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.12 (43772) covalent geometry : angle 0.51144 / 0.26 (59548) SS BOND : bond 0.00025 / 0.01 ( 4) SS BOND : angle 0.31219 / 0.19 ( 8) hydrogen bonds : bond 0.03961 / 2.62 ( 2396) hydrogen bonds : angle 3.90020 / 2.83 ( 7032) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10952 Ramachandran restraints generated. 5476 Oldfield, 0 Emsley, 5476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10952 Ramachandran restraints generated. 5476 Oldfield, 0 Emsley, 5476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 660 residues out of total 4700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 584 time to evaluate : 1.684 Fit side-chains REVERT: A 70 MET cc_start: 0.6749 (OUTLIER) cc_final: 0.5415 (pmm) REVERT: A 170 LEU cc_start: 0.7568 (tt) cc_final: 0.7186 (tm) REVERT: A 196 MET cc_start: 0.8035 (mmm) cc_final: 0.7828 (mmp) REVERT: A 416 LYS cc_start: 0.7242 (mttp) cc_final: 0.6528 (tttp) REVERT: A 456 MET cc_start: 0.5946 (mtp) cc_final: 0.5658 (tmm) REVERT: A 502 GLU cc_start: 0.7039 (tt0) cc_final: 0.6007 (tm-30) REVERT: A 506 ARG cc_start: 0.7080 (mpt180) cc_final: 0.6454 (mpt180) REVERT: A 553 ARG cc_start: 0.7425 (mmm-85) cc_final: 0.7036 (mtp180) REVERT: A 595 ARG cc_start: 0.7127 (mtm-85) cc_final: 0.6387 (mtp85) REVERT: A 614 ARG cc_start: 0.7348 (mtt180) cc_final: 0.6808 (mpp-170) REVERT: A 624 ASP cc_start: 0.7181 (p0) cc_final: 0.6872 (p0) REVERT: A 638 GLU cc_start: 0.6725 (mt-10) cc_final: 0.6456 (tm-30) REVERT: A 667 GLU cc_start: 0.7476 (tp30) cc_final: 0.7204 (mt-10) REVERT: A 686 GLU cc_start: 0.7754 (tt0) cc_final: 0.7270 (tp30) REVERT: A 697 LYS cc_start: 0.6998 (mmtt) cc_final: 0.6641 (mmtp) REVERT: A 702 ASN cc_start: 0.7962 (m-40) cc_final: 0.7331 (m-40) REVERT: A 729 HIS cc_start: 0.6847 (m90) cc_final: 0.6410 (m170) REVERT: A 797 LYS cc_start: 0.6918 (mttt) cc_final: 0.6575 (mtmt) REVERT: A 829 GLU cc_start: 0.8013 (mt-10) cc_final: 0.7363 (mm-30) REVERT: A 862 GLU cc_start: 0.6689 (tt0) cc_final: 0.6480 (pp20) REVERT: A 915 MET cc_start: 0.8954 (mtm) cc_final: 0.8650 (mtt) REVERT: A 935 MET cc_start: 0.8480 (tpp) cc_final: 0.8011 (mmm) REVERT: A 1042 MET cc_start: 0.8721 (mtm) cc_final: 0.8087 (mmt) REVERT: A 1059 LEU cc_start: 0.8010 (mt) cc_final: 0.7657 (mm) REVERT: A 1081 MET cc_start: 0.7061 (mtm) cc_final: 0.6764 (mtm) REVERT: A 1106 LYS cc_start: 0.6614 (ttmt) cc_final: 0.6302 (mtpp) REVERT: A 1108 LYS cc_start: 0.7231 (ttpp) cc_final: 0.6891 (ttmm) REVERT: A 1119 LYS cc_start: 0.7320 (mtpt) cc_final: 0.7018 (ttpp) REVERT: A 1122 ARG cc_start: 0.7037 (mtm-85) cc_final: 0.6792 (mtm-85) REVERT: A 1123 ARG cc_start: 0.7149 (ttp80) cc_final: 0.6575 (ttt-90) REVERT: A 1126 ARG cc_start: 0.6896 (ttm170) cc_final: 0.6469 (ttm170) REVERT: A 1130 GLU cc_start: 0.7260 (mt-10) cc_final: 0.6645 (mp0) REVERT: A 1131 MET cc_start: 0.7209 (mmp) cc_final: 0.6681 (mtp) REVERT: A 1452 ARG cc_start: 0.8432 (OUTLIER) cc_final: 0.8048 (ttp80) REVERT: B 70 MET cc_start: 0.6764 (OUTLIER) cc_final: 0.5431 (pmm) REVERT: B 170 LEU cc_start: 0.7581 (tt) cc_final: 0.7204 (tm) REVERT: B 196 MET cc_start: 0.8030 (mmm) cc_final: 0.7827 (mmp) REVERT: B 416 LYS cc_start: 0.7278 (mttp) cc_final: 0.6565 (tttp) REVERT: B 456 MET cc_start: 0.5926 (mtp) cc_final: 0.5613 (tmm) REVERT: B 506 ARG cc_start: 0.7092 (mpt180) cc_final: 0.6825 (mpt180) REVERT: B 553 ARG cc_start: 0.7433 (mmm-85) cc_final: 0.7044 (mtp180) REVERT: B 595 ARG cc_start: 0.7139 (mtm-85) cc_final: 0.6402 (mtp85) REVERT: B 614 ARG cc_start: 0.7360 (mtt180) cc_final: 0.6824 (mpp-170) REVERT: B 624 ASP cc_start: 0.7205 (p0) cc_final: 0.6895 (p0) REVERT: B 638 GLU cc_start: 0.6725 (mt-10) cc_final: 0.6465 (tm-30) REVERT: B 667 GLU cc_start: 0.7498 (tp30) cc_final: 0.7228 (mt-10) REVERT: B 686 GLU cc_start: 0.7752 (tt0) cc_final: 0.7263 (tp30) REVERT: B 697 LYS cc_start: 0.7000 (mmtt) cc_final: 0.6565 (mmtp) REVERT: B 702 ASN cc_start: 0.7965 (m-40) cc_final: 0.7344 (m-40) REVERT: B 729 HIS cc_start: 0.6842 (m90) cc_final: 0.6405 (m170) REVERT: B 797 LYS cc_start: 0.6926 (mttt) cc_final: 0.6584 (mtmt) REVERT: B 829 GLU cc_start: 0.8004 (mt-10) cc_final: 0.7360 (mm-30) REVERT: B 862 GLU cc_start: 0.6698 (tt0) cc_final: 0.6489 (pp20) REVERT: B 915 MET cc_start: 0.8960 (mtm) cc_final: 0.8659 (mtt) REVERT: B 935 MET cc_start: 0.8478 (tpp) cc_final: 0.8007 (mmm) REVERT: B 1042 MET cc_start: 0.8742 (mtm) cc_final: 0.8123 (mmt) REVERT: B 1059 LEU cc_start: 0.8022 (mt) cc_final: 0.7670 (mm) REVERT: B 1081 MET cc_start: 0.7088 (mtm) cc_final: 0.6790 (mtm) REVERT: B 1106 LYS cc_start: 0.6661 (ttmt) cc_final: 0.6347 (mtpp) REVERT: B 1108 LYS cc_start: 0.7231 (ttpp) cc_final: 0.6892 (ttmm) REVERT: B 1119 LYS cc_start: 0.7406 (mtpt) cc_final: 0.7067 (ttpp) REVERT: B 1123 ARG cc_start: 0.7161 (ttp80) cc_final: 0.6585 (ttt-90) REVERT: B 1125 GLU cc_start: 0.6418 (mm-30) cc_final: 0.6193 (mp0) REVERT: B 1126 ARG cc_start: 0.6897 (ttm170) cc_final: 0.6435 (ttm170) REVERT: B 1130 GLU cc_start: 0.7273 (mt-10) cc_final: 0.6654 (mp0) REVERT: B 1131 MET cc_start: 0.7228 (mmp) cc_final: 0.6702 (mtt) REVERT: B 1452 ARG cc_start: 0.8427 (OUTLIER) cc_final: 0.8009 (ttp80) REVERT: C 70 MET cc_start: 0.6769 (OUTLIER) cc_final: 0.5438 (pmm) REVERT: C 170 LEU cc_start: 0.7581 (tt) cc_final: 0.7203 (tm) REVERT: C 196 MET cc_start: 0.8027 (mmm) cc_final: 0.7819 (mmp) REVERT: C 416 LYS cc_start: 0.7264 (mttp) cc_final: 0.6554 (tttp) REVERT: C 456 MET cc_start: 0.5932 (mtp) cc_final: 0.5610 (tmm) REVERT: C 506 ARG cc_start: 0.7088 (mpt180) cc_final: 0.6822 (mpt180) REVERT: C 553 ARG cc_start: 0.7422 (mmm-85) cc_final: 0.7028 (mtp180) REVERT: C 595 ARG cc_start: 0.7155 (mtm-85) cc_final: 0.6414 (mtp85) REVERT: C 614 ARG cc_start: 0.7364 (mtt180) cc_final: 0.6821 (mpp-170) REVERT: C 624 ASP cc_start: 0.7215 (p0) cc_final: 0.6908 (p0) REVERT: C 638 GLU cc_start: 0.6728 (mt-10) cc_final: 0.6459 (tm-30) REVERT: C 667 GLU cc_start: 0.7494 (tp30) cc_final: 0.7224 (mt-10) REVERT: C 686 GLU cc_start: 0.7753 (tt0) cc_final: 0.7265 (tp30) REVERT: C 697 LYS cc_start: 0.7003 (mmtt) cc_final: 0.6647 (mmtp) REVERT: C 702 ASN cc_start: 0.7962 (m-40) cc_final: 0.7332 (m-40) REVERT: C 729 HIS cc_start: 0.6848 (m90) cc_final: 0.6408 (m170) REVERT: C 797 LYS cc_start: 0.6919 (mttt) cc_final: 0.6574 (mtmt) REVERT: C 829 GLU cc_start: 0.8000 (mt-10) cc_final: 0.7358 (mm-30) REVERT: C 862 GLU cc_start: 0.6692 (tt0) cc_final: 0.6484 (pp20) REVERT: C 915 MET cc_start: 0.8958 (mtm) cc_final: 0.8656 (mtt) REVERT: C 935 MET cc_start: 0.8490 (tpp) cc_final: 0.8018 (mmm) REVERT: C 1042 MET cc_start: 0.8739 (mtm) cc_final: 0.8119 (mmt) REVERT: C 1059 LEU cc_start: 0.8015 (mt) cc_final: 0.7662 (mm) REVERT: C 1081 MET cc_start: 0.7080 (mtm) cc_final: 0.6781 (mtm) REVERT: C 1106 LYS cc_start: 0.6639 (ttmt) cc_final: 0.6325 (mtpp) REVERT: C 1108 LYS cc_start: 0.7207 (ttpp) cc_final: 0.6871 (ttmm) REVERT: C 1119 LYS cc_start: 0.7384 (mtpt) cc_final: 0.6982 (ttpp) REVERT: C 1123 ARG cc_start: 0.7162 (ttp80) cc_final: 0.6577 (ttt-90) REVERT: C 1126 ARG cc_start: 0.6901 (ttm170) cc_final: 0.6477 (ttm170) REVERT: C 1130 GLU cc_start: 0.7268 (mt-10) cc_final: 0.6653 (mp0) REVERT: C 1131 MET cc_start: 0.7236 (mmp) cc_final: 0.6704 (mtt) REVERT: C 1452 ARG cc_start: 0.8427 (OUTLIER) cc_final: 0.8010 (ttp80) REVERT: D 70 MET cc_start: 0.6764 (OUTLIER) cc_final: 0.5440 (pmm) REVERT: D 170 LEU cc_start: 0.7581 (tt) cc_final: 0.7206 (tm) REVERT: D 196 MET cc_start: 0.8029 (mmm) cc_final: 0.7822 (mmp) REVERT: D 416 LYS cc_start: 0.7274 (mttp) cc_final: 0.6565 (tttp) REVERT: D 452 MET cc_start: 0.6938 (tpt) cc_final: 0.6653 (tpt) REVERT: D 456 MET cc_start: 0.5951 (mtp) cc_final: 0.5628 (tmm) REVERT: D 506 ARG cc_start: 0.7113 (mpt180) cc_final: 0.6891 (mpt180) REVERT: D 553 ARG cc_start: 0.7418 (mmm-85) cc_final: 0.7030 (mtp180) REVERT: D 595 ARG cc_start: 0.7155 (mtm-85) cc_final: 0.6416 (mtp85) REVERT: D 614 ARG cc_start: 0.7381 (mtt180) cc_final: 0.6840 (mpp-170) REVERT: D 624 ASP cc_start: 0.7200 (p0) cc_final: 0.6893 (p0) REVERT: D 638 GLU cc_start: 0.6722 (mt-10) cc_final: 0.6469 (tm-30) REVERT: D 667 GLU cc_start: 0.7500 (tp30) cc_final: 0.7226 (mt-10) REVERT: D 686 GLU cc_start: 0.7771 (tt0) cc_final: 0.7283 (tp30) REVERT: D 697 LYS cc_start: 0.7003 (mmtt) cc_final: 0.6571 (mmtp) REVERT: D 702 ASN cc_start: 0.7981 (m-40) cc_final: 0.7360 (m-40) REVERT: D 729 HIS cc_start: 0.6838 (m90) cc_final: 0.6402 (m170) REVERT: D 797 LYS cc_start: 0.6925 (mttt) cc_final: 0.6580 (mtmt) REVERT: D 829 GLU cc_start: 0.8007 (mt-10) cc_final: 0.7360 (mm-30) REVERT: D 862 GLU cc_start: 0.6699 (tt0) cc_final: 0.6486 (pp20) REVERT: D 915 MET cc_start: 0.8965 (mtm) cc_final: 0.8665 (mtt) REVERT: D 935 MET cc_start: 0.8471 (tpp) cc_final: 0.8012 (mmm) REVERT: D 1042 MET cc_start: 0.8720 (mtm) cc_final: 0.8087 (mmt) REVERT: D 1059 LEU cc_start: 0.8027 (mt) cc_final: 0.7682 (mm) REVERT: D 1081 MET cc_start: 0.7111 (mtm) cc_final: 0.6827 (mtm) REVERT: D 1106 LYS cc_start: 0.6609 (ttmt) cc_final: 0.6298 (mtpp) REVERT: D 1108 LYS cc_start: 0.7223 (ttpp) cc_final: 0.6884 (ttmm) REVERT: D 1119 LYS cc_start: 0.7380 (mtpt) cc_final: 0.7042 (ttpp) REVERT: D 1123 ARG cc_start: 0.7168 (ttp80) cc_final: 0.6583 (ttt-90) REVERT: D 1126 ARG cc_start: 0.6904 (ttm170) cc_final: 0.6476 (ttm170) REVERT: D 1130 GLU cc_start: 0.7270 (mt-10) cc_final: 0.6657 (mp0) REVERT: D 1131 MET cc_start: 0.7221 (mmp) cc_final: 0.6702 (mtt) REVERT: D 1348 ASP cc_start: 0.8323 (t0) cc_final: 0.8115 (t0) REVERT: D 1452 ARG cc_start: 0.8429 (OUTLIER) cc_final: 0.8019 (ttp80) outliers start: 76 outliers final: 25 residues processed: 620 average time/residue: 0.8513 time to fit residues: 633.7667 Evaluate side-chains 571 residues out of total 4700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 538 time to evaluate : 1.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 MET Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 946 LEU Chi-restraints excluded: chain A residue 1365 MET Chi-restraints excluded: chain A residue 1452 ARG Chi-restraints excluded: chain B residue 70 MET Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 615 MET Chi-restraints excluded: chain B residue 946 LEU Chi-restraints excluded: chain B residue 1365 MET Chi-restraints excluded: chain B residue 1452 ARG Chi-restraints excluded: chain C residue 70 MET Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 493 LEU Chi-restraints excluded: chain C residue 615 MET Chi-restraints excluded: chain C residue 946 LEU Chi-restraints excluded: chain C residue 1365 MET Chi-restraints excluded: chain C residue 1452 ARG Chi-restraints excluded: chain D residue 70 MET Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 311 GLN Chi-restraints excluded: chain D residue 493 LEU Chi-restraints excluded: chain D residue 615 MET Chi-restraints excluded: chain D residue 946 LEU Chi-restraints excluded: chain D residue 1365 MET Chi-restraints excluded: chain D residue 1452 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 548 random chunks: chunk 507 optimal weight: 0.9990 chunk 251 optimal weight: 4.9990 chunk 163 optimal weight: 3.9990 chunk 294 optimal weight: 4.9990 chunk 460 optimal weight: 2.9990 chunk 482 optimal weight: 4.9990 chunk 202 optimal weight: 7.9990 chunk 308 optimal weight: 8.9990 chunk 197 optimal weight: 7.9990 chunk 140 optimal weight: 7.9990 chunk 406 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 132 GLN A 514 HIS A 598 GLN A 696 ASN A 992 ASN B 132 GLN B 514 HIS B 598 GLN B 696 ASN C 132 GLN C 514 HIS C 598 GLN C 696 ASN C 992 ASN C1166 GLN D 132 GLN D 514 HIS D 598 GLN D 696 ASN D 992 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.156354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.111841 restraints weight = 53950.197| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 2.16 r_work: 0.3108 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.4288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.081 43776 Z= 0.298 Angle : 0.710 8.857 59556 Z= 0.368 Chirality : 0.046 0.171 6768 Planarity : 0.005 0.053 7544 Dihedral : 9.310 101.880 7016 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.85 % Favored : 97.08 % Rotamer: Outliers : 2.72 % Allowed : 10.89 % Favored : 86.