Starting phenix.real_space_refine on Thu Dec 26 06:03:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sre_40728/12_2024/8sre_40728.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sre_40728/12_2024/8sre_40728.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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8sre_40728/12_2024/8sre_40728.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sre_40728/12_2024/8sre_40728.map" model { file = "/net/cci-nas-00/data/ceres_data/8sre_40728/12_2024/8sre_40728.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sre_40728/12_2024/8sre_40728.cif" } resolution = 2.52 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.094 sd= 1.548 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 27440 2.51 5 N 7320 2.21 5 O 7740 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 42781 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 10531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1377, 10531 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: 398 Unresolved non-hydrogen angles: 496 Unresolved non-hydrogen dihedrals: 326 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 19, 'TYR:plan': 1, 'ASN:plan1': 6, 'HIS:plan': 7, 'PHE:plan': 4, 'GLU:plan': 16, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 261 Chain: "C" Number of atoms: 10531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1377, 10531 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: 398 Unresolved non-hydrogen angles: 496 Unresolved non-hydrogen dihedrals: 326 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 19, 'TYR:plan': 1, 'ASN:plan1': 6, 'HIS:plan': 7, 'PHE:plan': 4, 'GLU:plan': 16, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 261 Chain: "A" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 162 Unusual residues: {' MG': 6, 'APR': 2, 'CLR': 3} Classifications: {'undetermined': 11} Link IDs: {None: 10} Chain: "C" Number of atoms: 161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 161 Unusual residues: {' MG': 5, 'APR': 2, 'CLR': 3} Classifications: {'undetermined': 10} Link IDs: {None: 9} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Restraints were copied for chains: B, D Time building chain proxies: 60.32, per 1000 atoms: 1.41 Number of scatterers: 42781 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 7740 8.00 N 7320 7.00 C 27440 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 997 " - pdb=" SG CYS A1006 " 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: 10.77 Conformation dependent library (CDL) restraints added in 5.4 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: 228 helices and 36 sheets defined 59.5% alpha, 9.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.36 Creating SS restraints... Processing helix chain 'A' and resid 72 through 76 Processing helix chain 'A' and resid 118 through 135 removed outlier: 3.657A pdb=" N ALA A 122 " --> pdb=" O ASP A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 176 Processing helix chain 'A' and resid 186 through 203 removed outlier: 3.571A pdb=" N LYS A 190 " --> pdb=" O THR A 186 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LYS A 201 " --> pdb=" O GLU A 197 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N THR A 202 " --> pdb=" O ALA A 198 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLN A 203 " --> pdb=" O LEU A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 227 removed outlier: 3.803A pdb=" N ARG A 227 " --> pdb=" O ASP A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 287 Processing helix chain 'A' and resid 298 through 311 removed outlier: 3.504A 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 343 removed outlier: 3.537A pdb=" N PHE A 342 " --> pdb=" O LEU A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 359 removed outlier: 3.500A pdb=" N ASN A 359 " --> pdb=" O ALA A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 377 removed outlier: 3.716A 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: 3.590A pdb=" N ALA A 427 " --> pdb=" O GLN A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 457 removed outlier: 4.526A pdb=" N ASN A 448 " --> pdb=" O ALA A 444 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N ASP A 449 " --> pdb=" O ALA A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 469 removed outlier: 3.654A pdb=" N PHE A 469 " --> pdb=" O LEU A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 476 removed outlier: 4.081A pdb=" N LEU A 476 " --> pdb=" O ILE A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 492 Processing helix chain 'A' and resid 494 through 509 removed outlier: 3.583A pdb=" N LEU A 498 " --> pdb=" O PRO A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 523 removed outlier: 3.812A pdb=" N ARG A 517 " --> pdb=" O SER A 513 " (cutoff:3.500A) removed outlier: 4.199A 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: 3.774A pdb=" N SER A 569 " --> pdb=" O ALA A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 586 removed outlier: 3.944A pdb=" N ILE A 580 " --> pdb=" O ASP A 577 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N TYR A 581 " --> pdb=" O PHE A 578 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N SER A 583 " --> pdb=" O ILE A 580 " (cutoff:3.500A) removed outlier: 6.454A 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) removed outlier: 3.510A pdb=" N ASP A 586 " --> pdb=" O SER A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 590 through 611 removed outlier: 3.501A pdb=" N ARG A 594 " --> pdb=" O GLY A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 623 Processing helix chain 'A' and resid 625 through 642 Processing helix chain 'A' and resid 643 through 647 removed outlier: 3.810A 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 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: 3.559A pdb=" N VAL A 749 " --> pdb=" O PHE A 745 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU A 750 " --> pdb=" O PRO A 746 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 745 through 750' Processing helix chain 'A' and resid 788 through 800 removed outlier: 3.750A 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: 3.769A pdb=" N ASP A 866 " --> pdb=" O GLU A 862 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 889 removed outlier: 3.615A pdb=" N ARG A 870 " --> pdb=" O ASP A 866 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ASP A 889 " --> pdb=" O THR A 885 " (cutoff:3.500A) Processing helix chain 'A' and resid 892 through 915 removed outlier: 4.012A pdb=" N PHE A 905 " --> pdb=" O GLY A 901 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N MET A 915 " --> pdb=" O TRP A 911 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 921 removed outlier: 4.105A pdb=" N LEU A 920 " --> pdb=" O TYR A 917 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 961 removed outlier: 3.852A pdb=" N LYS A 927 " --> pdb=" O ASN A 923 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N LYS A 936 " --> pdb=" O MET A 932 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ASP A 937 " --> pdb=" O GLU A 933 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ILE A 947 " --> pdb=" O PHE A 943 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N PHE A 948 " --> pdb=" O LEU A 944 " (cutoff:3.500A) Processing helix chain 'A' and resid 967 through 981 removed outlier: 3.659A pdb=" N PHE A 971 " --> pdb=" O SER A 967 " (cutoff:3.500A) removed outlier: 4.528A 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 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: 5.347A pdb=" N ALA A1047 " --> pdb=" O LYS A1043 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N TYR A1057 " --> pdb=" O ARG A1053 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ASP A1065 " --> pdb=" O ALA A1061 " (cutoff:3.500A) Processing helix chain 'A' and resid 1073 through 1090 removed outlier: 4.171A 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 1170 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 removed outlier: 3.780A pdb=" N GLY A1384 " --> pdb=" O ALA A1380 " (cutoff:3.500A) Processing helix chain 'A' and resid 1402 through 1414 Processing helix chain 'A' and resid 1478 through 1491 Processing helix chain 'D' and resid 72 through 76 Processing helix chain 'D' and resid 118 through 135 removed outlier: 3.657A pdb=" N ALA D 122 " --> pdb=" O ASP D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 176 Processing helix chain 'D' and resid 186 through 203 removed outlier: 3.571A pdb=" N LYS D 190 " --> pdb=" O THR D 186 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LYS D 201 " --> pdb=" O GLU D 197 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N THR D 202 " --> pdb=" O ALA D 198 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLN D 203 " --> pdb=" O LEU D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 227 removed outlier: 3.803A pdb=" N ARG D 227 " --> pdb=" O ASP D 223 " (cutoff:3.500A) Processing helix chain 'D' and resid 271 through 287 Processing helix chain 'D' and resid 298 through 311 removed outlier: 3.504A 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 343 removed outlier: 3.537A pdb=" N PHE D 342 " --> pdb=" O LEU D 339 " (cutoff:3.500A) Processing helix chain 'D' and resid 346 through 359 removed outlier: 3.500A pdb=" N ASN D 359 " --> pdb=" O ALA D 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 362 through 377 removed outlier: 3.716A 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: 3.590A pdb=" N ALA D 427 " --> pdb=" O GLN D 423 " (cutoff:3.500A) Processing helix chain 'D' and resid 439 through 457 removed outlier: 4.526A pdb=" N ASN D 448 " --> pdb=" O ALA D 444 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N ASP D 449 " --> pdb=" O ALA D 445 " (cutoff:3.500A) Processing helix chain 'D' and resid 459 through 469 removed outlier: 3.654A pdb=" N PHE D 469 " --> pdb=" O LEU D 465 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 476 removed outlier: 4.081A pdb=" N LEU D 476 " --> pdb=" O ILE D 473 " (cutoff:3.500A) Processing helix chain 'D' and resid 487 through 492 Processing helix chain 'D' and resid 494 through 509 removed outlier: 3.583A pdb=" N LEU D 498 " --> pdb=" O PRO D 494 " (cutoff:3.500A) Processing helix chain 'D' and resid 513 through 523 removed outlier: 3.812A pdb=" N ARG D 517 " --> pdb=" O SER D 513 " (cutoff:3.500A) removed outlier: 4.199A 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: 3.773A pdb=" N SER D 569 " --> pdb=" O ALA D 565 " (cutoff:3.500A) Processing helix chain 'D' and resid 577 through 586 removed outlier: 3.944A pdb=" N ILE D 580 " --> pdb=" O ASP D 577 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N TYR D 581 " --> pdb=" O PHE D 578 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N SER D 583 " --> pdb=" O ILE D 580 " (cutoff:3.500A) removed outlier: 6.454A 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) removed outlier: 3.510A pdb=" N ASP D 586 " --> pdb=" O SER D 583 " (cutoff:3.500A) Processing helix chain 'D' and resid 590 through 611 removed outlier: 3.501A pdb=" N ARG D 594 " --> pdb=" O GLY D 590 " (cutoff:3.500A) Processing helix chain 'D' and resid 612 through 623 Processing helix chain 'D' and resid 625 through 642 Processing helix chain 'D' and resid 643 through 647 removed outlier: 3.810A 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 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: 3.559A pdb=" N VAL D 749 " --> pdb=" O PHE D 745 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU D 750 " --> pdb=" O PRO D 746 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 745 through 750' Processing helix chain 'D' and resid 788 through 800 removed outlier: 3.750A 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: 3.769A pdb=" N ASP D 866 " --> pdb=" O GLU D 862 " (cutoff:3.500A) Processing helix chain 'D' and resid 866 through 889 removed outlier: 3.615A pdb=" N ARG D 870 " --> pdb=" O ASP D 866 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ASP D 889 " --> pdb=" O THR D 885 " (cutoff:3.500A) Processing helix chain 'D' and resid 892 through 915 removed outlier: 4.011A pdb=" N PHE D 905 " --> pdb=" O GLY D 901 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N MET D 915 " --> pdb=" O TRP D 911 " (cutoff:3.500A) Processing helix chain 'D' and resid 916 through 921 removed outlier: 4.105A pdb=" N LEU D 920 " --> pdb=" O TYR D 917 " (cutoff:3.500A) Processing helix chain 'D' and resid 923 through 961 removed outlier: 3.852A pdb=" N LYS D 927 " --> pdb=" O ASN D 923 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N LYS D 936 " --> pdb=" O MET D 932 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N ASP D 937 " --> pdb=" O GLU D 933 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ILE D 947 " --> pdb=" O PHE D 943 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N PHE D 948 " --> pdb=" O LEU D 944 " (cutoff:3.500A) Processing helix chain 'D' and resid 967 through 981 removed outlier: 3.659A pdb=" N PHE D 971 " --> pdb=" O SER D 967 " (cutoff:3.500A) removed outlier: 4.529A 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 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: 5.347A pdb=" N ALA D1047 " --> pdb=" O LYS D1043 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N TYR D1057 " --> pdb=" O ARG D1053 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ASP D1065 " --> pdb=" O ALA D1061 " (cutoff:3.500A) Processing helix chain 'D' and resid 1073 through 1090 removed outlier: 4.171A 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 1170 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 removed outlier: 3.780A pdb=" N GLY D1384 " --> pdb=" O ALA D1380 " (cutoff:3.500A) Processing helix chain 'D' and resid 1402 through 1414 Processing helix chain 'D' and resid 1478 through 1491 Processing helix chain 'B' and resid 72 through 76 Processing helix chain 'B' and resid 118 through 135 removed outlier: 3.657A pdb=" N ALA B 122 " --> pdb=" O ASP B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 176 Processing helix chain 'B' and resid 186 through 203 removed outlier: 3.571A pdb=" N LYS B 190 " --> pdb=" O THR B 186 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LYS B 201 " --> pdb=" O GLU B 197 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N THR B 202 " --> pdb=" O ALA B 198 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLN B 203 " --> pdb=" O LEU B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 227 removed outlier: 3.803A pdb=" N ARG B 227 " --> pdb=" O ASP B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 287 Processing helix chain 'B' and resid 298 through 311 removed outlier: 3.504A 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 343 removed outlier: 3.537A pdb=" N PHE B 342 " --> pdb=" O LEU B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 359 removed outlier: 3.500A pdb=" N ASN B 359 " --> pdb=" O ALA B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 377 removed outlier: 3.716A 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: 3.591A pdb=" N ALA B 427 " --> pdb=" O GLN B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 457 removed outlier: 4.526A pdb=" N ASN B 448 " --> pdb=" O ALA B 444 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N ASP B 449 " --> pdb=" O ALA B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 469 removed outlier: 3.654A pdb=" N PHE B 469 " --> pdb=" O LEU B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 476 removed outlier: 4.081A pdb=" N LEU B 476 " --> pdb=" O ILE B 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 492 Processing helix chain 'B' and resid 494 through 509 removed outlier: 3.583A pdb=" N LEU B 498 " --> pdb=" O PRO B 494 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 523 removed outlier: 3.812A pdb=" N ARG B 517 " --> pdb=" O SER B 513 " (cutoff:3.500A) removed outlier: 4.199A 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: 3.774A pdb=" N SER B 569 " --> pdb=" O ALA B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 577 through 586 removed outlier: 3.944A pdb=" N ILE B 580 " --> pdb=" O ASP B 577 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N TYR B 581 " --> pdb=" O PHE B 578 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N SER B 583 " --> pdb=" O ILE B 580 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N LYS B 584 " --> pdb=" O TYR B 581 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N TYR B 585 " --> pdb=" O ASP B 582 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASP B 586 " --> pdb=" O SER B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 590 through 611 removed outlier: 3.501A pdb=" N ARG B 594 " --> pdb=" O GLY B 590 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 623 Processing helix chain 'B' and resid 625 through 642 Processing helix chain 'B' and resid 643 through 647 removed outlier: 3.810A 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 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: 3.559A pdb=" N VAL B 749 " --> pdb=" O PHE B 745 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU B 750 " --> pdb=" O PRO B 746 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 745 through 750' Processing helix chain 'B' and resid 788 through 800 removed outlier: 3.750A 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: 3.769A pdb=" N ASP B 866 " --> pdb=" O GLU B 862 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 889 removed outlier: 3.615A pdb=" N ARG B 870 " --> pdb=" O ASP B 866 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ASP B 889 " --> pdb=" O THR B 885 " (cutoff:3.500A) Processing helix chain 'B' and resid 892 through 915 removed outlier: 4.012A pdb=" N PHE B 905 " --> pdb=" O GLY B 901 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N MET B 915 " --> pdb=" O TRP B 911 " (cutoff:3.500A) Processing helix chain 'B' and resid 916 through 921 removed outlier: 4.105A pdb=" N LEU B 920 " --> pdb=" O TYR B 917 " (cutoff:3.500A) Processing helix chain 'B' and resid 923 through 961 removed outlier: 3.852A pdb=" N LYS B 927 " --> pdb=" O ASN B 923 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N LYS B 936 " --> pdb=" O MET B 932 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N ASP B 937 " --> pdb=" O GLU B 933 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ILE B 947 " --> pdb=" O PHE B 943 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N PHE B 948 " --> pdb=" O LEU B 944 " (cutoff:3.500A) Processing helix chain 'B' and resid 967 through 981 removed outlier: 3.658A pdb=" N PHE B 971 " --> pdb=" O SER B 967 " (cutoff:3.500A) removed outlier: 4.528A 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 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: 5.347A pdb=" N ALA B1047 " --> pdb=" O LYS B1043 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N TYR B1057 " --> pdb=" O ARG B1053 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ASP B1065 " --> pdb=" O ALA B1061 " (cutoff:3.500A) Processing helix chain 'B' and resid 1073 through 1090 removed outlier: 4.171A 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 1170 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 removed outlier: 3.780A pdb=" N GLY B1384 " --> pdb=" O ALA B1380 " (cutoff:3.500A) Processing helix chain 'B' and resid 1402 through 1414 Processing helix chain 'B' and resid 1478 through 1491 Processing helix chain 'C' and resid 72 through 76 Processing helix chain 'C' and resid 118 through 135 removed outlier: 3.657A pdb=" N ALA C 122 " --> pdb=" O ASP C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 176 Processing helix chain 'C' and resid 186 through 203 removed outlier: 3.571A pdb=" N LYS C 190 " --> pdb=" O THR C 186 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LYS C 201 " --> pdb=" O GLU C 197 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N THR C 202 " --> pdb=" O ALA C 198 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLN C 203 " --> pdb=" O LEU C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 227 removed outlier: 3.802A pdb=" N ARG C 227 " --> pdb=" O ASP C 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 287 Processing helix chain 'C' and resid 298 through 311 removed outlier: 3.504A 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 343 removed outlier: 3.537A pdb=" N PHE C 342 " --> pdb=" O LEU C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 359 removed outlier: 3.500A pdb=" N ASN C 359 " --> pdb=" O ALA C 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 377 removed outlier: 3.717A 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: 3.590A pdb=" N ALA C 427 " --> pdb=" O GLN C 423 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 457 removed outlier: 4.526A pdb=" N ASN C 448 " --> pdb=" O ALA C 444 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N ASP C 449 " --> pdb=" O ALA C 445 " (cutoff:3.500A) Processing helix chain 'C' and resid 459 through 469 removed outlier: 3.654A pdb=" N PHE C 469 " --> pdb=" O LEU C 465 " (cutoff:3.500A) Processing helix chain 'C' and resid 472 through 476 removed outlier: 4.080A pdb=" N LEU C 476 " --> pdb=" O ILE C 473 " (cutoff:3.500A) Processing helix chain 'C' and resid 487 through 492 Processing helix chain 'C' and resid 494 through 509 removed outlier: 3.583A pdb=" N LEU C 498 " --> pdb=" O PRO C 494 " (cutoff:3.500A) Processing helix chain 'C' and resid 513 through 523 removed outlier: 3.811A pdb=" N ARG C 517 " --> pdb=" O SER C 513 " (cutoff:3.500A) removed outlier: 4.199A 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: 3.774A pdb=" N SER C 569 " --> pdb=" O ALA C 565 " (cutoff:3.500A) Processing helix chain 'C' and resid 577 through 586 removed outlier: 3.944A pdb=" N ILE C 580 " --> pdb=" O ASP C 577 