Starting phenix.real_space_refine on Sun Feb 8 07:57:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sre_40728/02_2026/8sre_40728.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sre_40728/02_2026/8sre_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_40728/02_2026/8sre_40728.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sre_40728/02_2026/8sre_40728.map" model { file = "/net/cci-nas-00/data/ceres_data/8sre_40728/02_2026/8sre_40728.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sre_40728/02_2026/8sre_40728.cif" } resolution = 2.52 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.094 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-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 42781 Number of models: 1 Model: "" Number of chains: 12 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: {'GLU:plan': 16, 'ASP:plan': 19, 'GLN:plan1': 4, 'HIS:plan': 7, 'ARG:plan': 8, 'ASN:plan1': 6, 'TYR:plan': 1, 'PHE:plan': 4} Unresolved non-hydrogen planarities: 261 Chain: "D" 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: {'GLU:plan': 16, 'ASP:plan': 19, 'GLN:plan1': 4, 'HIS:plan': 7, 'ARG:plan': 8, 'ASN:plan1': 6, 'TYR:plan': 1, 'PHE:plan': 4} Unresolved non-hydrogen planarities: 261 Chain: "B" 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: {'GLU:plan': 16, 'ASP:plan': 19, 'GLN:plan1': 4, 'HIS:plan': 7, 'ARG:plan': 8, 'ASN:plan1': 6, 'TYR:plan': 1, 'PHE:plan': 4} 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: {'GLU:plan': 16, 'ASP:plan': 19, 'GLN:plan1': 4, 'HIS:plan': 7, 'ARG:plan': 8, 'ASN:plan1': 6, 'TYR:plan': 1, 'PHE:plan': 4} 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: "D" 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: "B" 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: "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} Time building chain proxies: 10.18, per 1000 atoms: 0.24 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=4, 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 Simple disulfide: pdb=" SG CYS B 997 " - pdb=" SG CYS B1006 " distance=2.03 Simple disulfide: pdb=" SG CYS C 997 " - pdb=" SG CYS C1006 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.63 Conformation dependent library (CDL) restraints added in 1.7 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: 1.96 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: 10.53 Time building geometry restraints manager: 4.86 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: 24376 17.73 - 35.46: 2047 35.46 - 53.19: 313 53.19 - 70.93: 36 70.93 - 88.66: 48 Dihedral angle restraints: 26820 sinusoidal: 10808 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 26817 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: 144 2.46 - 3.07: 21579 3.07 - 3.68: 67005 3.68 - 4.29: 94658 4.29 - 4.90: 162437 Nonbonded interactions: 345823 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=" OE2 GLU C1390 " pdb="MG MG C6006 " model vdw 2.036 2.170 ... (remaining 345818 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: 5.