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.11), residues: 5476 helix: 1.64 (0.09), residues: 3044 sheet: -0.53 (0.24), residues: 388 loop : -0.50 (0.14), residues: 2044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C1347 TYR 0.024 0.003 TYR D1063 PHE 0.021 0.003 PHE B 879 TRP 0.016 0.002 TRP B1366 HIS 0.006 0.002 HIS A 254 Details of bonding type rmsd/Z covalent geometry : bond 0.00682 / 0.30 (43772) covalent geometry : angle 0.70965 / 0.37 (59548) SS BOND : bond 0.00008 / 0.00 ( 4) SS BOND : angle 0.82148 / 0.50 ( 8) hydrogen bonds : bond 0.05822 / 3.84 ( 2396) hydrogen bonds : angle 4.42843 / 3.23 ( 7032) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10952 Ramachandran restraints generated. 5476 Oldfield, 0 Emsley, 5476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10952 Ramachandran restraints generated. 5476 Oldfield, 0 Emsley, 5476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 682 residues out of total 4700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 567 time to evaluate : 1.566 Fit side-chains REVERT: A 70 MET cc_start: 0.6969 (OUTLIER) cc_final: 0.5638 (pmm) REVERT: A 196 MET cc_start: 0.8194 (mmm) cc_final: 0.7958 (mmp) REVERT: A 284 GLN cc_start: 0.7640 (mm110) cc_final: 0.7394 (mm110) REVERT: A 456 MET cc_start: 0.6338 (mtt) cc_final: 0.5842 (mmm) REVERT: A 614 ARG cc_start: 0.7657 (mtt180) cc_final: 0.6998 (mtm-85) REVERT: A 624 ASP cc_start: 0.7046 (p0) cc_final: 0.6758 (p0) REVERT: A 659 GLN cc_start: 0.7204 (mm-40) cc_final: 0.6960 (mm110) REVERT: A 666 GLU cc_start: 0.7802 (tt0) cc_final: 0.7360 (tt0) REVERT: A 686 GLU cc_start: 0.7669 (tt0) cc_final: 0.7131 (tp30) REVERT: A 697 LYS cc_start: 0.7119 (mmtt) cc_final: 0.6877 (mmtp) REVERT: A 702 ASN cc_start: 0.8101 (m-40) cc_final: 0.7715 (m-40) REVERT: A 829 GLU cc_start: 0.7982 (mt-10) cc_final: 0.7299 (mm-30) REVERT: A 862 GLU cc_start: 0.6700 (tt0) cc_final: 0.6255 (pp20) REVERT: A 915 MET cc_start: 0.9161 (mtm) cc_final: 0.8783 (mtt) REVERT: A 935 MET cc_start: 0.8467 (OUTLIER) cc_final: 0.7913 (mmm) REVERT: A 1059 LEU cc_start: 0.8043 (mt) cc_final: 0.7707 (mm) REVERT: A 1081 MET cc_start: 0.7084 (mtm) cc_final: 0.6784 (mtm) REVERT: A 1108 LYS cc_start: 0.7174 (ttpp) cc_final: 0.6941 (ttmm) REVERT: A 1119 LYS cc_start: 0.7575 (mtpt) cc_final: 0.7257 (ttpp) REVERT: A 1123 ARG cc_start: 0.7330 (ttp80) cc_final: 0.6820 (ttt-90) REVERT: A 1124 TRP cc_start: 0.7267 (t60) cc_final: 0.7033 (t60) REVERT: A 1130 GLU cc_start: 0.7533 (mt-10) cc_final: 0.6914 (mp0) REVERT: A 1150 MET cc_start: 0.8263 (tpp) cc_final: 0.7480 (mtt) REVERT: A 1348 ASP cc_start: 0.8511 (t0) cc_final: 0.8293 (t0) REVERT: A 1452 ARG cc_start: 0.8594 (OUTLIER) cc_final: 0.7959 (ttp80) REVERT: B 70 MET cc_start: 0.6989 (OUTLIER) cc_final: 0.5654 (pmm) REVERT: B 196 MET cc_start: 0.8198 (mmm) cc_final: 0.7960 (mmp) REVERT: B 284 GLN cc_start: 0.7689 (mm110) cc_final: 0.7445 (mm110) REVERT: B 419 MET cc_start: 0.7865 (tmm) cc_final: 0.7651 (ttm) REVERT: B 456 MET cc_start: 0.6309 (mtt) cc_final: 0.5829 (mmm) REVERT: B 567 LEU cc_start: 0.7728 (mt) cc_final: 0.7520 (mt) REVERT: B 614 ARG cc_start: 0.7664 (mtt180) cc_final: 0.7006 (mtm-85) REVERT: B 624 ASP cc_start: 0.7051 (p0) cc_final: 0.6761 (p0) REVERT: B 659 GLN cc_start: 0.7205 (mm-40) cc_final: 0.6961 (mm110) REVERT: B 666 GLU cc_start: 0.7801 (tt0) cc_final: 0.7361 (tt0) REVERT: B 686 GLU cc_start: 0.7672 (tt0) cc_final: 0.7138 (tp30) REVERT: B 697 LYS cc_start: 0.7135 (mmtt) cc_final: 0.6889 (mmtp) REVERT: B 702 ASN cc_start: 0.8095 (m-40) cc_final: 0.7736 (m-40) REVERT: B 829 GLU cc_start: 0.7979 (mt-10) cc_final: 0.7308 (mm-30) REVERT: B 862 GLU cc_start: 0.6702 (tt0) cc_final: 0.6265 (pp20) REVERT: B 915 MET cc_start: 0.9164 (mtm) cc_final: 0.8788 (mtt) REVERT: B 935 MET cc_start: 0.8469 (OUTLIER) cc_final: 0.7919 (mmm) REVERT: B 1059 LEU cc_start: 0.8040 (mt) cc_final: 0.7705 (mm) REVERT: B 1081 MET cc_start: 0.7074 (mtm) cc_final: 0.6773 (mtm) REVERT: B 1108 LYS cc_start: 0.7170 (ttpp) cc_final: 0.6936 (ttmm) REVERT: B 1119 LYS cc_start: 0.7572 (mtpt) cc_final: 0.7201 (ttpp) REVERT: B 1123 ARG cc_start: 0.7365 (ttp80) cc_final: 0.6904 (ttt-90) REVERT: B 1125 GLU cc_start: 0.6524 (mm-30) cc_final: 0.6250 (mp0) REVERT: B 1130 GLU cc_start: 0.7542 (mt-10) cc_final: 0.6920 (mp0) REVERT: B 1150 MET cc_start: 0.7991 (OUTLIER) cc_final: 0.7464 (mtt) REVERT: B 1348 ASP cc_start: 0.8500 (t0) cc_final: 0.8281 (t0) REVERT: B 1452 ARG cc_start: 0.8590 (OUTLIER) cc_final: 0.7985 (ttp80) REVERT: C 70 MET cc_start: 0.6971 (OUTLIER) cc_final: 0.5643 (pmm) REVERT: C 196 MET cc_start: 0.8198 (mmm) cc_final: 0.7959 (mmp) REVERT: C 284 GLN cc_start: 0.7689 (mm110) cc_final: 0.7443 (mm110) REVERT: C 419 MET cc_start: 0.7856 (tmm) cc_final: 0.7640 (ttm) REVERT: C 456 MET cc_start: 0.6302 (mtt) cc_final: 0.5821 (mmm) REVERT: C 567 LEU cc_start: 0.7737 (mt) cc_final: 0.7531 (mt) REVERT: C 614 ARG cc_start: 0.7649 (mtt180) cc_final: 0.6992 (mtm-85) REVERT: C 624 ASP cc_start: 0.7046 (p0) cc_final: 0.6759 (p0) REVERT: C 659 GLN cc_start: 0.7207 (mm-40) cc_final: 0.6964 (mm110) REVERT: C 666 GLU cc_start: 0.7789 (tt0) cc_final: 0.7349 (tt0) REVERT: C 686 GLU cc_start: 0.7663 (tt0) cc_final: 0.7128 (tp30) REVERT: C 697 LYS cc_start: 0.7115 (mmtt) cc_final: 0.6873 (mmtp) REVERT: C 702 ASN cc_start: 0.8100 (m-40) cc_final: 0.7711 (m-40) REVERT: C 829 GLU cc_start: 0.7974 (mt-10) cc_final: 0.7304 (mm-30) REVERT: C 862 GLU cc_start: 0.6696 (tt0) cc_final: 0.6262 (pp20) REVERT: C 915 MET cc_start: 0.9163 (mtm) cc_final: 0.8788 (mtt) REVERT: C 935 MET cc_start: 0.8469 (OUTLIER) cc_final: 0.7917 (mmm) REVERT: C 1059 LEU cc_start: 0.8034 (mt) cc_final: 0.7697 (mm) REVERT: C 1081 MET cc_start: 0.7085 (mtm) cc_final: 0.6784 (mtm) REVERT: C 1108 LYS cc_start: 0.7172 (ttpp) cc_final: 0.6939 (ttmm) REVERT: C 1119 LYS cc_start: 0.7603 (mtpt) cc_final: 0.7221 (ttpp) REVERT: C 1123 ARG cc_start: 0.7343 (ttp80) cc_final: 0.6823 (ttt-90) REVERT: C 1130 GLU cc_start: 0.7537 (mt-10) cc_final: 0.6917 (mp0) REVERT: C 1147 MET cc_start: 0.8089 (mtm) cc_final: 0.7870 (mtp) REVERT: C 1348 ASP cc_start: 0.8516 (t0) cc_final: 0.8296 (t0) REVERT: C 1452 ARG cc_start: 0.8587 (OUTLIER) cc_final: 0.7959 (ttp80) REVERT: D 70 MET cc_start: 0.6986 (OUTLIER) cc_final: 0.5670 (pmm) REVERT: D 196 MET cc_start: 0.8219 (mmm) cc_final: 0.7976 (mmp) REVERT: D 284 GLN cc_start: 0.7638 (mm110) cc_final: 0.7387 (mm110) REVERT: D 419 MET cc_start: 0.7873 (tmm) cc_final: 0.7661 (ttm) REVERT: D 456 MET cc_start: 0.6346 (mtt) cc_final: 0.5853 (mmm) REVERT: D 567 LEU cc_start: 0.7746 (mt) cc_final: 0.7541 (mt) REVERT: D 614 ARG cc_start: 0.7677 (mtt180) cc_final: 0.7020 (mtm-85) REVERT: D 624 ASP cc_start: 0.7059 (p0) cc_final: 0.6770 (p0) REVERT: D 659 GLN cc_start: 0.7213 (mm-40) cc_final: 0.6969 (mm110) REVERT: D 666 GLU cc_start: 0.7809 (tt0) cc_final: 0.7370 (tt0) REVERT: D 686 GLU cc_start: 0.7667 (tt0) cc_final: 0.7133 (tp30) REVERT: D 697 LYS cc_start: 0.7146 (mmtt) cc_final: 0.6903 (mmtp) REVERT: D 702 ASN cc_start: 0.8105 (m-40) cc_final: 0.7747 (m-40) REVERT: D 829 GLU cc_start: 0.7986 (mt-10) cc_final: 0.7309 (mm-30) REVERT: D 862 GLU cc_start: 0.6705 (tt0) cc_final: 0.6272 (pp20) REVERT: D 915 MET cc_start: 0.9159 (mtm) cc_final: 0.8782 (mtt) REVERT: D 935 MET cc_start: 0.8439 (OUTLIER) cc_final: 0.7887 (mmm) REVERT: D 1059 LEU cc_start: 0.8045 (mt) cc_final: 0.7718 (mm) REVERT: D 1081 MET cc_start: 0.7102 (mtm) cc_final: 0.6797 (mtm) REVERT: D 1108 LYS cc_start: 0.7176 (ttpp) cc_final: 0.6940 (ttmm) REVERT: D 1119 LYS cc_start: 0.7576 (mtpt) cc_final: 0.7206 (ttpp) REVERT: D 1123 ARG cc_start: 0.7335 (ttp80) cc_final: 0.6813 (ttt-90) REVERT: D 1130 GLU cc_start: 0.7534 (mt-10) cc_final: 0.6911 (mp0) REVERT: D 1348 ASP cc_start: 0.8516 (t0) cc_final: 0.8280 (t0) REVERT: D 1452 ARG cc_start: 0.8589 (OUTLIER) cc_final: 0.7981 (ttp80) outliers start: 115 outliers final: 42 residues processed: 626 average time/residue: 0.8306 time to fit residues: 627.4639 Evaluate side-chains 598 residues out of total 4700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 543 time to evaluate : 1.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 MET Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 341 ARG Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 683 MET Chi-restraints excluded: chain A residue 935 MET Chi-restraints excluded: chain A residue 946 LEU Chi-restraints excluded: chain A residue 1144 VAL Chi-restraints excluded: chain A residue 1204 VAL Chi-restraints excluded: chain A residue 1452 ARG Chi-restraints excluded: chain B residue 70 MET Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 341 ARG Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 366 LEU Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 683 MET Chi-restraints excluded: chain B residue 864 ILE Chi-restraints excluded: chain B residue 935 MET Chi-restraints excluded: chain B residue 946 LEU Chi-restraints excluded: chain B residue 1144 VAL Chi-restraints excluded: chain B residue 1150 MET Chi-restraints excluded: chain B residue 1204 VAL Chi-restraints excluded: chain B residue 1452 ARG Chi-restraints excluded: chain C residue 70 MET Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 309 VAL Chi-restraints excluded: chain C residue 341 ARG Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 366 LEU Chi-restraints excluded: chain C residue 493 LEU Chi-restraints excluded: chain C residue 683 MET Chi-restraints excluded: chain C residue 864 ILE Chi-restraints excluded: chain C residue 935 MET Chi-restraints excluded: chain C residue 946 LEU Chi-restraints excluded: chain C residue 1144 VAL Chi-restraints excluded: chain C residue 1150 MET Chi-restraints excluded: chain C residue 1204 VAL Chi-restraints excluded: chain C residue 1452 ARG Chi-restraints excluded: chain D residue 70 MET Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 309 VAL Chi-restraints excluded: chain D residue 341 ARG Chi-restraints excluded: chain D residue 366 LEU Chi-restraints excluded: chain D residue 493 LEU Chi-restraints excluded: chain D residue 683 MET Chi-restraints excluded: chain D residue 935 MET Chi-restraints excluded: chain D residue 946 LEU Chi-restraints excluded: chain D residue 1144 VAL Chi-restraints excluded: chain D residue 1204 VAL Chi-restraints excluded: chain D residue 1452 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 548 random chunks: chunk 251 optimal weight: 1.9990 chunk 107 optimal weight: 20.0000 chunk 531 optimal weight: 1.9990 chunk 500 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 494 optimal weight: 1.9990 chunk 491 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 chunk 489 optimal weight: 3.9990 chunk 141 optimal weight: 0.9990 chunk 203 optimal weight: 3.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 514 HIS A 660 HIS A 696 ASN A1166 GLN B 514 HIS B 660 HIS B 696 ASN B1166 GLN C 514 HIS C 660 HIS C 696 ASN D 514 HIS D 660 HIS D1166 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.157905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.112519 restraints weight = 53832.331| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 2.36 r_work: 0.3122 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.4289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 43776 Z= 0.172 Angle : 0.565 7.678 59556 Z= 0.289 Chirality : 0.040 0.146 6768 Planarity : 0.004 0.050 7544 Dihedral : 8.453 98.451 7016 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.08 % Allowed : 12.38 % Favored : 85.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.11), residues: 5476 helix: 1.88 (0.09), residues: 3016 sheet: -0.69 (0.22), residues: 436 loop : -0.45 (0.14), residues: 2024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C1107 TYR 0.028 0.002 TYR D 420 PHE 0.018 0.002 PHE B 879 TRP 0.012 0.001 TRP D1366 HIS 0.005 0.001 HIS A 813 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.17 (43772) covalent geometry : angle 0.56461 / 0.29 (59548) SS BOND : bond 0.00009 / 0.00 ( 4) SS BOND : angle 0.53075 / 0.32 ( 8) hydrogen bonds : bond 0.04603 / 3.04 ( 2396) hydrogen bonds : angle 4.13850 / 3.01 ( 7032) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10952 Ramachandran restraints generated. 