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N TYR C 581 " --> pdb=" O PHE C 578 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N SER C 583 " --> pdb=" O ILE C 580 " (cutoff:3.500A) removed outlier: 6.454A 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) removed outlier: 3.510A pdb=" N ASP C 586 " --> pdb=" O SER C 583 " (cutoff:3.500A) Processing helix chain 'C' and resid 590 through 611 removed outlier: 3.501A pdb=" N ARG C 594 " --> pdb=" O GLY C 590 " (cutoff:3.500A) Processing helix chain 'C' and resid 612 through 623 Processing helix chain 'C' and resid 625 through 642 Processing helix chain 'C' and resid 643 through 647 removed outlier: 3.811A 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 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: 3.560A pdb=" N VAL C 749 " --> pdb=" O PHE C 745 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU C 750 " --> pdb=" O PRO C 746 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 745 through 750' Processing helix chain 'C' and resid 788 through 800 removed outlier: 3.750A 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: 3.769A pdb=" N ASP C 866 " --> pdb=" O GLU C 862 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 889 removed outlier: 3.614A pdb=" N ARG C 870 " --> pdb=" O ASP C 866 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ASP C 889 " --> pdb=" O THR C 885 " (cutoff:3.500A) Processing helix chain 'C' and resid 892 through 915 removed outlier: 4.012A pdb=" N PHE C 905 " --> pdb=" O GLY C 901 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N MET C 915 " --> pdb=" O TRP C 911 " (cutoff:3.500A) Processing helix chain 'C' and resid 916 through 921 removed outlier: 4.105A pdb=" N LEU C 920 " --> pdb=" O TYR C 917 " (cutoff:3.500A) Processing helix chain 'C' and resid 923 through 961 removed outlier: 3.852A pdb=" N LYS C 927 " --> pdb=" O ASN C 923 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N LYS C 936 " --> pdb=" O MET C 932 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ASP C 937 " --> pdb=" O GLU C 933 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ILE C 947 " --> pdb=" O PHE C 943 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N PHE C 948 " --> pdb=" O LEU C 944 " (cutoff:3.500A) Processing helix chain 'C' and resid 967 through 981 removed outlier: 3.659A pdb=" N PHE C 971 " --> pdb=" O SER C 967 " (cutoff:3.500A) removed outlier: 4.528A 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 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: 5.347A pdb=" N ALA C1047 " --> pdb=" O LYS C1043 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N TYR C1057 " --> pdb=" O ARG C1053 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ASP C1065 " --> pdb=" O ALA C1061 " (cutoff:3.500A) Processing helix chain 'C' and resid 1073 through 1090 removed outlier: 4.172A 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 1170 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 removed outlier: 3.780A pdb=" N GLY C1384 " --> pdb=" O ALA C1380 " (cutoff:3.500A) Processing helix chain 'C' and resid 1402 through 1414 Processing helix chain 'C' 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: 7.797A pdb=" N TRP A 96 " --> pdb=" O PRO A 231 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N ILE A 233 " --> pdb=" O TRP A 96 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N THR A 98 " --> pdb=" O ILE A 233 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N LEU A 259 " --> pdb=" O PRO A 109 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N LEU A 111 " --> pdb=" O LEU A 259 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N ASP A 261 " --> pdb=" O LEU A 111 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N LEU A 113 " --> pdb=" O ASP A 261 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N VAL A 179 " --> pdb=" O ILE A 211 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N ILE A 213 " --> pdb=" O VAL A 179 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N THR A 181 " --> pdb=" O ILE A 213 " (cutoff:3.500A) removed outlier: 8.516A pdb=" N THR A 215 " --> pdb=" O THR A 181 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ILE A 144 " --> pdb=" O VAL A 291 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N ILE A 293 " --> pdb=" O ILE A 144 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N SER A 146 " --> pdb=" O ILE A 293 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N VAL A 295 " --> pdb=" O SER A 146 " (cutoff:3.500A) removed outlier: 6.424A 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: 5.988A pdb=" N VAL A1251 " --> pdb=" O THR A1315 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N ARG A1317 " --> pdb=" O VAL A1251 " (cutoff:3.500A) removed outlier: 7.929A 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: 4.123A 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: 5.320A pdb=" N VAL A1333 " --> pdb=" O VAL A1356 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N ILE A1358 " --> pdb=" O THR A1331 " (cutoff:3.500A) removed outlier: 11.235A pdb=" N THR A1331 " --> pdb=" O ILE A1358 " (cutoff:3.500A) removed outlier: 13.713A pdb=" N ARG A1360 " --> pdb=" O ALA A1329 " (cutoff:3.500A) removed outlier: 17.460A pdb=" N ALA A1329 " --> pdb=" O ARG A1360 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N GLY A1324 " --> pdb=" O TRP A1434 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N GLU A1436 " --> pdb=" O GLY A1324 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N ASN A1326 " --> pdb=" O GLU A1436 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N THR A1438 " --> pdb=" O ASN A1326 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ALA A1328 " --> pdb=" O THR A1438 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N VAL A1440 " --> pdb=" O ALA A1328 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N ASP A1330 " --> pdb=" O VAL A1440 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N PHE A1442 " --> pdb=" O ASP A1330 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N VAL A1332 " --> pdb=" O PHE A1442 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N ASP A1444 " --> pdb=" O VAL A1332 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N THR A1334 " --> pdb=" O ASP A1444 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ALA A1420 " --> pdb=" O CYS A1439 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ASN A1441 " --> pdb=" O ILE A1418 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N ILE A1418 " --> pdb=" O ASN A1441 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N HIS A1443 " --> pdb=" O GLY A1416 " (cutoff:3.500A) removed outlier: 7.185A 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: 17.460A pdb=" N ALA A1329 " --> pdb=" O ARG A1360 " (cutoff:3.500A) removed outlier: 13.713A pdb=" N ARG A1360 " --> pdb=" O ALA A1329 " (cutoff:3.500A) removed outlier: 11.235A pdb=" N THR A1331 " --> pdb=" O ILE A1358 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N ILE A1358 " --> pdb=" O THR A1331 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N VAL A1333 " --> pdb=" O VAL A1356 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N LEU A1353 " --> pdb=" O MET A1468 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N MET A1468 " --> pdb=" O LEU A1353 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N PHE A1355 " --> pdb=" O TRP A1466 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N TRP A1466 " --> pdb=" O PHE A1355 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ALA A1357 " --> pdb=" O ALA A1464 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ALA A1464 " --> pdb=" O ALA A1357 " (cutoff:3.500A) removed outlier: 6.580A 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 'D' and resid 56 through 60 Processing sheet with id=AB2, first strand: chain 'D' and resid 80 through 81 Processing sheet with id=AB3, first strand: chain 'D' and resid 231 through 236 removed outlier: 7.796A pdb=" N TRP D 96 " --> pdb=" O PRO D 231 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N ILE D 233 " --> pdb=" O TRP D 96 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N THR D 98 " --> pdb=" O ILE D 233 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N LEU D 259 " --> pdb=" O PRO D 109 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N LEU D 111 " --> pdb=" O LEU D 259 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N ASP D 261 " --> pdb=" O LEU D 111 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N LEU D 113 " --> pdb=" O ASP D 261 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N VAL D 179 " --> pdb=" O ILE D 211 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N ILE D 213 " --> pdb=" O VAL D 179 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N THR D 181 " --> pdb=" O ILE D 213 " (cutoff:3.500A) removed outlier: 8.516A pdb=" N THR D 215 " --> pdb=" O THR D 181 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ILE D 144 " --> pdb=" O VAL D 291 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N ILE D 293 " --> pdb=" O ILE D 144 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N SER D 146 " --> pdb=" O ILE D 293 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N VAL D 295 " --> pdb=" O SER D 146 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N THR D 148 " --> pdb=" O VAL D 295 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 1251 through 1254 removed outlier: 5.988A pdb=" N VAL D1251 " --> pdb=" O THR D1315 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N ARG D1317 " --> pdb=" O VAL D1251 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N TYR D1253 " --> pdb=" O ARG D1317 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'D' and resid 1279 through 1281 Processing sheet with id=AB6, first strand: chain 'D' and resid 1297 through 1298 removed outlier: 4.122A pdb=" N SER D1297 " --> pdb=" O ILE D1306 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 1366 through 1367 removed outlier: 5.320A pdb=" N VAL D1333 " --> pdb=" O VAL D1356 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N ILE D1358 " --> pdb=" O THR D1331 " (cutoff:3.500A) removed outlier: 11.234A pdb=" N THR D1331 " --> pdb=" O ILE D1358 " (cutoff:3.500A) removed outlier: 13.713A pdb=" N ARG D1360 " --> pdb=" O ALA D1329 " (cutoff:3.500A) removed outlier: 17.459A pdb=" N ALA D1329 " --> pdb=" O ARG D1360 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N GLY D1324 " --> pdb=" O TRP D1434 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N GLU D1436 " --> pdb=" O GLY D1324 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N ASN D1326 " --> pdb=" O GLU D1436 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N THR D1438 " --> pdb=" O ASN D1326 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ALA D1328 " --> pdb=" O THR D1438 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N VAL D1440 " --> pdb=" O ALA D1328 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N ASP D1330 " --> pdb=" O VAL D1440 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N PHE D1442 " --> pdb=" O ASP D1330 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N VAL D1332 " --> pdb=" O PHE D1442 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N ASP D1444 " --> pdb=" O VAL D1332 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N THR D1334 " --> pdb=" O ASP D1444 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ALA D1420 " --> pdb=" O CYS D1439 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ASN D1441 " --> pdb=" O ILE D1418 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N ILE D1418 " --> pdb=" O ASN D1441 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N HIS D1443 " --> pdb=" O GLY D1416 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N GLY D1416 " --> pdb=" O HIS D1443 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 1370 through 1372 removed outlier: 17.459A pdb=" N ALA D1329 " --> pdb=" O ARG D1360 " (cutoff:3.500A) removed outlier: 13.713A pdb=" N ARG D1360 " --> pdb=" O ALA D1329 " (cutoff:3.500A) removed outlier: 11.234A pdb=" N THR D1331 " --> pdb=" O ILE D1358 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N ILE D1358 " --> pdb=" O THR D1331 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N VAL D1333 " --> pdb=" O VAL D1356 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N LEU D1353 " --> pdb=" O MET D1468 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N MET D1468 " --> pdb=" O LEU D1353 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N PHE D1355 " --> pdb=" O TRP D1466 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N TRP D1466 " --> pdb=" O PHE D1355 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ALA D1357 " --> pdb=" O ALA D1464 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N ALA D1464 " --> pdb=" O ALA D1357 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N GLN D1359 " --> pdb=" O GLU D1462 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 1346 through 1347 Processing sheet with id=AC1, first strand: chain 'B' and resid 56 through 60 Processing sheet with id=AC2, first strand: chain 'B' and resid 80 through 81 Processing sheet with id=AC3, first strand: chain 'B' and resid 231 through 236 removed outlier: 7.797A pdb=" N TRP B 96 " --> pdb=" O PRO B 231 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N ILE B 233 " --> pdb=" O TRP B 96 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N THR B 98 " --> pdb=" O ILE B 233 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N LEU B 259 " --> pdb=" O PRO B 109 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N LEU B 111 " --> pdb=" O LEU B 259 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N ASP B 261 " --> pdb=" O LEU B 111 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N LEU B 113 " --> pdb=" O ASP B 261 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N VAL B 179 " --> pdb=" O ILE B 211 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N ILE B 213 " --> pdb=" O VAL B 179 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N THR B 181 " --> pdb=" O ILE B 213 " (cutoff:3.500A) removed outlier: 8.516A pdb=" N THR B 215 " --> pdb=" O THR B 181 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ILE B 144 " --> pdb=" O VAL B 291 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N ILE B 293 " --> pdb=" O ILE B 144 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N SER B 146 " --> pdb=" O ILE B 293 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N VAL B 295 " --> pdb=" O SER B 146 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N THR B 148 " --> pdb=" O VAL B 295 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 1251 through 1254 removed outlier: 5.989A pdb=" N VAL B1251 " --> pdb=" O THR B1315 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N ARG B1317 " --> pdb=" O VAL B1251 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N TYR B1253 " --> pdb=" O ARG B1317 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'B' and resid 1279 through 1281 Processing sheet with id=AC6, first strand: chain 'B' and resid 1297 through 1298 removed outlier: 4.123A pdb=" N SER B1297 " --> pdb=" O ILE B1306 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 1366 through 1367 removed outlier: 5.320A pdb=" N VAL B1333 " --> pdb=" O VAL B1356 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N ILE B1358 " --> pdb=" O THR B1331 " (cutoff:3.500A) removed outlier: 11.234A pdb=" N THR B1331 " --> pdb=" O ILE B1358 " (cutoff:3.500A) removed outlier: 13.713A pdb=" N ARG B1360 " --> pdb=" O ALA B1329 " (cutoff:3.500A) removed outlier: 17.460A pdb=" N ALA B1329 " --> pdb=" O ARG B1360 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N GLY B1324 " --> pdb=" O TRP B1434 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N GLU B1436 " --> pdb=" O GLY B1324 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N ASN B1326 " --> pdb=" O GLU B1436 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N THR B1438 " --> pdb=" O ASN B1326 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ALA B1328 " --> pdb=" O THR B1438 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N VAL B1440 " --> pdb=" O ALA B1328 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N ASP B1330 " --> pdb=" O VAL B1440 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N PHE B1442 " --> pdb=" O ASP B1330 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N VAL B1332 " --> pdb=" O PHE B1442 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N ASP B1444 " --> pdb=" O VAL B1332 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N THR B1334 " --> pdb=" O ASP B1444 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ALA B1420 " --> pdb=" O CYS B1439 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ASN B1441 " --> pdb=" O ILE B1418 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N ILE B1418 " --> pdb=" O ASN B1441 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N HIS B1443 " --> pdb=" O GLY B1416 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N GLY B1416 " --> pdb=" O HIS B1443 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 1370 through 1372 removed outlier: 17.460A pdb=" N ALA B1329 " --> pdb=" O ARG B1360 " (cutoff:3.500A) removed outlier: 13.713A pdb=" N ARG B1360 " --> pdb=" O ALA B1329 " (cutoff:3.500A) removed outlier: 11.234A pdb=" N THR B1331 " --> pdb=" O ILE B1358 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N ILE B1358 " --> pdb=" O THR B1331 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N VAL B1333 " --> pdb=" O VAL B1356 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N LEU B1353 " --> pdb=" O MET B1468 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N MET B1468 " --> pdb=" O LEU B1353 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N PHE B1355 " --> pdb=" O TRP B1466 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N TRP B1466 " --> pdb=" O PHE B1355 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ALA B1357 " --> pdb=" O ALA B1464 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ALA B1464 " --> pdb=" O ALA B1357 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N GLN B1359 " --> pdb=" O GLU B1462 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 1346 through 1347 Processing sheet with id=AD1, first strand: chain 'C' and resid 56 through 60 Processing sheet with id=AD2, first strand: chain 'C' and resid 80 through 81 Processing sheet with id=AD3, first strand: chain 'C' and resid 231 through 236 removed outlier: 7.797A pdb=" N TRP C 96 " --> pdb=" O PRO C 231 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N ILE C 233 " --> pdb=" O TRP C 96 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N THR C 98 " --> pdb=" O ILE C 233 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N LEU C 259 " --> pdb=" O PRO C 109 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N LEU C 111 " --> pdb=" O LEU C 259 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N ASP C 261 " --> pdb=" O LEU C 111 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N LEU C 113 " --> pdb=" O ASP C 261 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N VAL C 179 " --> pdb=" O ILE C 211 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N ILE C 213 " --> pdb=" O VAL C 179 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N THR C 181 " --> pdb=" O ILE C 213 " (cutoff:3.500A) removed outlier: 8.516A pdb=" N THR C 215 " --> pdb=" O THR C 181 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ILE C 144 " --> pdb=" O VAL C 291 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N ILE C 293 " --> pdb=" O ILE C 144 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N SER C 146 " --> pdb=" O ILE C 293 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N VAL C 295 " --> pdb=" O SER C 146 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N THR C 148 " --> pdb=" O VAL C 295 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 1251 through 1254 removed outlier: 5.988A pdb=" N VAL C1251 " --> pdb=" O THR C1315 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N ARG C1317 " --> pdb=" O VAL C1251 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N TYR C1253 " --> pdb=" O ARG C1317 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'C' and resid 1279 through 1281 Processing sheet with id=AD6, first strand: chain 'C' and resid 1297 through 1298 removed outlier: 4.123A pdb=" N SER C1297 " --> pdb=" O ILE C1306 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 1366 through 1367 removed outlier: 5.321A pdb=" N VAL C1333 " --> pdb=" O VAL C1356 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N ILE C1358 " --> pdb=" O THR C1331 " (cutoff:3.500A) removed outlier: 11.236A pdb=" N THR C1331 " --> pdb=" O ILE C1358 " (cutoff:3.500A) removed outlier: 13.713A pdb=" N ARG C1360 " --> pdb=" O ALA C1329 " (cutoff:3.500A) removed outlier: 17.460A pdb=" N ALA C1329 " --> pdb=" O ARG C1360 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N GLY C1324 " --> pdb=" O TRP C1434 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N GLU C1436 " --> pdb=" O GLY C1324 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N ASN C1326 " --> pdb=" O GLU C1436 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N THR C1438 " --> pdb=" O ASN C1326 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ALA C1328 " --> pdb=" O THR C1438 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N VAL C1440 " --> pdb=" O ALA C1328 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N ASP C1330 " --> pdb=" O VAL C1440 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N PHE C1442 " --> pdb=" O ASP C1330 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N VAL C1332 " --> pdb=" O PHE C1442 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N ASP C1444 " --> pdb=" O VAL C1332 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N THR C1334 " --> pdb=" O ASP C1444 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ALA C1420 " --> pdb=" O CYS C1439 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ASN C1441 " --> pdb=" O ILE C1418 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N ILE C1418 " --> pdb=" O ASN C1441 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N HIS C1443 " --> pdb=" O GLY C1416 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N GLY C1416 " --> pdb=" O HIS C1443 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 1370 through 1372 removed outlier: 17.460A pdb=" N ALA C1329 " --> pdb=" O ARG C1360 " (cutoff:3.500A) removed outlier: 13.713A pdb=" N ARG C1360 " --> pdb=" O ALA C1329 " (cutoff:3.500A) removed outlier: 11.236A pdb=" N THR C1331 " --> pdb=" O ILE C1358 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N ILE C1358 " --> pdb=" O THR C1331 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N VAL C1333 " --> pdb=" O VAL C1356 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N LEU C1353 " --> pdb=" O MET C1468 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N MET C1468 " --> pdb=" O LEU C1353 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N PHE C1355 " --> pdb=" O TRP C1466 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N TRP C1466 " --> pdb=" O PHE C1355 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ALA C1357 " --> pdb=" O ALA C1464 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ALA C1464 " --> pdb=" O ALA C1357 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N GLN C1359 " --> pdb=" O GLU C1462 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 1346 through 1347 2376 hydrogen bonds defined for protein. 