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.660 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 41.040 Find NCS groups from input model: 1.240 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.570 ------------------------------------------------------------------------------- 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 43764 Z= 0.667 Angle : 1.775 13.273 59548 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (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 ARG 0.053 0.002 ARG D1088 TYR 0.049 0.006 TYR D 466 PHE 0.055 0.007 PHE B 941 TRP 0.032 0.003 TRP B 726 HIS 0.011 0.002 HIS B 660 Details of bonding type rmsd covalent geometry : bond 0.01254 (43760) covalent geometry : angle 1.77532 (59540) SS BOND : bond 0.00572 ( 4) SS BOND : angle 2.36681 ( 8) hydrogen bonds : bond 0.16755 ( 2364) hydrogen bonds : angle 7.05686 ( 6960) *********************** 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 : 1.588 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: 0.8629 time to fit residues: 1033.6451 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 : 1.672 ------------------------------------------------------------------------------- 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 394 optimal weight: 0.8980 chunk 430 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 265 optimal weight: 6.9990 chunk 523 optimal weight: 0.8980 chunk 497 optimal weight: 3.9990 chunk 414 optimal weight: 0.0040 chunk 310 optimal weight: 6.9990 chunk 488 optimal weight: 7.9990 chunk 366 optimal weight: 0.9980 chunk 223 optimal weight: 3.9990 overall best weight: 0.7594 ------------------------------------------------------------------------------- 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 813 HIS 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 813 HIS C 996 ASN C1038 ASN C1101 GLN C1116 ASN C1156 HIS C1282 ASN C1441 ASN C1463 HIS Total number of N/Q/H flips: 45 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.172796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.126833 restraints weight = 51914.048| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 1.95 r_work: 0.3362 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3230 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 43764 Z= 0.139 Angle : 0.534 6.977 59548 Z= 0.284 Chirality : 0.040 0.147 6772 Planarity : 0.005 0.073 7540 Dihedral : 8.311 85.900 7108 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.44 % Allowed : 8.06 % Favored : 90.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.11), residues: 5476 helix: 1.96 (0.09), residues: 3028 sheet: -1.09 (0.22), residues: 412 loop : -0.41 (0.14), residues: 2036 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 112 TYR 0.046 0.002 TYR D 420 PHE 0.014 0.002 PHE B 856 TRP 0.013 0.001 TRP A 726 HIS 0.006 0.001 HIS C 514 Details of bonding type rmsd covalent geometry : bond 0.00292 (43760) covalent geometry : angle 0.53362 (59540) SS BOND : bond 0.00150 ( 4) SS BOND : angle 0.21407 ( 8) hydrogen bonds : bond 0.04478 ( 2364) hydrogen bonds : angle 3.97247 ( 6960) *********************** 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 778 residues out of total 4700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 717 time to evaluate : 1.702 Fit side-chains REVERT: A 60 GLU cc_start: 0.6083 (mp0) cc_final: 0.5811 (mm-30) REVERT: A 80 HIS cc_start: 0.6240 (m-70) cc_final: 0.5756 (m170) REVERT: A 166 LYS cc_start: 0.7232 (tttm) cc_final: 0.6988 (ttmm) REVERT: A 262 ASP cc_start: 0.7127 (p0) cc_final: 0.6606 (p0) REVERT: A 