5476 Oldfield, 0 Emsley, 5476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10952 Ramachandran restraints generated. 5476 Oldfield, 0 Emsley, 5476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 650 residues out of total 4700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 562 time to evaluate : 1.625 Fit side-chains REVERT: A 70 MET cc_start: 0.6882 (OUTLIER) cc_final: 0.5524 (pmm) REVERT: A 196 MET cc_start: 0.8123 (mmm) cc_final: 0.7914 (mmp) REVERT: A 229 GLU cc_start: 0.5016 (OUTLIER) cc_final: 0.4693 (pp20) REVERT: A 284 GLN cc_start: 0.7657 (mm110) cc_final: 0.7441 (mm110) REVERT: A 456 MET cc_start: 0.6321 (mtt) cc_final: 0.5818 (mmm) REVERT: A 595 ARG cc_start: 0.7053 (mtm-85) cc_final: 0.6828 (mtt180) REVERT: A 614 ARG cc_start: 0.7598 (mtt180) cc_final: 0.6944 (mtm-85) REVERT: A 624 ASP cc_start: 0.6833 (p0) cc_final: 0.6590 (p0) REVERT: A 667 GLU cc_start: 0.7845 (mt-10) cc_final: 0.7508 (tt0) REVERT: A 686 GLU cc_start: 0.7670 (tt0) cc_final: 0.7125 (tp30) REVERT: A 697 LYS cc_start: 0.7195 (mmtt) cc_final: 0.6974 (mmtp) REVERT: A 702 ASN cc_start: 0.8109 (m-40) cc_final: 0.7753 (m-40) REVERT: A 805 ARG cc_start: 0.8394 (OUTLIER) cc_final: 0.8069 (mtp85) REVERT: A 829 GLU cc_start: 0.8023 (mt-10) cc_final: 0.7285 (mm-30) REVERT: A 862 GLU cc_start: 0.6737 (tt0) cc_final: 0.6399 (pp20) REVERT: A 915 MET cc_start: 0.9131 (mtm) cc_final: 0.8756 (mtt) REVERT: A 935 MET cc_start: 0.8467 (tpp) cc_final: 0.7958 (mmm) REVERT: A 1059 LEU cc_start: 0.8004 (mt) cc_final: 0.7676 (mm) REVERT: A 1081 MET cc_start: 0.7097 (mtm) cc_final: 0.6713 (mtm) REVERT: A 1107 ARG cc_start: 0.6125 (mtm110) cc_final: 0.5705 (ttp80) REVERT: A 1108 LYS cc_start: 0.7159 (ttpp) cc_final: 0.6836 (ttmm) REVERT: A 1119 LYS cc_start: 0.7567 (mtpt) cc_final: 0.7204 (ttpp) REVERT: A 1123 ARG cc_start: 0.7278 (ttp80) cc_final: 0.6711 (ttt-90) REVERT: A 1130 GLU cc_start: 0.7419 (mt-10) cc_final: 0.6797 (mp0) REVERT: A 1157 MET cc_start: 0.8612 (mmt) cc_final: 0.8339 (mmt) REVERT: A 1348 ASP cc_start: 0.8460 (t0) cc_final: 0.8210 (t0) REVERT: A 1452 ARG cc_start: 0.8580 (OUTLIER) cc_final: 0.7906 (ttp80) REVERT: B 70 MET cc_start: 0.6870 (OUTLIER) cc_final: 0.5511 (pmm) REVERT: B 196 MET cc_start: 0.8128 (mmm) cc_final: 0.7916 (mmp) REVERT: B 229 GLU cc_start: 0.5033 (OUTLIER) cc_final: 0.4706 (pp20) REVERT: B 284 GLN cc_start: 0.7720 (mm110) cc_final: 0.7504 (mm110) REVERT: B 456 MET cc_start: 0.6336 (mtt) cc_final: 0.5830 (mmm) REVERT: B 567 LEU cc_start: 0.7752 (mt) cc_final: 0.7506 (mt) REVERT: B 595 ARG cc_start: 0.7071 (mtm-85) cc_final: 0.6844 (mtt180) REVERT: B 614 ARG cc_start: 0.7591 (mtt180) cc_final: 0.6939 (mtm-85) REVERT: B 624 ASP cc_start: 0.6840 (p0) cc_final: 0.6597 (p0) REVERT: B 666 GLU cc_start: 0.7829 (tt0) cc_final: 0.7409 (tt0) REVERT: B 667 GLU cc_start: 0.7859 (mt-10) cc_final: 0.7530 (tt0) REVERT: B 686 GLU cc_start: 0.7679 (tt0) cc_final: 0.7123 (tp30) REVERT: B 697 LYS cc_start: 0.7153 (mmtt) cc_final: 0.6919 (mmtp) REVERT: B 702 ASN cc_start: 0.8104 (m-40) cc_final: 0.7746 (m-40) REVERT: B 805 ARG cc_start: 0.8397 (OUTLIER) cc_final: 0.8080 (mtp85) REVERT: B 829 GLU cc_start: 0.8013 (mt-10) cc_final: 0.7279 (mm-30) REVERT: B 862 GLU cc_start: 0.6723 (tt0) cc_final: 0.6365 (pp20) REVERT: B 915 MET cc_start: 0.9133 (mtm) cc_final: 0.8759 (mtt) REVERT: B 935 MET cc_start: 0.8467 (tpp) cc_final: 0.7966 (mmm) REVERT: B 1059 LEU cc_start: 0.8005 (mt) cc_final: 0.7676 (mm) REVERT: B 1081 MET cc_start: 0.7091 (mtm) cc_final: 0.6710 (mtm) REVERT: B 1107 ARG cc_start: 0.6128 (mtm110) cc_final: 0.5706 (ttp80) REVERT: B 1108 LYS cc_start: 0.7151 (ttpp) cc_final: 0.6830 (ttmm) REVERT: B 1119 LYS cc_start: 0.7550 (mtpt) cc_final: 0.7221 (ttpp) REVERT: B 1123 ARG cc_start: 0.7344 (ttp80) cc_final: 0.6770 (ttt-90) REVERT: B 1125 GLU cc_start: 0.6600 (mm-30) cc_final: 0.6284 (mp0) REVERT: B 1130 GLU cc_start: 0.7421 (mt-10) cc_final: 0.6798 (mp0) REVERT: B 1150 MET cc_start: 0.7864 (OUTLIER) cc_final: 0.7542 (mtt) REVERT: B 1348 ASP cc_start: 0.8478 (t0) cc_final: 0.8230 (t0) REVERT: B 1452 ARG cc_start: 0.8592 (OUTLIER) cc_final: 0.7977 (ttp80) REVERT: C 70 MET cc_start: 0.6868 (OUTLIER) cc_final: 0.5518 (pmm) REVERT: C 196 MET cc_start: 0.8124 (mmm) cc_final: 0.7915 (mmp) REVERT: C 229 GLU cc_start: 0.5024 (OUTLIER) cc_final: 0.4709 (pp20) REVERT: C 284 GLN cc_start: 0.7722 (mm110) cc_final: 0.7504 (mm110) REVERT: C 456 MET cc_start: 0.6324 (mtt) cc_final: 0.5815 (mmm) REVERT: C 567 LEU cc_start: 0.7755 (mt) cc_final: 0.7511 (mt) REVERT: C 595 ARG cc_start: 0.7069 (mtm-85) cc_final: 0.6841 (mtt180) REVERT: C 614 ARG cc_start: 0.7597 (mtt180) cc_final: 0.6951 (mtm-85) REVERT: C 624 ASP cc_start: 0.6827 (p0) cc_final: 0.6585 (p0) REVERT: C 666 GLU cc_start: 0.7814 (tt0) cc_final: 0.7394 (tt0) REVERT: C 667 GLU cc_start: 0.7847 (mt-10) cc_final: 0.7519 (tt0) REVERT: C 686 GLU cc_start: 0.7679 (tt0) cc_final: 0.7125 (tp30) REVERT: C 697 LYS cc_start: 0.7216 (mmtt) cc_final: 0.6990 (mmtp) REVERT: C 702 ASN cc_start: 0.8112 (m-40) cc_final: 0.7757 (m-40) REVERT: C 805 ARG cc_start: 0.8396 (OUTLIER) cc_final: 0.8076 (mtp85) REVERT: C 829 GLU cc_start: 0.8022 (mt-10) cc_final: 0.7291 (mm-30) REVERT: C 862 GLU cc_start: 0.6719 (tt0) cc_final: 0.6363 (pp20) REVERT: C 915 MET cc_start: 0.9127 (mtm) cc_final: 0.8749 (mtt) REVERT: C 935 MET cc_start: 0.8461 (tpp) cc_final: 0.7957 (mmm) REVERT: C 1059 LEU cc_start: 0.7999 (mt) cc_final: 0.7671 (mm) REVERT: C 1081 MET cc_start: 0.7098 (mtm) cc_final: 0.6715 (mtm) REVERT: C 1107 ARG cc_start: 0.6116 (mtm110) cc_final: 0.5698 (ttp80) REVERT: C 1108 LYS cc_start: 0.7151 (ttpp) cc_final: 0.6832 (ttmm) REVERT: C 1119 LYS cc_start: 0.7522 (mtpt) cc_final: 0.7157 (ttpp) REVERT: C 1123 ARG cc_start: 0.7259 (ttp80) cc_final: 0.6658 (ttt-90) REVERT: C 1124 TRP cc_start: 0.7166 (t60) cc_final: 0.6943 (t60) REVERT: C 1130 GLU cc_start: 0.7416 (mt-10) cc_final: 0.6794 (mp0) REVERT: C 1348 ASP cc_start: 0.8446 (t0) cc_final: 0.8199 (t0) REVERT: C 1452 ARG cc_start: 0.8574 (OUTLIER) cc_final: 0.7900 (ttp80) REVERT: D 70 MET cc_start: 0.6850 (OUTLIER) cc_final: 0.5533 (pmm) REVERT: D 196 MET cc_start: 0.8123 (mmm) cc_final: 0.7909 (mmp) REVERT: D 229 GLU cc_start: 0.4963 (OUTLIER) cc_final: 0.4659 (pp20) REVERT: D 284 GLN cc_start: 0.7676 (mm110) cc_final: 0.7457 (mm110) REVERT: D 456 MET cc_start: 0.6322 (mtt) cc_final: 0.5817 (mmm) REVERT: D 567 LEU cc_start: 0.7767 (mt) cc_final: 0.7522 (mt) REVERT: D 577 ASP cc_start: 0.6333 (t70) cc_final: 0.6098 (t0) REVERT: D 595 ARG cc_start: 0.7075 (mtm-85) cc_final: 0.6849 (mtt180) REVERT: D 614 ARG cc_start: 0.7601 (mtt180) cc_final: 0.6958 (mtm-85) REVERT: D 624 ASP cc_start: 0.6830 (p0) cc_final: 0.6586 (p0) REVERT: D 666 GLU cc_start: 0.7841 (tt0) cc_final: 0.7419 (tt0) REVERT: D 667 GLU cc_start: 0.7875 (mt-10) cc_final: 0.7549 (tt0) REVERT: D 686 GLU cc_start: 0.7683 (tt0) cc_final: 0.7130 (tp30) REVERT: D 697 LYS cc_start: 0.7142 (mmtt) cc_final: 0.6916 (mmtp) REVERT: D 702 ASN cc_start: 0.8126 (m-40) cc_final: 0.7773 (m-40) REVERT: D 805 ARG cc_start: 0.8409 (OUTLIER) cc_final: 0.8084 (mtp85) REVERT: D 829 GLU cc_start: 0.8018 (mt-10) cc_final: 0.7288 (mm-30) REVERT: D 862 GLU cc_start: 0.6743 (tt0) cc_final: 0.6410 (pp20) REVERT: D 915 MET cc_start: 0.9122 (mtm) cc_final: 0.8748 (mtt) REVERT: D 935 MET cc_start: 0.8477 (tpp) cc_final: 0.7965 (mmm) REVERT: D 1059 LEU cc_start: 0.8012 (mt) cc_final: 0.7693 (mm) REVERT: D 1081 MET cc_start: 0.7102 (mtm) cc_final: 0.6721 (mtm) REVERT: D 1107 ARG cc_start: 0.6140 (mtm110) cc_final: 0.5718 (ttp80) REVERT: D 1108 LYS cc_start: 0.7166 (ttpp) cc_final: 0.6840 (ttmm) REVERT: D 1119 LYS cc_start: 0.7513 (mtpt) cc_final: 0.7153 (ttpp) REVERT: D 1123 ARG cc_start: 0.7265 (ttp80) cc_final: 0.6660 (ttt-90) REVERT: D 1124 TRP cc_start: 0.7174 (t60) cc_final: 0.6953 (t60) REVERT: D 1130 GLU cc_start: 0.7423 (mt-10) cc_final: 0.6802 (mp0) REVERT: D 1150 MET cc_start: 0.8041 (tpp) cc_final: 0.7366 (mtt) REVERT: D 1157 MET cc_start: 0.8597 (mmt) cc_final: 0.8363 (mmt) REVERT: D 1348 ASP cc_start: 0.8486 (t0) cc_final: 0.8259 (t0) REVERT: D 1452 ARG cc_start: 0.8586 (OUTLIER) cc_final: 0.7975 (ttp80) outliers start: 88 outliers final: 35 residues processed: 605 average time/residue: 0.8581 time to fit residues: 622.0650 Evaluate side-chains 585 residues out of total 4700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 533 time to evaluate : 1.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 MET Chi-restraints excluded: chain A residue 229 GLU Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 341 ARG Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 805 ARG Chi-restraints excluded: chain A residue 864 ILE Chi-restraints excluded: chain A residue 946 LEU Chi-restraints excluded: chain A residue 1044 VAL Chi-restraints excluded: chain A residue 1125 GLU Chi-restraints excluded: chain A residue 1164 LEU Chi-restraints excluded: chain A residue 1452 ARG Chi-restraints excluded: chain B residue 70 MET Chi-restraints excluded: chain B residue 229 GLU Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 341 ARG Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 366 LEU Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 805 ARG Chi-restraints excluded: chain B residue 946 LEU Chi-restraints excluded: chain B residue 1044 VAL Chi-restraints excluded: chain B residue 1150 MET Chi-restraints excluded: chain B residue 1452 ARG Chi-restraints excluded: chain C residue 70 MET Chi-restraints excluded: chain C residue 229 GLU Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 340 THR Chi-restraints excluded: chain C residue 341 ARG Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 366 LEU Chi-restraints excluded: chain C residue 493 LEU Chi-restraints excluded: chain C residue 805 ARG Chi-restraints excluded: chain C residue 946 LEU Chi-restraints excluded: chain C residue 1044 VAL Chi-restraints excluded: chain C residue 1164 LEU Chi-restraints excluded: chain C residue 1452 ARG Chi-restraints excluded: chain D residue 70 MET Chi-restraints excluded: chain D residue 229 GLU Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 340 THR Chi-restraints excluded: chain D residue 341 ARG Chi-restraints excluded: chain D residue 346 THR Chi-restraints excluded: chain D residue 366 LEU Chi-restraints excluded: chain D residue 493 LEU Chi-restraints excluded: chain D residue 805 ARG Chi-restraints excluded: chain D residue 946 LEU Chi-restraints excluded: chain D residue 1044 VAL Chi-restraints excluded: chain D residue 1452 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 548 random chunks: chunk 308 optimal weight: 0.9980 chunk 322 optimal weight: 7.9990 chunk 207 optimal weight: 4.9990 chunk 523 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 506 optimal weight: 0.9980 chunk 71 optimal weight: 0.8980 chunk 518 optimal weight: 0.7980 chunk 82 optimal weight: 3.9990 chunk 385 optimal weight: 2.9990 chunk 291 optimal weight: 0.7980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 514 HIS A 660 HIS A 682 HIS A 696 ASN A1101 GLN B 514 HIS B 660 HIS B 682 HIS B 696 ASN C 368 ASN C 514 HIS C 660 HIS C 682 HIS C 696 ASN D 514 HIS D 660 HIS D 682 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.158971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.114047 restraints weight = 53957.250| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 2.01 r_work: 0.3185 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.4335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 43776 Z= 0.129 Angle : 0.521 7.081 59556 Z= 0.265 Chirality : 0.038 0.142 6768 Planarity : 0.004 0.049 7544 Dihedral : 7.898 95.958 7016 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.91 % Allowed : 13.45 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.11), residues: 5476 helix: 2.08 (0.09), residues: 3016 sheet: -0.98 (0.21), residues: 460 loop : -0.43 (0.14), residues: 2000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1107 TYR 0.032 0.002 TYR B 420 PHE 0.016 0.001 PHE D 879 TRP 0.010 0.001 TRP B1216 HIS 0.005 0.001 HIS C 682 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 (43772) covalent geometry : angle 0.52136 / 0.27 (59548) SS BOND : bond 0.00011 / 0.01 ( 4) SS BOND : angle 0.36093 / 0.22 ( 8) hydrogen bonds : bond 0.04104 / 2.72 ( 2396) hydrogen bonds : angle 3.96586 / 2.88 ( 7032) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10952 Ramachandran restraints generated. 