6960 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: 21.46 Time building geometry restraints manager: 12.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8984 1.33 - 1.45: 10220 1.45 - 1.57: 24064 1.57 - 1.70: 56 1.70 - 1.82: 436 Bond restraints: 43760 Sorted by residual: bond pdb=" C CYS B1245 " pdb=" N PRO B1246 " ideal model delta sigma weight residual 1.336 1.400 -0.064 1.25e-02 6.40e+03 2.64e+01 bond pdb=" C CYS D1245 " pdb=" N PRO D1246 " ideal model delta sigma weight residual 1.336 1.400 -0.064 1.25e-02 6.40e+03 2.62e+01 bond pdb=" C CYS C1245 " pdb=" N PRO C1246 " ideal model delta sigma weight residual 1.336 1.400 -0.064 1.25e-02 6.40e+03 2.62e+01 bond pdb=" C CYS A1245 " pdb=" N PRO A1246 " ideal model delta sigma weight residual 1.336 1.400 -0.064 1.25e-02 6.40e+03 2.62e+01 bond pdb=" C VAL D1014 " pdb=" N PRO D1015 " ideal model delta sigma weight residual 1.335 1.396 -0.061 1.36e-02 5.41e+03 1.99e+01 ... (remaining 43755 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.65: 52767 2.65 - 5.31: 5619 5.31 - 7.96: 943 7.96 - 10.62: 191 10.62 - 13.27: 20 Bond angle restraints: 59540 Sorted by residual: angle pdb=" N VAL B 844 " pdb=" CA VAL B 844 " pdb=" C VAL B 844 " ideal model delta sigma weight residual 110.53 104.26 6.27 9.40e-01 1.13e+00 4.44e+01 angle pdb=" N VAL D 844 " pdb=" CA VAL D 844 " pdb=" C VAL D 844 " ideal model delta sigma weight residual 110.53 104.27 6.26 9.40e-01 1.13e+00 4.43e+01 angle pdb=" N VAL C 844 " pdb=" CA VAL C 844 " pdb=" C VAL C 844 " ideal model delta sigma weight residual 110.53 104.27 6.26 9.40e-01 1.13e+00 4.43e+01 angle pdb=" N VAL A 844 " pdb=" CA VAL A 844 " pdb=" C VAL A 844 " ideal model delta sigma weight residual 110.53 104.27 6.26 9.40e-01 1.13e+00 4.43e+01 angle pdb=" C PHE B 154 " pdb=" CA PHE B 154 " pdb=" CB PHE B 154 " ideal model delta sigma weight residual 110.16 119.34 -9.18 1.44e+00 4.82e-01 4.06e+01 ... (remaining 59535 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 24374 17.73 - 35.46: 2043 35.46 - 53.19: 313 53.19 - 70.93: 36 70.93 - 88.66: 48 Dihedral angle restraints: 26814 sinusoidal: 10802 harmonic: 16012 Sorted by residual: dihedral pdb=" C ILE C 443 " pdb=" N ILE C 443 " pdb=" CA ILE C 443 " pdb=" CB ILE C 443 " ideal model delta harmonic sigma weight residual -122.00 -133.17 11.17 0 2.50e+00 1.60e-01 2.00e+01 dihedral pdb=" C ILE A 443 " pdb=" N ILE A 443 " pdb=" CA ILE A 443 " pdb=" CB ILE A 443 " ideal model delta harmonic sigma weight residual -122.00 -133.13 11.13 0 2.50e+00 1.60e-01 1.98e+01 dihedral pdb=" C ILE D 443 " pdb=" N ILE D 443 " pdb=" CA ILE D 443 " pdb=" CB ILE D 443 " ideal model delta harmonic sigma weight residual -122.00 -133.13 11.13 0 2.50e+00 1.60e-01 1.98e+01 ... (remaining 26811 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.102: 5353 0.102 - 0.205: 1152 0.205 - 0.307: 199 0.307 - 0.409: 56 0.409 - 0.511: 12 Chirality restraints: 6772 Sorted by residual: chirality pdb=" CB VAL B1011 " pdb=" CA VAL B1011 " pdb=" CG1 VAL B1011 " pdb=" CG2 VAL B1011 " both_signs ideal model delta sigma weight residual False -2.63 -2.12 -0.51 2.00e-01 2.50e+01 6.54e+00 chirality pdb=" CB VAL A1011 " pdb=" CA VAL A1011 " pdb=" CG1 VAL A1011 " pdb=" CG2 VAL A1011 " both_signs ideal model delta sigma weight residual False -2.63 -2.12 -0.51 2.00e-01 2.50e+01 6.54e+00 chirality pdb=" CB VAL C1011 " pdb=" CA VAL C1011 " pdb=" CG1 VAL C1011 " pdb=" CG2 VAL C1011 " both_signs ideal model delta sigma weight residual False -2.63 -2.12 -0.51 2.00e-01 2.50e+01 6.52e+00 ... (remaining 6769 not shown) Planarity restraints: 7540 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU B 229 " 0.097 5.00e-02 4.00e+02 1.46e-01 3.40e+01 pdb=" N PRO B 230 " -0.252 5.00e-02 4.00e+02 pdb=" CA PRO B 230 " 0.078 5.00e-02 4.00e+02 pdb=" CD PRO B 230 " 0.077 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU D 229 " 0.097 5.00e-02 4.00e+02 1.46e-01 3.40e+01 pdb=" N PRO D 230 " -0.252 5.00e-02 4.00e+02 pdb=" CA PRO D 230 " 0.078 5.00e-02 4.00e+02 pdb=" CD PRO D 230 " 0.077 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 229 " 0.097 5.00e-02 4.00e+02 1.46e-01 3.39e+01 pdb=" N PRO A 230 " -0.252 5.00e-02 4.00e+02 pdb=" CA PRO A 230 " 0.078 5.00e-02 4.00e+02 pdb=" CD PRO A 230 " 0.077 5.00e-02 4.00e+02 ... (remaining 7537 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.46: 146 2.46 - 3.07: 21581 3.07 - 3.68: 67007 3.68 - 4.29: 94658 4.29 - 4.90: 162437 Nonbonded interactions: 345829 Sorted by model distance: nonbonded pdb=" OE1 GLU A1386 " pdb="MG MG A1705 " model vdw 1.852 2.170 nonbonded pdb=" OE1 GLU B1386 " pdb="MG MG B1705 " model vdw 1.852 2.170 nonbonded pdb=" OE1 GLU D1386 " pdb="MG MG D6007 " model vdw 1.852 2.170 nonbonded pdb=" OE1 GLU C1386 " pdb="MG MG C6007 " model vdw 1.852 2.170 nonbonded pdb=" SG CYS C 997 " pdb=" SG CYS C1006 " model vdw 2.025 3.760 ... (remaining 345824 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 1704 through 1706 or resid 1709)) \ selection = (chain 'B' and (resid 51 through 1494 or resid 1704 through 1706 or resid 1709)) \ selection = (chain 'C' and (resid 51 through 1494 or resid 6004 through 6006 or resid 6009)) \ selection = (chain 'D' and (resid 51 through 1494 or resid 6004 through 6006 or resid 6009)) \ } 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: 9.240 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: 0.060 Extract box with map and model: 1.790 Check model and map are aligned: 0.330 Set scattering table: 0.420 Process input model: 134.680 Find NCS groups from input model: 2.820 Set up NCS constraints: 0.160 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: 0.020 Load rotamer database and sin/cos tables:12.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 162.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7050 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 : 0.013 0.148 43760 Z= 0.821 Angle : 1.775 13.273 59540 Z= 1.103 Chirality : 0.091 0.511 6772 Planarity : 0.012 0.146 7540 Dihedral : 13.338 88.658 16440 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.47 % Allowed : 1.39 % Favored : 98.13 % Cbeta Deviations : 0.46 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.11), residues: 5476 helix: 1.25 (0.09), residues: 2924 sheet: -0.91 (0.22), residues: 448 loop : -0.32 (0.14), residues: 2104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP B 726 HIS 0.011 0.002 HIS B 660 PHE 0.055 0.007 PHE B 941 TYR 0.049 0.006 TYR D 466 ARG 0.053 0.002 ARG D1088 *********************** 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 1001 residues out of total 4700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 981 time to evaluate : 4.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 ILE cc_start: 0.6791 (pt) cc_final: 0.6579 (mp) REVERT: A 80 HIS cc_start: 0.5577 (m-70) cc_final: 0.5195 (m-70) REVERT: A 145 LEU cc_start: 0.7897 (tp) cc_final: 0.7657 (mt) REVERT: A 166 LYS cc_start: 0.6507 (tttm) cc_final: 0.5943 (ttmm) REVERT: A 169 ARG cc_start: 0.6716 (ttm110) cc_final: 0.6454 (ttm110) REVERT: A 240 HIS cc_start: 0.6061 (m-70) cc_final: 0.5742 (m-70) REVERT: A 280 ASN cc_start: 0.7456 (t0) cc_final: 0.7041 (t0) REVERT: A 307 GLN cc_start: 0.6928 (mm110) cc_final: 0.6543 (mp-120) REVERT: A 368 ASN cc_start: 0.7009 (m-40) cc_final: 0.6478 (m110) REVERT: A 395 GLU cc_start: 0.6066 (tt0) cc_final: 0.5786 (pt0) REVERT: A 417 GLN cc_start: 0.6389 (mm-40) cc_final: 0.5803 (mm110) REVERT: A 502 GLU cc_start: 0.6039 (tt0) cc_final: 0.5502 (mt-10) REVERT: A 569 SER cc_start: 0.5870 (t) cc_final: 0.5667 (m) REVERT: A 592 GLN cc_start: 0.5880 (tt0) cc_final: 0.5414 (tp40) REVERT: A 611 ASP cc_start: 0.6619 (t0) cc_final: 0.6359 (t70) REVERT: A 618 HIS cc_start: 0.6180 (t70) cc_final: 0.5950 (t70) REVERT: A 626 SER cc_start: 0.6962 (m) cc_final: 0.6329 (p) REVERT: A 663 LYS cc_start: 0.6292 (mmpt) cc_final: 0.5782 (mppt) REVERT: A 686 GLU cc_start: 0.5862 (tt0) cc_final: 0.5089 (tp30) REVERT: A 690 SER cc_start: 0.7007 (p) cc_final: 0.6804 (m) REVERT: A 702 ASN cc_start: 0.6411 (t0) cc_final: 0.6057 (t0) REVERT: A 706 ASP cc_start: 0.6673 (m-30) cc_final: 0.6415 (m-30) REVERT: A 827 LYS cc_start: 0.7044 (ptmm) cc_final: 0.6765 (ptpt) REVERT: A 854 MET cc_start: 0.6040 (ttm) cc_final: 0.5672 (mtp) REVERT: A 870 ARG cc_start: 0.6791 (mtt180) cc_final: 0.6480 (mtt180) REVERT: A 889 ASP cc_start: 0.6350 (t0) cc_final: 0.6058 (t0) REVERT: A 915 MET cc_start: 0.7909 (mtm) cc_final: 0.7565 (mtt) REVERT: A 916 ARG cc_start: 0.6523 (tpt-90) cc_final: 0.5684 (tpm170) REVERT: A 933 GLU cc_start: 0.6001 (tp30) cc_final: 0.5275 (tp30) REVERT: A 963 ASP cc_start: 0.5992 (t70) cc_final: 0.5610 (t0) REVERT: A 964 GLU cc_start: 0.5567 (mm-30) cc_final: 0.5349 (tt0) REVERT: A 969 ARG cc_start: 0.6436 (mtp-110) cc_final: 0.5505 (mtp85) REVERT: A 1000 ASP cc_start: 0.7512 (m-30) cc_final: 0.7184 (m-30) REVERT: A 1059 LEU cc_start: 0.6677 (mt) cc_final: 0.6211 (mm) REVERT: A 1085 ARG cc_start: 0.4401 (tpp80) cc_final: 0.3334 (ttt180) REVERT: A 1107 ARG cc_start: 0.5575 (ttp-110) cc_final: 0.4971 (ptm-80) REVERT: A 1122 ARG cc_start: 0.5406 (mtm110) cc_final: 0.5144 (mtm110) REVERT: A 1123 ARG cc_start: 0.5925 (ttp80) cc_final: 0.5678 (ttp80) REVERT: A 1125 GLU cc_start: 0.5349 (mm-30) cc_final: 0.5029 (mm-30) REVERT: A 1129 GLN cc_start: 0.5435 (mm-40) cc_final: 0.5211 (mm-40) REVERT: A 1131 MET cc_start: 0.5704 (tpt) cc_final: 0.5338 (mtt) REVERT: A 1145 GLN cc_start: 0.7097 (tt0) cc_final: 0.6776 (tt0) REVERT: A 1162 PHE cc_start: 0.7741 (t80) cc_final: 0.7346 (t80) REVERT: A 1297 SER cc_start: 0.8160 (m) cc_final: 0.7960 (p) REVERT: A 1394 MET cc_start: 0.7997 (OUTLIER) cc_final: 0.7689 (mtp) REVERT: A 1401 MET cc_start: 0.5883 (mtm) cc_final: 0.5559 (mtp) REVERT: A 1460 ASP cc_start: 0.7628 (t70) cc_final: 0.7362 (p0) REVERT: D 80 HIS cc_start: 0.5568 (m-70) cc_final: 0.5189 (m-70) REVERT: D 145 LEU cc_start: 0.7898 (tp) cc_final: 0.7645 (mt) REVERT: D 166 LYS cc_start: 0.6455 (tttm) cc_final: 0.5892 (ttmm) REVERT: D 169 ARG cc_start: 0.6750 (ttm110) cc_final: 0.6484 (ttm110) REVERT: D 240 HIS cc_start: 0.6059 (m-70) cc_final: 0.5761 (m-70) REVERT: D 280 ASN cc_start: 0.7446 (t0) cc_final: 0.7021 (t0) REVERT: D 307 GLN cc_start: 0.6923 (mm110) cc_final: 0.6666 (mm-40) REVERT: D 368 ASN cc_start: 0.7024 (m-40) cc_final: 0.6493 (m110) REVERT: D 395 GLU cc_start: 0.6053 (tt0) cc_final: 0.5781 (pt0) REVERT: D 417 GLN cc_start: 0.6418 (mm-40) cc_final: 0.5822 (mm110) REVERT: D 428 LYS cc_start: 0.5713 (ttmt) cc_final: 0.5340 (tptp) REVERT: D 461 HIS cc_start: 0.5775 (m90) cc_final: 0.5526 (m-70) REVERT: D 502 GLU cc_start: 0.6038 (tt0) cc_final: 0.5497 (mt-10) REVERT: D 569 SER cc_start: 0.5893 (t) cc_final: 0.5669 (m) REVERT: D 595 ARG cc_start: 0.6149 (mtt180) cc_final: 0.5916 (mtt180) REVERT: D 611 ASP cc_start: 0.6594 (t0) cc_final: 0.6342 (t70) REVERT: D 618 HIS cc_start: 0.6174 (t70) cc_final: 0.5936 (t70) REVERT: D 626 SER cc_start: 0.6935 (m) cc_final: 0.6322 (p) REVERT: D 663 LYS cc_start: 0.6127 (mmpt) cc_final: 0.5634 (mppt) REVERT: D 686 GLU cc_start: 0.6019 (tt0) cc_final: 0.5229 (tp30) REVERT: D 690 SER cc_start: 0.7023 (p) cc_final: 0.6797 (m) REVERT: D 702 ASN cc_start: 0.6509 (t0) cc_final: 0.6062 (t0) REVERT: D 706 ASP cc_start: 0.6624 (m-30) cc_final: 0.6266 (m-30) REVERT: D 708 LYS cc_start: 0.7328 (mttp) cc_final: 0.6947 (mmtt) REVERT: D 827 LYS cc_start: 0.7055 (ptmm) cc_final: 0.6755 (ptpt) REVERT: D 854 MET cc_start: 0.6027 (ttm) cc_final: 0.5665 (mtp) REVERT: D 870 ARG cc_start: 0.6762 (mtt180) cc_final: 0.6435 (mtt180) REVERT: D 889 ASP cc_start: 0.6360 (t0) cc_final: 0.6057 (t0) REVERT: D 915 MET cc_start: 0.7907 (mtm) cc_final: 0.7575 (mtt) REVERT: D 916 ARG cc_start: 0.6508 (tpt-90) cc_final: 0.5682 (tpm170) REVERT: D 923 ASN cc_start: 0.6931 (m-40) cc_final: 0.6721 (m110) REVERT: D 933 GLU cc_start: 0.5966 (tp30) cc_final: 0.5251 (tp30) REVERT: D 963 ASP cc_start: 0.5966 (t70) cc_final: 0.5586 (t0) REVERT: D 964 GLU cc_start: 0.5581 (mm-30) cc_final: 0.5349 (tt0) REVERT: D 969 ARG cc_start: 0.6382 (mtp-110) cc_final: 0.5497 (mtp85) REVERT: D 1000 ASP cc_start: 0.7526 (m-30) cc_final: 0.7224 (m-30) REVERT: D 1059 LEU cc_start: 0.6661 (mt) cc_final: 0.6209 (mm) REVERT: D 1085 ARG cc_start: 0.4436 (tpp80) cc_final: 0.3363 (ttt180) REVERT: D 1107 ARG cc_start: 0.5642 (ttp-110) cc_final: 0.5030 (ptm-80) REVERT: D 1122 ARG cc_start: 0.5433 (mtm110) cc_final: 0.5158 (mtm110) REVERT: D 1123 ARG cc_start: 0.5934 (ttp80) cc_final: 0.5733 (ttp80) REVERT: D 1125 GLU cc_start: 0.5391 (mm-30) cc_final: 0.5073 (mm-30) REVERT: D 1129 GLN cc_start: 0.5477 (mm-40) cc_final: 0.5221 (mm-40) REVERT: D 1131 MET cc_start: 0.5631 (tpt) cc_final: 0.5214 (mtt) REVERT: D 1145 GLN cc_start: 0.7121 (tt0) cc_final: 0.6803 (tt0) REVERT: D 1157 MET cc_start: 0.7648 (mmm) cc_final: 0.7434 (mmt) REVERT: D 1162 PHE cc_start: 0.7746 (t80) cc_final: 0.7341 (t80) REVERT: D 1297 SER cc_start: 0.8140 (m) cc_final: 0.7927 (p) REVERT: D 1394 MET cc_start: 0.7993 (OUTLIER) cc_final: 0.7686 (mtp) REVERT: D 1401 MET cc_start: 0.5902 (mtm) cc_final: 0.5571 (mtp) REVERT: D 1460 ASP cc_start: 0.7622 (t70) cc_final: 0.7357 (p0) REVERT: B 80 HIS cc_start: 0.5567 (m-70) cc_final: 0.5192 (m-70) REVERT: B 145 LEU cc_start: 0.7897 (tp) cc_final: 0.7645 (mt) REVERT: B 166 LYS cc_start: 0.6453 (tttm) cc_final: 0.5889 (ttmm) REVERT: B 169 ARG cc_start: 0.6719 (ttm110) cc_final: 0.6458 (ttm110) REVERT: B 240 HIS cc_start: 0.6058 (m-70) cc_final: 0.5761 (m-70) REVERT: B 280 ASN cc_start: 0.7450 (t0) cc_final: 0.7026 (t0) REVERT: B 307 GLN cc_start: 0.6927 (mm110) cc_final: 0.6668 (mm-40) REVERT: B 368 ASN cc_start: 0.7020 (m-40) cc_final: 0.6489 (m110) REVERT: B 395 GLU cc_start: 0.6054 (tt0) cc_final: 0.5774 (pt0) REVERT: B 417 GLN cc_start: 0.6418 (mm-40) cc_final: 0.5824 (mm110) REVERT: B 428 LYS cc_start: 0.5715 (ttmt) cc_final: 0.5342 (tptp) REVERT: B 461 HIS cc_start: 0.5775 (m90) cc_final: 0.5525 (m-70) REVERT: B 502 GLU cc_start: 0.6039 (tt0) cc_final: 0.5499 (mt-10) REVERT: B 569 SER cc_start: 0.5893 (t) cc_final: 0.5669 (m) REVERT: B 595 ARG cc_start: 0.6149 (mtt180) cc_final: 0.5919 (mtt180) REVERT: B 611 ASP cc_start: 0.6595 (t0) cc_final: 0.6342 (t70) REVERT: B 618 HIS cc_start: 0.6175 (t70) cc_final: 0.5936 (t70) REVERT: B 626 SER cc_start: 0.6936 (m) cc_final: 0.6323 (p) REVERT: B 663 LYS cc_start: 0.6143 (mmpt) cc_final: 0.5646 (mppt) REVERT: B 686 GLU cc_start: 0.6020 (tt0) cc_final: 0.5217 (tp30) REVERT: B 690 SER cc_start: 0.7033 (p) cc_final: 0.6816 (m) REVERT: B 702 ASN cc_start: 0.6509 (t0) cc_final: 0.6063 (t0) REVERT: B 706 ASP cc_start: 0.6655 (m-30) cc_final: 0.6314 (m-30) REVERT: B 708 LYS cc_start: 0.7329 (mttp) cc_final: 0.6948 (mmtt) REVERT: B 827 LYS cc_start: 0.7021 (ptmm) cc_final: 0.6754 (ptpt) REVERT: B 854 MET cc_start: 0.6027 (ttm) cc_final: 0.5664 (mtp) REVERT: B 870 ARG cc_start: 0.6764 (mtt180) cc_final: 0.6437 (mtt180) REVERT: B 889 ASP cc_start: 0.6360 (t0) cc_final: 0.6058 (t0) REVERT: B 915 MET cc_start: 0.7909 (mtm) cc_final: 0.7576 (mtt) REVERT: B 916 ARG cc_start: 0.6509 (tpt-90) cc_final: 0.5681 (tpm170) REVERT: B 933 GLU cc_start: 0.5967 (tp30) cc_final: 0.5185 (tp30) REVERT: B 936 LYS cc_start: 0.5864 (mttt) cc_final: 0.5494 (mtpt) REVERT: B 963 ASP cc_start: 0.6010 (t70) cc_final: 0.5635 (t0) REVERT: B 964 GLU cc_start: 0.5617 (mm-30) cc_final: 0.5389 (tt0) REVERT: B 969 ARG cc_start: 0.6374 (mtp-110) cc_final: 0.5482 (mtp85) REVERT: B 1000 ASP cc_start: 0.7527 (m-30) cc_final: 0.7226 (m-30) REVERT: B 1059 LEU cc_start: 0.6661 (mt) cc_final: 0.6210 (mm) REVERT: B 1085 ARG cc_start: 0.4436 (tpp80) cc_final: 0.3363 (ttt180) REVERT: B 1107 ARG cc_start: 0.5574 (ttp-110) cc_final: 0.4967 (ptm-80) REVERT: B 1122 ARG cc_start: 0.5434 (mtm110) cc_final: 0.5152 (mtm110) REVERT: B 1123 ARG cc_start: 0.5935 (ttp80) cc_final: 0.5733 (ttp80) REVERT: B 1125 GLU cc_start: 0.5391 (mm-30) cc_final: 0.5072 (mm-30) REVERT: B 1129 GLN cc_start: 0.5478 (mm-40) cc_final: 0.5222 (mm-40) REVERT: B 1131 MET cc_start: 0.5631 (tpt) cc_final: 0.5214 (mtt) REVERT: B 1145 GLN cc_start: 0.7124 (tt0) cc_final: 0.6806 (tt0) REVERT: B 1162 PHE cc_start: 0.7748 (t80) cc_final: 0.7345 (t80) REVERT: B 1297 SER cc_start: 0.8143 (m) cc_final: 0.7926 (p) REVERT: B 1394 MET cc_start: 0.7994 (OUTLIER) cc_final: 0.7688 (mtp) REVERT: B 1401 MET cc_start: 0.5901 (mtm) cc_final: 0.5557 (mtp) REVERT: B 1460 ASP cc_start: 0.7620 (t70) cc_final: 0.7396 (p0) REVERT: C 59 ILE cc_start: 0.6758 (pt) cc_final: 0.6551 (mp) REVERT: C 80 HIS cc_start: 0.5575 (m-70) cc_final: 0.5194 (m-70) REVERT: C 145 LEU cc_start: 0.7891 (tp) cc_final: 0.7644 (mt) REVERT: C 166 LYS cc_start: 0.6456 (tttm) cc_final: 0.5891 (ttmm) REVERT: C 169 ARG cc_start: 0.6743 (ttm110) cc_final: 0.6482 (ttm110) REVERT: C 240 HIS cc_start: 0.6063 (m-70) cc_final: 0.5768 (m-70) REVERT: C 280 ASN cc_start: 0.7451 (t0) cc_final: 0.7036 (t0) REVERT: C 307 GLN cc_start: 0.6929 (mm110) cc_final: 0.6518 (mp-120) REVERT: C 368 ASN cc_start: 0.7017 (m-40) cc_final: 0.6490 (m110) REVERT: C 395 GLU cc_start: 0.6056 (tt0) cc_final: 0.5775 (pt0) REVERT: C 417 GLN cc_start: 0.6418 (mm-40) cc_final: 0.5828 (mm110) REVERT: C 428 LYS cc_start: 0.5703 (ttmt) cc_final: 0.5334 (tptp) REVERT: C 502 GLU cc_start: 0.6037 (tt0) cc_final: 0.5498 (mt-10) REVERT: C 569 SER cc_start: 0.5874 (t) cc_final: 0.5659 (m) REVERT: C 595 ARG cc_start: 0.6152 (mtt180) cc_final: 0.5921 (mtt180) REVERT: C 611 ASP cc_start: 0.6591 (t0) cc_final: 0.6334 (t70) REVERT: C 618 HIS cc_start: 0.6177 (t70) cc_final: 0.5946 (t70) REVERT: C 626 SER cc_start: 0.6936 (m) cc_final: 0.6321 (p) REVERT: C 663 LYS cc_start: 0.6143 (mmpt) cc_final: 0.5646 (mppt) REVERT: C 686 GLU cc_start: 0.6019 (tt0) cc_final: 0.5219 (tp30) REVERT: C 690 SER cc_start: 0.7031 (p) cc_final: 0.6816 (m) REVERT: C 702 ASN cc_start: 0.6505 (t0) cc_final: 0.6059 (t0) REVERT: C 706 ASP cc_start: 0.6666 (m-30) cc_final: 0.6326 (m-30) REVERT: C 708 LYS cc_start: 0.7324 (mttp) cc_final: 0.6944 (mmtt) REVERT: C 827 LYS cc_start: 0.7031 (ptmm) cc_final: 0.6763 (ptpt) REVERT: C 854 MET cc_start: 0.6028 (ttm) cc_final: 0.5666 (mtp) REVERT: C 870 ARG cc_start: 0.6775 (mtt180) cc_final: 0.6449 (mtt180) REVERT: C 889 ASP cc_start: 0.6357 (t0) cc_final: 0.6077 (t0) REVERT: C 915 MET cc_start: 0.7908 (mtm) cc_final: 0.7575 (mtt) REVERT: C 916 ARG cc_start: 0.6507 (tpt-90) cc_final: 0.5681 (tpm170) REVERT: C 923 ASN cc_start: 0.6930 (m-40) cc_final: 0.6717 (m110) REVERT: C 933 GLU cc_start: 0.5960 (tp30) cc_final: 0.5238 (tp30) REVERT: C 963 ASP cc_start: 0.6011 (t70) cc_final: 0.5637 (t0) REVERT: C 964 GLU cc_start: 0.5608 (mm-30) cc_final: 0.5383 (tt0) REVERT: C 969 ARG cc_start: 0.6382 (mtp-110) cc_final: 0.5498 (mtp85) REVERT: C 1000 ASP cc_start: 0.7524 (m-30) cc_final: 0.7220 (m-30) REVERT: C 1059 LEU cc_start: 0.6664 (mt) cc_final: 0.6214 (mm) REVERT: C 1085 ARG cc_start: 0.4434 (tpp80) cc_final: 0.3361 (ttt180) REVERT: C 1107 ARG cc_start: 0.5573 (ttp-110) cc_final: 0.4966 (ptm-80) REVERT: C 1122 ARG cc_start: 0.5436 (mtm110) cc_final: 0.5161 (mtm110) REVERT: C 1123 ARG cc_start: 0.5901 (ttp80) cc_final: 0.5688 (ttp80) REVERT: C 1125 GLU cc_start: 0.5394 (mm-30) cc_final: 0.5076 (mm-30) REVERT: C 1129 GLN cc_start: 0.5478 (mm-40) cc_final: 0.5223 (mm-40) REVERT: C 1131 MET cc_start: 0.5707 (tpt) cc_final: 0.5302 (mtt) REVERT: C 1145 GLN cc_start: 0.7157 (tt0) cc_final: 0.6835 (tt0) REVERT: C 1162 PHE cc_start: 0.7747 (t80) cc_final: 0.7344 (t80) REVERT: C 1297 SER cc_start: 0.8162 (m) cc_final: 0.7961 (p) REVERT: C 1394 MET cc_start: 0.7997 (OUTLIER) cc_final: 0.7688 (mtp) REVERT: C 1401 MET cc_start: 0.5897 (mtm) cc_final: 0.5556 (mtp) REVERT: C 1460 ASP cc_start: 0.7628 (t70) cc_final: 0.7366 (p0) outliers start: 20 outliers final: 4 residues processed: 997 average time/residue: 1.7686 time to fit residues: 2127.8852 Evaluate side-chains 695 residues out of total 4700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 687 time to evaluate : 5.