5476 Oldfield, 0 Emsley, 5476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10952 Ramachandran restraints generated. 5476 Oldfield, 0 Emsley, 5476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 636 residues out of total 4700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 555 time to evaluate : 1.707 Fit side-chains REVERT: A 70 MET cc_start: 0.6962 (OUTLIER) cc_final: 0.5661 (pmm) REVERT: A 196 MET cc_start: 0.8082 (mmm) cc_final: 0.7806 (mmp) REVERT: A 284 GLN cc_start: 0.7589 (mm110) cc_final: 0.7374 (mm110) REVERT: A 341 ARG cc_start: 0.8219 (OUTLIER) cc_final: 0.7893 (ptm160) REVERT: A 395 GLU cc_start: 0.7158 (mt-10) cc_final: 0.6601 (pt0) REVERT: A 456 MET cc_start: 0.6291 (mtt) cc_final: 0.5798 (mmm) REVERT: A 577 ASP cc_start: 0.6276 (t70) cc_final: 0.6069 (t0) REVERT: A 595 ARG cc_start: 0.6998 (mtm-85) cc_final: 0.6749 (mtt180) REVERT: A 614 ARG cc_start: 0.7595 (mtt180) cc_final: 0.6955 (mtm-85) REVERT: A 624 ASP cc_start: 0.6766 (p0) cc_final: 0.6495 (p0) REVERT: A 667 GLU cc_start: 0.7713 (mt-10) cc_final: 0.7424 (tt0) REVERT: A 686 GLU cc_start: 0.7581 (tt0) cc_final: 0.7021 (tp30) REVERT: A 697 LYS cc_start: 0.7244 (mmtt) cc_final: 0.7028 (mmtp) REVERT: A 702 ASN cc_start: 0.8038 (m-40) cc_final: 0.7611 (m-40) REVERT: A 829 GLU cc_start: 0.7938 (mt-10) cc_final: 0.7241 (mm-30) REVERT: A 862 GLU cc_start: 0.6708 (tt0) cc_final: 0.6312 (pp20) REVERT: A 915 MET cc_start: 0.9099 (mtm) cc_final: 0.8727 (mtt) REVERT: A 935 MET cc_start: 0.8452 (OUTLIER) cc_final: 0.7948 (mmm) REVERT: A 1059 LEU cc_start: 0.7987 (mt) cc_final: 0.7657 (mm) REVERT: A 1081 MET cc_start: 0.7103 (mtm) cc_final: 0.6727 (mtm) REVERT: A 1108 LYS cc_start: 0.7253 (ttpp) cc_final: 0.6901 (ttmm) REVERT: A 1119 LYS cc_start: 0.7525 (mtpt) cc_final: 0.7169 (ttpp) REVERT: A 1123 ARG cc_start: 0.7217 (ttp80) cc_final: 0.6634 (ttt-90) REVERT: A 1124 TRP cc_start: 0.7180 (t60) cc_final: 0.6956 (t60) REVERT: A 1150 MET cc_start: 0.8056 (tpp) cc_final: 0.7276 (mtt) REVERT: A 1157 MET cc_start: 0.8516 (mmt) cc_final: 0.8299 (mmt) REVERT: A 1348 ASP cc_start: 0.8366 (t0) cc_final: 0.8154 (t0) REVERT: A 1452 ARG cc_start: 0.8515 (OUTLIER) cc_final: 0.7920 (ttp80) REVERT: B 70 MET cc_start: 0.6937 (OUTLIER) cc_final: 0.5654 (pmm) REVERT: B 81 MET cc_start: 0.8034 (ptt) cc_final: 0.7701 (ptt) REVERT: B 196 MET cc_start: 0.8077 (mmm) cc_final: 0.7800 (mmp) REVERT: B 284 GLN cc_start: 0.7656 (mm110) cc_final: 0.7415 (mm110) REVERT: B 341 ARG cc_start: 0.8247 (OUTLIER) cc_final: 0.7951 (ptm160) REVERT: B 395 GLU cc_start: 0.7171 (mt-10) cc_final: 0.6598 (pt0) REVERT: B 456 MET cc_start: 0.6295 (mtt) cc_final: 0.5808 (mmm) REVERT: B 567 LEU cc_start: 0.7705 (mt) cc_final: 0.7461 (mt) REVERT: B 577 ASP cc_start: 0.6285 (t70) cc_final: 0.6080 (t0) REVERT: B 595 ARG cc_start: 0.7025 (mtm-85) cc_final: 0.6781 (mtt180) REVERT: B 614 ARG cc_start: 0.7590 (mtt180) cc_final: 0.6957 (mtm-85) REVERT: B 624 ASP cc_start: 0.6771 (p0) cc_final: 0.6499 (p0) REVERT: B 666 GLU cc_start: 0.7784 (tt0) cc_final: 0.7362 (tt0) REVERT: B 667 GLU cc_start: 0.7730 (mt-10) cc_final: 0.7442 (tt0) REVERT: B 686 GLU cc_start: 0.7584 (tt0) cc_final: 0.7017 (tp30) REVERT: B 697 LYS cc_start: 0.7241 (mmtt) cc_final: 0.7025 (mmtp) REVERT: B 702 ASN cc_start: 0.8038 (m-40) cc_final: 0.7611 (m-40) REVERT: B 829 GLU cc_start: 0.7924 (mt-10) cc_final: 0.7232 (mm-30) REVERT: B 862 GLU cc_start: 0.6727 (tt0) cc_final: 0.6228 (pp20) REVERT: B 915 MET cc_start: 0.9098 (mtm) cc_final: 0.8723 (mtt) REVERT: B 935 MET cc_start: 0.8450 (OUTLIER) cc_final: 0.7951 (mmm) REVERT: B 1059 LEU cc_start: 0.7987 (mt) cc_final: 0.7655 (mm) REVERT: B 1081 MET cc_start: 0.7094 (mtm) cc_final: 0.6719 (mtm) REVERT: B 1108 LYS cc_start: 0.7262 (ttpp) cc_final: 0.6913 (ttmm) REVERT: B 1119 LYS cc_start: 0.7437 (mtpt) cc_final: 0.7116 (ttpp) REVERT: B 1123 ARG cc_start: 0.7334 (ttp80) cc_final: 0.6777 (ttt-90) REVERT: B 1125 GLU cc_start: 0.6613 (mm-30) cc_final: 0.6258 (mp0) REVERT: B 1129 GLN cc_start: 0.6531 (mm110) cc_final: 0.5918 (mt0) REVERT: B 1130 GLU cc_start: 0.7359 (mt-10) cc_final: 0.6763 (mp0) REVERT: B 1150 MET cc_start: 0.7818 (mtp) cc_final: 0.7496 (mtt) REVERT: B 1348 ASP cc_start: 0.8375 (t0) cc_final: 0.8157 (t0) REVERT: B 1452 ARG cc_start: 0.8528 (OUTLIER) cc_final: 0.7934 (ttp80) REVERT: C 70 MET cc_start: 0.6940 (OUTLIER) cc_final: 0.5655 (pmm) REVERT: C 75 PHE cc_start: 0.8092 (t80) cc_final: 0.7871 (t80) REVERT: C 81 MET cc_start: 0.8032 (ptt) cc_final: 0.7700 (ptt) REVERT: C 196 MET cc_start: 0.8083 (mmm) cc_final: 0.7805 (mmp) REVERT: C 284 GLN cc_start: 0.7657 (mm110) cc_final: 0.7414 (mm110) REVERT: C 341 ARG cc_start: 0.8208 (OUTLIER) cc_final: 0.7883 (ptm160) REVERT: C 395 GLU cc_start: 0.7169 (mt-10) cc_final: 0.6598 (pt0) REVERT: C 456 MET cc_start: 0.6293 (mtt) cc_final: 0.5792 (mmm) REVERT: C 567 LEU cc_start: 0.7711 (mt) cc_final: 0.7467 (mt) REVERT: C 577 ASP cc_start: 0.6283 (t70) cc_final: 0.6082 (t0) REVERT: C 595 ARG cc_start: 0.7012 (mtm-85) cc_final: 0.6762 (mtt180) REVERT: C 614 ARG cc_start: 0.7588 (mtt180) cc_final: 0.6953 (mtm-85) REVERT: C 624 ASP cc_start: 0.6762 (p0) cc_final: 0.6493 (p0) REVERT: C 666 GLU cc_start: 0.7782 (tt0) cc_final: 0.7361 (tt0) REVERT: C 667 GLU cc_start: 0.7725 (mt-10) cc_final: 0.7441 (tt0) REVERT: C 686 GLU cc_start: 0.7585 (tt0) cc_final: 0.7013 (tp30) REVERT: C 697 LYS cc_start: 0.7235 (mmtt) cc_final: 0.7017 (mmtp) REVERT: C 702 ASN cc_start: 0.8044 (m-40) cc_final: 0.7618 (m-40) REVERT: C 829 GLU cc_start: 0.7922 (mt-10) cc_final: 0.7238 (mm-30) REVERT: C 862 GLU cc_start: 0.6725 (tt0) cc_final: 0.6217 (pp20) REVERT: C 915 MET cc_start: 0.9092 (mtm) cc_final: 0.8716 (mtt) REVERT: C 935 MET cc_start: 0.8445 (OUTLIER) cc_final: 0.7939 (mmm) REVERT: C 1059 LEU cc_start: 0.7990 (mt) cc_final: 0.7662 (mm) REVERT: C 1081 MET cc_start: 0.7107 (mtm) cc_final: 0.6732 (mtm) REVERT: C 1108 LYS cc_start: 0.7244 (ttpp) cc_final: 0.6892 (ttmm) REVERT: C 1119 LYS cc_start: 0.7480 (mtpt) cc_final: 0.7121 (ttpp) REVERT: C 1123 ARG cc_start: 0.7217 (ttp80) cc_final: 0.6620 (ttt-90) REVERT: C 1130 GLU cc_start: 0.7376 (mt-10) cc_final: 0.6735 (mp0) REVERT: C 1348 ASP cc_start: 0.8358 (t0) cc_final: 0.8143 (t0) REVERT: C 1452 ARG cc_start: 0.8515 (OUTLIER) cc_final: 0.7922 (ttp80) REVERT: D 70 MET cc_start: 0.6931 (OUTLIER) cc_final: 0.5639 (pmm) REVERT: D 81 MET cc_start: 0.8055 (ptt) cc_final: 0.7663 (ptt) REVERT: D 196 MET cc_start: 0.8082 (mmm) cc_final: 0.7803 (mmp) REVERT: D 284 GLN cc_start: 0.7593 (mm110) cc_final: 0.7374 (mm110) REVERT: D 341 ARG cc_start: 0.8222 (OUTLIER) cc_final: 0.7900 (ptm160) REVERT: D 395 GLU cc_start: 0.7185 (mt-10) cc_final: 0.6615 (pt0) REVERT: D 456 MET cc_start: 0.6281 (mtt) cc_final: 0.5789 (mmm) REVERT: D 567 LEU cc_start: 0.7715 (mt) cc_final: 0.7472 (mt) REVERT: D 577 ASP cc_start: 0.6221 (t70) cc_final: 0.6004 (t0) REVERT: D 595 ARG cc_start: 0.7026 (mtm-85) cc_final: 0.6771 (mtt180) REVERT: D 614 ARG cc_start: 0.7597 (mtt180) cc_final: 0.6964 (mtm-85) REVERT: D 624 ASP cc_start: 0.6773 (p0) cc_final: 0.6502 (p0) REVERT: D 666 GLU cc_start: 0.7797 (tt0) cc_final: 0.7374 (tt0) REVERT: D 667 GLU cc_start: 0.7740 (mt-10) cc_final: 0.7455 (tt0) REVERT: D 686 GLU cc_start: 0.7584 (tt0) cc_final: 0.7019 (tp30) REVERT: D 697 LYS cc_start: 0.7212 (mmtt) cc_final: 0.6997 (mmtp) REVERT: D 702 ASN cc_start: 0.8050 (m-40) cc_final: 0.7626 (m-40) REVERT: D 829 GLU cc_start: 0.7926 (mt-10) cc_final: 0.7234 (mm-30) REVERT: D 862 GLU cc_start: 0.6673 (tt0) cc_final: 0.6264 (pp20) REVERT: D 915 MET cc_start: 0.9104 (mtm) cc_final: 0.8732 (mtt) REVERT: D 935 MET cc_start: 0.8463 (OUTLIER) cc_final: 0.7951 (mmm) REVERT: D 1059 LEU cc_start: 0.8009 (mt) cc_final: 0.7678 (mm) REVERT: D 1081 MET cc_start: 0.7118 (mtm) cc_final: 0.6744 (mtm) REVERT: D 1108 LYS cc_start: 0.7250 (ttpp) cc_final: 0.6896 (ttmm) REVERT: D 1119 LYS cc_start: 0.7476 (mtpt) cc_final: 0.7118 (ttpp) REVERT: D 1123 ARG cc_start: 0.7208 (ttp80) cc_final: 0.6608 (ttt-90) REVERT: D 1348 ASP cc_start: 0.8368 (t0) cc_final: 0.8163 (t0) REVERT: D 1452 ARG cc_start: 0.8519 (OUTLIER) cc_final: 0.7932 (ttp80) outliers start: 81 outliers final: 23 residues processed: 596 average time/residue: 0.8514 time to fit residues: 610.2328 Evaluate side-chains 575 residues out of total 4700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 536 time to evaluate : 1.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 MET Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 341 ARG Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 935 MET Chi-restraints excluded: chain A residue 946 LEU Chi-restraints excluded: chain A residue 1044 VAL Chi-restraints excluded: chain A residue 1164 LEU Chi-restraints excluded: chain A residue 1452 ARG Chi-restraints excluded: chain B residue 70 MET Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 341 ARG Chi-restraints excluded: chain B residue 366 LEU Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 935 MET Chi-restraints excluded: chain B residue 946 LEU Chi-restraints excluded: chain B residue 1044 VAL Chi-restraints excluded: chain B residue 1452 ARG Chi-restraints excluded: chain C residue 70 MET Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 341 ARG Chi-restraints excluded: chain C residue 366 LEU Chi-restraints excluded: chain C residue 493 LEU Chi-restraints excluded: chain C residue 935 MET Chi-restraints excluded: chain C residue 946 LEU Chi-restraints excluded: chain C residue 1044 VAL Chi-restraints excluded: chain C residue 1164 LEU Chi-restraints excluded: chain C residue 1452 ARG Chi-restraints excluded: chain D residue 70 MET Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 341 ARG Chi-restraints excluded: chain D residue 346 THR Chi-restraints excluded: chain D residue 366 LEU Chi-restraints excluded: chain D residue 493 LEU Chi-restraints excluded: chain D residue 935 MET Chi-restraints excluded: chain D residue 946 LEU Chi-restraints excluded: chain D residue 1044 VAL Chi-restraints excluded: chain D residue 1452 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 548 random chunks: chunk 418 optimal weight: 0.1980 chunk 237 optimal weight: 9.9990 chunk 292 optimal weight: 0.9990 chunk 354 optimal weight: 5.9990 chunk 333 optimal weight: 10.0000 chunk 310 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 400 optimal weight: 1.9990 chunk 532 optimal weight: 4.9990 chunk 177 optimal weight: 10.0000 chunk 202 optimal weight: 0.6980 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 514 HIS A 660 HIS A 682 HIS A 696 ASN B 514 HIS B 660 HIS B 682 HIS B 696 ASN C 514 HIS C 660 HIS C 682 HIS C 696 ASN C1101 GLN D 514 HIS D 660 HIS D 682 HIS D 992 ASN D1101 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.159098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.114934 restraints weight = 53563.314| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 2.18 r_work: 0.3160 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.4441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 43776 Z= 0.148 Angle : 0.548 7.467 59556 Z= 0.277 Chirality : 0.039 0.145 6768 Planarity : 0.004 0.049 7544 Dihedral : 7.865 96.583 7016 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.01 % Allowed : 13.85 % Favored : 84.