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 683 MET Chi-restraints excluded: chain A residue 1394 MET Chi-restraints excluded: chain D residue 683 MET Chi-restraints excluded: chain D residue 1394 MET Chi-restraints excluded: chain B residue 683 MET Chi-restraints excluded: chain B residue 1394 MET Chi-restraints excluded: chain C residue 683 MET Chi-restraints excluded: chain C residue 1394 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 548 random chunks: chunk 462 optimal weight: 0.9990 chunk 415 optimal weight: 0.9990 chunk 230 optimal weight: 0.9980 chunk 141 optimal weight: 1.9990 chunk 280 optimal weight: 2.9990 chunk 221 optimal weight: 0.9980 chunk 429 optimal weight: 2.9990 chunk 166 optimal weight: 0.9980 chunk 261 optimal weight: 1.9990 chunk 319 optimal weight: 2.9990 chunk 497 optimal weight: 3.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 266 ASN A 450 ASN A 813 HIS A 996 ASN A1038 ASN A1080 HIS A1101 GLN A1116 ASN A1156 HIS A1282 ASN A1441 ASN A1463 HIS D 266 ASN D 450 ASN D 996 ASN D1038 ASN D1101 GLN D1116 ASN D1156 HIS D1282 ASN D1441 ASN D1463 HIS B 266 ASN B 450 ASN B 813 HIS B 996 ASN B1038 ASN B1101 GLN B1116 ASN B1156 HIS B1282 ASN B1441 ASN B1463 HIS C 266 ASN C 450 ASN C 996 ASN C1038 ASN C1080 HIS C1101 GLN C1116 ASN C1156 HIS C1282 ASN C1441 ASN C1463 HIS Total number of N/Q/H flips: 44 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7071 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 43760 Z= 0.220 Angle : 0.549 6.963 59540 Z= 0.291 Chirality : 0.041 0.168 6772 Planarity : 0.005 0.071 7540 Dihedral : 8.377 86.287 7108 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.54 % Allowed : 7.94 % Favored : 90.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.11), residues: 5476 helix: 1.95 (0.09), residues: 3028 sheet: -1.10 (0.23), residues: 376 loop : -0.37 (0.14), residues: 2072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 726 HIS 0.006 0.001 HIS C 240 PHE 0.013 0.002 PHE A 879 TYR 0.043 0.002 TYR C 420 ARG 0.007 0.001 ARG B 112 *********************** 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 769 residues out of total 4700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 704 time to evaluate : 5.119 Fit side-chains REVERT: A 78 ARG cc_start: 0.5670 (ptp-170) cc_final: 0.5447 (ptp-170) REVERT: A 80 HIS cc_start: 0.5635 (m-70) cc_final: 0.5125 (m170) REVERT: A 145 LEU cc_start: 0.7863 (tp) cc_final: 0.7548 (mt) REVERT: A 166 LYS cc_start: 0.6202 (tttm) cc_final: 0.5968 (ttmm) REVERT: A 262 ASP cc_start: 0.6951 (p0) cc_final: 0.6415 (p0) REVERT: A 284 GLN cc_start: 0.7327 (mm-40) cc_final: 0.6783 (mt0) REVERT: A 368 ASN cc_start: 0.7204 (m-40) cc_final: 0.6762 (m110) REVERT: A 395 GLU cc_start: 0.5973 (tt0) cc_final: 0.5545 (mt-10) REVERT: A 502 GLU cc_start: 0.5937 (tt0) cc_final: 0.5392 (mt-10) REVERT: A 569 SER cc_start: 0.5572 (t) cc_final: 0.5155 (m) REVERT: A 618 HIS cc_start: 0.5638 (t70) cc_final: 0.5431 (t70) REVERT: A 663 LYS cc_start: 0.5807 (mmpt) cc_final: 0.5397 (mtmt) REVERT: A 675 GLU cc_start: 0.6116 (tp30) cc_final: 0.5774 (tp30) REVERT: A 686 GLU cc_start: 0.5744 (tt0) cc_final: 0.5209 (tp30) REVERT: A 691 LYS cc_start: 0.7404 (mttt) cc_final: 0.7026 (mttp) REVERT: A 702 ASN cc_start: 0.6162 (t0) cc_final: 0.5744 (t0) REVERT: A 706 ASP cc_start: 0.6207 (m-30) cc_final: 0.6005 (m-30) REVERT: A 797 LYS cc_start: 0.6309 (mttt) cc_final: 0.5944 (mtpm) REVERT: A 827 LYS cc_start: 0.7136 (ptmm) cc_final: 0.6846 (ptpt) REVERT: A 889 ASP cc_start: 0.6150 (t0) cc_final: 0.5906 (t0) REVERT: A 930 MET cc_start: 0.5891 (tpp) cc_final: 0.5622 (tpp) REVERT: A 936 LYS cc_start: 0.6018 (mttt) cc_final: 0.5714 (mtpt) REVERT: A 969 ARG cc_start: 0.6331 (mtp-110) cc_final: 0.5570 (mtp85) REVERT: A 1000 ASP cc_start: 0.7440 (m-30) cc_final: 0.7179 (m-30) REVERT: A 1064 LYS cc_start: 0.6334 (OUTLIER) cc_final: 0.5665 (mmtm) REVERT: A 1085 ARG cc_start: 0.4459 (tpp80) cc_final: 0.3412 (ttp-170) REVERT: A 1107 ARG cc_start: 0.5412 (ttp-110) cc_final: 0.4852 (ptm-80) REVERT: A 1122 ARG cc_start: 0.5093 (mtm110) cc_final: 0.4540 (ttp80) REVERT: A 1128 ARG cc_start: 0.5439 (OUTLIER) cc_final: 0.4907 (ttp-110) REVERT: A 1129 GLN cc_start: 0.5481 (mm-40) cc_final: 0.5195 (mm-40) REVERT: A 1162 PHE cc_start: 0.7459 (t80) cc_final: 0.7185 (t80) REVERT: A 1269 ASP cc_start: 0.8476 (t0) cc_final: 0.8244 (t70) REVERT: A 1297 SER cc_start: 0.8339 (m) cc_final: 0.7999 (p) REVERT: A 1348 ASP cc_start: 0.7932 (t0) cc_final: 0.7727 (t0) REVERT: A 1401 MET cc_start: 0.6331 (mtm) cc_final: 0.6123 (mtp) REVERT: A 1459 ASP cc_start: 0.8415 (t70) cc_final: 0.7915 (t70) REVERT: D 80 HIS cc_start: 0.5611 (m-70) cc_final: 0.5105 (m170) REVERT: D 145 LEU cc_start: 0.7861 (tp) cc_final: 0.7540 (mt) REVERT: D 166 LYS cc_start: 0.6217 (tttm) cc_final: 0.5978 (ttmm) REVERT: D 262 ASP cc_start: 0.6970 (p0) cc_final: 0.6435 (p0) REVERT: D 284 GLN cc_start: 0.7374 (mm-40) cc_final: 0.6815 (mt0) REVERT: D 368 ASN cc_start: 0.7230 (m-40) cc_final: 0.6786 (m110) REVERT: D 395 GLU cc_start: 0.5970 (tt0) cc_final: 0.5544 (mt-10) REVERT: D 502 GLU cc_start: 0.5927 (tt0) cc_final: 0.5380 (mt-10) REVERT: D 569 SER cc_start: 0.5691 (t) cc_final: 0.5273 (m) REVERT: D 595 ARG cc_start: 0.5724 (mtt180) cc_final: 0.5499 (mtt180) REVERT: D 663 LYS cc_start: 0.5790 (mmpt) cc_final: 0.5390 (mtmt) REVERT: D 675 GLU cc_start: 0.6095 (tp30) cc_final: 0.5748 (tp30) REVERT: D 686 GLU cc_start: 0.5778 (tt0) cc_final: 0.5157 (tp30) REVERT: D 691 LYS cc_start: 0.7385 (mttt) cc_final: 0.7001 (mttp) REVERT: D 702 ASN cc_start: 0.6177 (t0) cc_final: 0.5757 (t0) REVERT: D 706 ASP cc_start: 0.6195 (m-30) cc_final: 0.5967 (m-30) REVERT: D 708 LYS cc_start: 0.6832 (mttp) cc_final: 0.6393 (mmtm) REVERT: D 797 LYS cc_start: 0.6335 (mttt) cc_final: 0.5860 (mtpm) REVERT: D 827 LYS cc_start: 0.7106 (ptmm) cc_final: 0.6823 (ptpt) REVERT: D 889 ASP cc_start: 0.6164 (t0) cc_final: 0.5903 (t0) REVERT: D 930 MET cc_start: 0.5889 (tpp) cc_final: 0.5634 (tpp) REVERT: D 936 LYS cc_start: 0.6005 (mttt) cc_final: 0.5704 (mtpt) REVERT: D 969 ARG cc_start: 0.6346 (mtp-110) cc_final: 0.5568 (mtp85) REVERT: D 1000 ASP cc_start: 0.7449 (m-30) cc_final: 0.7191 (m-30) REVERT: D 1065 ASP cc_start: 0.6458 (m-30) cc_final: 0.5926 (t0) REVERT: D 1085 ARG cc_start: 0.4453 (tpp80) cc_final: 0.3435 (ttp-170) REVERT: D 1107 ARG cc_start: 0.5455 (ttp-110) cc_final: 0.4893 (ptm-80) REVERT: D 1122 ARG cc_start: 0.5239 (mtm110) cc_final: 0.4683 (ttp80) REVERT: D 1123 ARG cc_start: 0.5711 (ttp80) cc_final: 0.5498 (ttp80) REVERT: D 1128 ARG cc_start: 0.5431 (OUTLIER) cc_final: 0.4915 (ttp-110) REVERT: D 1129 GLN cc_start: 0.5454 (mm-40) cc_final: 0.5167 (mm-40) REVERT: D 1157 MET cc_start: 0.7244 (mmm) cc_final: 0.7032 (mmt) REVERT: D 1162 PHE cc_start: 0.7481 (t80) cc_final: 0.7166 (t80) REVERT: D 1269 ASP cc_start: 0.8479 (t0) cc_final: 0.8246 (t70) REVERT: D 1297 SER cc_start: 0.8337 (m) cc_final: 0.8006 (p) REVERT: D 1401 MET cc_start: 0.6325 (mtm) cc_final: 0.6106 (mtp) REVERT: D 1459 ASP cc_start: 0.8432 (t70) cc_final: 0.7932 (t70) REVERT: B 60 GLU cc_start: 0.5937 (mp0) cc_final: 0.5736 (mm-30) REVERT: B 80 HIS cc_start: 0.5623 (m-70) cc_final: 0.5120 (m170) REVERT: B 145 LEU cc_start: 0.7862 (tp) cc_final: 0.7541 (mt) REVERT: B 166 LYS cc_start: 0.6214 (tttm) cc_final: 0.5975 (ttmm) REVERT: B 262 ASP cc_start: 0.6954 (p0) cc_final: 0.6422 (p0) REVERT: B 284 GLN cc_start: 0.7368 (mm-40) cc_final: 0.6814 (mt0) REVERT: B 368 ASN cc_start: 0.7214 (m-40) cc_final: 0.6773 (m110) REVERT: B 395 GLU cc_start: 0.5970 (tt0) cc_final: 0.5543 (mt-10) REVERT: B 502 GLU cc_start: 0.5927 (tt0) cc_final: 0.5372 (mt-10) REVERT: B 569 SER cc_start: 0.5692 (t) cc_final: 0.5274 (m) REVERT: B 595 ARG cc_start: 0.5724 (mtt180) cc_final: 0.5500 (mtt180) REVERT: B 618 HIS cc_start: 0.5640 (t70) cc_final: 0.5432 (t70) REVERT: B 663 LYS cc_start: 0.5787 (mmpt) cc_final: 0.5387 (mtmt) REVERT: B 675 GLU cc_start: 0.6093 (tp30) cc_final: 0.5747 (tp30) REVERT: B 686 GLU cc_start: 0.5777 (tt0) cc_final: 0.5156 (tp30) REVERT: B 691 LYS cc_start: 0.7386 (mttt) cc_final: 0.7001 (mttp) REVERT: B 702 ASN cc_start: 0.6176 (t0) cc_final: 0.5758 (t0) REVERT: B 706 ASP cc_start: 0.6194 (m-30) cc_final: 0.5973 (m-30) REVERT: B 708 LYS cc_start: 0.6832 (mttp) cc_final: 0.6392 (mmtm) REVERT: B 797 LYS cc_start: 0.6335 (mttt) cc_final: 0.5860 (mtpm) REVERT: B 827 LYS cc_start: 0.7105 (ptmm) cc_final: 0.6821 (ptpt) REVERT: B 889 ASP cc_start: 0.6164 (t0) cc_final: 0.5930 (t0) REVERT: B 933 GLU cc_start: 0.6026 (tp30) cc_final: 0.5825 (mm-30) REVERT: B 936 LYS cc_start: 0.6003 (mttt) cc_final: 0.5703 (mtpt) REVERT: B 969 ARG cc_start: 0.6343 (mtp-110) cc_final: 0.5560 (mtp85) REVERT: B 1000 ASP cc_start: 0.7440 (m-30) cc_final: 0.7174 (m-30) REVERT: B 1064 LYS cc_start: 0.6320 (OUTLIER) cc_final: 0.5640 (mmtm) REVERT: B 1085 ARG cc_start: 0.4452 (tpp80) cc_final: 0.3434 (ttp-170) REVERT: B 1107 ARG cc_start: 0.5475 (ttp-110) cc_final: 0.4918 (ptm-80) REVERT: B 1122 ARG cc_start: 0.5157 (mtm110) cc_final: 0.4611 (ttp80) REVERT: B 1123 ARG cc_start: 0.5828 (ttp80) cc_final: 0.5612 (ttp80) REVERT: B 1128 ARG cc_start: 0.5432 (OUTLIER) cc_final: 0.4906 (ttp-110) REVERT: B 1129 GLN cc_start: 0.5454 (mm-40) cc_final: 0.5165 (mm-40) REVERT: B 1162 PHE cc_start: 0.7461 (t80) cc_final: 0.7183 (t80) REVERT: B 1269 ASP cc_start: 0.8478 (t0) cc_final: 0.8247 (t70) REVERT: B 1297 SER cc_start: 0.8337 (m) cc_final: 0.8002 (p) REVERT: B 1401 MET cc_start: 0.6331 (mtm) cc_final: 0.6112 (mtp) REVERT: B 1459 ASP cc_start: 0.8433 (t70) cc_final: 0.7932 (t70) REVERT: C 78 ARG cc_start: 0.5589 (ptp-170) cc_final: 0.5371 (ptp-170) REVERT: C 80 HIS cc_start: 0.5634 (m-70) cc_final: 0.5126 (m170) REVERT: C 145 LEU cc_start: 0.7863 (tp) cc_final: 0.7546 (mt) REVERT: C 166 LYS cc_start: 0.6218 (tttm) cc_final: 0.5977 (ttmm) REVERT: C 262 ASP cc_start: 0.6954 (p0) cc_final: 0.6425 (p0) REVERT: C 284 GLN cc_start: 0.7335 (mm-40) cc_final: 0.6773 (mt0) REVERT: C 368 ASN cc_start: 0.7201 (m-40) cc_final: 0.6761 (m110) REVERT: C 395 GLU cc_start: 0.5970 (tt0) cc_final: 0.5542 (mt-10) REVERT: C 502 GLU cc_start: 0.5936 (tt0) cc_final: 0.5392 (mt-10) REVERT: C 569 SER cc_start: 0.5590 (t) cc_final: 0.5170 (m) REVERT: C 595 ARG cc_start: 0.5725 (mtt180) cc_final: 0.5501 (mtt180) REVERT: C 618 HIS cc_start: 0.5641 (t70) cc_final: 0.5436 (t70) REVERT: C 663 LYS cc_start: 0.5788 (mmpt) cc_final: 0.5387 (mtmt) REVERT: C 675 GLU cc_start: 0.6095 (tp30) cc_final: 0.5749 (tp30) REVERT: C 686 GLU cc_start: 0.5776 (tt0) cc_final: 0.5159 (tp30) REVERT: C 691 LYS cc_start: 0.7388 (mttt) cc_final: 0.7005 (mttp) REVERT: C 702 ASN cc_start: 0.6175 (t0) cc_final: 0.5757 (t0) REVERT: C 706 ASP cc_start: 0.6194 (m-30) cc_final: 0.5972 (m-30) REVERT: C 708 LYS cc_start: 0.6828 (mttp) cc_final: 0.6393 (mmtm) REVERT: C 797 LYS cc_start: 0.6333 (mttt) cc_final: 0.5917 (mtpm) REVERT: C 827 LYS cc_start: 0.7113 (ptmm) cc_final: 0.6829 (ptpt) REVERT: C 889 ASP cc_start: 0.6161 (t0) cc_final: 0.5899 (t0) REVERT: C 930 MET cc_start: 0.5884 (tpp) cc_final: 0.5628 (tpp) REVERT: C 936 LYS cc_start: 0.6005 (mttt) cc_final: 0.5704 (mtpt) REVERT: C 969 ARG cc_start: 0.6348 (mtp-110) cc_final: 0.5569 (mtp85) REVERT: C 1000 ASP cc_start: 0.7437 (m-30) cc_final: 0.7169 (m-30) REVERT: C 1064 LYS cc_start: 0.6324 (OUTLIER) cc_final: 0.5647 (mmtm) REVERT: C 1085 ARG cc_start: 0.4453 (tpp80) cc_final: 0.3435 (ttp-170) REVERT: C 1107 ARG cc_start: 0.5433 (ttp-110) cc_final: 0.4872 (ptm-80) REVERT: C 1122 ARG cc_start: 0.5160 (mtm110) cc_final: 0.4614 (ttp80) REVERT: C 1123 ARG cc_start: 0.5828 (ttp80) cc_final: 0.5611 (ttp80) REVERT: C 1128 ARG cc_start: 0.5435 (OUTLIER) cc_final: 0.4906 (ttp-110) REVERT: C 1129 GLN cc_start: 0.5462 (mm-40) cc_final: 0.5172 (mm-40) REVERT: C 1150 MET cc_start: 0.6159 (OUTLIER) cc_final: 0.5309 (mmt) REVERT: C 1157 MET cc_start: 0.7568 (mmm) cc_final: 0.7217 (mmt) REVERT: C 1162 PHE cc_start: 0.7467 (t80) cc_final: 0.7189 (t80) REVERT: C 1269 ASP cc_start: 0.8477 (t0) cc_final: 0.8244 (t70) REVERT: C 1297 SER cc_start: 0.8341 (m) cc_final: 0.8005 (p) REVERT: C 1459 ASP cc_start: 0.8416 (t70) cc_final: 0.7917 (t70) outliers start: 65 outliers final: 20 residues processed: 718 average time/residue: 1.7997 time to fit residues: 1556.2790 Evaluate side-chains 656 residues out of total 4700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 628 time to evaluate : 4.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1064 LYS Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1128 ARG Chi-restraints excluded: chain A residue 1164 LEU Chi-restraints excluded: chain A residue 1229 VAL Chi-restraints excluded: chain A residue 1243 ILE Chi-restraints excluded: chain A residue 1299 ASP Chi-restraints excluded: chain D residue 1082 LEU Chi-restraints excluded: chain D residue 1128 ARG Chi-restraints excluded: chain D residue 1164 LEU Chi-restraints excluded: chain D residue 1229 VAL Chi-restraints excluded: chain D residue 1243 ILE Chi-restraints excluded: chain D residue 1299 ASP Chi-restraints excluded: chain B residue 1064 LYS Chi-restraints excluded: chain B residue 1082 LEU Chi-restraints excluded: chain B residue 1128 ARG Chi-restraints excluded: chain B residue 1164 LEU Chi-restraints excluded: chain B residue 1229 VAL Chi-restraints excluded: chain B residue 1243 ILE Chi-restraints excluded: chain B residue 1299 ASP Chi-restraints excluded: chain C residue 1064 LYS Chi-restraints excluded: chain C residue 1082 LEU Chi-restraints excluded: chain C residue 1128 ARG Chi-restraints excluded: chain C residue 1150 MET Chi-restraints excluded: chain C residue 1164 LEU Chi-restraints excluded: chain C residue 1229 VAL Chi-restraints excluded: chain C residue 1243 ILE Chi-restraints excluded: chain C residue 1299 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 548 random chunks: chunk 276 optimal weight: 0.2980 chunk 154 optimal weight: 0.0050 chunk 414 optimal weight: 9.9990 chunk 338 optimal weight: 4.9990 chunk 137 optimal weight: 9.9990 chunk 498 optimal weight: 0.8980 chunk 538 optimal weight: 3.9990 chunk 443 optimal weight: 4.9990 chunk 494 optimal weight: 2.9990 chunk 169 optimal weight: 4.9990 chunk 399 optimal weight: 0.3980 overall best weight: 0.9196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 HIS A 280 ASN A 450 ASN A 660 HIS A1101 GLN A1282 ASN D 280 ASN D 660 HIS D 692 ASN D1080 HIS D1282 ASN B 280 ASN B 660 HIS B 692 ASN B1080 HIS B1282 ASN C 240 HIS C 280 ASN C 660 HIS C 692 ASN C1101 GLN C1282 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7094 moved from start: 0.3137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 43760 Z= 0.188 Angle : 0.508 6.652 59540 Z= 0.269 Chirality : 0.039 0.171 6772 Planarity : 0.004 0.050 7540 Dihedral : 8.225 88.481 7084 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.87 % Allowed : 9.92 % Favored : 88.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.11), residues: 5476 helix: 2.12 (0.09), residues: 3032 sheet: -1.01 (0.22), residues: 384 loop : -0.28 (0.14), residues: 2060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 726 HIS 0.006 0.001 HIS B 514 PHE 0.014 0.001 PHE C 879 TYR 0.028 0.002 TYR C 420 ARG 0.009 0.001 ARG A 152 *********************** 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 710 residues out of total 4700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 631 time to evaluate : 4.931 Fit side-chains REVERT: A 80 HIS cc_start: 0.5884 (m-70) cc_final: 0.5443 (m170) REVERT: A 145 LEU cc_start: 0.7932 (tp) cc_final: 0.7617 (mt) REVERT: A 166 LYS cc_start: 0.6091 (tttm) cc_final: 0.5857 (ttmm) REVERT: A 240 HIS cc_start: 0.6203 (m-70) cc_final: 0.5959 (m-70) REVERT: A 284 GLN cc_start: 0.7450 (mm-40) cc_final: 0.6929 (mt0) REVERT: A 335 MET cc_start: 0.8702 (mtp) cc_final: 0.8437 (mtp) REVERT: A 368 ASN cc_start: 0.7355 (m-40) cc_final: 0.6928 (m110) REVERT: A 395 GLU cc_start: 0.5864 (tt0) cc_final: 0.5441 (pt0) REVERT: A 502 GLU cc_start: 0.6042 (tt0) cc_final: 0.5560 (mt-10) REVERT: A 510 LYS cc_start: 0.5253 (mttm) cc_final: 0.5035 (mttm) REVERT: A 663 LYS cc_start: 0.5897 (mmpt) cc_final: 0.5419 (mtmt) REVERT: A 666 GLU cc_start: 0.5610 (tt0) cc_final: 0.5280 (tt0) REVERT: A 686 GLU cc_start: 0.5776 (tt0) cc_final: 0.5111 (tp30) REVERT: A 691 LYS cc_start: 0.7320 (mttt) cc_final: 0.6959 (mttp) REVERT: A 706 ASP cc_start: 0.6460 (m-30) cc_final: 0.6169 (m-30) REVERT: A 797 LYS cc_start: 0.6251 (mttt) cc_final: 0.5863 (mtpm) REVERT: A 827 LYS cc_start: 0.7174 (ptmm) cc_final: 0.6897 (ptpt) REVERT: A 923 ASN cc_start: 0.6616 (m110) cc_final: 0.6396 (m110) REVERT: A 930 MET cc_start: 0.5906 (tpp) cc_final: 0.5691 (tpp) REVERT: A 932 MET cc_start: 0.5565 (mmt) cc_final: 0.5163 (mmm) REVERT: A 933 GLU cc_start: 0.6147 (mm-30) cc_final: 0.5830 (mm-30) REVERT: A 936 LYS cc_start: 0.5631 (mttt) cc_final: 0.5418 (mtpt) REVERT: A 969 ARG cc_start: 0.6538 (mtp-110) cc_final: 0.5767 (mtp85) REVERT: A 1000 ASP cc_start: 0.7499 (m-30) cc_final: 0.7226 (m-30) REVERT: A 1107 ARG cc_start: 0.5559 (ttp-110) cc_final: 0.4980 (ptm-80) REVERT: A 1122 ARG cc_start: 0.4961 (mtm110) cc_final: 0.4441 (ttp80) REVERT: A 1128 ARG cc_start: 0.5758 (OUTLIER) cc_final: 0.5307 (ttp-110) REVERT: A 1131 MET cc_start: 0.5671 (OUTLIER) cc_final: 0.5328 (tpp) REVERT: A 1157 MET cc_start: 0.7605 (OUTLIER) cc_final: 0.7341 (mmm) REVERT: A 1269 ASP cc_start: 0.8516 (t0) cc_final: 0.8259 (t70) REVERT: A 1348 ASP cc_start: 0.7869 (t0) cc_final: 0.7562 (t70) REVERT: A 1350 LYS cc_start: 0.7342 (mttt) cc_final: 0.7082 (mttm) REVERT: A 1365 MET cc_start: 0.8232 (ptm) cc_final: 0.7841 (ptm) REVERT: A 1401 MET cc_start: 0.6137 (mtm) cc_final: 0.5895 (mtp) REVERT: D 80 HIS cc_start: 0.5861 (m-70) cc_final: 0.5403 (m170) REVERT: D 145 LEU cc_start: 0.7933 (tp) cc_final: 0.7637 (mt) REVERT: D 166 LYS cc_start: 0.6045 (tttm) cc_final: 0.5826 (ttmm) REVERT: D 239 MET cc_start: 0.5991 (ppp) cc_final: 0.5713 (ppp) REVERT: D 240 HIS cc_start: 0.6245 (m-70) cc_final: 0.5973 (m-70) REVERT: D 284 GLN cc_start: 0.7454 (mm-40) cc_final: 0.6933 (mt0) REVERT: D 335 MET cc_start: 0.8705 (mtp) cc_final: 0.8441 (mtp) REVERT: D 368 ASN cc_start: 0.7356 (m-40) cc_final: 0.6911 (m110) REVERT: D 395 GLU cc_start: 0.5849 (tt0) cc_final: 0.5436 (pt0) REVERT: D 502 GLU cc_start: 0.6048 (tt0) cc_final: 0.5556 (mt-10) REVERT: D 510 LYS cc_start: 0.5239 (mttm) cc_final: 0.5009 (mttm) REVERT: D 663 LYS cc_start: 0.5896 (mmpt) cc_final: 0.5419 (mtmt) REVERT: D 666 GLU cc_start: 0.5593 (tt0) cc_final: 0.5259 (tt0) REVERT: D 675 GLU cc_start: 0.6068 (tp30) cc_final: 0.5665 (tp30) REVERT: D 686 GLU cc_start: 0.5774 (tt0) cc_final: 0.5110 (tp30) REVERT: D 691 LYS cc_start: 0.7251 (mttt) cc_final: 0.6884 (mttp) REVERT: D 702 ASN cc_start: 0.6055 (t0) cc_final: 0.5739 (t160) REVERT: D 706 ASP cc_start: 0.6399 (m-30) cc_final: 0.6100 (m-30) REVERT: D 708 LYS cc_start: 0.6833 (mttp) cc_final: 0.6488 (mttm) REVERT: D 797 LYS cc_start: 0.6250 (mttt) cc_final: 0.5872 (mtpm) REVERT: D 827 LYS cc_start: 0.7149 (ptmm) cc_final: 0.6899 (ptpt) REVERT: D 889 ASP cc_start: 0.5992 (t0) cc_final: 0.5785 (t0) REVERT: D 923 ASN cc_start: 0.6655 (m-40) cc_final: 0.6450 (m110) REVERT: D 930 MET cc_start: 0.5813 (tpp) cc_final: 0.5597 (tpp) REVERT: D 932 MET cc_start: 0.5541 (mmt) cc_final: 0.5130 (mmm) REVERT: D 933 GLU cc_start: 0.6105 (mm-30) cc_final: 0.5785 (mm-30) REVERT: D 936 LYS cc_start: 0.5751 (mttt) cc_final: 0.5535 (mtpt) REVERT: D 969 ARG cc_start: 0.6536 (mtp-110) cc_final: 0.5756 (mtp85) REVERT: D 1000 ASP cc_start: 0.7506 (m-30) cc_final: 0.7235 (m-30) REVERT: D 1065 ASP cc_start: 0.6471 (m-30) cc_final: 0.6037 (t0) REVERT: D 1107 ARG cc_start: 0.5540 (ttp-110) cc_final: 0.4965 (ptm-80) REVERT: D 1122 ARG cc_start: 0.4941 (mtm110) cc_final: 0.4413 (ttp80) REVERT: D 1123 ARG cc_start: 0.5672 (ttp80) cc_final: 0.5454 (ttp80) REVERT: D 1128 ARG cc_start: 0.5547 (OUTLIER) cc_final: 0.5075 (ttp-110) REVERT: D 1131 MET cc_start: 0.5662 (OUTLIER) cc_final: 0.5320 (tpp) REVERT: D 1157 MET cc_start: 0.7445 (mmm) cc_final: 0.7143 (mmt) REVERT: D 1269 ASP cc_start: 0.8516 (t0) cc_final: 0.8259 (t70) REVERT: D 1348 ASP cc_start: 0.7710 (t0) cc_final: 0.7431 (t70) REVERT: D 1350 LYS cc_start: 0.7463 (mttt) cc_final: 0.7187 (mttm) REVERT: D 1365 MET cc_start: 0.8231 (ptm) cc_final: 0.7856 (ptm) REVERT: D 1401 MET cc_start: 0.6146 (mtm) cc_final: 0.5918 (mtp) REVERT: B 80 HIS cc_start: 0.5867 (m-70) cc_final: 0.5409 (m170) REVERT: B 145 LEU cc_start: 0.7932 (tp) cc_final: 0.7637 (mt) REVERT: B 166 LYS cc_start: 0.6042 (tttm) cc_final: 0.5824 (ttmm) REVERT: B 239 MET cc_start: 0.5983 (ppp) cc_final: 0.5707 (ppp) REVERT: B 240 HIS cc_start: 0.6264 (m-70) cc_final: 0.5994 (m-70) REVERT: B 284 GLN cc_start: 0.7449 (mm-40) cc_final: 0.6926 (mt0) REVERT: B 335 MET cc_start: 0.8705 (mtp) cc_final: 0.8440 (mtp) REVERT: B 368 ASN cc_start: 0.7358 (m-40) cc_final: 0.6930 (m110) REVERT: B 395 GLU cc_start: 0.5849 (tt0) cc_final: 0.5437 (pt0) REVERT: B 502 GLU cc_start: 0.6049 (tt0) cc_final: 0.5557 (mt-10) REVERT: B 510 LYS cc_start: 0.5252 (mttm) cc_final: 0.5022 (mttm) REVERT: B 663 LYS cc_start: 0.5895 (mmpt) cc_final: 0.5417 (mtmt) REVERT: B 675 GLU cc_start: 0.6063 (tp30) cc_final: 0.5662 (tp30) REVERT: B 686 GLU cc_start: 0.5774 (tt0) cc_final: 0.5110 (tp30) REVERT: B 691 LYS cc_start: 0.7251 (mttt) cc_final: 0.6884 (mttp) REVERT: B 706 ASP cc_start: 0.6437 (m-30) cc_final: 0.6147 (m-30) REVERT: B 708 LYS cc_start: 0.6827 (mttp) cc_final: 0.6473 (mttm) REVERT: B 797 LYS cc_start: 0.6250 (mttt) cc_final: 0.5873 (mtpm) REVERT: B 827 LYS cc_start: 0.7163 (ptmm) cc_final: 0.6908 (ptpt) REVERT: B 889 ASP cc_start: 0.5981 (t0) cc_final: 0.5773 (t0) REVERT: B 923 ASN cc_start: 0.6650 (m110) cc_final: 0.6433 (m110) REVERT: B 932 MET cc_start: 0.5542 (mmt) cc_final: 0.5149 (mmm) REVERT: B 933 GLU cc_start: 0.6296 (tp30) cc_final: 0.5909 (mm-30) REVERT: B 936 LYS cc_start: 0.5749 (mttt) cc_final: 0.5531 (mtpt) REVERT: B 969 ARG cc_start: 0.6525 (mtp-110) cc_final: 0.5743 (mtp85) REVERT: B 1000 ASP cc_start: 0.7559 (m-30) cc_final: 0.7259 (m-30) REVERT: B 1005 GLU cc_start: 0.7036 (mt-10) cc_final: 0.6836 (mt-10) REVERT: B 1107 ARG cc_start: 0.5541 (ttp-110) cc_final: 0.4965 (ptm-80) REVERT: B 1122 ARG cc_start: 0.4947 (mtm110) cc_final: 0.4430 (ttp80) REVERT: B 1128 ARG cc_start: 0.5747 (OUTLIER) cc_final: 0.5275 (ttp-110) REVERT: B 1131 MET cc_start: 0.5662 (OUTLIER) cc_final: 0.5320 (tpp) REVERT: B 1160 PHE cc_start: 0.6661 (m-10) cc_final: 0.6335 (t80) REVERT: B 1269 ASP cc_start: 0.8515 (t0) cc_final: 0.8260 (t70) REVERT: B 1348 ASP cc_start: 0.7715 (t0) cc_final: 0.7435 (t70) REVERT: B 1350 LYS cc_start: 0.7464 (mttt) cc_final: 0.7188 (mttm) REVERT: B 1365 MET cc_start: 0.8235 (ptm) cc_final: 0.7861 (ptm) REVERT: B 1401 MET cc_start: 0.6150 (mtm) cc_final: 0.5921 (mtp) REVERT: C 80 HIS cc_start: 0.5884 (m-70) cc_final: 0.5443 (m170) REVERT: C 145 LEU cc_start: 0.7933 (tp) cc_final: 0.7638 (mt) REVERT: C 166 LYS cc_start: 0.6060 (tttm) cc_final: 0.5824 (ttmm) REVERT: C 284 GLN cc_start: 0.7450 (mm-40) cc_final: 0.6928 (mt0) REVERT: C 335 MET cc_start: 0.8704 (mtp) cc_final: 0.8440 (mtp) REVERT: C 368 ASN cc_start: 0.7352 (m-40) cc_final: 0.6903 (m110) REVERT: C 395 GLU cc_start: 0.5853 (tt0) cc_final: 0.5440 (pt0) REVERT: C 502 GLU cc_start: 0.6048 (tt0) cc_final: 0.5557 (mt-10) REVERT: C 510 LYS cc_start: 0.5253 (mttm) cc_final: 0.5020 (mttm) REVERT: C 663 LYS cc_start: 0.5895 (mmpt) cc_final: 0.5417 (mtmt) REVERT: C 675 GLU cc_start: 0.6077 (tp30) cc_final: 0.5674 (tp30) REVERT: C 686 GLU cc_start: 0.5794 (tt0) cc_final: 0.5130 (tp30) REVERT: C 691 LYS cc_start: 0.7238 (mttt) cc_final: 0.6891 (mttp) REVERT: C 706 ASP cc_start: 0.6437 (m-30) cc_final: 0.6147 (m-30) REVERT: C 708 LYS cc_start: 0.6826 (mttp) cc_final: 0.6473 (mttm) REVERT: C 797 LYS cc_start: 0.6250 (mttt) cc_final: 0.5866 (mtpm) REVERT: C 827 LYS cc_start: 0.7136 (ptmm) cc_final: 0.6878 (ptpt) REVERT: C 889 ASP cc_start: 0.5991 (t0) cc_final: 0.5784 (t0) REVERT: C 923 ASN cc_start: 0.6656 (m-40) cc_final: 0.6450 (m110) REVERT: C 930 MET cc_start: 0.5814 (tpp) cc_final: 0.5599 (tpp) REVERT: C 932 MET cc_start: 0.5556 (mmt) cc_final: 0.5147 (mmm) REVERT: C 933 GLU cc_start: 0.6104 (mm-30) cc_final: 0.5787 (mm-30) REVERT: C 936 LYS cc_start: 0.5747 (mttt) cc_final: 0.5531 (mtpt) REVERT: C 969 ARG cc_start: 0.6536 (mtp-110) cc_final: 0.5755 (mtp85) REVERT: C 1000 ASP cc_start: 0.7557 (m-30) cc_final: 0.7261 (m-30) REVERT: C 1005 GLU cc_start: 0.7036 (mt-10) cc_final: 0.6825 (mt-10) REVERT: C 1107 ARG cc_start: 0.5559 (ttp-110) cc_final: 0.4981 (ptm-80) REVERT: C 1122 ARG cc_start: 0.4930 (mtm110) cc_final: 0.4414 (ttp80) REVERT: C 1128 ARG cc_start: 0.5647 (OUTLIER) cc_final: 0.5153 (ttp-110) REVERT: C 1131 MET cc_start: 0.5662 (OUTLIER) cc_final: 0.5320 (tpp) REVERT: C 1157 MET cc_start: 0.7699 (mmm) cc_final: 0.7496 (mmt) REVERT: C 1269 ASP cc_start: 0.8516 (t0) cc_final: 0.8259 (t70) REVERT: C 1348 ASP cc_start: 0.7727 (t0) cc_final: 0.7438 (t70) REVERT: C 1350 LYS cc_start: 0.7466 (mttt) cc_final: 0.7191 (mttm) REVERT: C 1365 MET cc_start: 0.8232 (ptm) cc_final: 0.7842 (ptm) outliers start: 79 outliers final: 24 residues processed: 649 average time/residue: 1.9431 time to fit residues: 1499.9871 Evaluate side-chains 621 residues out of total 4700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 588 time to evaluate : 4.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 683 MET Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1128 ARG Chi-restraints excluded: chain A residue 1131 MET Chi-restraints excluded: chain A residue 1157 MET Chi-restraints excluded: chain A residue 1229 VAL Chi-restraints excluded: chain A residue 1243 ILE Chi-restraints excluded: chain A residue 1299 ASP Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 683 MET Chi-restraints excluded: chain D residue 1082 LEU Chi-restraints excluded: chain D residue 1128 ARG Chi-restraints excluded: chain D residue 1131 MET Chi-restraints excluded: chain D residue 1229 VAL Chi-restraints excluded: chain D residue 1243 ILE Chi-restraints excluded: chain D residue 1299 ASP Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 683 MET Chi-restraints excluded: chain B residue 1082 LEU Chi-restraints excluded: chain B residue 1128 ARG Chi-restraints excluded: chain B residue 1131 MET Chi-restraints excluded: chain B residue 1229 VAL Chi-restraints excluded: chain B residue 1243 ILE Chi-restraints excluded: chain B residue 1299 ASP Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 683 MET Chi-restraints excluded: chain C residue 1082 LEU Chi-restraints excluded: chain C residue 1128 ARG Chi-restraints excluded: chain C residue 1131 MET Chi-restraints excluded: chain C residue 1229 VAL Chi-restraints excluded: chain C residue 1243 ILE Chi-restraints excluded: chain C residue 1299 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 548 random chunks: chunk 492 optimal weight: 5.9990 chunk 374 optimal weight: 10.0000 chunk 258 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 237 optimal weight: 10.0000 chunk 334 optimal weight: 3.9990 chunk 500 optimal weight: 3.9990 chunk 529 optimal weight: 0.0000 chunk 261 optimal weight: 1.9990 chunk 474 optimal weight: 3.9990 chunk 142 optimal weight: 4.9990 overall best weight: 2.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 813 HIS A1282 ASN D1156 HIS D1282 ASN B1282 ASN C1282 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7141 moved from start: 0.3995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 43760 Z= 0.425 Angle : 0.645 8.225 59540 Z= 0.339 Chirality : 0.045 0.168 6772 Planarity : 0.005 0.051 7540 Dihedral : 8.705 89.909 7084 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.15 % Allowed : 12.10 % Favored : 85.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.11), residues: 5476 helix: 1.82 (0.09), residues: 3044 sheet: -1.07 (0.21), residues: 436 loop : -0.49 (0.14), residues: 1996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 606 HIS 0.006 0.001 HIS A 254 PHE 0.024 0.003 PHE D 879 TYR 0.024 0.003 TYR C1063 ARG 0.010 0.001 ARG B 152 *********************** 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 718 residues out of total 4700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 627 time to evaluate : 4.800 Fit side-chains REVERT: A 166 LYS cc_start: 0.6123 (tttm) cc_final: 0.5667 (ttmm) REVERT: A 170 LEU cc_start: 0.6614 (OUTLIER) cc_final: 0.6177 (mm) REVERT: A 284 GLN cc_start: 0.7504 (mm-40) cc_final: 0.6964 (mt0) REVERT: A 335 MET cc_start: 0.8687 (mtp) cc_final: 0.8471 (mtp) REVERT: A 395 GLU cc_start: 0.5933 (tt0) cc_final: 0.5478 (mt-10) REVERT: A 477 LYS cc_start: 0.6379 (mptt) cc_final: 0.6055 (mmtp) REVERT: A 502 GLU cc_start: 0.5965 (tt0) cc_final: 0.5527 (mt-10) REVERT: A 507 GLU cc_start: 0.5925 (tp30) cc_final: 0.5578 (tp30) REVERT: A 592 GLN cc_start: 0.6154 (OUTLIER) cc_final: 0.5649 (tp40) REVERT: A 663 LYS cc_start: 0.5814 (mmpt) cc_final: 0.5454 (mtmt) REVERT: A 666 GLU cc_start: 0.5771 (tt0) cc_final: 0.5438 (tt0) REVERT: A 667 GLU cc_start: 0.5670 (mt-10) cc_final: 0.5344 (mm-30) REVERT: A 686 GLU cc_start: 0.5770 (tt0) cc_final: 0.5137 (tp30) REVERT: A 691 LYS cc_start: 0.7095 (mttt) cc_final: 0.6778 (mttt) REVERT: A 706 ASP cc_start: 0.6606 (m-30) cc_final: 0.6395 (m-30) REVERT: A 797 LYS cc_start: 0.6081 (mttt) cc_final: 0.5679 (mtpm) REVERT: A 827 LYS cc_start: 0.7283 (ptmm) cc_final: 0.7081 (ptpt) REVERT: A 969 ARG cc_start: 0.6517 (mtp-110) cc_final: 0.5844 (mtp85) REVERT: A 1000 ASP cc_start: 0.7623 (m-30) cc_final: 0.7365 (m-30) REVERT: A 1005 GLU cc_start: 0.6692 (mt-10) cc_final: 0.6418 (mt-10) REVERT: A 1107 ARG cc_start: 0.5584 (ttp-110) cc_final: 0.4994 (ptm-80) REVERT: A 1108 LYS cc_start: 0.6127 (tmmt) cc_final: 0.5636 (ttpp) REVERT: A 1122 ARG cc_start: 0.5002 (mtm110) cc_final: 0.4560 (ttp80) REVERT: A 1128 ARG cc_start: 0.5823 (OUTLIER) cc_final: 0.5353 (ttp-110) REVERT: A 1151 ASP cc_start: 0.6843 (m-30) cc_final: 0.6626 (m-30) REVERT: A 1348 ASP cc_start: 0.7972 (t0) cc_final: 0.7655 (t0) REVERT: A 1365 MET cc_start: 0.8285 (ptm) cc_final: 0.7861 (ptm) REVERT: D 166 LYS cc_start: 0.6124 (tttm) cc_final: 0.5673 (ttmm) REVERT: D 170 LEU cc_start: 0.6605 (OUTLIER) cc_final: 0.6166 (mm) REVERT: D 239 MET cc_start: 0.6039 (ppp) cc_final: 0.4967 (mtm) REVERT: D 284 GLN cc_start: 0.7486 (mm-40) cc_final: 0.6943 (mt0) REVERT: D 335 MET cc_start: 0.8691 (mtp) cc_final: 0.8482 (mtp) REVERT: D 395 GLU cc_start: 0.5930 (tt0) cc_final: 0.5470 (mt-10) REVERT: D 477 LYS cc_start: 0.6377 (mptt) cc_final: 0.6050 (mmtp) REVERT: D 502 GLU cc_start: 0.6000 (tt0) cc_final: 0.5569 (mt-10) REVERT: D 507 GLU cc_start: 0.5913 (tp30) cc_final: 0.5631 (tp30) REVERT: D 663 LYS cc_start: 0.5813 (mmpt) cc_final: 0.5453 (mtmt) REVERT: D 666 GLU cc_start: 0.5817 (tt0) cc_final: 0.5459 (tt0) REVERT: D 667 GLU cc_start: 0.5660 (mt-10) cc_final: 0.5332 (mm-30) REVERT: D 686 GLU cc_start: 0.5764 (tt0) cc_final: 0.5138 (tp30) REVERT: D 691 LYS cc_start: 0.7071 (mttt) cc_final: 0.6735 (mttt) REVERT: D 694 MET cc_start: 0.5444 (OUTLIER) cc_final: 0.5226 (ttp) REVERT: D 706 ASP cc_start: 0.6520 (m-30) cc_final: 0.6263 (m-30) REVERT: D 708 LYS cc_start: 0.6955 (mttp) cc_final: 0.6555 (mttm) REVERT: D 797 LYS cc_start: 0.6082 (mttt) cc_final: 0.5682 (mtpm) REVERT: D 827 LYS cc_start: 0.7269 (ptmm) cc_final: 0.7067 (ptpt) REVERT: D 969 ARG cc_start: 0.6510 (mtp-110) cc_final: 0.5842 (mtp85) REVERT: D 1000 ASP cc_start: 0.7618 (m-30) cc_final: 0.7366 (m-30) REVERT: D 1005 GLU cc_start: 0.6713 (mt-10) cc_final: 0.6442 (mt-10) REVERT: D 1065 ASP cc_start: 0.6493 (m-30) cc_final: 0.6126 (t0) REVERT: D 1107 ARG cc_start: 0.5518 (ttp-110) cc_final: 0.4936 (ptm-80) REVERT: D 1108 LYS cc_start: 0.6037 (ttmt) cc_final: 0.5530 (ttpp) REVERT: D 1122 ARG cc_start: 0.5012 (mtm110) cc_final: 0.4558 (ttp80) REVERT: D 1128 ARG cc_start: 0.5649 (OUTLIER) cc_final: 0.5142 (ttp-110) REVERT: D 1151 ASP cc_start: 0.6714 (m-30) cc_final: 0.6451 (m-30) REVERT: D 1157 MET cc_start: 0.7461 (mmm) cc_final: 0.7181 (mmt) REVERT: D 1348 ASP cc_start: 0.7937 (t0) cc_final: 0.7662 (t0) REVERT: D 1365 MET cc_start: 0.8281 (ptm) cc_final: 0.7842 (ptm) REVERT: B 71 GLU cc_start: 0.5297 (OUTLIER) cc_final: 0.4720 (tm-30) REVERT: B 80 HIS cc_start: 0.5633 (m-70) cc_final: 0.5188 (m170) REVERT: B 166 LYS cc_start: 0.6124 (tttm) cc_final: 0.5674 (ttmm) REVERT: B 170 LEU cc_start: 0.6606 (OUTLIER) cc_final: 0.6168 (mm) REVERT: B 239 MET cc_start: 0.6039 (ppp) cc_final: 0.4967 (mtm) REVERT: B 284 GLN cc_start: 0.7488 (mm-40) cc_final: 0.6941 (mt0) REVERT: B 335 MET cc_start: 0.8691 (mtp) cc_final: 0.8480 (mtp) REVERT: B 395 GLU cc_start: 0.5930 (tt0) cc_final: 0.5469 (mt-10) REVERT: B 472 LYS cc_start: 0.5346 (mmmm) cc_final: 0.5016 (mtmt) REVERT: B 477 LYS cc_start: 0.6383 (mptt) cc_final: 0.6052 (mmtp) REVERT: B 502 GLU cc_start: 0.5985 (tt0) cc_final: 0.5546 (mt-10) REVERT: B 507 GLU cc_start: 0.5934 (tp30) cc_final: 0.5667 (tp30) REVERT: B 592 GLN cc_start: 0.6249 (OUTLIER) cc_final: 0.6044 (tm-30) REVERT: B 663 LYS cc_start: 0.5813 (mmpt) cc_final: 0.5454 (mtmt) REVERT: B 666 GLU cc_start: 0.5739 (tt0) cc_final: 0.5425 (tt0) REVERT: B 667 GLU cc_start: 0.5670 (mt-10) cc_final: 0.5344 (mm-30) REVERT: B 686 GLU cc_start: 0.5763 (tt0) cc_final: 0.5138 (tp30) REVERT: B 691 LYS cc_start: 0.7071 (mttt) cc_final: 0.6735 (mttt) REVERT: B 694 MET cc_start: 0.5453 (OUTLIER) cc_final: 0.5235 (ttp) REVERT: B 706 ASP cc_start: 0.6615 (m-30) cc_final: 0.6378 (m-30) REVERT: B 708 LYS cc_start: 0.6948 (mttp) cc_final: 0.6547 (mttm) REVERT: B 797 LYS cc_start: 0.6083 (mttt) cc_final: 0.5683 (mtpm) REVERT: B 827 LYS cc_start: 0.7263 (ptmm) cc_final: 0.7060 (ptpt) REVERT: B 932 MET cc_start: 0.5477 (mmt) cc_final: 0.5119 (mmm) REVERT: B 969 ARG cc_start: 0.6500 (mtp-110) cc_final: 0.5828 (mtp85) REVERT: B 1000 ASP cc_start: 0.7622 (m-30) cc_final: 0.7369 (m-30) REVERT: B 1005 GLU cc_start: 0.6776 (mt-10) cc_final: 0.6528 (mt-10) REVERT: B 1107 ARG cc_start: 0.5518 (ttp-110) cc_final: 0.4936 (ptm-80) REVERT: B 1108 LYS cc_start: 0.6037 (ttmt) cc_final: 0.5530 (ttpp) REVERT: B 1122 ARG cc_start: 0.4999 (mtm110) cc_final: 0.4553 (ttp80) REVERT: B 1128 ARG cc_start: 0.5725 (OUTLIER) cc_final: 0.5265 (ttp-110) REVERT: B 1151 ASP cc_start: 0.6784 (m-30) cc_final: 0.6489 (m-30) REVERT: B 1348 ASP cc_start: 0.7939 (t0) cc_final: 0.7664 (t0) REVERT: B 1365 MET cc_start: 0.8281 (ptm) cc_final: 0.7840 (ptm) REVERT: C 166 LYS cc_start: 0.6126 (tttm) cc_final: 0.5674 (ttmm) REVERT: C 170 LEU cc_start: 0.6608 (OUTLIER) cc_final: 0.6172 (mm) REVERT: C 284 GLN cc_start: 0.7503 (mm-40) cc_final: 0.6963 (mt0) REVERT: C 335 MET cc_start: 0.8688 (mtp) cc_final: 0.8479 (mtp) REVERT: C 395 GLU cc_start: 0.5932 (tt0) cc_final: 0.5478 (mt-10) REVERT: C 472 LYS cc_start: 0.5348 (mmmm) cc_final: 0.5015 (mtmt) REVERT: C 477 LYS cc_start: 0.6376 (mptt) cc_final: 0.6050 (mmtp) REVERT: C 502 GLU cc_start: 0.5984 (tt0) cc_final: 0.5548 (mt-10) REVERT: C 507 GLU cc_start: 0.5913 (tp30) cc_final: 0.5628 (tp30) REVERT: C 580 ILE cc_start: 0.6452 (pt) cc_final: 0.6245 (pt) REVERT: C 595 ARG cc_start: 0.5735 (mtt180) cc_final: 0.5442 (mtt180) REVERT: C 663 LYS cc_start: 0.5815 (mmpt) cc_final: 0.5456 (mtmt) REVERT: C 666 GLU cc_start: 0.5741 (tt0) cc_final: 0.5426 (tt0) REVERT: C 667 GLU cc_start: 0.5671 (mt-10) cc_final: 0.5345 (mm-30) REVERT: C 686 GLU cc_start: 0.5780 (tt0) cc_final: 0.5136 (tp30) REVERT: C 691 LYS cc_start: 0.7068 (mttt) cc_final: 0.6736 (mttt) REVERT: C 694 MET cc_start: 0.5499 (OUTLIER) cc_final: 0.5282 (ttp) REVERT: C 706 ASP cc_start: 0.6617 (m-30) cc_final: 0.6380 (m-30) REVERT: C 708 LYS cc_start: 0.6950 (mttp) cc_final: 0.6550 (mttm) REVERT: C 797 LYS cc_start: 0.6082 (mttt) cc_final: 0.5681 (mtpm) REVERT: C 827 LYS cc_start: 0.7281 (ptmm) cc_final: 0.7081 (ptpt) REVERT: C 969 ARG cc_start: 0.6510 (mtp-110) cc_final: 0.5843 (mtp85) REVERT: C 1000 ASP cc_start: 0.7618 (m-30) cc_final: 0.7365 (m-30) REVERT: C 1005 GLU cc_start: 0.6778 (mt-10) cc_final: 0.6531 (mt-10) REVERT: C 1107 ARG cc_start: 0.5548 (ttp-110) cc_final: 0.4959 (ptm-80) REVERT: C 1108 LYS cc_start: 0.6084 (ttmt) cc_final: 0.5625 (ttpp) REVERT: C 1122 ARG cc_start: 0.5065 (mtm110) cc_final: 0.4627 (ttp80) REVERT: C 1128 ARG cc_start: 0.5727 (OUTLIER) cc_final: 0.5291 (ttp-110) REVERT: C 1151 ASP cc_start: 0.6812 (m-30) cc_final: 0.6594 (m-30) REVERT: C 1157 MET cc_start: 0.7747 (mmm) cc_final: 0.7427 (mmt) REVERT: C 1348 ASP cc_start: 0.7955 (t0) cc_final: 0.7689 (t0) REVERT: C 1365 MET cc_start: 0.8285 (ptm) cc_final: 0.7857 (ptm) outliers start: 91 outliers final: 43 residues processed: 657 average time/residue: 2.0228 time to fit residues: 1578.4035 Evaluate side-chains 645 residues out of total 4700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 588 time to evaluate : 5.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 310 ARG Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 592 GLN Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 683 MET Chi-restraints excluded: chain A residue 694 MET Chi-restraints excluded: chain A residue 1075 LEU Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1128 ARG Chi-restraints excluded: chain A residue 1164 LEU Chi-restraints excluded: chain A residue 1229 VAL Chi-restraints excluded: chain A residue 1238 MET Chi-restraints excluded: chain A residue 1243 ILE Chi-restraints excluded: chain D residue 70 MET Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 310 ARG Chi-restraints excluded: chain D residue 357 THR Chi-restraints excluded: chain D residue 615 MET Chi-restraints excluded: chain D residue 683 MET Chi-restraints excluded: chain D residue 694 MET Chi-restraints excluded: chain D residue 1064 LYS Chi-restraints excluded: chain D residue 1082 LEU Chi-restraints excluded: chain D residue 1128 ARG Chi-restraints excluded: chain D residue 1229 VAL Chi-restraints excluded: chain D residue 1238 MET Chi-restraints excluded: chain D residue 1243 ILE Chi-restraints excluded: chain B residue 70 MET Chi-restraints excluded: chain B residue 71 GLU Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 310 ARG Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 592 GLN Chi-restraints excluded: chain B residue 615 MET Chi-restraints excluded: chain B residue 683 MET Chi-restraints excluded: chain B residue 694 MET Chi-restraints excluded: chain B residue 1082 LEU Chi-restraints excluded: chain B residue 1128 ARG Chi-restraints excluded: chain B residue 1229 VAL Chi-restraints excluded: chain B residue 1238 MET Chi-restraints excluded: chain B residue 1243 ILE Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 310 ARG Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 615 MET Chi-restraints excluded: chain C residue 683 MET Chi-restraints excluded: chain C residue 694 MET Chi-restraints excluded: chain C residue 1082 LEU Chi-restraints excluded: chain C residue 1128 ARG Chi-restraints excluded: chain C residue 1164 LEU Chi-restraints excluded: chain C residue 1229 VAL Chi-restraints excluded: chain C residue 1238 MET Chi-restraints excluded: chain C residue 1243 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 548 random chunks: chunk 441 optimal weight: 0.9980 chunk 300 optimal weight: 4.9990 chunk 7 optimal weight: 0.6980 chunk 394 optimal weight: 0.9990 chunk 218 optimal weight: 1.9990 chunk 452 optimal weight: 4.9990 chunk 366 optimal weight: 0.6980 chunk 0 optimal weight: 7.9990 chunk 270 optimal weight: 0.6980 chunk 475 optimal weight: 1.9990 chunk 133 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN D 61 ASN D1145 GLN C 61 ASN C1145 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7114 moved from start: 0.3929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 43760 Z= 0.172 Angle : 0.487 7.830 59540 Z= 0.257 Chirality : 0.039 0.166 6772 Planarity : 0.004 0.045 7540 Dihedral : 8.250 89.090 7084 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.80 % Allowed : 12.67 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.11), residues: 5476 helix: 2.12 (0.09), residues: 3016 sheet: -1.23 (0.21), residues: 416 loop : -0.34 (0.14), residues: 2044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B1124 HIS 0.003 0.001 HIS A 813 PHE 0.016 0.001 PHE B 879 TYR 0.023 0.002 TYR A 420 ARG 0.008 0.000 ARG B 152 *********************** 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 685 residues out of total 4700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 609 time to evaluate : 4.887 Fit side-chains REVERT: A 166 LYS cc_start: 0.6170 (tttm) cc_final: 0.5726 (ttmm) REVERT: A 170 LEU cc_start: 0.6638 (OUTLIER) cc_final: 0.6185 (mm) REVERT: A 284 GLN cc_start: 0.7468 (mm-40) cc_final: 0.6913 (mt0) REVERT: A 335 MET cc_start: 0.8685 (mtp) cc_final: 0.8447 (mtp) REVERT: A 395 GLU cc_start: 0.5923 (tt0) cc_final: 0.5330 (pt0) REVERT: A 477 LYS cc_start: 0.6378 (mptt) cc_final: 0.6045 (mmtp) REVERT: A 502 GLU cc_start: 0.5976 (tt0) cc_final: 0.5651 (mt-10) REVERT: A 507 GLU cc_start: 0.5951 (tp30) cc_final: 0.5608 (tp30) REVERT: A 510 LYS cc_start: 0.5122 (mttm) cc_final: 0.4908 (mttm) REVERT: A 618 HIS cc_start: 0.5724 (t70) cc_final: 0.5450 (t70) REVERT: A 663 LYS cc_start: 0.5943 (mmpt) cc_final: 0.5481 (mtmt) REVERT: A 666 GLU cc_start: 0.5614 (tt0) cc_final: 0.5261 (tt0) REVERT: A 686 GLU cc_start: 0.5691 (tt0) cc_final: 0.5103 (tp30) REVERT: A 691 LYS cc_start: 0.7062 (mttt) cc_final: 0.6764 (mttt) REVERT: A 706 ASP cc_start: 0.6607 (m-30) cc_final: 0.6379 (m-30) REVERT: A 797 LYS cc_start: 0.6020 (mttt) cc_final: 0.5606 (mtpm) REVERT: A 827 LYS cc_start: 0.7314 (ptmm) cc_final: 0.7018 (ptpt) REVERT: A 933 GLU cc_start: 0.6079 (mm-30) cc_final: 0.5721 (mm-30) REVERT: A 969 ARG cc_start: 0.6505 (mtp-110) cc_final: 0.5680 (mtp85) REVERT: A 1000 ASP cc_start: 0.7646 (m-30) cc_final: 0.7335 (m-30) REVERT: A 1005 GLU cc_start: 0.6890 (mt-10) cc_final: 0.6560 (mt-10) REVERT: A 1107 ARG cc_start: 0.5744 (ttp-110) cc_final: 0.5094 (ptm-80) REVERT: A 1108 LYS cc_start: 0.6107 (tmmt) cc_final: 0.5642 (ttpp) REVERT: A 1122 ARG cc_start: 0.5058 (mtm110) cc_final: 0.4655 (ttp80) REVERT: A 1128 ARG cc_start: 0.5909 (OUTLIER) cc_final: 0.5469 (ttp-110) REVERT: A 1151 ASP cc_start: 0.6863 (m-30) cc_final: 0.6501 (m-30) REVERT: A 1160 PHE cc_start: 0.6817 (m-10) cc_final: 0.6176 (t80) REVERT: A 1348 ASP cc_start: 0.7894 (t0) cc_final: 0.7510 (t70) REVERT: A 1365 MET cc_start: 0.8212 (ptm) cc_final: 0.7936 (ptm) REVERT: A 1401 MET cc_start: 0.6919 (mtp) cc_final: 0.6589 (mtp) REVERT: A 1463 HIS cc_start: 0.8248 (m90) cc_final: 0.8012 (m-70) REVERT: D 80 HIS cc_start: 0.5709 (m-70) cc_final: 0.5230 (m170) REVERT: D 166 LYS cc_start: 0.6141 (tttm) cc_final: 0.5687 (ttmm) REVERT: D 170 LEU cc_start: 0.6630 (OUTLIER) cc_final: 0.6183 (mm) REVERT: D 284 GLN cc_start: 0.7451 (mm-40) cc_final: 0.6893 (mt0) REVERT: D 335 MET cc_start: 0.8685 (mtp) cc_final: 0.8452 (mtp) REVERT: D 395 GLU cc_start: 0.5923 (tt0) cc_final: 0.5330 (pt0) REVERT: D 456 MET cc_start: 0.4863 (OUTLIER) cc_final: 0.4265 (ttp) REVERT: D 477 LYS cc_start: 0.6373 (mptt) cc_final: 0.6039 (mmtp) REVERT: D 502 GLU cc_start: 0.6007 (tt0) cc_final: 