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.11), residues: 5476 helix: 2.08 (0.09), residues: 3016 sheet: -1.02 (0.21), residues: 460 loop : -0.46 (0.14), residues: 2000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 594 TYR 0.016 0.002 TYR C 917 PHE 0.018 0.002 PHE A 879 TRP 0.010 0.001 TRP A1309 HIS 0.006 0.001 HIS A 682 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 (43772) covalent geometry : angle 0.54790 / 0.28 (59548) SS BOND : bond 0.00022 / 0.01 ( 4) SS BOND : angle 0.45053 / 0.27 ( 8) hydrogen bonds : bond 0.04276 / 2.83 ( 2396) hydrogen bonds : angle 3.98409 / 2.89 ( 7032) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10952 Ramachandran restraints generated. 5476 Oldfield, 0 Emsley, 5476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10952 Ramachandran restraints generated. 5476 Oldfield, 0 Emsley, 5476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 633 residues out of total 4700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 548 time to evaluate : 1.582 Fit side-chains REVERT: A 70 MET cc_start: 0.6911 (OUTLIER) cc_final: 0.5587 (pmm) REVERT: A 196 MET cc_start: 0.8081 (mmm) cc_final: 0.7826 (mmp) REVERT: A 229 GLU cc_start: 0.4824 (OUTLIER) cc_final: 0.4563 (pp20) REVERT: A 284 GLN cc_start: 0.7613 (mm110) cc_final: 0.7386 (mm110) REVERT: A 341 ARG cc_start: 0.8221 (OUTLIER) cc_final: 0.7908 (ptm160) REVERT: A 395 GLU cc_start: 0.7172 (mt-10) cc_final: 0.6586 (pt0) REVERT: A 456 MET cc_start: 0.6336 (mtt) cc_final: 0.5834 (mmm) REVERT: A 577 ASP cc_start: 0.6392 (t70) cc_final: 0.6177 (t0) REVERT: A 595 ARG cc_start: 0.7057 (mtm-85) cc_final: 0.6803 (mtt180) REVERT: A 614 ARG cc_start: 0.7633 (mtt180) cc_final: 0.6986 (mtm-85) REVERT: A 624 ASP cc_start: 0.6796 (p0) cc_final: 0.6523 (p0) REVERT: A 667 GLU cc_start: 0.7765 (mt-10) cc_final: 0.7443 (tt0) REVERT: A 686 GLU cc_start: 0.7608 (tt0) cc_final: 0.7053 (tp30) REVERT: A 697 LYS cc_start: 0.7357 (mmtt) cc_final: 0.7150 (mmtp) REVERT: A 702 ASN cc_start: 0.8059 (m-40) cc_final: 0.7650 (m-40) REVERT: A 805 ARG cc_start: 0.8421 (OUTLIER) cc_final: 0.8063 (mtp85) REVERT: A 829 GLU cc_start: 0.7951 (mt-10) cc_final: 0.7247 (mm-30) REVERT: A 862 GLU cc_start: 0.6745 (tt0) cc_final: 0.6234 (pp20) REVERT: A 915 MET cc_start: 0.9106 (mtm) cc_final: 0.8733 (mtt) REVERT: A 935 MET cc_start: 0.8479 (OUTLIER) cc_final: 0.7973 (mmm) REVERT: A 1059 LEU cc_start: 0.7999 (mt) cc_final: 0.7666 (mm) REVERT: A 1081 MET cc_start: 0.7136 (mtm) cc_final: 0.6756 (mtm) REVERT: A 1107 ARG cc_start: 0.6115 (ttp-110) cc_final: 0.5882 (ttm110) REVERT: A 1119 LYS cc_start: 0.7483 (mtpt) cc_final: 0.7124 (ttpp) REVERT: A 1123 ARG cc_start: 0.7212 (ttp80) cc_final: 0.6758 (ttt-90) REVERT: A 1150 MET cc_start: 0.8065 (OUTLIER) cc_final: 0.7561 (mtt) REVERT: A 1348 ASP cc_start: 0.8413 (t0) cc_final: 0.8191 (t0) REVERT: A 1452 ARG cc_start: 0.8543 (OUTLIER) cc_final: 0.7951 (ttp80) REVERT: B 70 MET cc_start: 0.6872 (OUTLIER) cc_final: 0.5566 (pmm) REVERT: B 196 MET cc_start: 0.8081 (mmm) cc_final: 0.7821 (mmp) REVERT: B 229 GLU cc_start: 0.4827 (OUTLIER) cc_final: 0.4564 (pp20) REVERT: B 284 GLN cc_start: 0.7660 (mm110) cc_final: 0.7429 (mm110) REVERT: B 341 ARG cc_start: 0.8258 (OUTLIER) cc_final: 0.7978 (ptm160) REVERT: B 395 GLU cc_start: 0.7157 (mt-10) cc_final: 0.6567 (pt0) REVERT: B 456 MET cc_start: 0.6342 (mtt) cc_final: 0.5845 (mmm) REVERT: B 567 LEU cc_start: 0.7650 (mt) cc_final: 0.7408 (mt) REVERT: B 577 ASP cc_start: 0.6400 (t70) cc_final: 0.6192 (t0) REVERT: B 595 ARG cc_start: 0.7076 (mtm-85) cc_final: 0.6822 (mtt180) REVERT: B 614 ARG cc_start: 0.7627 (mtt180) cc_final: 0.6985 (mtm-85) REVERT: B 624 ASP cc_start: 0.6792 (p0) cc_final: 0.6520 (p0) REVERT: B 667 GLU cc_start: 0.7778 (mt-10) cc_final: 0.7456 (tt0) REVERT: B 686 GLU cc_start: 0.7606 (tt0) cc_final: 0.7054 (tp30) REVERT: B 697 LYS cc_start: 0.7303 (mmtt) cc_final: 0.7095 (mmtp) REVERT: B 702 ASN cc_start: 0.8064 (m-40) cc_final: 0.7648 (m-40) REVERT: B 805 ARG cc_start: 0.8425 (OUTLIER) cc_final: 0.8067 (mtp85) REVERT: B 829 GLU cc_start: 0.7945 (mt-10) cc_final: 0.7241 (mm-30) REVERT: B 862 GLU cc_start: 0.6741 (tt0) cc_final: 0.6236 (pp20) REVERT: B 915 MET cc_start: 0.9110 (mtm) cc_final: 0.8737 (mtt) REVERT: B 935 MET cc_start: 0.8475 (OUTLIER) cc_final: 0.7961 (mmm) REVERT: B 1059 LEU cc_start: 0.8008 (mt) cc_final: 0.7676 (mm) REVERT: B 1081 MET cc_start: 0.7123 (mtm) cc_final: 0.6743 (mtm) REVERT: B 1107 ARG cc_start: 0.6114 (ttp-110) cc_final: 0.5878 (ttm110) REVERT: B 1119 LYS cc_start: 0.7476 (mtpt) cc_final: 0.7124 (ttpp) REVERT: B 1123 ARG cc_start: 0.7343 (ttp80) cc_final: 0.6778 (ttt-90) REVERT: B 1125 GLU cc_start: 0.6664 (mm-30) cc_final: 0.6325 (mp0) REVERT: B 1130 GLU cc_start: 0.7408 (mt-10) cc_final: 0.6768 (mp0) REVERT: B 1150 MET cc_start: 0.7779 (mtp) cc_final: 0.7558 (mtp) REVERT: B 1157 MET cc_start: 0.8729 (mmt) cc_final: 0.8319 (mmt) REVERT: B 1348 ASP cc_start: 0.8422 (t0) cc_final: 0.8191 (t0) REVERT: B 1452 ARG cc_start: 0.8537 (OUTLIER) cc_final: 0.7951 (ttp80) REVERT: C 70 MET cc_start: 0.6904 (OUTLIER) cc_final: 0.5607 (pmm) REVERT: C 196 MET cc_start: 0.8092 (mmm) cc_final: 0.7838 (mmp) REVERT: C 229 GLU cc_start: 0.4816 (OUTLIER) cc_final: 0.4569 (pp20) REVERT: C 284 GLN cc_start: 0.7660 (mm110) cc_final: 0.7427 (mm110) REVERT: C 341 ARG cc_start: 0.8209 (OUTLIER) cc_final: 0.7896 (ptm160) REVERT: C 395 GLU cc_start: 0.7166 (mt-10) cc_final: 0.6578 (pt0) REVERT: C 456 MET cc_start: 0.6336 (mtt) cc_final: 0.5833 (mmm) REVERT: C 567 LEU cc_start: 0.7652 (mt) cc_final: 0.7411 (mt) REVERT: C 577 ASP cc_start: 0.6405 (t70) cc_final: 0.6195 (t0) REVERT: C 595 ARG cc_start: 0.7070 (mtm-85) cc_final: 0.6811 (mtt180) REVERT: C 614 ARG cc_start: 0.7635 (mtt180) cc_final: 0.6991 (mtm-85) REVERT: C 624 ASP cc_start: 0.6776 (p0) cc_final: 0.6504 (p0) REVERT: C 667 GLU cc_start: 0.7771 (mt-10) cc_final: 0.7446 (tt0) REVERT: C 686 GLU cc_start: 0.7605 (tt0) cc_final: 0.7054 (tp30) REVERT: C 697 LYS cc_start: 0.7357 (mmtt) cc_final: 0.7149 (mmtp) REVERT: C 702 ASN cc_start: 0.8032 (m-40) cc_final: 0.7623 (m-40) REVERT: C 805 ARG cc_start: 0.8421 (OUTLIER) cc_final: 0.8058 (mtp85) REVERT: C 829 GLU cc_start: 0.7936 (mt-10) cc_final: 0.7252 (mm-30) REVERT: C 862 GLU cc_start: 0.6734 (tt0) cc_final: 0.6231 (pp20) REVERT: C 915 MET cc_start: 0.9098 (mtm) cc_final: 0.8723 (mtt) REVERT: C 935 MET cc_start: 0.8479 (OUTLIER) cc_final: 0.7966 (mmm) REVERT: C 1059 LEU cc_start: 0.7996 (mt) cc_final: 0.7665 (mm) REVERT: C 1081 MET cc_start: 0.7133 (mtm) cc_final: 0.6752 (mtm) REVERT: C 1107 ARG cc_start: 0.6119 (ttp-110) cc_final: 0.5878 (ttm110) REVERT: C 1119 LYS cc_start: 0.7480 (mtpt) cc_final: 0.7158 (ttpp) REVERT: C 1123 ARG cc_start: 0.7146 (ttp80) cc_final: 0.6675 (ttt-90) REVERT: C 1130 GLU cc_start: 0.7382 (mt-10) cc_final: 0.6774 (mp0) REVERT: C 1157 MET cc_start: 0.8748 (mmt) cc_final: 0.8277 (mmt) REVERT: C 1348 ASP cc_start: 0.8399 (t0) cc_final: 0.8173 (t0) REVERT: C 1452 ARG cc_start: 0.8541 (OUTLIER) cc_final: 0.7950 (ttp80) REVERT: D 70 MET cc_start: 0.6880 (OUTLIER) cc_final: 0.5565 (pmm) REVERT: D 81 MET cc_start: 0.8066 (ptt) cc_final: 0.7718 (ptt) REVERT: D 196 MET cc_start: 0.8074 (mmm) cc_final: 0.7804 (mmp) REVERT: D 229 GLU cc_start: 0.4829 (OUTLIER) cc_final: 0.4583 (pp20) REVERT: D 284 GLN cc_start: 0.7615 (mm110) cc_final: 0.7389 (mm110) REVERT: D 341 ARG cc_start: 0.8225 (OUTLIER) cc_final: 0.7933 (ptm160) REVERT: D 395 GLU cc_start: 0.7180 (mt-10) cc_final: 0.6598 (pt0) REVERT: D 456 MET cc_start: 0.6348 (mtt) cc_final: 0.5841 (mmm) REVERT: D 567 LEU cc_start: 0.7649 (mt) cc_final: 0.7409 (mt) REVERT: D 577 ASP cc_start: 0.6243 (t70) cc_final: 0.6015 (t0) REVERT: D 595 ARG cc_start: 0.7108 (mtm-85) cc_final: 0.6839 (mtt180) REVERT: D 614 ARG cc_start: 0.7640 (mtt180) cc_final: 0.7004 (mtm-85) REVERT: D 624 ASP cc_start: 0.6801 (p0) cc_final: 0.6529 (p0) REVERT: D 667 GLU cc_start: 0.7791 (mt-10) cc_final: 0.7470 (tt0) REVERT: D 686 GLU cc_start: 0.7608 (tt0) cc_final: 0.7055 (tp30) REVERT: D 697 LYS cc_start: 0.7320 (mmtt) cc_final: 0.7102 (mmtp) REVERT: D 702 ASN cc_start: 0.8040 (m-40) cc_final: 0.7632 (m-40) REVERT: D 805 ARG cc_start: 0.8428 (OUTLIER) cc_final: 0.8068 (mtp85) REVERT: D 829 GLU cc_start: 0.7940 (mt-10) cc_final: 0.7246 (mm-30) REVERT: D 862 GLU cc_start: 0.6761 (tt0) cc_final: 0.6234 (pp20) REVERT: D 915 MET cc_start: 0.9109 (mtm) cc_final: 0.8736 (mtt) REVERT: D 935 MET cc_start: 0.8485 (OUTLIER) cc_final: 0.7975 (mmm) REVERT: D 1059 LEU cc_start: 0.8012 (mt) cc_final: 0.7681 (mm) REVERT: D 1081 MET cc_start: 0.7145 (mtm) cc_final: 0.6768 (mtm) REVERT: D 1107 ARG cc_start: 0.6129 (ttp-110) cc_final: 0.5894 (ttm110) REVERT: D 1119 LYS cc_start: 0.7514 (mtpt) cc_final: 0.7161 (ttpp) REVERT: D 1123 ARG cc_start: 0.7147 (ttp80) cc_final: 0.6673 (ttt-90) REVERT: D 1157 MET cc_start: 0.8716 (mmt) cc_final: 0.8213 (mmt) REVERT: D 1348 ASP cc_start: 0.8392 (t0) cc_final: 0.8186 (t0) REVERT: D 1452 ARG cc_start: 0.8554 (OUTLIER) cc_final: 0.7915 (ttp80) outliers start: 85 outliers final: 33 residues processed: 593 average time/residue: 0.7939 time to fit residues: 568.0864 Evaluate side-chains 585 residues out of total 4700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 527 time to evaluate : 1.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 MET Chi-restraints excluded: chain A residue 229 GLU Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 341 ARG Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 800 SER Chi-restraints excluded: chain A residue 805 ARG Chi-restraints excluded: chain A residue 935 MET Chi-restraints excluded: chain A residue 946 LEU Chi-restraints excluded: chain A residue 1044 VAL Chi-restraints excluded: chain A residue 1150 MET Chi-restraints excluded: chain A residue 1163 SER Chi-restraints excluded: chain A residue 1164 LEU Chi-restraints excluded: chain A residue 1452 ARG Chi-restraints excluded: chain B residue 70 MET Chi-restraints excluded: chain B residue 229 GLU Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 341 ARG Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 366 LEU Chi-restraints excluded: chain B residue 800 SER Chi-restraints excluded: chain B residue 805 ARG Chi-restraints excluded: chain B residue 935 MET Chi-restraints excluded: chain B residue 946 LEU Chi-restraints excluded: chain B residue 1044 VAL Chi-restraints excluded: chain B residue 1164 LEU Chi-restraints excluded: chain B residue 1452 ARG Chi-restraints excluded: chain C residue 70 MET Chi-restraints excluded: chain C residue 229 GLU Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 340 THR Chi-restraints excluded: chain C residue 341 ARG Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 366 LEU Chi-restraints excluded: chain C residue 800 SER Chi-restraints excluded: chain C residue 805 ARG Chi-restraints excluded: chain C residue 935 MET Chi-restraints excluded: chain C residue 946 LEU Chi-restraints excluded: chain C residue 1044 VAL Chi-restraints excluded: chain C residue 1163 SER Chi-restraints excluded: chain C residue 1164 LEU Chi-restraints excluded: chain C residue 1452 ARG Chi-restraints excluded: chain D residue 70 MET Chi-restraints excluded: chain D residue 229 GLU Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 341 ARG Chi-restraints excluded: chain D residue 346 THR Chi-restraints excluded: chain D residue 366 LEU Chi-restraints excluded: chain D residue 800 SER Chi-restraints excluded: chain D residue 805 ARG Chi-restraints excluded: chain D residue 935 MET Chi-restraints excluded: chain D residue 946 LEU Chi-restraints excluded: chain D residue 1044 VAL Chi-restraints excluded: chain D residue 1164 LEU Chi-restraints excluded: chain D residue 1452 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 548 random chunks: chunk 78 optimal weight: 2.9990 chunk 323 optimal weight: 0.2980 chunk 331 optimal weight: 8.9990 chunk 304 optimal weight: 1.9990 chunk 377 optimal weight: 9.9990 chunk 336 optimal weight: 5.9990 chunk 243 optimal weight: 0.6980 chunk 286 optimal weight: 4.9990 chunk 454 optimal weight: 30.0000 chunk 108 optimal weight: 4.9990 chunk 48 optimal weight: 10.0000 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 514 HIS A 660 HIS A 682 HIS A 696 ASN B 514 HIS B 682 HIS B 696 ASN B1101 GLN C 514 HIS C 682 HIS C 696 ASN D 368 ASN D 514 HIS D 660 HIS D 682 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.156438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.111837 restraints weight = 54185.199| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 1.97 r_work: 0.3139 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.4677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 43776 Z= 0.220 Angle : 0.616 7.996 59556 Z= 0.314 Chirality : 0.042 0.149 6768 Planarity : 0.005 0.052 7544 Dihedral : 8.480 100.363 7016 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.01 % Allowed : 14.46 % Favored : 83.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.11), residues: 5476 helix: 1.91 (0.09), residues: 3020 sheet: -0.81 (0.22), residues: 436 loop : -0.67 (0.14), residues: 2020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C1452 TYR 0.020 0.002 TYR C 917 PHE 0.020 0.002 PHE B 879 TRP 0.013 0.002 TRP B1309 HIS 0.007 0.001 HIS A 813 Details of bonding type rmsd/Z covalent geometry : bond 0.00505 / 0.22 (43772) covalent geometry : angle 0.61626 / 0.31 (59548) SS BOND : bond 0.00046 / 0.02 ( 4) SS BOND : angle 0.67935 / 0.41 ( 8) hydrogen bonds : bond 0.04950 / 3.27 ( 2396) hydrogen bonds : angle 4.19664 / 3.05 ( 7032) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10952 Ramachandran restraints generated. 5476 Oldfield, 0 Emsley, 5476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10952 Ramachandran restraints generated. 5476 Oldfield, 0 Emsley, 5476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 621 residues out of total 4700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 536 time to evaluate : 1.245 Fit side-chains REVERT: A 70 MET cc_start: 0.6829 (OUTLIER) cc_final: 0.5549 (pmm) REVERT: A 196 MET cc_start: 0.8186 (mmm) cc_final: 0.7914 (mmp) REVERT: A 284 GLN cc_start: 0.7628 (mm110) cc_final: 0.7407 (mm110) REVERT: A 395 GLU cc_start: 0.7174 (mt-10) cc_final: 0.6579 (pt0) REVERT: A 577 ASP cc_start: 0.6539 (t70) cc_final: 0.6260 (t0) REVERT: A 614 ARG cc_start: 0.7696 (mtt180) cc_final: 0.7042 (mtm-85) REVERT: A 624 ASP cc_start: 0.6808 (p0) cc_final: 0.6497 (p0) REVERT: A 686 GLU cc_start: 0.7678 (tt0) cc_final: 0.7125 (tp30) REVERT: A 692 ASN cc_start: 0.6579 (t0) cc_final: 0.6262 (t0) REVERT: A 702 ASN cc_start: 0.8158 (m-40) cc_final: 0.7793 (m-40) REVERT: A 805 ARG cc_start: 0.8426 (OUTLIER) cc_final: 0.8062 (mtp85) REVERT: A 829 GLU cc_start: 0.7942 (mt-10) cc_final: 0.7259 (mm-30) REVERT: A 862 GLU cc_start: 0.6759 (tt0) cc_final: 0.6290 (pp20) REVERT: A 915 MET cc_start: 0.9148 (mtm) cc_final: 0.8756 (mtt) REVERT: A 935 MET cc_start: 0.8465 (OUTLIER) cc_final: 0.7948 (mmm) REVERT: A 1059 LEU cc_start: 0.8001 (mt) cc_final: 0.7664 (mm) REVERT: A 1081 MET cc_start: 0.7141 (mtm) cc_final: 0.6749 (mtm) REVERT: A 1107 ARG cc_start: 0.6065 (ttp-110) cc_final: 0.5851 (ttm110) REVERT: A 1119 LYS cc_start: 0.7570 (mtpt) cc_final: 0.7231 (ttpp) REVERT: A 1123 ARG cc_start: 0.7208 (ttp80) cc_final: 0.6744 (ttt-90) REVERT: A 1150 MET cc_start: 0.8150 (OUTLIER) cc_final: 0.7630 (mtt) REVERT: A 1157 MET cc_start: 0.8803 (mmt) cc_final: 0.8313 (mmt) REVERT: A 1348 ASP cc_start: 0.8445 (t0) cc_final: 0.8232 (t0) REVERT: A 1452 ARG cc_start: 0.8563 (OUTLIER) cc_final: 0.7894 (ttp80) REVERT: B 70 MET cc_start: 0.6836 (OUTLIER) cc_final: 0.5542 (pmm) REVERT: B 81 MET cc_start: 0.8069 (ptt) cc_final: 0.7661 (ptt) REVERT: B 196 MET cc_start: 0.8194 (mmm) cc_final: 0.7921 (mmp) REVERT: B 284 GLN cc_start: 0.7708 (mm110) cc_final: 0.7462 (mm110) REVERT: B 395 GLU cc_start: 0.7169 (mt-10) cc_final: 0.6582 (pt0) REVERT: B 567 LEU cc_start: 0.7609 (mt) cc_final: 0.7381 (mt) REVERT: B 577 ASP cc_start: 0.6530 (t70) cc_final: 0.6263 (t0) REVERT: B 614 ARG cc_start: 0.7695 (mtt180) cc_final: 0.7050 (mtm-85) REVERT: B 624 ASP cc_start: 0.6803 (p0) cc_final: 0.6491 (p0) REVERT: B 667 GLU cc_start: 0.7793 (mt-10) cc_final: 0.7411 (tt0) REVERT: B 686 GLU cc_start: 0.7637 (tt0) cc_final: 0.7121 (tp30) REVERT: B 692 ASN cc_start: 0.6619 (t0) cc_final: 0.6321 (t0) REVERT: B 702 ASN cc_start: 0.8161 (m-40) cc_final: 0.7795 (m-40) REVERT: B 805 ARG cc_start: 0.8425 (OUTLIER) cc_final: 0.8060 (mtp85) REVERT: B 829 GLU cc_start: 0.7931 (mt-10) cc_final: 0.7250 (mm-30) REVERT: B 862 GLU cc_start: 0.6754 (tt0) cc_final: 0.6292 (pp20) REVERT: B 915 MET cc_start: 0.9146 (mtm) cc_final: 0.8753 (mtt) REVERT: B 935 MET cc_start: 0.8470 (OUTLIER) cc_final: 0.7950 (mmm) REVERT: B 1059 LEU cc_start: 0.8005 (mt) cc_final: 0.7667 (mm) REVERT: B 1081 MET cc_start: 0.7128 (mtm) cc_final: 0.6731 (mtm) REVERT: B 1107 ARG cc_start: 0.6068 (ttp-110) cc_final: 0.5853 (ttm110) REVERT: B 1119 LYS cc_start: 0.7531 (mtpt) cc_final: 0.7168 (ttpp) REVERT: B 1123 ARG cc_start: 0.7369 (ttp80) cc_final: 0.6794 (ttt-90) REVERT: B 1125 GLU cc_start: 0.6674 (mm-30) cc_final: 0.6296 (mp0) REVERT: B 1130 GLU cc_start: 0.7454 (mt-10) cc_final: 0.6836 (mp0) REVERT: B 1150 MET cc_start: 0.7818 (mtp) cc_final: 0.7597 (mtp) REVERT: B 1348 ASP cc_start: 0.8454 (t0) cc_final: 0.8236 (t0) REVERT: B 1452 ARG cc_start: 0.8575 (OUTLIER) cc_final: 0.7929 (ttp80) REVERT: C 70 MET cc_start: 0.6847 (OUTLIER) cc_final: 0.5552 (pmm) REVERT: C 81 MET cc_start: 0.8066 (ptt) cc_final: 0.7658 (ptt) REVERT: C 196 MET cc_start: 0.8196 (mmm) cc_final: 0.7927 (mmp) REVERT: C 284 GLN cc_start: 0.7713 (mm110) cc_final: 0.7469 (mm110) REVERT: C 395 GLU cc_start: 0.7161 (mt-10) cc_final: 0.6572 (pt0) REVERT: C 567 LEU cc_start: 0.7622 (mt) cc_final: 0.7395 (mt) REVERT: C 577 ASP cc_start: 0.6543 (t70) cc_final: 0.6277 (t0) REVERT: C 614 ARG cc_start: 0.7700 (mtt180) cc_final: 0.7050 (mtm-85) REVERT: C 624 ASP cc_start: 0.6790 (p0) cc_final: 0.6480 (p0) REVERT: C 667 GLU cc_start: 0.7798 (mt-10) cc_final: 0.7411 (tt0) REVERT: C 686 GLU cc_start: 0.7638 (tt0) cc_final: 0.7125 (tp30) REVERT: C 692 ASN cc_start: 0.6585 (t0) cc_final: 0.6272 (t0) REVERT: C 702 ASN cc_start: 0.8166 (m-40) cc_final: 0.7799 (m-40) REVERT: C 805 ARG cc_start: 0.8431 (OUTLIER) cc_final: 0.8043 (mtp85) REVERT: C 829 GLU cc_start: 0.7930 (mt-10) cc_final: 0.7256 (mm-30) REVERT: C 862 GLU cc_start: 0.6756 (tt0) cc_final: 0.6295 (pp20) REVERT: C 915 MET cc_start: 0.9140 (mtm) cc_final: 0.8746 (mtt) REVERT: C 935 MET cc_start: 0.8463 (OUTLIER) cc_final: 0.7943 (mmm) REVERT: C 1059 LEU cc_start: 0.8003 (mt) cc_final: 0.7664 (mm) REVERT: C 1081 MET cc_start: 0.7131 (mtm) cc_final: 0.6736 (mtm) REVERT: C 1107 ARG cc_start: 0.6071 (ttp-110) cc_final: 0.5854 (ttm110) REVERT: C 1119 LYS cc_start: 0.7523 (mtpt) cc_final: 0.7153 (ttpp) REVERT: C 1123 ARG cc_start: 0.7197 (ttp80) cc_final: 0.6715 (ttt-90) REVERT: C 1130 GLU cc_start: 0.7451 (mt-10) cc_final: 0.6827 (mp0) REVERT: C 1348 ASP cc_start: 0.8447 (t0) cc_final: 0.8235 (t0) REVERT: C 1452 ARG cc_start: 0.8564 (OUTLIER) cc_final: 0.7897 (ttp80) REVERT: D 70 MET cc_start: 0.6846 (OUTLIER) cc_final: 0.5561 (pmm) REVERT: D 196 MET cc_start: 0.8184 (mmm) cc_final: 0.7914 (mmp) REVERT: D 395 GLU cc_start: 0.7173 (mt-10) cc_final: 0.6588 (pt0) REVERT: D 567 LEU cc_start: 0.7614 (mt) cc_final: 0.7387 (mt) REVERT: D 577 ASP cc_start: 0.6468 (t70) cc_final: 0.6212 (t0) REVERT: D 614 ARG cc_start: 0.7703 (mtt180) cc_final: 0.7058 (mtm-85) REVERT: D 624 ASP cc_start: 0.6799 (p0) cc_final: 0.6486 (p0) REVERT: D 667 GLU cc_start: 0.7831 (mt-10) cc_final: 0.7441 (tt0) REVERT: D 686 GLU cc_start: 0.7645 (tt0) cc_final: 0.7135 (tp30) REVERT: D 692 ASN cc_start: 0.6629 (t0) cc_final: 0.6314 (t0) REVERT: D 697 LYS cc_start: 0.7318 (mmtt) cc_final: 0.7104 (mmtp) REVERT: D 702 ASN cc_start: 0.8174 (m-40) cc_final: 0.7845 (m-40) REVERT: D 805 ARG cc_start: 0.8431 (OUTLIER) cc_final: 0.8072 (mtp85) REVERT: D 829 GLU cc_start: 0.7933 (mt-10) cc_final: 0.7257 (mm-30) REVERT: D 862 GLU cc_start: 0.6752 (tt0) cc_final: 0.6284 (pp20) REVERT: D 915 MET cc_start: 0.9146 (mtm) cc_final: 0.8752 (mtt) REVERT: D 935 MET cc_start: 0.8474 (OUTLIER) cc_final: 0.7956 (mmm) REVERT: D 1059 LEU cc_start: 0.8020 (mt) cc_final: 0.7687 (mm) REVERT: D 1081 MET cc_start: 0.7149 (mtm) cc_final: 0.6757 (mtm) REVERT: D 1107 ARG cc_start: 0.6091 (ttp-110) cc_final: 0.5876 (ttm110) REVERT: D 1119 LYS cc_start: 0.7547 (mtpt) cc_final: 0.7177 (ttpp) REVERT: D 1123 ARG cc_start: 0.7123 (ttp80) cc_final: 0.6638 (ttt-90) REVERT: D 1348 ASP cc_start: 0.8418 (t0) cc_final: 0.8213 (t0) REVERT: D 1452 ARG cc_start: 0.8555 (OUTLIER) cc_final: 0.7957 (ttp80) outliers start: 85 outliers final: 38 residues processed: 581 average time/residue: 0.8227 time to fit residues: 572.0199 Evaluate side-chains 573 residues out of total 4700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 518 time to evaluate : 1.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 MET Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 341 ARG Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 800 SER Chi-restraints excluded: chain A residue 805 ARG Chi-restraints excluded: chain A residue 935 MET Chi-restraints excluded: chain A residue 946 LEU Chi-restraints excluded: chain A residue 1150 MET Chi-restraints excluded: chain A residue 1163 SER Chi-restraints excluded: chain A residue 1164 LEU Chi-restraints excluded: chain A residue 1452 ARG Chi-restraints excluded: chain B residue 70 MET Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 341 ARG Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 366 LEU Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 800 SER Chi-restraints excluded: chain B residue 805 ARG Chi-restraints excluded: chain B residue 864 ILE Chi-restraints excluded: chain B residue 935 MET Chi-restraints excluded: chain B residue 946 LEU Chi-restraints excluded: chain B residue 1452 ARG Chi-restraints excluded: chain C residue 70 MET Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 340 THR Chi-restraints excluded: chain C residue 341 ARG Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 366 LEU Chi-restraints excluded: chain C residue 493 LEU Chi-restraints excluded: chain C residue 800 SER Chi-restraints excluded: chain C residue 805 ARG Chi-restraints excluded: chain C residue 864 ILE Chi-restraints excluded: chain C residue 935 MET Chi-restraints excluded: chain C residue 946 LEU Chi-restraints excluded: chain C residue 1150 MET Chi-restraints excluded: chain C residue 1163 SER Chi-restraints excluded: chain C residue 1164 LEU Chi-restraints excluded: chain C residue 1452 ARG Chi-restraints excluded: chain D residue 70 MET Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 340 THR Chi-restraints excluded: chain D residue 341 ARG Chi-restraints excluded: chain D residue 346 THR Chi-restraints excluded: chain D residue 366 LEU Chi-restraints excluded: chain D residue 493 LEU Chi-restraints excluded: chain D residue 800 SER Chi-restraints excluded: chain D residue 805 ARG Chi-restraints excluded: chain D residue 935 MET Chi-restraints excluded: chain D residue 946 LEU Chi-restraints excluded: chain D residue 1452 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 548 random chunks: chunk 144 optimal weight: 0.9990 chunk 221 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 466 optimal weight: 0.9990 chunk 174 optimal weight: 0.9990 chunk 525 optimal weight: 0.9990 chunk 384 optimal weight: 0.1980 chunk 429 optimal weight: 0.5980 chunk 382 optimal weight: 4.9990 chunk 336 optimal weight: 4.9990 chunk 389 optimal weight: 0.7980 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 514 HIS A 647 GLN A 660 HIS A 682 HIS A 696 ASN A 992 ASN B 368 ASN B 514 HIS B 647 GLN B 660 HIS B 682 HIS B 696 ASN C 514 HIS C 647 GLN C 660 HIS C 682 HIS C 696 ASN C 992 ASN D 514 HIS D 647 GLN D 660 HIS D 682 HIS Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.158934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.114257 restraints weight = 53927.827| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 2.25 r_work: 0.3172 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.4593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 43776 Z= 0.123 Angle : 0.537 8.077 59556 Z= 0.269 Chirality : 0.038 0.143 6768 Planarity : 0.004 0.050 7544 Dihedral : 7.898 96.847 7016 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.56 % Allowed : 14.93 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.35 (0.11), residues: 5476 helix: 2.13 (0.09), residues: 3020 sheet: -1.05 (0.21), residues: 460 loop : -0.52 (0.14), residues: 1996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 594 TYR 0.013 0.001 TYR D 705 PHE 0.016 0.001 PHE D 879 TRP 0.015 0.001 TRP D 726 HIS 0.006 0.001 HIS D 682 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (43772) covalent geometry : angle 0.53696 / 0.27 (59548) SS BOND : bond 0.00012 / 0.01 ( 4) SS BOND : angle 0.30876 / 0.18 ( 8) hydrogen bonds : bond 0.03984 / 2.64 ( 2396) hydrogen bonds : angle 3.97328 / 2.88 ( 7032) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10952 Ramachandran restraints generated. 