0.5652 (mt-10) REVERT: D 507 GLU cc_start: 0.6019 (tp30) cc_final: 0.5685 (tp30) REVERT: D 663 LYS cc_start: 0.5936 (mmpt) cc_final: 0.5478 (mtmt) REVERT: D 666 GLU cc_start: 0.5615 (tt0) cc_final: 0.5285 (tt0) REVERT: D 686 GLU cc_start: 0.5713 (tt0) cc_final: 0.5101 (tp30) REVERT: D 691 LYS cc_start: 0.7069 (mttt) cc_final: 0.6785 (mttp) REVERT: D 694 MET cc_start: 0.5430 (OUTLIER) cc_final: 0.5226 (ttp) REVERT: D 706 ASP cc_start: 0.6622 (m-30) cc_final: 0.6343 (m-30) REVERT: D 708 LYS cc_start: 0.6914 (mttp) cc_final: 0.6514 (mttm) REVERT: D 797 LYS cc_start: 0.6035 (mttt) cc_final: 0.5626 (mtpm) REVERT: D 827 LYS cc_start: 0.7304 (ptmm) cc_final: 0.7016 (ptpt) REVERT: D 923 ASN cc_start: 0.6733 (m-40) cc_final: 0.6527 (m110) REVERT: D 969 ARG cc_start: 0.6505 (mtp-110) cc_final: 0.5682 (mtp85) REVERT: D 1000 ASP cc_start: 0.7649 (m-30) cc_final: 0.7346 (m-30) REVERT: D 1005 GLU cc_start: 0.6872 (mt-10) cc_final: 0.6537 (mt-10) REVERT: D 1065 ASP cc_start: 0.6447 (m-30) cc_final: 0.6090 (t0) REVERT: D 1107 ARG cc_start: 0.5723 (ttp-110) cc_final: 0.5070 (ptm-80) REVERT: D 1108 LYS cc_start: 0.6173 (ttmt) cc_final: 0.5659 (ttpp) REVERT: D 1122 ARG cc_start: 0.5037 (mtm110) cc_final: 0.4534 (ttp80) REVERT: D 1128 ARG cc_start: 0.5804 (OUTLIER) cc_final: 0.5371 (ttp-110) REVERT: D 1151 ASP cc_start: 0.6889 (m-30) cc_final: 0.6547 (m-30) REVERT: D 1157 MET cc_start: 0.7422 (mmm) cc_final: 0.6998 (mmt) REVERT: D 1348 ASP cc_start: 0.7790 (t0) cc_final: 0.7451 (t70) REVERT: D 1365 MET cc_start: 0.8199 (ptm) cc_final: 0.7912 (ptm) REVERT: D 1401 MET cc_start: 0.6907 (mtp) cc_final: 0.6589 (mtp) REVERT: D 1463 HIS cc_start: 0.8248 (m-70) cc_final: 0.8011 (m-70) REVERT: B 71 GLU cc_start: 0.5277 (tm-30) cc_final: 0.4740 (tm-30) REVERT: B 80 HIS cc_start: 0.5714 (m-70) cc_final: 0.5254 (m170) REVERT: B 166 LYS cc_start: 0.6139 (tttm) cc_final: 0.5686 (ttmm) REVERT: B 170 LEU cc_start: 0.6630 (OUTLIER) cc_final: 0.6183 (mm) REVERT: B 284 GLN cc_start: 0.7449 (mm-40) cc_final: 0.6908 (mt0) REVERT: B 335 MET cc_start: 0.8686 (mtp) cc_final: 0.8453 (mtp) REVERT: B 395 GLU cc_start: 0.5923 (tt0) cc_final: 0.5330 (pt0) REVERT: B 456 MET cc_start: 0.4882 (ttm) cc_final: 0.4252 (ttp) REVERT: B 477 LYS cc_start: 0.6385 (mptt) cc_final: 0.6039 (mmtp) REVERT: B 502 GLU cc_start: 0.6056 (tt0) cc_final: 0.5719 (mt-10) REVERT: B 507 GLU cc_start: 0.6022 (tp30) cc_final: 0.5689 (tp30) REVERT: B 618 HIS cc_start: 0.5723 (t70) cc_final: 0.5469 (t70) REVERT: B 663 LYS cc_start: 0.5968 (mmpt) cc_final: 0.5523 (mtmt) REVERT: B 666 GLU cc_start: 0.5668 (tt0) cc_final: 0.5342 (tt0) REVERT: B 686 GLU cc_start: 0.5714 (tt0) cc_final: 0.5101 (tp30) REVERT: B 691 LYS cc_start: 0.7069 (mttt) cc_final: 0.6785 (mttp) REVERT: B 694 MET cc_start: 0.5455 (OUTLIER) cc_final: 0.5251 (ttp) REVERT: B 706 ASP cc_start: 0.6571 (m-30) cc_final: 0.6344 (m-30) REVERT: B 708 LYS cc_start: 0.6917 (mttp) cc_final: 0.6521 (mttm) REVERT: B 797 LYS cc_start: 0.6021 (mttt) cc_final: 0.5609 (mtpm) REVERT: B 827 LYS cc_start: 0.7294 (ptmm) cc_final: 0.7004 (ptpt) REVERT: B 969 ARG cc_start: 0.6505 (mtp-110) cc_final: 0.5676 (mtp85) REVERT: B 1000 ASP cc_start: 0.7659 (m-30) cc_final: 0.7366 (m-30) REVERT: B 1107 ARG cc_start: 0.5722 (ttp-110) cc_final: 0.5069 (ptm-80) REVERT: B 1108 LYS cc_start: 0.6146 (ttmt) cc_final: 0.5633 (ttpp) REVERT: B 1122 ARG cc_start: 0.5058 (mtm110) cc_final: 0.4555 (ttp80) REVERT: B 1128 ARG cc_start: 0.5882 (OUTLIER) cc_final: 0.5455 (ttp-110) REVERT: B 1151 ASP cc_start: 0.6847 (m-30) cc_final: 0.6506 (m-30) REVERT: B 1348 ASP cc_start: 0.7790 (t0) cc_final: 0.7452 (t70) REVERT: B 1365 MET cc_start: 0.8198 (ptm) cc_final: 0.7910 (ptm) REVERT: B 1401 MET cc_start: 0.6930 (mtp) cc_final: 0.6605 (mtp) REVERT: B 1463 HIS cc_start: 0.8249 (m-70) cc_final: 0.8010 (m-70) REVERT: C 166 LYS cc_start: 0.6171 (tttm) cc_final: 0.5727 (ttmm) REVERT: C 170 LEU cc_start: 0.6639 (OUTLIER) cc_final: 0.6186 (mm) REVERT: C 284 GLN cc_start: 0.7448 (mm-40) cc_final: 0.6910 (mt0) REVERT: C 335 MET cc_start: 0.8686 (mtp) cc_final: 0.8453 (mtp) REVERT: C 395 GLU cc_start: 0.5925 (tt0) cc_final: 0.5332 (pt0) REVERT: C 456 MET cc_start: 0.4869 (OUTLIER) cc_final: 0.4271 (ttp) REVERT: C 472 LYS cc_start: 0.5334 (mmmm) cc_final: 0.4931 (mtmt) REVERT: C 477 LYS cc_start: 0.6373 (mptt) cc_final: 0.6041 (mmtp) REVERT: C 502 GLU cc_start: 0.6067 (tt0) cc_final: 0.5730 (mt-10) REVERT: C 507 GLU cc_start: 0.6020 (tp30) cc_final: 0.5721 (tp30) REVERT: C 510 LYS cc_start: 0.5269 (mttm) cc_final: 0.5039 (mttm) REVERT: C 618 HIS cc_start: 0.5722 (t70) cc_final: 0.5465 (t70) REVERT: C 663 LYS cc_start: 0.5967 (mmpt) cc_final: 0.5523 (mtmt) REVERT: C 666 GLU cc_start: 0.5668 (tt0) cc_final: 0.5343 (tt0) REVERT: C 686 GLU cc_start: 0.5688 (tt0) cc_final: 0.5102 (tp30) REVERT: C 691 LYS cc_start: 0.7025 (mttt) cc_final: 0.6740 (mttp) REVERT: C 694 MET cc_start: 0.5410 (OUTLIER) cc_final: 0.5202 (ttp) REVERT: C 706 ASP cc_start: 0.6571 (m-30) cc_final: 0.6343 (m-30) REVERT: C 708 LYS cc_start: 0.6919 (mttp) cc_final: 0.6523 (mttm) REVERT: C 797 LYS cc_start: 0.6021 (mttt) cc_final: 0.5609 (mtpm) REVERT: C 827 LYS cc_start: 0.7298 (ptmm) cc_final: 0.7000 (ptpt) REVERT: C 923 ASN cc_start: 0.6734 (m-40) cc_final: 0.6525 (m110) REVERT: C 933 GLU cc_start: 0.6050 (mm-30) cc_final: 0.5707 (mm-30) REVERT: C 969 ARG cc_start: 0.6505 (mtp-110) cc_final: 0.5682 (mtp85) REVERT: C 1000 ASP cc_start: 0.7656 (m-30) cc_final: 0.7362 (m-30) REVERT: C 1107 ARG cc_start: 0.5739 (ttp-110) cc_final: 0.5083 (ptm-80) REVERT: C 1108 LYS cc_start: 0.6159 (ttmt) cc_final: 0.5659 (ttpp) REVERT: C 1122 ARG cc_start: 0.5045 (mtm110) cc_final: 0.4544 (ttp80) REVERT: C 1128 ARG cc_start: 0.5873 (OUTLIER) cc_final: 0.5417 (ttp-110) REVERT: C 1151 ASP cc_start: 0.6755 (m-30) cc_final: 0.6429 (m-30) REVERT: C 1157 MET cc_start: 0.7646 (mmm) cc_final: 0.7388 (mmt) REVERT: C 1348 ASP cc_start: 0.7771 (t0) cc_final: 0.7443 (t70) REVERT: C 1365 MET cc_start: 0.8207 (ptm) cc_final: 0.7930 (ptm) REVERT: C 1463 HIS cc_start: 0.8250 (m90) cc_final: 0.8018 (m-70) outliers start: 76 outliers final: 37 residues processed: 631 average time/residue: 1.9560 time to fit residues: 1475.8380 Evaluate side-chains 637 residues out of total 4700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 587 time to evaluate : 5.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 683 MET Chi-restraints excluded: chain A residue 694 MET Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1128 ARG Chi-restraints excluded: chain A residue 1229 VAL Chi-restraints excluded: chain A residue 1238 MET Chi-restraints excluded: chain A residue 1243 ILE Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 456 MET Chi-restraints excluded: chain D residue 615 MET Chi-restraints excluded: chain D residue 646 LEU Chi-restraints excluded: chain D residue 683 MET Chi-restraints excluded: chain D residue 694 MET Chi-restraints excluded: chain D residue 1064 LYS Chi-restraints excluded: chain D residue 1082 LEU Chi-restraints excluded: chain D residue 1128 ARG Chi-restraints excluded: chain D residue 1229 VAL Chi-restraints excluded: chain D residue 1238 MET Chi-restraints excluded: chain D residue 1243 ILE Chi-restraints excluded: chain B residue 70 MET Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 615 MET Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 683 MET Chi-restraints excluded: chain B residue 694 MET Chi-restraints excluded: chain B residue 1082 LEU Chi-restraints excluded: chain B residue 1128 ARG Chi-restraints excluded: chain B residue 1229 VAL Chi-restraints excluded: chain B residue 1238 MET Chi-restraints excluded: chain B residue 1243 ILE Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 456 MET Chi-restraints excluded: chain C residue 615 MET Chi-restraints excluded: chain C residue 646 LEU Chi-restraints excluded: chain C residue 683 MET Chi-restraints excluded: chain C residue 694 MET Chi-restraints excluded: chain C residue 1082 LEU Chi-restraints excluded: chain C residue 1128 ARG Chi-restraints excluded: chain C residue 1229 VAL Chi-restraints excluded: chain C residue 1238 MET Chi-restraints excluded: chain C residue 1243 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 548 random chunks: chunk 178 optimal weight: 9.9990 chunk 477 optimal weight: 2.9990 chunk 104 optimal weight: 7.9990 chunk 310 optimal weight: 10.0000 chunk 130 optimal weight: 2.9990 chunk 530 optimal weight: 1.9990 chunk 440 optimal weight: 4.9990 chunk 245 optimal weight: 2.9990 chunk 44 optimal weight: 6.9990 chunk 175 optimal weight: 0.0370 chunk 278 optimal weight: 5.9990 overall best weight: 2.2066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN A 82 HIS D 61 ASN D 82 HIS D 450 ASN D1101 GLN B 61 ASN B 82 HIS B 450 ASN B1101 GLN B1156 HIS C 61 ASN C 82 HIS C 450 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7139 moved from start: 0.4179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 43760 Z= 0.335 Angle : 0.582 7.904 59540 Z= 0.305 Chirality : 0.042 0.180 6772 Planarity : 0.005 0.046 7540 Dihedral : 8.532 89.375 7084 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.24 % Allowed : 12.78 % Favored : 84.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.11), residues: 5476 helix: 1.95 (0.09), residues: 3036 sheet: -1.29 (0.21), residues: 436 loop : -0.51 (0.14), residues: 2004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C1124 HIS 0.005 0.001 HIS A1156 PHE 0.029 0.002 PHE B 496 TYR 0.021 0.002 TYR A1063 ARG 0.009 0.001 ARG C 152 *********************** 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 678 residues out of total 4700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 583 time to evaluate : 4.948 Fit side-chains REVERT: A 166 LYS cc_start: 0.6207 (tttm) cc_final: 0.5903 (ttmm) REVERT: A 284 GLN cc_start: 0.7546 (mm-40) cc_final: 0.6961 (mt0) REVERT: A 335 MET cc_start: 0.8690 (mtp) cc_final: 0.8420 (mtp) REVERT: A 395 GLU cc_start: 0.5953 (tt0) cc_final: 0.5463 (mt-10) REVERT: A 477 LYS cc_start: 0.6504 (mptt) cc_final: 0.5842 (mmtp) REVERT: A 507 GLU cc_start: 0.5967 (tp30) cc_final: 0.5640 (tp30) REVERT: A 618 HIS cc_start: 0.5733 (t70) cc_final: 0.5460 (t70) REVERT: A 663 LYS cc_start: 0.5842 (mmpt) cc_final: 0.5378 (mtmt) REVERT: A 666 GLU cc_start: 0.5764 (tt0) cc_final: 0.5439 (tt0) REVERT: A 686 GLU cc_start: 0.5840 (tt0) cc_final: 0.5199 (tp30) REVERT: A 691 LYS cc_start: 0.7107 (mttt) cc_final: 0.6793 (mttp) REVERT: A 706 ASP cc_start: 0.6592 (m-30) cc_final: 0.6373 (m-30) REVERT: A 827 LYS cc_start: 0.7336 (ptmm) cc_final: 0.7084 (ptpt) REVERT: A 932 MET cc_start: 0.5509 (mmt) cc_final: 0.5140 (mmm) REVERT: A 969 ARG cc_start: 0.6526 (mtp-110) cc_final: 0.5687 (mtp85) REVERT: A 1000 ASP cc_start: 0.7624 (m-30) cc_final: 0.7318 (m-30) REVERT: A 1005 GLU cc_start: 0.6760 (mt-10) cc_final: 0.6418 (mt-10) REVERT: A 1107 ARG cc_start: 0.5595 (ttp-110) cc_final: 0.4987 (ptm-80) REVERT: A 1108 LYS cc_start: 0.6102 (tmmt) cc_final: 0.5616 (ttpp) REVERT: A 1122 ARG cc_start: 0.5119 (mtm110) cc_final: 0.4690 (ttp80) REVERT: A 1128 ARG cc_start: 0.5868 (OUTLIER) cc_final: 0.5439 (ttp-110) REVERT: A 1147 MET cc_start: 0.6572 (mmm) cc_final: 0.6278 (mtm) REVERT: A 1151 ASP cc_start: 0.6809 (m-30) cc_final: 0.6434 (m-30) REVERT: A 1252 GLU cc_start: 0.8538 (OUTLIER) cc_final: 0.8305 (tp30) REVERT: A 1348 ASP cc_start: 0.7955 (t0) cc_final: 0.7567 (t70) REVERT: A 1365 MET cc_start: 0.8238 (ptm) cc_final: 0.7905 (ptm) REVERT: A 1401 MET cc_start: 0.7015 (mtp) cc_final: 0.6692 (mtp) REVERT: D 166 LYS cc_start: 0.6149 (tttm) cc_final: 0.5843 (ttmm) REVERT: D 284 GLN cc_start: 0.7532 (mm-40) cc_final: 0.6904 (mt0) REVERT: D 335 MET cc_start: 0.8697 (mtp) cc_final: 0.8432 (mtp) REVERT: D 395 GLU cc_start: 0.5950 (tt0) cc_final: 0.5461 (mt-10) REVERT: D 456 MET cc_start: 0.5096 (OUTLIER) cc_final: 0.4479 (ttp) REVERT: D 477 LYS cc_start: 0.6500 (mptt) cc_final: 0.5824 (mmtp) REVERT: D 502 GLU cc_start: 0.5942 (tt0) cc_final: 0.5650 (mt-10) REVERT: D 507 GLU cc_start: 0.5967 (tp30) cc_final: 0.5647 (tp30) REVERT: D 663 LYS cc_start: 0.5856 (mmpt) cc_final: 0.5393 (mtmt) REVERT: D 666 GLU cc_start: 0.5760 (tt0) cc_final: 0.5420 (tt0) REVERT: D 686 GLU cc_start: 0.5747 (tt0) cc_final: 0.5117 (tp30) REVERT: D 694 MET cc_start: 0.5471 (OUTLIER) cc_final: 0.5254 (ttp) REVERT: D 706 ASP cc_start: 0.6587 (m-30) cc_final: 0.6358 (m-30) REVERT: D 708 LYS cc_start: 0.6947 (mttp) cc_final: 0.6526 (mttm) REVERT: D 827 LYS cc_start: 0.7321 (ptmm) cc_final: 0.7068 (ptpt) REVERT: D 932 MET cc_start: 0.5503 (mmt) cc_final: 0.5133 (mmm) REVERT: D 969 ARG cc_start: 0.6529 (mtp-110) cc_final: 0.5689 (mtp85) REVERT: D 1000 ASP cc_start: 0.7623 (m-30) cc_final: 0.7324 (m-30) REVERT: D 1005 GLU cc_start: 0.6806 (mt-10) cc_final: 0.6458 (mt-10) REVERT: D 1065 ASP cc_start: 0.6542 (m-30) cc_final: 0.6198 (t0) REVERT: D 1107 ARG cc_start: 0.5540 (ttp-110) cc_final: 0.4940 (ptm-80) REVERT: D 1108 LYS cc_start: 0.6047 (ttmt) cc_final: 0.5556 (ttpp) REVERT: D 1122 ARG cc_start: 0.5045 (mtm110) cc_final: 0.4618 (ttp80) REVERT: D 1128 ARG cc_start: 0.5752 (OUTLIER) cc_final: 0.5294 (ttp-110) REVERT: D 1151 ASP cc_start: 0.6710 (m-30) cc_final: 0.6328 (m-30) REVERT: D 1252 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.8258 (tp30) REVERT: D 1348 ASP cc_start: 0.7879 (t0) cc_final: 0.7495 (t70) REVERT: D 1365 MET cc_start: 0.8194 (ptm) cc_final: 0.7846 (ptm) REVERT: D 1401 MET cc_start: 0.7012 (mtp) cc_final: 0.6697 (mtp) REVERT: B 71 GLU cc_start: 0.5355 (tm-30) cc_final: 0.4837 (tm-30) REVERT: B 166 LYS cc_start: 0.6188 (tttm) cc_final: 0.5885 (ttmm) REVERT: B 284 GLN cc_start: 0.7533 (mm-40) cc_final: 0.6929 (mt0) REVERT: B 335 MET cc_start: 0.8691 (mtp) cc_final: 0.8427 (mtp) REVERT: B 395 GLU cc_start: 0.5950 (tt0) cc_final: 0.5461 (mt-10) REVERT: B 477 LYS cc_start: 0.6502 (mptt) cc_final: 0.5826 (mmtp) REVERT: B 502 GLU cc_start: 0.5935 (tt0) cc_final: 0.5657 (mt-10) REVERT: B 507 GLU cc_start: 0.6040 (tp30) cc_final: 0.5708 (tp30) REVERT: B 618 HIS cc_start: 0.5714 (t70) cc_final: 0.5469 (t70) REVERT: B 663 LYS cc_start: 0.5855 (mmpt) cc_final: 0.5392 (mtmt) REVERT: B 666 GLU cc_start: 0.5729 (tt0) cc_final: 0.5421 (tt0) REVERT: B 686 GLU cc_start: 0.5746 (tt0) cc_final: 0.5117 (tp30) REVERT: B 694 MET cc_start: 0.5468 (OUTLIER) cc_final: 0.5254 (ttp) REVERT: B 708 LYS cc_start: 0.6934 (mttp) cc_final: 0.6514 (mttm) REVERT: B 827 LYS cc_start: 0.7327 (ptmm) cc_final: 0.7073 (ptpt) REVERT: B 932 MET cc_start: 0.5486 (mmt) cc_final: 0.5098 (mmm) REVERT: B 969 ARG cc_start: 0.6502 (mtp-110) cc_final: 0.5657 (mtp85) REVERT: B 1000 ASP cc_start: 0.7659 (m-30) cc_final: 0.7409 (m-30) REVERT: B 1107 ARG cc_start: 0.5540 (ttp-110) cc_final: 0.4939 (ptm-80) REVERT: B 1108 LYS cc_start: 0.6047 (ttmt) cc_final: 0.5556 (ttpp) REVERT: B 1122 ARG cc_start: 0.5044 (mtm110) cc_final: 0.4633 (ttp80) REVERT: B 1128 ARG cc_start: 0.5846 (OUTLIER) cc_final: 0.5417 (ttp-110) REVERT: B 1147 MET cc_start: 0.6429 (mmm) cc_final: 0.6201 (mtm) REVERT: B 1151 ASP cc_start: 0.6874 (m-30) cc_final: 0.6486 (m-30) REVERT: B 1252 GLU cc_start: 0.8538 (OUTLIER) cc_final: 0.8306 (tp30) REVERT: B 1348 ASP cc_start: 0.7882 (t0) cc_final: 0.7498 (t70) REVERT: B 1365 MET cc_start: 0.8202 (ptm) cc_final: 0.7858 (ptm) REVERT: B 1401 MET cc_start: 0.7010 (mtp) cc_final: 0.6704 (mtp) REVERT: C 166 LYS cc_start: 0.6205 (tttm) cc_final: 0.5902 (ttmm) REVERT: C 284 GLN cc_start: 0.7544 (mm-40) cc_final: 0.6955 (mt0) REVERT: C 335 MET cc_start: 0.8700 (mtp) cc_final: 0.8436 (mtp) REVERT: C 395 GLU cc_start: 0.5951 (tt0) cc_final: 0.5461 (mt-10) REVERT: C 456 MET cc_start: 0.5101 (ttm) cc_final: 0.4476 (ttp) REVERT: C 477 LYS cc_start: 0.6506 (mptt) cc_final: 0.5832 (mmtp) REVERT: C 502 GLU cc_start: 0.5932 (tt0) cc_final: 0.5649 (mt-10) REVERT: C 507 GLU cc_start: 0.5932 (tp30) cc_final: 0.5618 (tp30) REVERT: C 595 ARG cc_start: 0.5513 (mtp180) cc_final: 0.5229 (mtt180) REVERT: C 618 HIS cc_start: 0.5714 (t70) cc_final: 0.5471 (t70) REVERT: C 663 LYS cc_start: 0.5856 (mmpt) cc_final: 0.5392 (mtmt) REVERT: C 666 GLU cc_start: 0.5728 (tt0) cc_final: 0.5420 (tt0) REVERT: C 686 GLU cc_start: 0.5725 (tt0) cc_final: 0.5123 (tp30) REVERT: C 694 MET cc_start: 0.5445 (OUTLIER) cc_final: 0.5230 (ttp) REVERT: C 708 LYS cc_start: 0.6934 (mttp) cc_final: 0.6514 (mttm) REVERT: C 827 LYS cc_start: 0.7340 (ptmm) cc_final: 0.7084 (ptpt) REVERT: C 969 ARG cc_start: 0.6530 (mtp-110) cc_final: 0.5690 (mtp85) REVERT: C 1000 ASP cc_start: 0.7657 (m-30) cc_final: 0.7406 (m-30) REVERT: C 1107 ARG cc_start: 0.5636 (ttp-110) cc_final: 0.5024 (ptm-80) REVERT: C 1108 LYS cc_start: 0.6097 (ttmt) cc_final: 0.5603 (ttpp) REVERT: C 1122 ARG cc_start: 0.5118 (mtm110) cc_final: 0.4690 (ttp80) REVERT: C 1128 ARG cc_start: 0.5897 (OUTLIER) cc_final: 0.5473 (ttp-110) REVERT: C 1151 ASP cc_start: 0.6833 (m-30) cc_final: 0.6548 (m-30) REVERT: C 1157 MET cc_start: 0.7662 (mmm) cc_final: 0.7376 (mmt) REVERT: C 1252 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.8313 (tp30) REVERT: C 1348 ASP cc_start: 0.7860 (t0) cc_final: 0.7488 (t70) REVERT: C 1365 MET cc_start: 0.8244 (ptm) cc_final: 0.7910 (ptm) outliers start: 95 outliers final: 48 residues processed: 622 average time/residue: 1.9828 time to fit residues: 1469.3688 Evaluate side-chains 630 residues out of total 4700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 570 time to evaluate : 4.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 310 ARG Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 683 MET Chi-restraints excluded: chain A residue 694 MET Chi-restraints excluded: chain A residue 1075 LEU Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1128 ARG Chi-restraints excluded: chain A residue 1229 VAL Chi-restraints excluded: chain A residue 1238 MET Chi-restraints excluded: chain A residue 1243 ILE Chi-restraints excluded: chain A residue 1252 GLU Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 310 ARG Chi-restraints excluded: chain D residue 456 MET Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 615 MET Chi-restraints excluded: chain D residue 646 LEU Chi-restraints excluded: chain D residue 683 MET Chi-restraints excluded: chain D residue 694 MET Chi-restraints excluded: chain D residue 1064 LYS Chi-restraints excluded: chain D residue 1082 LEU Chi-restraints excluded: chain D residue 1128 ARG Chi-restraints excluded: chain D residue 1229 VAL Chi-restraints excluded: chain D residue 1238 MET Chi-restraints excluded: chain D residue 1243 ILE Chi-restraints excluded: chain D residue 1252 GLU Chi-restraints excluded: chain B residue 70 MET Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 310 ARG Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 615 MET Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 683 MET Chi-restraints excluded: chain B residue 694 MET Chi-restraints excluded: chain B residue 1011 VAL Chi-restraints excluded: chain B residue 1082 LEU Chi-restraints excluded: chain B residue 1128 ARG Chi-restraints excluded: chain B residue 1229 VAL Chi-restraints excluded: chain B residue 1238 MET Chi-restraints excluded: chain B residue 1243 ILE Chi-restraints excluded: chain B residue 1252 GLU Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 310 ARG Chi-restraints excluded: chain C residue 574 VAL Chi-restraints excluded: chain C residue 615 MET Chi-restraints excluded: chain C residue 646 LEU Chi-restraints excluded: chain C residue 683 MET Chi-restraints excluded: chain C residue 694 MET Chi-restraints excluded: chain C residue 1011 VAL Chi-restraints excluded: chain C residue 1082 LEU Chi-restraints excluded: chain C residue 1128 ARG Chi-restraints excluded: chain C residue 1150 MET Chi-restraints excluded: chain C residue 1229 VAL Chi-restraints excluded: chain C residue 1238 MET Chi-restraints excluded: chain C residue 1243 ILE Chi-restraints excluded: chain C residue 1252 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 548 random chunks: chunk 511 optimal weight: 0.1980 chunk 59 optimal weight: 1.9990 chunk 302 optimal weight: 2.9990 chunk 387 optimal weight: 0.6980 chunk 299 optimal weight: 4.9990 chunk 446 optimal weight: 4.9990 chunk 296 optimal weight: 0.8980 chunk 528 optimal weight: 1.9990 chunk 330 optimal weight: 3.9990 chunk 322 optimal weight: 0.0050 chunk 243 optimal weight: 0.7980 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN D 61 ASN D 813 HIS B 61 ASN C 61 ASN C 813 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7104 moved from start: 0.4102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 43760 Z= 0.151 Angle : 0.472 7.171 59540 Z= 0.247 Chirality : 0.038 0.165 6772 Planarity : 0.004 0.045 7540 Dihedral : 8.068 89.040 7084 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.06 % Allowed : 13.26 % Favored : 84.