5476 Oldfield, 0 Emsley, 5476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10952 Ramachandran restraints generated. 5476 Oldfield, 0 Emsley, 5476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 605 residues out of total 4700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 539 time to evaluate : 1.627 Fit side-chains REVERT: A 70 MET cc_start: 0.6824 (OUTLIER) cc_final: 0.5510 (pmm) REVERT: A 81 MET cc_start: 0.8264 (ptp) cc_final: 0.8028 (ptt) REVERT: A 196 MET cc_start: 0.8059 (mmm) cc_final: 0.7771 (mmp) REVERT: A 284 GLN cc_start: 0.7628 (mm110) cc_final: 0.7376 (mm110) REVERT: A 341 ARG cc_start: 0.8240 (OUTLIER) cc_final: 0.7951 (ptm160) REVERT: A 395 GLU cc_start: 0.7167 (mt-10) cc_final: 0.6557 (pt0) REVERT: A 452 MET cc_start: 0.6945 (tpt) cc_final: 0.6735 (tpt) REVERT: A 577 ASP cc_start: 0.6399 (t70) cc_final: 0.6137 (t0) REVERT: A 614 ARG cc_start: 0.7643 (mtt180) cc_final: 0.6979 (mtm-85) REVERT: A 624 ASP cc_start: 0.6788 (p0) cc_final: 0.6494 (p0) REVERT: A 667 GLU cc_start: 0.7768 (mt-10) cc_final: 0.7446 (tt0) REVERT: A 686 GLU cc_start: 0.7581 (tt0) cc_final: 0.7015 (tp30) REVERT: A 702 ASN cc_start: 0.8097 (m-40) cc_final: 0.7742 (m-40) REVERT: A 805 ARG cc_start: 0.8412 (OUTLIER) cc_final: 0.8052 (mtp85) REVERT: A 829 GLU cc_start: 0.7964 (mt-10) cc_final: 0.7225 (mm-30) REVERT: A 862 GLU cc_start: 0.6777 (tt0) cc_final: 0.6274 (pp20) REVERT: A 915 MET cc_start: 0.9105 (mtm) cc_final: 0.8733 (mtt) REVERT: A 935 MET cc_start: 0.8433 (OUTLIER) cc_final: 0.7914 (mmm) REVERT: A 1059 LEU cc_start: 0.7978 (mt) cc_final: 0.7654 (mm) REVERT: A 1081 MET cc_start: 0.7126 (mtm) cc_final: 0.6732 (mtm) REVERT: A 1107 ARG cc_start: 0.6072 (ttp-110) cc_final: 0.5868 (ttm110) REVERT: A 1119 LYS cc_start: 0.7465 (mtpt) cc_final: 0.7094 (ttpp) REVERT: A 1123 ARG cc_start: 0.7093 (ttp80) cc_final: 0.6627 (ttt-90) REVERT: A 1150 MET cc_start: 0.8036 (OUTLIER) cc_final: 0.7546 (mtt) REVERT: A 1157 MET cc_start: 0.8659 (mmt) cc_final: 0.8280 (mmt) REVERT: A 1348 ASP cc_start: 0.8411 (t0) cc_final: 0.8202 (t0) REVERT: A 1452 ARG cc_start: 0.8533 (OUTLIER) cc_final: 0.7929 (ttp80) REVERT: B 70 MET cc_start: 0.6834 (OUTLIER) cc_final: 0.5575 (pmm) REVERT: B 81 MET cc_start: 0.8015 (ptt) cc_final: 0.7566 (ptt) REVERT: B 196 MET cc_start: 0.8051 (mmm) cc_final: 0.7761 (mmp) REVERT: B 284 GLN cc_start: 0.7688 (mm110) cc_final: 0.7434 (mm110) REVERT: B 341 ARG cc_start: 0.8237 (OUTLIER) cc_final: 0.7965 (ptm160) REVERT: B 395 GLU cc_start: 0.7165 (mt-10) cc_final: 0.6527 (pt0) REVERT: B 452 MET cc_start: 0.6950 (tpt) cc_final: 0.6738 (tpt) REVERT: B 567 LEU cc_start: 0.7585 (mt) cc_final: 0.7351 (mt) REVERT: B 577 ASP cc_start: 0.6405 (t70) cc_final: 0.6147 (t0) REVERT: B 614 ARG cc_start: 0.7635 (mtt180) cc_final: 0.6972 (mtm-85) REVERT: B 624 ASP cc_start: 0.6789 (p0) cc_final: 0.6487 (p0) REVERT: B 667 GLU cc_start: 0.7783 (mt-10) cc_final: 0.7462 (tt0) REVERT: B 686 GLU cc_start: 0.7561 (tt0) cc_final: 0.6988 (tp30) REVERT: B 692 ASN cc_start: 0.6601 (t0) cc_final: 0.6255 (t0) REVERT: B 702 ASN cc_start: 0.8092 (m-40) cc_final: 0.7672 (m-40) REVERT: B 805 ARG cc_start: 0.8418 (OUTLIER) cc_final: 0.8061 (mtp85) REVERT: B 829 GLU cc_start: 0.7953 (mt-10) cc_final: 0.7213 (mm-30) REVERT: B 862 GLU cc_start: 0.6770 (tt0) cc_final: 0.6276 (pp20) REVERT: B 915 MET cc_start: 0.9107 (mtm) cc_final: 0.8732 (mtt) REVERT: B 935 MET cc_start: 0.8451 (OUTLIER) cc_final: 0.7934 (mmm) REVERT: B 1059 LEU cc_start: 0.7981 (mt) cc_final: 0.7657 (mm) REVERT: B 1081 MET cc_start: 0.7099 (mtm) cc_final: 0.6703 (mtm) REVERT: B 1107 ARG cc_start: 0.6073 (ttp-110) cc_final: 0.5867 (ttm110) REVERT: B 1119 LYS cc_start: 0.7468 (mtpt) cc_final: 0.7119 (ttpp) REVERT: B 1123 ARG cc_start: 0.7326 (ttp80) cc_final: 0.6739 (ttt-90) REVERT: B 1125 GLU cc_start: 0.6643 (mm-30) cc_final: 0.6298 (mp0) REVERT: B 1130 GLU cc_start: 0.7362 (mt-10) cc_final: 0.6742 (mp0) REVERT: B 1147 MET cc_start: 0.8001 (OUTLIER) cc_final: 0.7618 (mtm) REVERT: B 1150 MET cc_start: 0.7790 (mtp) cc_final: 0.7580 (mtp) REVERT: B 1348 ASP cc_start: 0.8418 (t0) cc_final: 0.8202 (t0) REVERT: B 1452 ARG cc_start: 0.8541 (OUTLIER) cc_final: 0.7946 (ttp80) REVERT: C 70 MET cc_start: 0.6846 (OUTLIER) cc_final: 0.5581 (pmm) REVERT: C 81 MET cc_start: 0.7998 (ptt) cc_final: 0.7556 (ptt) REVERT: C 196 MET cc_start: 0.8058 (mmm) cc_final: 0.7772 (mmp) REVERT: C 284 GLN cc_start: 0.7687 (mm110) cc_final: 0.7432 (mm110) REVERT: C 341 ARG cc_start: 0.8217 (OUTLIER) cc_final: 0.7923 (ptm160) REVERT: C 395 GLU cc_start: 0.7166 (mt-10) cc_final: 0.6554 (pt0) REVERT: C 452 MET cc_start: 0.6945 (tpt) cc_final: 0.6742 (tpt) REVERT: C 567 LEU cc_start: 0.7630 (mt) cc_final: 0.7396 (mt) REVERT: C 577 ASP cc_start: 0.6406 (t70) cc_final: 0.6146 (t0) REVERT: C 614 ARG cc_start: 0.7636 (mtt180) cc_final: 0.6975 (mtm-85) REVERT: C 624 ASP cc_start: 0.6767 (p0) cc_final: 0.6471 (p0) REVERT: C 667 GLU cc_start: 0.7779 (mt-10) cc_final: 0.7456 (tt0) REVERT: C 686 GLU cc_start: 0.7570 (tt0) cc_final: 0.6999 (tp30) REVERT: C 702 ASN cc_start: 0.8098 (m-40) cc_final: 0.7681 (m-40) REVERT: C 805 ARG cc_start: 0.8418 (OUTLIER) cc_final: 0.8054 (mtp85) REVERT: C 829 GLU cc_start: 0.7960 (mt-10) cc_final: 0.7228 (mm-30) REVERT: C 862 GLU cc_start: 0.6770 (tt0) cc_final: 0.6273 (pp20) REVERT: C 915 MET cc_start: 0.9100 (mtm) cc_final: 0.8725 (mtt) REVERT: C 935 MET cc_start: 0.8444 (OUTLIER) cc_final: 0.7921 (mmm) REVERT: C 1059 LEU cc_start: 0.7981 (mt) cc_final: 0.7657 (mm) REVERT: C 1081 MET cc_start: 0.7119 (mtm) cc_final: 0.6723 (mtm) REVERT: C 1107 ARG cc_start: 0.6070 (ttp-110) cc_final: 0.5860 (ttm110) REVERT: C 1119 LYS cc_start: 0.7441 (mtpt) cc_final: 0.7083 (ttpp) REVERT: C 1123 ARG cc_start: 0.7054 (ttp80) cc_final: 0.6576 (ttt-90) REVERT: C 1130 GLU cc_start: 0.7418 (mt-10) cc_final: 0.6783 (mp0) REVERT: C 1348 ASP cc_start: 0.8413 (t0) cc_final: 0.8198 (t0) REVERT: C 1452 ARG cc_start: 0.8532 (OUTLIER) cc_final: 0.7928 (ttp80) REVERT: D 70 MET cc_start: 0.6861 (OUTLIER) cc_final: 0.5578 (pmm) REVERT: D 81 MET cc_start: 0.7948 (ptt) cc_final: 0.7661 (ptt) REVERT: D 196 MET cc_start: 0.8052 (mmm) cc_final: 0.7754 (mmp) REVERT: D 341 ARG cc_start: 0.8219 (OUTLIER) cc_final: 0.7936 (ptm160) REVERT: D 395 GLU cc_start: 0.7171 (mt-10) cc_final: 0.6567 (pt0) REVERT: D 567 LEU cc_start: 0.7630 (mt) cc_final: 0.7396 (mt) REVERT: D 577 ASP cc_start: 0.6225 (t70) cc_final: 0.5958 (t0) REVERT: D 614 ARG cc_start: 0.7642 (mtt180) cc_final: 0.6901 (mtm-85) REVERT: D 624 ASP cc_start: 0.6785 (p0) cc_final: 0.6491 (p0) REVERT: D 667 GLU cc_start: 0.7803 (mt-10) cc_final: 0.7446 (tt0) REVERT: D 686 GLU cc_start: 0.7575 (tt0) cc_final: 0.7007 (tp30) REVERT: D 702 ASN cc_start: 0.8097 (m-40) cc_final: 0.7679 (m-40) REVERT: D 805 ARG cc_start: 0.8420 (OUTLIER) cc_final: 0.8061 (mtp85) REVERT: D 829 GLU cc_start: 0.7952 (mt-10) cc_final: 0.7218 (mm-30) REVERT: D 862 GLU cc_start: 0.6774 (tt0) cc_final: 0.6280 (pp20) REVERT: D 915 MET cc_start: 0.9111 (mtm) cc_final: 0.8737 (mtt) REVERT: D 935 MET cc_start: 0.8445 (OUTLIER) cc_final: 0.7924 (mmm) REVERT: D 1059 LEU cc_start: 0.7999 (mt) cc_final: 0.7674 (mm) REVERT: D 1081 MET cc_start: 0.7121 (mtm) cc_final: 0.6725 (mtm) REVERT: D 1107 ARG cc_start: 0.6074 (ttp-110) cc_final: 0.5868 (ttm110) REVERT: D 1119 LYS cc_start: 0.7468 (mtpt) cc_final: 0.7111 (ttpp) REVERT: D 1123 ARG cc_start: 0.7090 (ttp80) cc_final: 0.6615 (ttt-90) REVERT: D 1348 ASP cc_start: 0.8388 (t0) cc_final: 0.8172 (t0) REVERT: D 1452 ARG cc_start: 0.8558 (OUTLIER) cc_final: 0.7897 (ttp80) outliers start: 66 outliers final: 22 residues processed: 572 average time/residue: 0.7527 time to fit residues: 520.0379 Evaluate side-chains 566 residues out of total 4700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 522 time to evaluate : 1.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 MET Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 341 ARG Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 805 ARG Chi-restraints excluded: chain A residue 935 MET Chi-restraints excluded: chain A residue 1011 VAL Chi-restraints excluded: chain A residue 1150 MET Chi-restraints excluded: chain A residue 1164 LEU Chi-restraints excluded: chain A residue 1452 ARG Chi-restraints excluded: chain B residue 70 MET Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 341 ARG Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 366 LEU Chi-restraints excluded: chain B residue 615 MET Chi-restraints excluded: chain B residue 805 ARG Chi-restraints excluded: chain B residue 935 MET Chi-restraints excluded: chain B residue 1011 VAL Chi-restraints excluded: chain B residue 1147 MET Chi-restraints excluded: chain B residue 1452 ARG Chi-restraints excluded: chain C residue 70 MET Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 341 ARG Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 366 LEU Chi-restraints excluded: chain C residue 615 MET Chi-restraints excluded: chain C residue 805 ARG Chi-restraints excluded: chain C residue 935 MET Chi-restraints excluded: chain C residue 1011 VAL Chi-restraints excluded: chain C residue 1164 LEU Chi-restraints excluded: chain C residue 1452 ARG Chi-restraints excluded: chain D residue 70 MET Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 341 ARG Chi-restraints excluded: chain D residue 346 THR Chi-restraints excluded: chain D residue 366 LEU Chi-restraints excluded: chain D residue 615 MET Chi-restraints excluded: chain D residue 805 ARG Chi-restraints excluded: chain D residue 935 MET Chi-restraints excluded: chain D residue 1011 VAL Chi-restraints excluded: chain D residue 1452 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 548 random chunks: chunk 318 optimal weight: 0.8980 chunk 98 optimal weight: 4.9990 chunk 143 optimal weight: 4.9990 chunk 342 optimal weight: 0.0970 chunk 460 optimal weight: 7.9990 chunk 506 optimal weight: 2.9990 chunk 485 optimal weight: 0.6980 chunk 99 optimal weight: 6.9990 chunk 19 optimal weight: 0.3980 chunk 62 optimal weight: 3.9990 chunk 117 optimal weight: 3.9990 overall best weight: 1.0180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 514 HIS A 660 HIS A 682 HIS A 696 ASN B 514 HIS B 660 HIS B 682 HIS B 696 ASN C 514 HIS C 660 HIS C 682 HIS C 696 ASN D 514 HIS D 660 HIS D 682 HIS D 696 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.158567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.114060 restraints weight = 53893.751| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 2.12 r_work: 0.3173 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.4628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 43776 Z= 0.138 Angle : 0.554 11.073 59556 Z= 0.278 Chirality : 0.039 0.144 6768 Planarity : 0.004 0.050 7544 Dihedral : 7.816 96.510 7016 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.23 % Allowed : 15.86 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.32 (0.11), residues: 5476 helix: 2.10 (0.09), residues: 3044 sheet: -1.02 (0.21), residues: 464 loop : -0.58 (0.14), residues: 1968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 594 TYR 0.015 0.002 TYR D 917 PHE 0.017 0.001 PHE D 879 TRP 0.014 0.001 TRP D 726 HIS 0.007 0.001 HIS C 682 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 (43772) covalent geometry : angle 0.55421 / 0.28 (59548) SS BOND : bond 0.00010 / 0.00 ( 4) SS BOND : angle 0.39852 / 0.24 ( 8) hydrogen bonds : bond 0.04150 / 2.75 ( 2396) hydrogen bonds : angle 3.97816 / 2.89 ( 7032) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10952 Ramachandran restraints generated. 