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.11), residues: 5476 helix: 2.19 (0.09), residues: 3040 sheet: -1.30 (0.22), residues: 412 loop : -0.38 (0.14), residues: 2024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1124 HIS 0.003 0.001 HIS C 240 PHE 0.027 0.001 PHE B 496 TYR 0.019 0.002 TYR D 420 ARG 0.009 0.000 ARG B 152 *********************** 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 684 residues out of total 4700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 597 time to evaluate : 4.691 Fit side-chains REVERT: A 166 LYS cc_start: 0.6188 (tttm) cc_final: 0.5723 (ttmm) REVERT: A 170 LEU cc_start: 0.6615 (OUTLIER) cc_final: 0.6160 (mm) REVERT: A 284 GLN cc_start: 0.7465 (mm-40) cc_final: 0.6902 (mt0) REVERT: A 395 GLU cc_start: 0.5993 (tt0) cc_final: 0.5357 (pt0) REVERT: A 477 LYS cc_start: 0.6550 (mptt) cc_final: 0.5899 (mmtp) REVERT: A 507 GLU cc_start: 0.6098 (tp30) cc_final: 0.5743 (tp30) REVERT: A 618 HIS cc_start: 0.5766 (t70) cc_final: 0.5488 (t70) REVERT: A 663 LYS cc_start: 0.5928 (mmpt) cc_final: 0.5482 (mtmt) REVERT: A 666 GLU cc_start: 0.5514 (tt0) cc_final: 0.5216 (tt0) REVERT: A 686 GLU cc_start: 0.5687 (tt0) cc_final: 0.5100 (tp30) REVERT: A 706 ASP cc_start: 0.6614 (m-30) cc_final: 0.6404 (m-30) REVERT: A 725 ASP cc_start: 0.6261 (m-30) cc_final: 0.5773 (m-30) REVERT: A 827 LYS cc_start: 0.7353 (ptmm) cc_final: 0.7045 (ptpt) REVERT: A 923 ASN cc_start: 0.6593 (m110) cc_final: 0.6379 (m110) REVERT: A 932 MET cc_start: 0.5677 (mmt) cc_final: 0.5266 (mmm) REVERT: A 933 GLU cc_start: 0.6081 (mm-30) cc_final: 0.5756 (mm-30) REVERT: A 969 ARG cc_start: 0.6545 (mtp-110) cc_final: 0.5685 (mtp85) REVERT: A 1000 ASP cc_start: 0.7635 (m-30) cc_final: 0.7323 (m-30) REVERT: A 1005 GLU cc_start: 0.6957 (mt-10) cc_final: 0.6577 (mt-10) REVERT: A 1107 ARG cc_start: 0.5739 (ttp-110) cc_final: 0.5080 (ptm-80) REVERT: A 1122 ARG cc_start: 0.5098 (mtm110) cc_final: 0.4678 (ttp80) REVERT: A 1128 ARG cc_start: 0.5887 (OUTLIER) cc_final: 0.5480 (ttp-110) REVERT: A 1147 MET cc_start: 0.6511 (mmm) cc_final: 0.6164 (mtm) REVERT: A 1151 ASP cc_start: 0.6894 (m-30) cc_final: 0.6481 (m-30) REVERT: A 1160 PHE cc_start: 0.6774 (m-10) cc_final: 0.6307 (t80) REVERT: A 1348 ASP cc_start: 0.7846 (t0) cc_final: 0.7462 (t70) REVERT: A 1401 MET cc_start: 0.7082 (mtp) cc_final: 0.6782 (mtp) REVERT: D 78 ARG cc_start: 0.5897 (ptp-170) cc_final: 0.5635 (ptp-110) REVERT: D 80 HIS cc_start: 0.5749 (m-70) cc_final: 0.5317 (m170) REVERT: D 166 LYS cc_start: 0.6174 (tttm) cc_final: 0.5705 (ttmm) REVERT: D 170 LEU cc_start: 0.6615 (OUTLIER) cc_final: 0.6162 (mm) REVERT: D 284 GLN cc_start: 0.7458 (mm-40) cc_final: 0.6888 (mt0) REVERT: D 395 GLU cc_start: 0.5979 (tt0) cc_final: 0.5359 (pt0) REVERT: D 456 MET cc_start: 0.4984 (ttm) cc_final: 0.4531 (ttp) REVERT: D 477 LYS cc_start: 0.6509 (mptt) cc_final: 0.5851 (mmtp) REVERT: D 502 GLU cc_start: 0.6014 (tt0) cc_final: 0.5734 (mt-10) REVERT: D 507 GLU cc_start: 0.6063 (tp30) cc_final: 0.5723 (tp30) REVERT: D 514 HIS cc_start: 0.5798 (p-80) cc_final: 0.5570 (p90) REVERT: D 663 LYS cc_start: 0.5948 (mmpt) cc_final: 0.5484 (mtmt) REVERT: D 666 GLU cc_start: 0.5490 (tt0) cc_final: 0.5173 (tt0) REVERT: D 667 GLU cc_start: 0.6094 (mt-10) cc_final: 0.5737 (mt-10) REVERT: D 686 GLU cc_start: 0.5703 (tt0) cc_final: 0.5079 (tp30) REVERT: D 708 LYS cc_start: 0.6806 (mttp) cc_final: 0.6382 (mttm) REVERT: D 725 ASP cc_start: 0.6257 (m-30) cc_final: 0.5781 (m-30) REVERT: D 797 LYS cc_start: 0.6079 (mttt) cc_final: 0.5629 (mtpm) REVERT: D 827 LYS cc_start: 0.7341 (ptmm) cc_final: 0.7042 (ptpt) REVERT: D 932 MET cc_start: 0.5557 (mmt) cc_final: 0.5152 (mmm) REVERT: D 933 GLU cc_start: 0.6086 (mm-30) cc_final: 0.5714 (mm-30) REVERT: D 969 ARG cc_start: 0.6547 (mtp-110) cc_final: 0.5691 (mtp85) REVERT: D 1000 ASP cc_start: 0.7635 (m-30) cc_final: 0.7326 (m-30) REVERT: D 1005 GLU cc_start: 0.6909 (mt-10) cc_final: 0.6531 (mt-10) REVERT: D 1065 ASP cc_start: 0.6527 (m-30) cc_final: 0.6203 (t0) REVERT: D 1107 ARG cc_start: 0.5770 (ttp-110) cc_final: 0.5097 (ptm-80) REVERT: D 1108 LYS cc_start: 0.6118 (ttmt) cc_final: 0.5625 (ttpp) REVERT: D 1122 ARG cc_start: 0.5098 (mtm110) cc_final: 0.4578 (ttp80) REVERT: D 1128 ARG cc_start: 0.5784 (OUTLIER) cc_final: 0.5358 (ttp-110) REVERT: D 1151 ASP cc_start: 0.6953 (m-30) cc_final: 0.6525 (m-30) REVERT: D 1157 MET cc_start: 0.7678 (mmt) cc_final: 0.7443 (mmt) REVERT: D 1252 GLU cc_start: 0.8484 (OUTLIER) cc_final: 0.8203 (tp30) REVERT: D 1348 ASP cc_start: 0.7833 (t0) cc_final: 0.7456 (t70) REVERT: D 1401 MET cc_start: 0.7072 (mtp) cc_final: 0.6771 (mtp) REVERT: B 80 HIS cc_start: 0.5675 (m-70) cc_final: 0.5205 (m170) REVERT: B 166 LYS cc_start: 0.6172 (tttm) cc_final: 0.5704 (ttmm) REVERT: B 170 LEU cc_start: 0.6616 (OUTLIER) cc_final: 0.6162 (mm) REVERT: B 284 GLN cc_start: 0.7486 (mm-40) cc_final: 0.6907 (mt0) REVERT: B 395 GLU cc_start: 0.5978 (tt0) cc_final: 0.5359 (pt0) REVERT: B 456 MET cc_start: 0.4842 (ttm) cc_final: 0.4400 (ttp) REVERT: B 477 LYS cc_start: 0.6506 (mptt) cc_final: 0.5844 (mmtp) REVERT: B 502 GLU cc_start: 0.6121 (tt0) cc_final: 0.5840 (mt-10) REVERT: B 507 GLU cc_start: 0.6016 (tp30) cc_final: 0.5727 (tp30) REVERT: B 618 HIS cc_start: 0.5740 (t70) cc_final: 0.5481 (t70) REVERT: B 663 LYS cc_start: 0.5942 (mmpt) cc_final: 0.5497 (mtmt) REVERT: B 666 GLU cc_start: 0.5576 (tt0) cc_final: 0.5218 (tt0) REVERT: B 686 GLU cc_start: 0.5703 (tt0) cc_final: 0.5079 (tp30) REVERT: B 708 LYS cc_start: 0.6847 (mttp) cc_final: 0.6433 (mttm) REVERT: B 725 ASP cc_start: 0.6258 (m-30) cc_final: 0.5781 (m-30) REVERT: B 797 LYS cc_start: 0.6081 (mttt) cc_final: 0.5631 (mtpm) REVERT: B 827 LYS cc_start: 0.7341 (ptmm) cc_final: 0.7041 (ptpt) REVERT: B 923 ASN cc_start: 0.6592 (m110) cc_final: 0.6378 (m110) REVERT: B 932 MET cc_start: 0.5573 (mmt) cc_final: 0.5170 (mmm) REVERT: B 933 GLU cc_start: 0.6092 (mm-30) cc_final: 0.5776 (mm-30) REVERT: B 969 ARG cc_start: 0.6544 (mtp-110) cc_final: 0.5681 (mtp85) REVERT: B 1000 ASP cc_start: 0.7607 (m-30) cc_final: 0.7368 (m-30) REVERT: B 1107 ARG cc_start: 0.5774 (ttp-110) cc_final: 0.5106 (ptm-80) REVERT: B 1108 LYS cc_start: 0.6120 (ttmt) cc_final: 0.5626 (ttpp) REVERT: B 1122 ARG cc_start: 0.5072 (mtm110) cc_final: 0.4571 (ttp80) REVERT: B 1128 ARG cc_start: 0.5888 (OUTLIER) cc_final: 0.5497 (ttp-110) REVERT: B 1151 ASP cc_start: 0.6874 (m-30) cc_final: 0.6470 (m-30) REVERT: B 1252 GLU cc_start: 0.8482 (OUTLIER) cc_final: 0.8199 (tp30) REVERT: B 1348 ASP cc_start: 0.7834 (t0) cc_final: 0.7458 (t70) REVERT: B 1365 MET cc_start: 0.8176 (ptm) cc_final: 0.7958 (ptm) REVERT: B 1401 MET cc_start: 0.7053 (mtp) cc_final: 0.6762 (mtp) REVERT: C 82 HIS cc_start: 0.6256 (m-70) cc_final: 0.5901 (m90) REVERT: C 166 LYS cc_start: 0.6178 (tttm) cc_final: 0.5707 (ttmm) REVERT: C 170 LEU cc_start: 0.6617 (OUTLIER) cc_final: 0.6162 (mm) REVERT: C 284 GLN cc_start: 0.7486 (mm-40) cc_final: 0.6908 (mt0) REVERT: C 395 GLU cc_start: 0.5980 (tt0) cc_final: 0.5359 (pt0) REVERT: C 456 MET cc_start: 0.4867 (ttm) cc_final: 0.4468 (ttp) REVERT: C 477 LYS cc_start: 0.6517 (mptt) cc_final: 0.5852 (mmtp) REVERT: C 502 GLU cc_start: 0.6012 (tt0) cc_final: 0.5741 (mt-10) REVERT: C 507 GLU cc_start: 0.6041 (tp30) cc_final: 0.5739 (tp30) REVERT: C 618 HIS cc_start: 0.5841 (t70) cc_final: 0.5586 (t70) REVERT: C 663 LYS cc_start: 0.5942 (mmpt) cc_final: 0.5497 (mtmt) REVERT: C 666 GLU cc_start: 0.5576 (tt0) cc_final: 0.5217 (tt0) REVERT: C 686 GLU cc_start: 0.5678 (tt0) cc_final: 0.5083 (tp30) REVERT: C 708 LYS cc_start: 0.6848 (mttp) cc_final: 0.6433 (mttm) REVERT: C 725 ASP cc_start: 0.6258 (m-30) cc_final: 0.5781 (m-30) REVERT: C 797 LYS cc_start: 0.6080 (mttt) cc_final: 0.5630 (mtpm) REVERT: C 827 LYS cc_start: 0.7338 (ptmm) cc_final: 0.7033 (ptpt) REVERT: C 932 MET cc_start: 0.5683 (mmt) cc_final: 0.5288 (mmm) REVERT: C 933 GLU cc_start: 0.6105 (mm-30) cc_final: 0.5752 (mm-30) REVERT: C 969 ARG cc_start: 0.6547 (mtp-110) cc_final: 0.5692 (mtp85) REVERT: C 1000 ASP cc_start: 0.7604 (m-30) cc_final: 0.7364 (m-30) REVERT: C 1107 ARG cc_start: 0.5739 (ttp-110) cc_final: 0.5071 (ptm-80) REVERT: C 1108 LYS cc_start: 0.6118 (ttmt) cc_final: 0.5626 (ttpp) REVERT: C 1122 ARG cc_start: 0.5092 (mtm110) cc_final: 0.4573 (ttp80) REVERT: C 1128 ARG cc_start: 0.5821 (OUTLIER) cc_final: 0.5416 (ttp-110) REVERT: C 1151 ASP cc_start: 0.6813 (m-30) cc_final: 0.6589 (m-30) REVERT: C 1157 MET cc_start: 0.7642 (mmm) cc_final: 0.7230 (mmt) REVERT: C 1252 GLU cc_start: 0.8483 (OUTLIER) cc_final: 0.8199 (tp30) REVERT: C 1348 ASP cc_start: 0.7797 (t0) cc_final: 0.7458 (t70) outliers start: 87 outliers final: 38 residues processed: 634 average time/residue: 1.9291 time to fit residues: 1460.5417 Evaluate side-chains 622 residues out of total 4700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 573 time to evaluate : 4.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 517 ARG Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 683 MET Chi-restraints excluded: chain A residue 1011 VAL Chi-restraints excluded: chain A residue 1075 LEU Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1128 ARG Chi-restraints excluded: chain A residue 1229 VAL Chi-restraints excluded: chain A residue 1238 MET Chi-restraints excluded: chain A residue 1243 ILE Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 517 ARG Chi-restraints excluded: chain D residue 615 MET Chi-restraints excluded: chain D residue 683 MET Chi-restraints excluded: chain D residue 1011 VAL Chi-restraints excluded: chain D residue 1064 LYS Chi-restraints excluded: chain D residue 1082 LEU Chi-restraints excluded: chain D residue 1128 ARG Chi-restraints excluded: chain D residue 1229 VAL Chi-restraints excluded: chain D residue 1238 MET Chi-restraints excluded: chain D residue 1243 ILE Chi-restraints excluded: chain D residue 1252 GLU Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 517 ARG Chi-restraints excluded: chain B residue 615 MET Chi-restraints excluded: chain B residue 683 MET Chi-restraints excluded: chain B residue 1011 VAL Chi-restraints excluded: chain B residue 1082 LEU Chi-restraints excluded: chain B residue 1128 ARG Chi-restraints excluded: chain B residue 1229 VAL Chi-restraints excluded: chain B residue 1238 MET Chi-restraints excluded: chain B residue 1243 ILE Chi-restraints excluded: chain B residue 1252 GLU Chi-restraints excluded: chain C residue 94 THR Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 517 ARG Chi-restraints excluded: chain C residue 615 MET Chi-restraints excluded: chain C residue 683 MET Chi-restraints excluded: chain C residue 1011 VAL Chi-restraints excluded: chain C residue 1082 LEU Chi-restraints excluded: chain C residue 1128 ARG Chi-restraints excluded: chain C residue 1150 MET Chi-restraints excluded: chain C residue 1229 VAL Chi-restraints excluded: chain C residue 1238 MET Chi-restraints excluded: chain C residue 1243 ILE Chi-restraints excluded: chain C residue 1252 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 548 random chunks: chunk 326 optimal weight: 0.2980 chunk 210 optimal weight: 7.9990 chunk 315 optimal weight: 10.0000 chunk 159 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 chunk 102 optimal weight: 5.9990 chunk 335 optimal weight: 9.9990 chunk 359 optimal weight: 6.9990 chunk 261 optimal weight: 0.1980 chunk 49 optimal weight: 7.9990 chunk 415 optimal weight: 2.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1156 HIS D 61 ASN D1152 GLN B 61 ASN B1152 GLN C 61 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7140 moved from start: 0.4302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 43760 Z= 0.342 Angle : 0.591 7.329 59540 Z= 0.307 Chirality : 0.042 0.168 6772 Planarity : 0.005 0.046 7540 Dihedral : 8.452 89.502 7084 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.96 % Allowed : 13.54 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.11), residues: 5476 helix: 2.05 (0.09), residues: 3012 sheet: -1.34 (0.21), residues: 436 loop : -0.50 (0.14), residues: 2028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D1124 HIS 0.006 0.001 HIS C1156 PHE 0.027 0.002 PHE C 496 TYR 0.022 0.003 TYR B1063 ARG 0.007 0.001 ARG D1126 *********************** 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 642 residues out of total 4700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 559 time to evaluate : 4.802 Fit side-chains revert: symmetry clash REVERT: A 166 LYS cc_start: 0.6212 (tttm) cc_final: 0.5689 (ttmm) REVERT: A 170 LEU cc_start: 0.6590 (OUTLIER) cc_final: 0.6147 (mm) REVERT: A 284 GLN cc_start: 0.7548 (mm-40) cc_final: 0.6991 (mt0) REVERT: A 395 GLU cc_start: 0.6115 (tt0) cc_final: 0.5458 (mt-10) REVERT: A 477 LYS cc_start: 0.6582 (mptt) cc_final: 0.5932 (mmtp) REVERT: A 507 GLU cc_start: 0.5994 (tp30) cc_final: 0.5634 (tp30) REVERT: A 618 HIS cc_start: 0.5720 (t70) cc_final: 0.5476 (t70) REVERT: A 663 LYS cc_start: 0.5819 (mmpt) cc_final: 0.5354 (mtmt) REVERT: A 666 GLU cc_start: 0.5744 (tt0) cc_final: 0.5415 (tt0) REVERT: A 686 GLU cc_start: 0.5749 (tt0) cc_final: 0.5125 (tp30) REVERT: A 706 ASP cc_start: 0.6594 (m-30) cc_final: 0.6378 (m-30) REVERT: A 969 ARG cc_start: 0.6534 (mtp-110) cc_final: 0.5700 (mtp85) REVERT: A 1000 ASP cc_start: 0.7639 (m-30) cc_final: 0.7333 (m-30) REVERT: A 1005 GLU cc_start: 0.6734 (mt-10) cc_final: 0.6372 (mt-10) REVERT: A 1107 ARG cc_start: 0.5672 (ttp-110) cc_final: 0.5064 (ptm-80) REVERT: A 1108 LYS cc_start: 0.6112 (tmmt) cc_final: 0.5628 (ttpp) REVERT: A 1122 ARG cc_start: 0.5181 (mtm110) cc_final: 0.4728 (ttp80) REVERT: A 1128 ARG cc_start: 0.5907 (OUTLIER) cc_final: 0.5533 (ttp-110) REVERT: A 1147 MET cc_start: 0.6503 (mmm) cc_final: 0.6234 (mtm) REVERT: A 1151 ASP cc_start: 0.6868 (m-30) cc_final: 0.6465 (m-30) REVERT: A 1348 ASP cc_start: 0.7939 (t0) cc_final: 0.7559 (t70) REVERT: A 1401 MET cc_start: 0.7021 (mtp) cc_final: 0.6709 (mtp) REVERT: D 166 LYS cc_start: 0.6208 (tttm) cc_final: 0.5686 (ttmm) REVERT: D 170 LEU cc_start: 0.6588 (OUTLIER) cc_final: 0.6147 (mm) REVERT: D 284 GLN cc_start: 0.7529 (mm-40) cc_final: 0.6967 (mt0) REVERT: D 364 GLN cc_start: 0.7047 (OUTLIER) cc_final: 0.6838 (tm-30) REVERT: D 395 GLU cc_start: 0.6137 (tt0) cc_final: 0.5530 (mt-10) REVERT: D 456 MET cc_start: 0.5097 (ttm) cc_final: 0.4629 (ttp) REVERT: D 477 LYS cc_start: 0.6575 (mptt) cc_final: 0.5918 (mmtp) REVERT: D 507 GLU cc_start: 0.6022 (tp30) cc_final: 0.5792 (tp30) REVERT: D 663 LYS cc_start: 0.5862 (mmpt) cc_final: 0.5407 (mtmt) REVERT: D 666 GLU cc_start: 0.5713 (tt0) cc_final: 0.5336 (tt0) REVERT: D 686 GLU cc_start: 0.5730 (tt0) cc_final: 0.5137 (tp30) REVERT: D 708 LYS cc_start: 0.6918 (mttp) cc_final: 0.6488 (mttm) REVERT: D 827 LYS cc_start: 0.7340 (ptmm) cc_final: 0.7084 (ptpt) REVERT: D 969 ARG cc_start: 0.6535 (mtp-110) cc_final: 0.5710 (mtp85) REVERT: D 1000 ASP cc_start: 0.7638 (m-30) cc_final: 0.7340 (m-30) REVERT: D 1005 GLU cc_start: 0.6756 (mt-10) cc_final: 0.6405 (mt-10) REVERT: D 1065 ASP cc_start: 0.6573 (m-30) cc_final: 0.6249 (t0) REVERT: D 1107 ARG cc_start: 0.5643 (ttp-110) cc_final: 0.5025 (ptm-80) REVERT: D 1108 LYS cc_start: 0.6094 (ttmt) cc_final: 0.5610 (ttpp) REVERT: D 1119 LYS cc_start: 0.5423 (mtpt) cc_final: 0.5047 (ttmt) REVERT: D 1122 ARG cc_start: 0.5189 (mtm110) cc_final: 0.4718 (ttp80) REVERT: D 1128 ARG cc_start: 0.5819 (OUTLIER) cc_final: 0.5408 (ttp-110) REVERT: D 1151 ASP cc_start: 0.6862 (m-30) cc_final: 0.6440 (m-30) REVERT: D 1348 ASP cc_start: 0.7898 (t0) cc_final: 0.7522 (t70) REVERT: D 1401 MET cc_start: 0.7052 (mtp) cc_final: 0.6757 (mtp) REVERT: B 166 LYS cc_start: 0.6208 (tttm) cc_final: 0.5686 (ttmm) REVERT: B 170 LEU cc_start: 0.6589 (OUTLIER) cc_final: 0.6147 (mm) REVERT: B 284 GLN cc_start: 0.7530 (mm-40) cc_final: 0.6962 (mt0) REVERT: B 364 GLN cc_start: 0.7045 (OUTLIER) cc_final: 0.6837 (tm-30) REVERT: B 395 GLU cc_start: 0.6137 (tt0) cc_final: 0.5527 (mt-10) REVERT: B 477 LYS cc_start: 0.6581 (mptt) cc_final: 0.5924 (mmtp) REVERT: B 507 GLU cc_start: 0.5915 (tp30) cc_final: 0.5623 (tp30) REVERT: B 618 HIS cc_start: 0.5686 (t70) cc_final: 0.5439 (t70) REVERT: B 663 LYS cc_start: 0.5839 (mmpt) cc_final: 0.5377 (mtmt) REVERT: B 666 GLU cc_start: 0.5772 (tt0) cc_final: 0.5456 (tt0) REVERT: B 686 GLU cc_start: 0.5729 (tt0) cc_final: 0.5135 (tp30) REVERT: B 708 LYS cc_start: 0.6940 (mttp) cc_final: 0.6502 (mttm) REVERT: B 827 LYS cc_start: 0.7336 (ptmm) cc_final: 0.7082 (ptpt) REVERT: B 932 MET cc_start: 0.5504 (mmt) cc_final: 0.5123 (mmm) REVERT: B 969 ARG cc_start: 0.6533 (mtp-110) cc_final: 0.5697 (mtp85) REVERT: B 1000 ASP cc_start: 0.7666 (m-30) cc_final: 0.7434 (m-30) REVERT: B 1107 ARG cc_start: 0.5643 (ttp-110) cc_final: 0.5025 (ptm-80) REVERT: B 1108 LYS cc_start: 0.6081 (ttmt) cc_final: 0.5595 (ttpp) REVERT: B 1122 ARG cc_start: 0.5175 (mtm110) cc_final: 0.4720 (ttp80) REVERT: B 1128 ARG cc_start: 0.5920 (OUTLIER) cc_final: 0.5542 (ttp-110) REVERT: B 1147 MET cc_start: 0.6481 (mmm) cc_final: 0.6194 (mtm) REVERT: B 1151 ASP cc_start: 0.6837 (m-30) cc_final: 0.6452 (m-30) REVERT: B 1348 ASP cc_start: 0.7899 (t0) cc_final: 0.7525 (t70) REVERT: B 1365 MET cc_start: 0.8249 (ptm) cc_final: 0.7917 (ptm) REVERT: B 1401 MET cc_start: 0.7093 (mtp) cc_final: 0.6819 (mtp) REVERT: C 82 HIS cc_start: 0.6112 (m-70) cc_final: 0.5906 (m170) REVERT: C 166 LYS cc_start: 0.6212 (tttm) cc_final: 0.5689 (ttmm) REVERT: C 170 LEU cc_start: 0.6591 (OUTLIER) cc_final: 0.6147 (mm) REVERT: C 284 GLN cc_start: 0.7546 (mm-40) cc_final: 0.6988 (mt0) REVERT: C 395 GLU cc_start: 0.6136 (tt0) cc_final: 0.5527 (mt-10) REVERT: C 456 MET cc_start: 0.5098 (OUTLIER) cc_final: 0.4517 (ttp) REVERT: C 477 LYS cc_start: 0.6600 (mptt) cc_final: 0.5943 (mmtp) REVERT: C 507 GLU cc_start: 0.6080 (tp30) cc_final: 0.5792 (tp30) REVERT: C 618 HIS cc_start: 0.5686 (t70) cc_final: 0.5440 (t70) REVERT: C 663 LYS cc_start: 0.5845 (mmpt) cc_final: 0.5390 (mtmt) REVERT: C 666 GLU cc_start: 0.5773 (tt0) cc_final: 0.5456 (tt0) REVERT: C 686 GLU cc_start: 0.5752 (tt0) cc_final: 0.5148 (tp30) REVERT: C 708 LYS cc_start: 0.6940 (mttp) cc_final: 0.6503 (mttm) REVERT: C 827 LYS cc_start: 0.7348 (ptmm) cc_final: 0.7091 (ptpt) REVERT: C 932 MET cc_start: 0.5507 (mmt) cc_final: 0.5134 (mmm) REVERT: C 969 ARG cc_start: 0.6536 (mtp-110) cc_final: 0.5710 (mtp85) REVERT: C 1000 ASP cc_start: 0.7664 (m-30) cc_final: 0.7431 (m-30) REVERT: C 1107 ARG cc_start: 0.5646 (ttp-110) cc_final: 0.5026 (ptm-80) REVERT: C 1108 LYS cc_start: 0.6094 (ttmt) cc_final: 0.5610 (ttpp) REVERT: C 1119 LYS cc_start: 0.5401 (mtpt) cc_final: 0.4767 (mttt) REVERT: C 1122 ARG cc_start: 0.5159 (mtm110) cc_final: 0.4702 (ttp80) REVERT: C 1128 ARG cc_start: 0.5924 (OUTLIER) cc_final: 0.5546 (ttp-110) REVERT: C 1151 ASP cc_start: 0.6797 (m-30) cc_final: 0.6531 (m-30) REVERT: C 1157 MET cc_start: 0.7596 (mmm) cc_final: 0.7242 (mmt) REVERT: C 1348 ASP cc_start: 0.7901 (t0) cc_final: 0.7517 (t70) outliers start: 83 outliers final: 47 residues processed: 600 average time/residue: 1.9410 time to fit residues: 1407.7220 Evaluate side-chains 608 residues out of total 4700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 550 time to evaluate : 5.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 683 MET Chi-restraints excluded: chain A residue 1011 VAL Chi-restraints excluded: chain A residue 1064 LYS Chi-restraints excluded: chain A residue 1075 LEU Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1128 ARG Chi-restraints excluded: chain A residue 1229 VAL Chi-restraints excluded: chain A residue 1238 MET Chi-restraints excluded: chain A residue 1243 ILE Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 364 GLN Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 615 MET Chi-restraints excluded: chain D residue 646 LEU Chi-restraints excluded: chain D residue 683 MET Chi-restraints excluded: chain D residue 1011 VAL Chi-restraints excluded: chain D residue 1064 LYS Chi-restraints excluded: chain D residue 1082 LEU Chi-restraints excluded: chain D residue 1128 ARG Chi-restraints excluded: chain D residue 1150 MET Chi-restraints excluded: chain D residue 1229 VAL Chi-restraints excluded: chain D residue 1238 MET Chi-restraints excluded: chain D residue 1243 ILE Chi-restraints excluded: chain B residue 70 MET Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 364 GLN Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 592 GLN Chi-restraints excluded: chain B residue 615 MET Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 683 MET Chi-restraints excluded: chain B residue 1011 VAL Chi-restraints excluded: chain B residue 1064 LYS Chi-restraints excluded: chain B residue 1082 LEU Chi-restraints excluded: chain B residue 1128 ARG Chi-restraints excluded: chain B residue 1150 MET Chi-restraints excluded: chain B residue 1229 VAL Chi-restraints excluded: chain B residue 1238 MET Chi-restraints excluded: chain B residue 1243 ILE Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 456 MET Chi-restraints excluded: chain C residue 574 VAL Chi-restraints excluded: chain C residue 615 MET Chi-restraints excluded: chain C residue 646 LEU Chi-restraints excluded: chain C residue 683 MET Chi-restraints excluded: chain C residue 1011 VAL Chi-restraints excluded: chain C residue 1064 LYS Chi-restraints excluded: chain C residue 1082 LEU Chi-restraints excluded: chain C residue 1128 ARG Chi-restraints excluded: chain C residue 1150 MET Chi-restraints excluded: chain C residue 1229 VAL Chi-restraints excluded: chain C residue 1238 MET Chi-restraints excluded: chain C residue 1243 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 548 random chunks: chunk 480 optimal weight: 8.9990 chunk 506 optimal weight: 2.9990 chunk 461 optimal weight: 0.9980 chunk 492 optimal weight: 4.9990 chunk 505 optimal weight: 0.5980 chunk 296 optimal weight: 1.9990 chunk 214 optimal weight: 6.9990 chunk 386 optimal weight: 0.5980 chunk 151 optimal weight: 6.9990 chunk 444 optimal weight: 0.8980 chunk 465 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN D 61 ASN D 692 ASN B 61 ASN C 61 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7116 moved from start: 0.4253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 43760 Z= 0.177 Angle : 0.496 7.347 59540 Z= 0.258 Chirality : 0.039 0.166 6772 Planarity : 0.004 0.045 7540 Dihedral : 8.122 89.733 7084 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.51 % Allowed : 14.01 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.11), residues: 5476 helix: 2.21 (0.09), residues: 3012 sheet: -1.33 (0.22), residues: 416 loop : -0.40 (0.14), residues: 2048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1124 HIS 0.003 0.001 HIS B 82 PHE 0.027 0.001 PHE C 496 TYR 0.017 0.002 TYR A 420 ARG 0.006 0.000 ARG D1126 *********************** 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 627 residues out of total 4700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 563 time to evaluate : 4.664 Fit side-chains REVERT: A 166 LYS cc_start: 0.6208 (tttm) cc_final: 0.5736 (ttmm) REVERT: A 170 LEU cc_start: 0.6612 (OUTLIER) cc_final: 0.6150 (mm) REVERT: A 284 GLN cc_start: 0.7501 (mm-40) cc_final: 0.6922 (mt0) REVERT: A 477 LYS cc_start: 0.6588 (mptt) cc_final: 0.5925 (mmtp) REVERT: A 507 GLU cc_start: 0.6093 (tp30) cc_final: 0.5780 (tp30) REVERT: A 618 HIS cc_start: 0.5762 (t70) cc_final: 0.5494 (t70) REVERT: A 663 LYS cc_start: 0.5814 (mmpt) cc_final: 0.5352 (mtmt) REVERT: A 666 GLU cc_start: 0.5460 (tt0) cc_final: 0.5139 (tt0) REVERT: A 686 GLU cc_start: 0.5702 (tt0) cc_final: 0.5115 (tp30) REVERT: A 923 ASN cc_start: 0.6581 (m110) cc_final: 0.6357 (m110) REVERT: A 933 GLU cc_start: 0.6027 (mm-30) cc_final: 0.5694 (mm-30) REVERT: A 969 ARG cc_start: 0.6534 (mtp-110) cc_final: 0.5673 (mtp85) REVERT: A 1000 ASP cc_start: 0.7643 (m-30) cc_final: 0.7388 (m-30) REVERT: A 1107 ARG cc_start: 0.5701 (ttp-110) cc_final: 0.5040 (ptm-80) REVERT: A 1122 ARG cc_start: 0.5147 (mtm110) cc_final: 0.4720 (ttp80) REVERT: A 1128 ARG cc_start: 0.5827 (OUTLIER) cc_final: 0.5439 (ttp-110) REVERT: A 1147 MET cc_start: 0.6472 (mmm) cc_final: 0.6161 (mtm) REVERT: A 1151 ASP cc_start: 0.6967 (m-30) cc_final: 0.6516 (m-30) REVERT: A 1348 ASP cc_start: 0.7860 (t0) cc_final: 0.7512 (t70) REVERT: A 1401 MET cc_start: 0.7173 (mtp) cc_final: 0.6902 (mtp) REVERT: D 80 HIS cc_start: 0.5768 (m-70) cc_final: 0.5302 (m170) REVERT: D 166 LYS cc_start: 0.6201 (tttm) cc_final: 0.5732 (ttmm) REVERT: D 170 LEU cc_start: 0.6610 (OUTLIER) cc_final: 0.6148 (mm) REVERT: D 284 GLN cc_start: 0.7515 (mm-40) cc_final: 0.6929 (mt0) REVERT: D 456 MET cc_start: 0.4974 (OUTLIER) cc_final: 0.4548 (ttp) REVERT: D 477 LYS cc_start: 0.6602 (mptt) cc_final: 0.5939 (mmtp) REVERT: D 507 GLU cc_start: 0.6107 (tp30) cc_final: 0.5669 (tp30) REVERT: D 527 LEU cc_start: 0.6546 (OUTLIER) cc_final: 0.6295 (mm) REVERT: D 595 ARG cc_start: 0.5369 (mtp180) cc_final: 0.5130 (mtt180) REVERT: D 663 LYS cc_start: 0.5809 (mmpt) cc_final: 0.5351 (mtmt) REVERT: D 666 GLU cc_start: 0.5455 (tt0) cc_final: 0.5122 (tt0) REVERT: D 686 GLU cc_start: 0.5735 (tt0) cc_final: 0.5114 (tp30) REVERT: D 692 ASN cc_start: 0.5660 (OUTLIER) cc_final: 0.5438 (t0) REVERT: D 708 LYS cc_start: 0.6824 (mttp) cc_final: 0.6386 (mttm) REVERT: D 827 LYS cc_start: 0.7350 (ptmm) cc_final: 0.7036 (ptpt) REVERT: D 933 GLU cc_start: 0.6012 (mm-30) cc_final: 0.5705 (mm-30) REVERT: D 969 ARG cc_start: 0.6541 (mtp-110) cc_final: 0.5685 (mtp85) REVERT: D 1000 ASP cc_start: 0.7645 (m-30) cc_final: 0.7348 (m-30) REVERT: D 1005 GLU cc_start: 0.6878 (mt-10) cc_final: 0.6507 (mt-10) REVERT: D 1065 ASP cc_start: 0.6611 (m-30) cc_final: 0.6318 (t0) REVERT: D 1107 ARG cc_start: 0.5687 (ttp-110) cc_final: 0.5021 (ptm-80) REVERT: D 1108 LYS cc_start: 0.6110 (ttmt) cc_final: 0.5620 (ttpp) REVERT: D 1122 ARG cc_start: 0.5171 (mtm110) cc_final: 0.4720 (ttp80) REVERT: D 1128 ARG cc_start: 0.5783 (OUTLIER) cc_final: 0.5382 (ttp-110) REVERT: D 1151 ASP cc_start: 0.6945 (m-30) cc_final: 0.6489 (m-30) REVERT: D 1348 ASP cc_start: 0.7848 (t0) cc_final: 0.7469 (t70) REVERT: D 1401 MET cc_start: 0.7173 (mtp) cc_final: 0.6896 (mtp) REVERT: B 80 HIS cc_start: 0.5784 (m-70) cc_final: 0.5346 (m170) REVERT: B 166 LYS cc_start: 0.6201 (tttm) cc_final: 0.5731 (ttmm) REVERT: B 170 LEU cc_start: 0.6614 (OUTLIER) cc_final: 0.6155 (mm) REVERT: B 284 GLN cc_start: 0.7501 (mm-40) cc_final: 0.6920 (mt0) REVERT: B 395 GLU cc_start: 0.6018 (tt0) cc_final: 0.5433 (mt-10) REVERT: B 456 MET cc_start: 0.5212 (ttm) cc_final: 0.4691 (ttp) REVERT: B 477 LYS cc_start: 0.6552 (mptt) cc_final: 0.5871 (mmtp) REVERT: B 507 GLU cc_start: 0.6042 (tp30) cc_final: 0.5701 (tp30) REVERT: B 595 ARG cc_start: 0.5372 (mtp180) cc_final: 0.5134 (mtt180) REVERT: B 618 HIS cc_start: 0.5690 (t70) cc_final: 0.5426 (t70) REVERT: B 663 LYS cc_start: 0.5813 (mmpt) cc_final: 0.5352 (mtmt) REVERT: B 666 GLU cc_start: 0.5503 (tt0) cc_final: 0.5231 (tt0) REVERT: B 686 GLU cc_start: 0.5734 (tt0) cc_final: 0.5114 (tp30) REVERT: B 708 LYS cc_start: 0.6947 (mttp) cc_final: 0.6513 (mttm) REVERT: B 827 LYS cc_start: 0.7348 (ptmm) cc_final: 0.7039 (ptpt) REVERT: B 923 ASN cc_start: 0.6580 (m110) cc_final: 0.6355 (m110) REVERT: B 932 MET cc_start: 0.5527 (mmt) cc_final: 0.5127 (mmm) REVERT: B 933 GLU cc_start: 0.6089 (mm-30) cc_final: 0.5820 (mm-30) REVERT: B 969 ARG cc_start: 0.6536 (mtp-110) cc_final: 0.5676 (mtp85) REVERT: B 1000 ASP cc_start: 0.7620 (m-30) cc_final: 0.7385 (m-30) REVERT: B 1107 ARG cc_start: 0.5688 (ttp-110) cc_final: 0.5021 (ptm-80) REVERT: B 1108 LYS cc_start: 0.6110 (ttmt) cc_final: 0.5620 (ttpp) REVERT: B 1122 ARG cc_start: 0.5162 (mtm110) cc_final: 0.4707 (ttp80) REVERT: B 1128 ARG cc_start: 0.5854 (OUTLIER) cc_final: 0.5459 (ttp-110) REVERT: B 1147 MET cc_start: 0.6391 (mmm) cc_final: 0.6061 (mtm) REVERT: B 1151 ASP cc_start: 0.6860 (m-30) cc_final: 0.6442 (m-30) REVERT: B 1160 PHE cc_start: 0.6727 (m-10) cc_final: 0.6345 (t80) REVERT: B 1348 ASP cc_start: 0.7851 (t0) cc_final: 0.7473 (t70) REVERT: B 1365 MET cc_start: 0.8188 (ptm) cc_final: 0.7967 (ptm) REVERT: B 1401 MET cc_start: 0.7220 (mtp) cc_final: 0.6942 (mtp) REVERT: C 166 LYS cc_start: 0.6212 (tttm) cc_final: 0.5737 (ttmm) REVERT: C 170 LEU cc_start: 0.6613 (OUTLIER) cc_final: 0.6152 (mm) REVERT: C 284 GLN cc_start: 0.7496 (mm-40) cc_final: 0.6958 (mt0) REVERT: C 395 GLU cc_start: 0.6020 (tt0) cc_final: 0.5434 (mt-10) REVERT: C 456 MET cc_start: 0.5068 (OUTLIER) cc_final: 0.4553 (ttp) REVERT: C 477 LYS cc_start: 0.6617 (mptt) cc_final: 0.5949 (mmtp) REVERT: C 507 GLU cc_start: 0.6123 (tp30) cc_final: 0.5815 (tp30) REVERT: C 618 HIS cc_start: 0.5689 (t70) cc_final: 0.5426 (t70) REVERT: C 663 LYS cc_start: 0.5813 (mmpt) cc_final: 0.5353 (mtmt) REVERT: C 666 GLU cc_start: 0.5502 (tt0) cc_final: 0.5230 (tt0) REVERT: C 686 GLU cc_start: 0.5711 (tt0) cc_final: 0.5121 (tp30) REVERT: C 708 LYS cc_start: 0.6947 (mttp) cc_final: 0.6513 (mttm) REVERT: C 827 LYS cc_start: 0.7344 (ptmm) cc_final: 0.7025 (ptpt) REVERT: C 932 MET cc_start: 0.5580 (mmt) cc_final: 0.5190 (mmm) REVERT: C 933 GLU cc_start: 0.6059 (mm-30) cc_final: 0.5741 (mm-30) REVERT: C 969 ARG cc_start: 0.6540 (mtp-110) cc_final: 0.5684 (mtp85) REVERT: C 1000 ASP cc_start: 0.7619 (m-30) cc_final: 0.7382 (m-30) REVERT: C 1107 ARG cc_start: 0.5681 (ttp-110) cc_final: 0.5015 (ptm-80) REVERT: C 1108 LYS cc_start: 0.6077 (ttmt) cc_final: 0.5607 (ttpp) REVERT: C 1119 LYS cc_start: 0.5385 (mtpt) cc_final: 0.4709 (mtmt) REVERT: C 1122 ARG cc_start: 0.5137 (mtm110) cc_final: 0.4674 (ttp80) REVERT: C 1128 ARG cc_start: 0.5821 (OUTLIER) cc_final: 0.5437 (ttp-110) REVERT: C 1151 ASP cc_start: 0.6839 (m-30) cc_final: 0.6563 (m-30) REVERT: C 1157 MET cc_start: 0.7530 (mmm) cc_final: 0.7246 (mmt) REVERT: C 1348 ASP cc_start: 0.7809 (t0) cc_final: 0.7470 (t70) outliers start: 64 outliers final: 39 residues processed: 587 average time/residue: 1.9305 time to fit residues: 1375.8654 Evaluate side-chains 609 residues out of total 4700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 558 time to evaluate : 4.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 683 MET Chi-restraints excluded: chain A residue 1011 VAL Chi-restraints excluded: chain A residue 1064 LYS Chi-restraints excluded: chain A residue 1075 LEU Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1128 ARG Chi-restraints excluded: chain A residue 1229 VAL Chi-restraints excluded: chain A residue 1238 MET Chi-restraints excluded: chain A residue 1243 ILE Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 456 MET Chi-restraints excluded: chain D residue 527 LEU Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 615 MET Chi-restraints excluded: chain D residue 683 MET Chi-restraints excluded: chain D residue 692 ASN Chi-restraints excluded: chain D residue 1011 VAL Chi-restraints excluded: chain D residue 1064 LYS Chi-restraints excluded: chain D residue 1082 LEU Chi-restraints excluded: chain D residue 1128 ARG Chi-restraints excluded: chain D residue 1150 MET Chi-restraints excluded: chain D residue 1229 VAL Chi-restraints excluded: chain D residue 1238 MET Chi-restraints excluded: chain D residue 1243 ILE Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 615 MET Chi-restraints excluded: chain B residue 683 MET Chi-restraints excluded: chain B residue 1011 VAL Chi-restraints excluded: chain B residue 1082 LEU Chi-restraints excluded: chain B residue 1128 ARG Chi-restraints excluded: chain B residue 1229 VAL Chi-restraints excluded: chain B residue 1238 MET Chi-restraints excluded: chain B residue 1243 ILE Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 456 MET Chi-restraints excluded: chain C residue 574 VAL Chi-restraints excluded: chain C residue 615 MET Chi-restraints excluded: chain C residue 683 MET Chi-restraints excluded: chain C residue 1011 VAL Chi-restraints excluded: chain C residue 1082 LEU Chi-restraints excluded: chain C residue 1128 ARG Chi-restraints excluded: chain C residue 1150 MET Chi-restraints excluded: chain C residue 1229 VAL Chi-restraints excluded: chain C residue 1238 MET Chi-restraints excluded: chain C residue 1243 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 548 random chunks: chunk 490 optimal weight: 3.9990 chunk 323 optimal weight: 4.9990 chunk 520 optimal weight: 5.9990 chunk 317 optimal weight: 4.9990 chunk 246 optimal weight: 6.9990 chunk 361 optimal weight: 6.9990 chunk 545 optimal weight: 3.9990 chunk 502 optimal weight: 0.0970 chunk 434 optimal weight: 0.1980 chunk 45 optimal weight: 9.9990 chunk 335 optimal weight: 9.9990 overall best weight: 2.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN D 61 ASN D 692 ASN B 61 ASN B 692 ASN C 61 ASN C 692 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7123 moved from start: 0.4263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.182 43760 Z= 0.326 Angle : 0.599 59.189 59540 Z= 0.330 Chirality : 0.042 0.355 6772 Planarity : 0.004 0.072 7540 Dihedral : 8.134 89.696 7084 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.35 % Allowed : 14.30 % Favored : 84.36 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.11), residues: 5476 helix: 2.19 (0.09), residues: 3012 sheet: -1.25 (0.22), residues: 436 loop : -0.45 (0.14), residues: 2028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A1124 HIS 0.006 0.001 HIS D 240 PHE 0.025 0.002 PHE C 496 TYR 0.016 0.002 TYR A 420 ARG 0.011 0.001 ARG C 595 ********************** 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 617 residues out of total 4700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 560 time to evaluate : 5.224 Fit side-chains REVERT: A 166 LYS cc_start: 0.6213 (tttm) cc_final: 0.5895 (ttmm) REVERT: A 284 GLN cc_start: 0.7518 (mm-40) cc_final: 0.6972 (mt0) REVERT: A 477 LYS cc_start: 0.6591 (mptt) cc_final: 0.5929 (mmtp) REVERT: A 507 GLU cc_start: 0.6086 (tp30) cc_final: 0.5844 (tp30) REVERT: A 618 HIS cc_start: 0.5768 (t70) cc_final: 0.5495 (t70) REVERT: A 663 LYS cc_start: 0.5815 (mmpt) cc_final: 0.5358 (mtmt) REVERT: A 666 GLU cc_start: 0.5470 (tt0) cc_final: 0.5131 (tt0) REVERT: A 686 GLU cc_start: 0.5703 (tt0) cc_final: 0.5150 (tp30) REVERT: A 923 ASN cc_start: 0.6587 (m110) cc_final: 0.6361 (m110) REVERT: A 933 GLU cc_start: 0.6030 (mm-30) cc_final: 0.5699 (mm-30) REVERT: A 969 ARG cc_start: 0.6539 (mtp-110) cc_final: 0.5703 (mtp85) REVERT: A 1000 ASP cc_start: 0.7657 (m-30) cc_final: 0.7403 (m-30) REVERT: A 1107 ARG cc_start: 0.5695 (ttp-110) cc_final: 0.5046 (ptm-80) REVERT: A 1108 LYS cc_start: 0.6071 (tmmt) cc_final: 0.5757 (ttpt) REVERT: A 1122 ARG cc_start: 0.5148 (mtm110) cc_final: 0.4720 (ttp80) REVERT: A 1128 ARG cc_start: 0.5815 (OUTLIER) cc_final: 0.5441 (ttp-110) REVERT: A 1147 MET cc_start: 0.6468 (mmm) cc_final: 0.6164 (mtm) REVERT: A 1151 ASP cc_start: 0.6969 (m-30) cc_final: 0.6522 (m-30) REVERT: A 1348 ASP cc_start: 0.7865 (t0) cc_final: 0.7511 (t70) REVERT: A 1401 MET cc_start: 0.7177 (mtp) cc_final: 0.6898 (mtp) REVERT: D 80 HIS cc_start: 0.5737 (m-70) cc_final: 0.5269 (m170) REVERT: D 166 LYS cc_start: 0.6206 (tttm) cc_final: 0.5891 (ttmm) REVERT: D 284 GLN cc_start: 0.7518 (mm-40) cc_final: 0.6972 (mt0) REVERT: D 456 MET cc_start: 0.4919 (ttm) cc_final: 0.4518 (ttp) REVERT: D 477 LYS cc_start: 0.6591 (mptt) cc_final: 0.5936 (mmtp) REVERT: D 507 GLU cc_start: 0.6075 (tp30) cc_final: 0.5670 (tp30) REVERT: D 527 LEU cc_start: 0.6571 (OUTLIER) cc_final: 0.6298 (mm) REVERT: D 595 ARG cc_start: 0.5373 (mtp180) cc_final: 0.5121 (mtt180) REVERT: D 663 LYS cc_start: 0.5802 (mmpt) cc_final: 0.5358 (mtmt) REVERT: D 666 GLU cc_start: 0.5496 (tt0) cc_final: 0.5148 (tt0) REVERT: D 686 GLU cc_start: 0.5735 (tt0) cc_final: 0.5116 (tp30) REVERT: D 708 LYS cc_start: 0.6828 (mttp) cc_final: 0.6389 (mttm) REVERT: D 827 LYS cc_start: 0.7350 (ptmm) cc_final: 0.7041 (ptpt) REVERT: D 969 ARG cc_start: 0.6545 (mtp-110) cc_final: 0.5715 (mtp85) REVERT: D 1000 ASP cc_start: 0.7648 (m-30) cc_final: 0.7351 (m-30) REVERT: D 1005 GLU cc_start: 0.6880 (mt-10) cc_final: 0.6507 (mt-10) REVERT: D 1065 ASP cc_start: 0.6615 (m-30) cc_final: 0.6323 (t0) REVERT: D 1107 ARG cc_start: 0.5706 (ttp-110) cc_final: 0.5047 (ptm-80) REVERT: D 1108 LYS cc_start: 0.6164 (ttmt) cc_final: 0.5674 (ttpp) REVERT: D 1122 ARG cc_start: 0.5162 (mtm110) cc_final: 0.4724 (ttp80) REVERT: D 1128 ARG cc_start: 0.5768 (OUTLIER) cc_final: 0.5386 (ttp-110) REVERT: D 1151 ASP cc_start: 0.6951 (m-30) cc_final: 0.6495 (m-30) REVERT: D 1348 ASP cc_start: 0.7853 (t0) cc_final: 0.7470 (t70) REVERT: D 1401 MET cc_start: 0.7177 (mtp) cc_final: 0.6898 (mtp) REVERT: B 80 HIS cc_start: 0.5805 (m-70) cc_final: 0.5353 (m170) REVERT: B 166 LYS cc_start: 0.6205 (tttm) cc_final: 0.5890 (ttmm) REVERT: B 284 GLN cc_start: 0.7499 (mm-40) cc_final: 0.6954 (mt0) REVERT: B 395 GLU cc_start: 0.6025 (tt0) cc_final: 0.5439 (mt-10) REVERT: B 456 MET cc_start: 0.5217 (ttm) cc_final: 0.4688 (ttp) REVERT: B 477 LYS cc_start: 0.6542 (mptt) cc_final: 0.5883 (mmtp) REVERT: B 507 GLU cc_start: 0.6038 (tp30) cc_final: 0.5704 (tp30) REVERT: B 595 ARG cc_start: 0.5377 (mtp180) cc_final: 0.5126 (mtt180) REVERT: B 618 HIS cc_start: 0.5696 (t70) cc_final: 0.5426 (t70) REVERT: B 663 LYS cc_start: 0.5812 (mmpt) cc_final: 0.5358 (mtmt) REVERT: B 666 GLU cc_start: 0.5514 (tt0) cc_final: 0.5204 (tt0) REVERT: B 686 GLU cc_start: 0.5734 (tt0) cc_final: 0.5116 (tp30) REVERT: B 692 ASN cc_start: 0.5806 (OUTLIER) cc_final: 0.5524 (t0) REVERT: B 708 LYS cc_start: 0.6949 (mttp) cc_final: 0.6515 (mttm) REVERT: B 827 LYS cc_start: 0.7350 (ptmm) cc_final: 0.7044 (ptpt) REVERT: B 923 ASN cc_start: 0.6585 (m110) cc_final: 0.6359 (m110) REVERT: B 932 MET cc_start: 0.5517 (mmt) cc_final: 0.5116 (mmm) REVERT: B 933 GLU cc_start: 0.6086 (mm-30) cc_final: 0.5814 (mm-30) REVERT: B 969 ARG cc_start: 0.6550 (mtp-110) cc_final: 0.5715 (mtp85) REVERT: B 1000 ASP cc_start: 0.7620 (m-30) cc_final: 0.7382 (m-30) REVERT: B 1107 ARG cc_start: 0.5689 (ttp-110) cc_final: 0.5022 (ptm-80) REVERT: B 1108 LYS cc_start: 0.6145 (ttmt) cc_final: 0.5675 (ttpp) REVERT: B 1122 ARG cc_start: 0.5155 (mtm110) cc_final: 0.4716 (ttp80) REVERT: B 1128 ARG cc_start: 0.5837 (OUTLIER) cc_final: 0.5462 (ttp-110) REVERT: B 1147 MET cc_start: 0.6399 (mmm) cc_final: 0.6070 (mtm) REVERT: B 1151 ASP cc_start: 0.6865 (m-30) cc_final: 0.6446 (m-30) REVERT: B 1160 PHE cc_start: 0.6737 (m-10) cc_final: 0.6348 (t80) REVERT: B 1348 ASP cc_start: 0.7855 (t0) cc_final: 0.7473 (t70) REVERT: B 1365 MET cc_start: 0.8204 (ptm) cc_final: 0.7954 (ptm) REVERT: B 1401 MET cc_start: 0.7202 (mtp) cc_final: 0.6921 (mtp) REVERT: C 80 HIS cc_start: 0.5686 (m-70) cc_final: 0.5210 (m170) REVERT: C 166 LYS cc_start: 0.6215 (tttm) cc_final: 0.5895 (ttmm) REVERT: C 284 GLN cc_start: 0.7494 (mm-40) cc_final: 0.6955 (mt0) REVERT: C 456 MET cc_start: 0.5003 (ttm) cc_final: 0.4501 (ttp) REVERT: C 477 LYS cc_start: 0.6622 (mptt) cc_final: 0.5952 (mmtp) REVERT: C 507 GLU cc_start: 0.6103 (tp30) cc_final: 0.5804 (tp30) REVERT: C 618 HIS cc_start: 0.5695 (t70) cc_final: 0.5428 (t70) REVERT: C 663 LYS cc_start: 0.5811 (mmpt) cc_final: 0.5358 (mtmt) REVERT: C 666 GLU cc_start: 0.5513 (tt0) cc_final: 0.5206 (tt0) REVERT: C 686 GLU cc_start: 0.5710 (tt0) cc_final: 0.5122 (tp30) REVERT: C 692 ASN cc_start: 0.5747 (OUTLIER) cc_final: 0.5472 (t0) REVERT: C 708 LYS cc_start: 0.6950 (mttp) cc_final: 0.6516 (mttm) REVERT: C 827 LYS cc_start: 0.7346 (ptmm) cc_final: 0.7031 (ptpt) REVERT: C 932 MET cc_start: 0.5577 (mmt) cc_final: 0.5184 (mmm) REVERT: C 933 GLU cc_start: 0.6055 (mm-30) cc_final: 0.5735 (mm-30) REVERT: C 969 ARG cc_start: 0.6544 (mtp-110) cc_final: 0.5713 (mtp85) REVERT: C 1000 ASP cc_start: 0.7618 (m-30) cc_final: 0.7380 (m-30) REVERT: C 1107 ARG cc_start: 0.5682 (ttp-110) cc_final: 0.5016 (ptm-80) REVERT: C 1108 LYS cc_start: 0.6123 (ttmt) cc_final: 0.5651 (ttpp) REVERT: C 1119 LYS cc_start: 0.5388 (mtpt) cc_final: 0.4711 (mtmt) REVERT: C 1122 ARG cc_start: 0.5156 (mtm110) cc_final: 0.4693 (ttp80) REVERT: C 1128 ARG cc_start: 0.5820 (OUTLIER) cc_final: 0.5451 (ttp-110) REVERT: C 1151 ASP cc_start: 0.6843 (m-30) cc_final: 0.6565 (m-30) REVERT: C 1157 MET cc_start: 0.7535 (mmm) cc_final: 0.7258 (mmt) REVERT: C 1348 ASP cc_start: 0.7813 (t0) cc_final: 0.7471 (t70) outliers start: 57 outliers final: 42 residues processed: 584 average time/residue: 1.8834 time to fit residues: 1319.2616 Evaluate side-chains 608 residues out of total 4700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 559 time to evaluate : 4.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 683 MET Chi-restraints excluded: chain A residue 1011 VAL Chi-restraints excluded: chain A residue 1064 LYS Chi-restraints excluded: chain A residue 1075 LEU Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1128 ARG Chi-restraints excluded: chain A residue 1229 VAL Chi-restraints excluded: chain A residue 1238 MET Chi-restraints excluded: chain A residue 1243 ILE Chi-restraints excluded: chain D residue 527 LEU Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 615 MET Chi-restraints excluded: chain D residue 646 LEU Chi-restraints excluded: chain D residue 683 MET Chi-restraints excluded: chain D residue 1011 VAL Chi-restraints excluded: chain D residue 1064 LYS Chi-restraints excluded: chain D residue 1082 LEU Chi-restraints excluded: chain D residue 1128 ARG Chi-restraints excluded: chain D residue 1150 MET Chi-restraints excluded: chain D residue 1229 VAL Chi-restraints excluded: chain D residue 1238 MET Chi-restraints excluded: chain D residue 1243 ILE Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 615 MET Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 683 MET Chi-restraints excluded: chain B residue 692 ASN Chi-restraints excluded: chain B residue 1011 VAL Chi-restraints excluded: chain B residue 1082 LEU Chi-restraints excluded: chain B residue 1128 ARG Chi-restraints excluded: chain B residue 1229 VAL Chi-restraints excluded: chain B residue 1238 MET Chi-restraints excluded: chain B residue 1243 ILE Chi-restraints excluded: chain C residue 574 VAL Chi-restraints excluded: chain C residue 615 MET Chi-restraints excluded: chain C residue 646 LEU Chi-restraints excluded: chain C residue 683 MET Chi-restraints excluded: chain C residue 692 ASN Chi-restraints excluded: chain C residue 1011 VAL Chi-restraints excluded: chain C residue 1082 LEU Chi-restraints excluded: chain C residue 1128 ARG Chi-restraints excluded: chain C residue 1150 MET Chi-restraints excluded: chain C residue 1164 LEU Chi-restraints excluded: chain C residue 1229 VAL Chi-restraints excluded: chain C residue 1238 MET Chi-restraints excluded: chain C residue 1243 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 548 random chunks: chunk 266 optimal weight: 0.8980 chunk 345 optimal weight: 5.9990 chunk 463 optimal weight: 8.9990 chunk 133 optimal weight: 4.9990 chunk 400 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 chunk 120 optimal weight: 0.8980 chunk 435 optimal weight: 0.0050 chunk 182 optimal weight: 4.9990 chunk 447 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 overall best weight: 0.8996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN D 61 ASN B 61 ASN B 692 ASN C 61 ASN C 692 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.167554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.122160 restraints weight = 50971.325| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 1.90 r_work: 0.3276 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.4266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 43760 Z= 0.186 Angle : 0.504 8.255 59540 Z= 0.262 Chirality : 0.039 0.166 6772 Planarity : 0.004 0.045 7540 Dihedral : 8.099 89.942 7084 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.39 % Allowed : 14.20 % Favored : 84.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.11), residues: 5476 helix: 2.24 (0.09), residues: 3012 sheet: -1.21 (0.22), residues: 436 loop : -0.41 (0.14), residues: 2028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D1124 HIS 0.003 0.001 HIS B 82 PHE 0.027 0.001 PHE C 496 TYR 0.018 0.002 TYR A 420 ARG 0.006 0.000 ARG D1126 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20785.40 seconds wall clock time: 374 minutes 3.02 seconds (22443.02 seconds total)