5476 Oldfield, 0 Emsley, 5476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10952 Ramachandran restraints generated. 5476 Oldfield, 0 Emsley, 5476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 574 residues out of total 4700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 522 time to evaluate : 1.553 Fit side-chains REVERT: A 70 MET cc_start: 0.6767 (OUTLIER) cc_final: 0.5512 (pmm) REVERT: A 81 MET cc_start: 0.8258 (ptp) cc_final: 0.7973 (ptt) REVERT: A 196 MET cc_start: 0.8101 (mmm) cc_final: 0.7877 (mmp) REVERT: A 284 GLN cc_start: 0.7608 (mm110) cc_final: 0.7364 (mm110) REVERT: A 341 ARG cc_start: 0.8211 (OUTLIER) cc_final: 0.7933 (ptm160) REVERT: A 395 GLU cc_start: 0.7177 (mt-10) cc_final: 0.6569 (pt0) REVERT: A 577 ASP cc_start: 0.6421 (t70) cc_final: 0.6166 (t0) REVERT: A 614 ARG cc_start: 0.7630 (mtt180) cc_final: 0.6899 (mtm-85) REVERT: A 624 ASP cc_start: 0.6752 (p0) cc_final: 0.6461 (p0) REVERT: A 667 GLU cc_start: 0.7748 (mt-10) cc_final: 0.7414 (tt0) REVERT: A 683 MET cc_start: 0.8350 (tpt) cc_final: 0.7989 (tpp) REVERT: A 686 GLU cc_start: 0.7566 (tt0) cc_final: 0.6992 (tp30) REVERT: A 692 ASN cc_start: 0.6624 (t0) cc_final: 0.6312 (t0) REVERT: A 702 ASN cc_start: 0.8049 (m-40) cc_final: 0.7695 (m-40) REVERT: A 805 ARG cc_start: 0.8396 (OUTLIER) cc_final: 0.8039 (mtp85) REVERT: A 829 GLU cc_start: 0.7933 (mt-10) cc_final: 0.7228 (mm-30) REVERT: A 862 GLU cc_start: 0.6777 (tt0) cc_final: 0.6264 (pp20) REVERT: A 915 MET cc_start: 0.9097 (mtm) cc_final: 0.8724 (mtt) REVERT: A 935 MET cc_start: 0.8450 (OUTLIER) cc_final: 0.7926 (mmm) REVERT: A 1059 LEU cc_start: 0.7975 (mt) cc_final: 0.7641 (mm) REVERT: A 1081 MET cc_start: 0.7160 (mtm) cc_final: 0.6779 (mtm) REVERT: A 1107 ARG cc_start: 0.6081 (ttp-110) cc_final: 0.5870 (ttm110) REVERT: A 1119 LYS cc_start: 0.7438 (mtpt) cc_final: 0.7063 (ttpp) REVERT: A 1123 ARG cc_start: 0.7098 (ttp80) cc_final: 0.6648 (ttt-90) REVERT: A 1150 MET cc_start: 0.8125 (OUTLIER) cc_final: 0.7708 (mtt) REVERT: A 1348 ASP cc_start: 0.8393 (t0) cc_final: 0.8169 (t0) REVERT: A 1452 ARG cc_start: 0.8548 (OUTLIER) cc_final: 0.7885 (ttp80) REVERT: B 70 MET cc_start: 0.6701 (OUTLIER) cc_final: 0.5396 (pmm) REVERT: B 81 MET cc_start: 0.8018 (ptt) cc_final: 0.7604 (ptt) REVERT: B 196 MET cc_start: 0.8096 (mmm) cc_final: 0.7868 (mmp) REVERT: B 284 GLN cc_start: 0.7648 (mm110) cc_final: 0.7393 (mm110) REVERT: B 341 ARG cc_start: 0.8168 (mtm110) cc_final: 0.7907 (ptm160) REVERT: B 395 GLU cc_start: 0.7170 (mt-10) cc_final: 0.6541 (pt0) REVERT: B 567 LEU cc_start: 0.7567 (mt) cc_final: 0.7350 (mt) REVERT: B 577 ASP cc_start: 0.6424 (t70) cc_final: 0.6185 (t0) REVERT: B 614 ARG cc_start: 0.7633 (mtt180) cc_final: 0.6897 (mtm-85) REVERT: B 624 ASP cc_start: 0.6753 (p0) cc_final: 0.6457 (p0) REVERT: B 667 GLU cc_start: 0.7747 (mt-10) cc_final: 0.7435 (tt0) REVERT: B 683 MET cc_start: 0.8332 (tpt) cc_final: 0.7970 (tpp) REVERT: B 686 GLU cc_start: 0.7561 (tt0) cc_final: 0.6990 (tp30) REVERT: B 692 ASN cc_start: 0.6655 (t0) cc_final: 0.6328 (t0) REVERT: B 702 ASN cc_start: 0.8020 (m-40) cc_final: 0.7662 (m-40) REVERT: B 805 ARG cc_start: 0.8407 (OUTLIER) cc_final: 0.8053 (mtp85) REVERT: B 829 GLU cc_start: 0.7930 (mt-10) cc_final: 0.7221 (mm-30) REVERT: B 862 GLU cc_start: 0.6765 (tt0) cc_final: 0.6264 (pp20) REVERT: B 915 MET cc_start: 0.9097 (mtm) cc_final: 0.8717 (mtt) REVERT: B 935 MET cc_start: 0.8454 (OUTLIER) cc_final: 0.7927 (mmm) REVERT: B 1059 LEU cc_start: 0.7980 (mt) cc_final: 0.7651 (mm) REVERT: B 1081 MET cc_start: 0.7134 (mtm) cc_final: 0.6751 (mtm) REVERT: B 1107 ARG cc_start: 0.6079 (ttp-110) cc_final: 0.5865 (ttm110) REVERT: B 1119 LYS cc_start: 0.7477 (mtpt) cc_final: 0.7125 (ttpp) REVERT: B 1123 ARG cc_start: 0.7346 (ttp80) cc_final: 0.6762 (ttt-90) REVERT: B 1125 GLU cc_start: 0.6676 (mm-30) cc_final: 0.6321 (mp0) REVERT: B 1130 GLU cc_start: 0.7386 (mt-10) cc_final: 0.6766 (mp0) REVERT: B 1348 ASP cc_start: 0.8402 (t0) cc_final: 0.8169 (t0) REVERT: B 1452 ARG cc_start: 0.8544 (OUTLIER) cc_final: 0.7933 (ttp80) REVERT: C 70 MET cc_start: 0.6705 (OUTLIER) cc_final: 0.5399 (pmm) REVERT: C 81 MET cc_start: 0.8012 (ptt) cc_final: 0.7593 (ptt) REVERT: C 196 MET cc_start: 0.8108 (mmm) cc_final: 0.7884 (mmp) REVERT: C 284 GLN cc_start: 0.7651 (mm110) cc_final: 0.7396 (mm110) REVERT: C 341 ARG cc_start: 0.8194 (OUTLIER) cc_final: 0.7912 (ptm160) REVERT: C 395 GLU cc_start: 0.7160 (mt-10) cc_final: 0.6559 (pt0) REVERT: C 502 GLU cc_start: 0.7312 (tt0) cc_final: 0.7100 (tt0) REVERT: C 577 ASP cc_start: 0.6434 (t70) cc_final: 0.6184 (t0) REVERT: C 614 ARG cc_start: 0.7615 (mtt180) cc_final: 0.6887 (mtm-85) REVERT: C 624 ASP cc_start: 0.6738 (p0) cc_final: 0.6450 (p0) REVERT: C 667 GLU cc_start: 0.7746 (mt-10) cc_final: 0.7416 (tt0) REVERT: C 683 MET cc_start: 0.8353 (tpt) cc_final: 0.7986 (tpp) REVERT: C 686 GLU cc_start: 0.7582 (tt0) cc_final: 0.7013 (tp30) REVERT: C 692 ASN cc_start: 0.6632 (t0) cc_final: 0.6319 (t0) REVERT: C 702 ASN cc_start: 0.8028 (m-40) cc_final: 0.7675 (m-40) REVERT: C 805 ARG cc_start: 0.8406 (OUTLIER) cc_final: 0.8044 (mtp85) REVERT: C 829 GLU cc_start: 0.7932 (mt-10) cc_final: 0.7230 (mm-30) REVERT: C 862 GLU cc_start: 0.6765 (tt0) cc_final: 0.6261 (pp20) REVERT: C 915 MET cc_start: 0.9090 (mtm) cc_final: 0.8710 (mtt) REVERT: C 935 MET cc_start: 0.8440 (OUTLIER) cc_final: 0.7910 (mmm) REVERT: C 1059 LEU cc_start: 0.7983 (mt) cc_final: 0.7653 (mm) REVERT: C 1081 MET cc_start: 0.7149 (mtm) cc_final: 0.6766 (mtm) REVERT: C 1107 ARG cc_start: 0.6077 (ttp-110) cc_final: 0.5860 (ttm110) REVERT: C 1119 LYS cc_start: 0.7423 (mtpt) cc_final: 0.7066 (ttpp) REVERT: C 1123 ARG cc_start: 0.7069 (ttp80) cc_final: 0.6617 (ttt-90) REVERT: C 1129 GLN cc_start: 0.6571 (mm110) cc_final: 0.5971 (mt0) REVERT: C 1130 GLU cc_start: 0.7392 (mt-10) cc_final: 0.6789 (mp0) REVERT: C 1348 ASP cc_start: 0.8387 (t0) cc_final: 0.8165 (t0) REVERT: C 1452 ARG cc_start: 0.8550 (OUTLIER) cc_final: 0.7944 (ttp80) REVERT: D 70 MET cc_start: 0.6724 (OUTLIER) cc_final: 0.5412 (pmm) REVERT: D 81 MET cc_start: 0.7981 (ptt) cc_final: 0.7635 (ptt) REVERT: D 196 MET cc_start: 0.8095 (mmm) cc_final: 0.7861 (mmp) REVERT: D 341 ARG cc_start: 0.8189 (OUTLIER) cc_final: 0.7918 (ptm160) REVERT: D 395 GLU cc_start: 0.7187 (mt-10) cc_final: 0.6564 (pt0) REVERT: D 577 ASP cc_start: 0.6326 (t70) cc_final: 0.6043 (t0) REVERT: D 614 ARG cc_start: 0.7621 (mtt180) cc_final: 0.6900 (mtm-85) REVERT: D 624 ASP cc_start: 0.6757 (p0) cc_final: 0.6467 (p0) REVERT: D 666 GLU cc_start: 0.7797 (tt0) cc_final: 0.7372 (tt0) REVERT: D 667 GLU cc_start: 0.7772 (mt-10) cc_final: 0.7467 (tt0) REVERT: D 683 MET cc_start: 0.8354 (tpt) cc_final: 0.7988 (tpp) REVERT: D 686 GLU cc_start: 0.7579 (tt0) cc_final: 0.7011 (tp30) REVERT: D 692 ASN cc_start: 0.6634 (t0) cc_final: 0.6350 (t0) REVERT: D 702 ASN cc_start: 0.8038 (m-40) cc_final: 0.7693 (m-40) REVERT: D 805 ARG cc_start: 0.8407 (OUTLIER) cc_final: 0.8050 (mtp85) REVERT: D 829 GLU cc_start: 0.7933 (mt-10) cc_final: 0.7229 (mm-30) REVERT: D 862 GLU cc_start: 0.6773 (tt0) cc_final: 0.6274 (pp20) REVERT: D 915 MET cc_start: 0.9098 (mtm) cc_final: 0.8720 (mtt) REVERT: D 935 MET cc_start: 0.8463 (OUTLIER) cc_final: 0.7935 (mmm) REVERT: D 1059 LEU cc_start: 0.7994 (mt) cc_final: 0.7665 (mm) REVERT: D 1081 MET cc_start: 0.7157 (mtm) cc_final: 0.6776 (mtm) REVERT: D 1107 ARG cc_start: 0.6088 (ttp-110) cc_final: 0.5874 (ttm110) REVERT: D 1119 LYS cc_start: 0.7474 (mtpt) cc_final: 0.7116 (ttpp) REVERT: D 1123 ARG cc_start: 0.7089 (ttp80) cc_final: 0.6634 (ttt-90) REVERT: D 1348 ASP cc_start: 0.8353 (t0) cc_final: 0.8137 (t0) REVERT: D 1452 ARG cc_start: 0.8523 (OUTLIER) cc_final: 0.7951 (ttp80) outliers start: 52 outliers final: 23 residues processed: 546 average time/residue: 0.6778 time to fit residues: 446.8793 Evaluate side-chains 567 residues out of total 4700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 524 time to evaluate : 1.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 MET Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 341 ARG Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 805 ARG Chi-restraints excluded: chain A residue 935 MET Chi-restraints excluded: chain A residue 1011 VAL Chi-restraints excluded: chain A residue 1150 MET Chi-restraints excluded: chain A residue 1164 LEU Chi-restraints excluded: chain A residue 1452 ARG Chi-restraints excluded: chain B residue 70 MET Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 346 THR Chi-restraints excluded: chain B residue 366 LEU Chi-restraints excluded: chain B residue 615 MET Chi-restraints excluded: chain B residue 805 ARG Chi-restraints excluded: chain B residue 935 MET Chi-restraints excluded: chain B residue 1011 VAL Chi-restraints excluded: chain B residue 1452 ARG Chi-restraints excluded: chain C residue 70 MET Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 341 ARG Chi-restraints excluded: chain C residue 346 THR Chi-restraints excluded: chain C residue 366 LEU Chi-restraints excluded: chain C residue 615 MET Chi-restraints excluded: chain C residue 805 ARG Chi-restraints excluded: chain C residue 935 MET Chi-restraints excluded: chain C residue 1011 VAL Chi-restraints excluded: chain C residue 1164 LEU Chi-restraints excluded: chain C residue 1452 ARG Chi-restraints excluded: chain D residue 70 MET Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 341 ARG Chi-restraints excluded: chain D residue 346 THR Chi-restraints excluded: chain D residue 366 LEU Chi-restraints excluded: chain D residue 615 MET Chi-restraints excluded: chain D residue 805 ARG Chi-restraints excluded: chain D residue 935 MET Chi-restraints excluded: chain D residue 1011 VAL Chi-restraints excluded: chain D residue 1444 ASP Chi-restraints excluded: chain D residue 1452 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 548 random chunks: chunk 49 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 520 optimal weight: 10.0000 chunk 250 optimal weight: 1.9990 chunk 140 optimal weight: 0.9990 chunk 269 optimal weight: 0.6980 chunk 260 optimal weight: 0.5980 chunk 484 optimal weight: 6.9990 chunk 57 optimal weight: 7.9990 chunk 515 optimal weight: 0.9980 chunk 526 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 514 HIS A 660 HIS A 682 HIS A 696 ASN B 514 HIS B 660 HIS B 682 HIS B 696 ASN C 514 HIS C 660 HIS C 682 HIS C 696 ASN D 514 HIS D 660 HIS D 682 HIS D 696 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.159021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.114718 restraints weight = 54179.332| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 1.98 r_work: 0.3187 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.4627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 43776 Z= 0.127 Angle : 0.548 11.550 59556 Z= 0.273 Chirality : 0.039 0.162 6768 Planarity : 0.004 0.050 7544 Dihedral : 7.707 95.838 7016 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.16 % Allowed : 15.81 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.35 (0.11), residues: 5476 helix: 2.13 (0.09), residues: 3044 sheet: -1.01 (0.21), residues: 460 loop : -0.58 (0.14), residues: 1972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 594 TYR 0.044 0.002 TYR A 420 PHE 0.016 0.001 PHE D 879 TRP 0.013 0.001 TRP D 726 HIS 0.008 0.001 HIS A 682 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 (43772) covalent geometry : angle 0.54773 / 0.27 (59548) SS BOND : bond 0.00010 / 0.01 ( 4) SS BOND : angle 0.35372 / 0.21 ( 8) hydrogen bonds : bond 0.04007 / 2.65 ( 2396) hydrogen bonds : angle 3.94415 / 2.86 ( 7032) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20490.05 seconds wall clock time: 348 minutes 8.84 seconds (20888.84 seconds total)