284 GLN cc_start: 0.7639 (mm-40) cc_final: 0.7329 (mt0) REVERT: A 368 ASN cc_start: 0.7623 (m-40) cc_final: 0.7391 (m110) REVERT: A 395 GLU cc_start: 0.6845 (tt0) cc_final: 0.6560 (mt-10) REVERT: A 502 GLU cc_start: 0.6699 (tt0) cc_final: 0.6218 (mt-10) REVERT: A 569 SER cc_start: 0.6517 (t) cc_final: 0.6071 (m) REVERT: A 663 LYS cc_start: 0.7449 (mmpt) cc_final: 0.6964 (mtmt) REVERT: A 667 GLU cc_start: 0.8051 (mt-10) cc_final: 0.7775 (mt-10) REVERT: A 675 GLU cc_start: 0.8002 (tp30) cc_final: 0.7675 (tp30) REVERT: A 686 GLU cc_start: 0.7364 (tt0) cc_final: 0.6749 (tp30) REVERT: A 691 LYS cc_start: 0.7990 (mttt) cc_final: 0.7731 (mttp) REVERT: A 702 ASN cc_start: 0.7810 (t0) cc_final: 0.7475 (t0) REVERT: A 706 ASP cc_start: 0.7755 (m-30) cc_final: 0.7483 (m-30) REVERT: A 797 LYS cc_start: 0.6864 (mttt) cc_final: 0.6436 (mtpm) REVERT: A 930 MET cc_start: 0.8152 (tpp) cc_final: 0.7909 (tpp) REVERT: A 932 MET cc_start: 0.7459 (mmt) cc_final: 0.7100 (mmm) REVERT: A 969 ARG cc_start: 0.8034 (mtp-110) cc_final: 0.7528 (mtp85) REVERT: A 1000 ASP cc_start: 0.8021 (m-30) cc_final: 0.7795 (m-30) REVERT: A 1064 LYS cc_start: 0.7895 (OUTLIER) cc_final: 0.7096 (mmtm) REVERT: A 1085 ARG cc_start: 0.5193 (tpp80) cc_final: 0.4048 (ttp-170) REVERT: A 1107 ARG cc_start: 0.6285 (ttp-110) cc_final: 0.5664 (ptm-80) REVERT: A 1122 ARG cc_start: 0.6596 (mtm110) cc_final: 0.5861 (ttp80) REVERT: A 1123 ARG cc_start: 0.7315 (ttp80) cc_final: 0.7060 (ttp80) REVERT: A 1128 ARG cc_start: 0.6722 (OUTLIER) cc_final: 0.6216 (ttp-110) REVERT: A 1162 PHE cc_start: 0.8295 (t80) cc_final: 0.8031 (t80) REVERT: D 60 GLU cc_start: 0.6008 (mp0) cc_final: 0.5753 (mm-30) REVERT: D 80 HIS cc_start: 0.6218 (m-70) cc_final: 0.5708 (m170) REVERT: D 166 LYS cc_start: 0.7235 (tttm) cc_final: 0.6992 (ttmm) REVERT: D 262 ASP cc_start: 0.7127 (p0) cc_final: 0.6593 (p0) REVERT: D 284 GLN cc_start: 0.7622 (mm-40) cc_final: 0.7317 (mt0) REVERT: D 368 ASN cc_start: 0.7638 (m-40) cc_final: 0.7398 (m110) REVERT: D 395 GLU cc_start: 0.6789 (tt0) cc_final: 0.6513 (mt-10) REVERT: D 502 GLU cc_start: 0.6724 (tt0) cc_final: 0.6225 (mt-10) REVERT: D 569 SER cc_start: 0.6504 (t) cc_final: 0.6062 (m) REVERT: D 595 ARG cc_start: 0.6863 (mtt180) cc_final: 0.6630 (mtt180) REVERT: D 663 LYS cc_start: 0.7397 (mmpt) cc_final: 0.6940 (mtmt) REVERT: D 675 GLU cc_start: 0.7992 (tp30) cc_final: 0.7672 (tp30) REVERT: D 686 GLU cc_start: 0.7376 (tt0) cc_final: 0.6761 (tp30) REVERT: D 691 LYS cc_start: 0.8013 (mttt) cc_final: 0.7738 (mttp) REVERT: D 702 ASN cc_start: 0.7821 (t0) cc_final: 0.7466 (t0) REVERT: D 706 ASP cc_start: 0.7697 (m-30) cc_final: 0.7473 (m-30) REVERT: D 708 LYS cc_start: 0.7694 (mttp) cc_final: 0.7356 (mmtm) REVERT: D 797 LYS cc_start: 0.6874 (mttt) cc_final: 0.6466 (mtpm) REVERT: D 889 ASP cc_start: 0.7352 (t0) cc_final: 0.7152 (t0) REVERT: D 930 MET cc_start: 0.8152 (tpp) cc_final: 0.7908 (tpp) REVERT: D 932 MET cc_start: 0.7567 (mmt) cc_final: 0.7201 (mmm) REVERT: D 936 LYS cc_start: 0.8098 (mttt) cc_final: 0.7894 (mtpt) REVERT: D 969 ARG cc_start: 0.8026 (mtp-110) cc_final: 0.7516 (mtp85) REVERT: D 1000 ASP cc_start: 0.8006 (m-30) cc_final: 0.7781 (m-30) REVERT: D 1085 ARG cc_start: 0.5185 (tpp80) cc_final: 0.4064 (ttp-170) REVERT: D 1107 ARG cc_start: 0.6304 (ttp-110) cc_final: 0.5656 (ptm-80) REVERT: D 1122 ARG cc_start: 0.6537 (mtm110) cc_final: 0.5805 (ttp80) REVERT: D 1123 ARG cc_start: 0.7312 (ttp80) cc_final: 0.7016 (ttp80) REVERT: D 1128 ARG cc_start: 0.6712 (OUTLIER) cc_final: 0.6222 (ttp-110) REVERT: D 1162 PHE cc_start: 0.8293 (t80) cc_final: 0.8092 (t80) REVERT: B 60 GLU cc_start: 0.6004 (mp0) cc_final: 0.5748 (mm-30) REVERT: B 80 HIS cc_start: 0.6223 (m-70) cc_final: 0.5756 (m170) REVERT: B 166 LYS cc_start: 0.7239 (tttm) cc_final: 0.6998 (ttmm) REVERT: B 262 ASP cc_start: 0.7127 (p0) cc_final: 0.6596 (p0) REVERT: B 284 GLN cc_start: 0.7607 (mm-40) cc_final: 0.7315 (mt0) REVERT: B 368 ASN cc_start: 0.7637 (m-40) cc_final: 0.7403 (m110) REVERT: B 395 GLU cc_start: 0.6804 (tt0) cc_final: 0.6523 (mt-10) REVERT: B 502 GLU cc_start: 0.6719 (tt0) cc_final: 0.6224 (mt-10) REVERT: B 569 SER cc_start: 0.6518 (t) cc_final: 0.6076 (m) REVERT: B 595 ARG cc_start: 0.6877 (mtt180) cc_final: 0.6645 (mtt180) REVERT: B 663 LYS cc_start: 0.7408 (mmpt) cc_final: 0.6954 (mtmt) REVERT: B 675 GLU cc_start: 0.7987 (tp30) cc_final: 0.7669 (tp30) REVERT: B 686 GLU cc_start: 0.7395 (tt0) cc_final: 0.6780 (tp30) REVERT: B 691 LYS cc_start: 0.7985 (mttt) cc_final: 0.7736 (mttp) REVERT: B 702 ASN cc_start: 0.7819 (t0) cc_final: 0.7461 (t0) REVERT: B 706 ASP cc_start: 0.7697 (m-30) cc_final: 0.7472 (m-30) REVERT: B 708 LYS cc_start: 0.7708 (mttp) cc_final: 0.7362 (mmtm) REVERT: B 797 LYS cc_start: 0.6868 (mttt) cc_final: 0.6463 (mtpm) REVERT: B 889 ASP cc_start: 0.7358 (t0) cc_final: 0.7157 (t0) REVERT: B 930 MET cc_start: 0.8136 (tpp) cc_final: 0.7892 (tpp) REVERT: B 932 MET cc_start: 0.7381 (mmt) cc_final: 0.6983 (mmm) REVERT: B 936 LYS cc_start: 0.8087 (mttt) cc_final: 0.7881 (mtpt) REVERT: B 969 ARG cc_start: 0.8037 (mtp-110) cc_final: 0.7523 (mtp85) REVERT: B 1000 ASP cc_start: 0.8007 (m-30) cc_final: 0.7784 (m-30) REVERT: B 1064 LYS cc_start: 0.7882 (OUTLIER) cc_final: 0.7075 (mmtm) REVERT: B 1085 ARG cc_start: 0.5189 (tpp80) cc_final: 0.4068 (ttp-170) REVERT: B 1107 ARG cc_start: 0.6306 (ttp-110) cc_final: 0.5657 (ptm-80) REVERT: B 1122 ARG cc_start: 0.6538 (mtm110) cc_final: 0.5808 (ttp80) REVERT: B 1123 ARG cc_start: 0.7321 (ttp80) cc_final: 0.7026 (ttp80) REVERT: B 1128 ARG cc_start: 0.6720 (OUTLIER) cc_final: 0.6229 (ttp-110) REVERT: B 1162 PHE cc_start: 0.8298 (t80) cc_final: 0.8094 (t80) REVERT: C 60 GLU cc_start: 0.6028 (mp0) cc_final: 0.5729 (mm-30) REVERT: C 80 HIS cc_start: 0.6235 (m-70) cc_final: 0.5770 (m170) REVERT: C 166 LYS cc_start: 0.7245 (tttm) cc_final: 0.7004 (ttmm) REVERT: C 262 ASP cc_start: 0.7124 (p0) cc_final: 0.6599 (p0) REVERT: C 284 GLN cc_start: 0.7607 (mm-40) cc_final: 0.7318 (mt0) REVERT: C 368 ASN cc_start: 0.7624 (m-40) cc_final: 0.7393 (m110) REVERT: C 395 GLU cc_start: 0.6800 (tt0) cc_final: 0.6529 (mt-10) REVERT: C 502 GLU cc_start: 0.6683 (tt0) cc_final: 0.6196 (mt-10) REVERT: C 569 SER cc_start: 0.6513 (t) cc_final: 0.6070 (m) REVERT: C 595 ARG cc_start: 0.6880 (mtt180) cc_final: 0.6651 (mtt180) REVERT: C 663 LYS cc_start: 0.7418 (mmpt) cc_final: 0.6962 (mtmt) REVERT: C 675 GLU cc_start: 0.7998 (tp30) cc_final: 0.7683 (tp30) REVERT: C 686 GLU cc_start: 0.7387 (tt0) cc_final: 0.6773 (tp30) REVERT: C 691 LYS cc_start: 0.7994 (mttt) cc_final: 0.7749 (mttp) REVERT: C 702 ASN cc_start: 0.7823 (t0) cc_final: 0.7469 (t0) REVERT: C 706 ASP cc_start: 0.7700 (m-30) cc_final: 0.7470 (m-30) REVERT: C 708 LYS cc_start: 0.7689 (mttp) cc_final: 0.7359 (mmtm) REVERT: C 797 LYS cc_start: 0.6863 (mttt) cc_final: 0.6445 (mtpm) REVERT: C 930 MET cc_start: 0.8132 (tpp) cc_final: 0.7888 (tpp) REVERT: C 932 MET cc_start: 0.7431 (mmt) cc_final: 0.7032 (mmm) REVERT: C 936 LYS cc_start: 0.8092 (mttt) cc_final: 0.7886 (mtpt) REVERT: C 969 ARG cc_start: 0.8034 (mtp-110) cc_final: 0.7524 (mtp85) REVERT: C 1000 ASP cc_start: 0.8007 (m-30) cc_final: 0.7779 (m-30) REVERT: C 1064 LYS cc_start: 0.7882 (OUTLIER) cc_final: 0.7078 (mmtm) REVERT: C 1085 ARG cc_start: 0.5187 (tpp80) cc_final: 0.4048 (ttp-170) REVERT: C 1107 ARG cc_start: 0.6293 (ttp-110) cc_final: 0.5670 (ptm-80) REVERT: C 1122 ARG cc_start: 0.6542 (mtm110) cc_final: 0.5809 (ttp80) REVERT: C 1123 ARG cc_start: 0.7319 (ttp80) cc_final: 0.7022 (ttp80) REVERT: C 1128 ARG cc_start: 0.6721 (OUTLIER) cc_final: 0.6233 (ttp-110) REVERT: C 1150 MET cc_start: 0.7921 (OUTLIER) cc_final: 0.6623 (mmt) REVERT: C 1162 PHE cc_start: 0.8294 (t80) cc_final: 0.8094 (t80) outliers start: 61 outliers final: 20 residues processed: 731 average time/residue: 0.8727 time to fit residues: 764.7402 Evaluate side-chains 640 residues out of total 4700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 612 time to evaluate : 1.623 ------------------------------------------------------------------------------- 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 7 optimal weight: 1.9990 chunk 359 optimal weight: 5.9990 chunk 146 optimal weight: 4.9990 chunk 330 optimal weight: 3.9990 chunk 13 optimal weight: 6.9990 chunk 454 optimal weight: 0.9980 chunk 352 optimal weight: 1.9990 chunk 438 optimal weight: 0.9990 chunk 490 optimal weight: 1.9990 chunk 297 optimal weight: 3.9990 chunk 147 optimal weight: 7.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 ASN A 660 HIS A 813 HIS A1101 GLN A1282 ASN D 280 ASN D 660 HIS D 692 ASN D 813 HIS D 893 GLN D1080 HIS D1101 GLN D1282 ASN B 240 HIS B 280 ASN B 660 HIS B 692 ASN B 813 HIS B 893 GLN B1080 HIS B1101 GLN B1282 ASN C 280 ASN C 660 HIS C 692 ASN C 813 HIS C1080 HIS C1101 GLN C1282 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.166684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.120439 restraints weight = 51390.319| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 1.94 r_work: 0.3246 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.3514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 43764 Z= 0.188 Angle : 0.582 7.065 59548 Z= 0.308 Chirality : 0.042 0.167 6772 Planarity : 0.005 0.047 7540 Dihedral : 8.588 89.982 7084 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.91 % Allowed : 10.35 % Favored : 87.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.11), residues: 5476 helix: 1.93 (0.09), residues: 3044 sheet: -0.93 (0.21), residues: 436 loop : -0.38 (0.14), residues: 1996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 152 TYR 0.026 0.002 TYR B 420 PHE 0.020 0.002 PHE C 879 TRP 0.010 0.002 TRP C 726 HIS 0.007 0.001 HIS C 240 Details of bonding type rmsd covalent geometry : bond 0.00423 (43760) covalent geometry : angle 0.58225 (59540) SS BOND : bond 0.00085 ( 4) SS BOND : angle 0.47625 ( 8) hydrogen bonds : bond 0.05061 ( 2364) hydrogen bonds : angle 3.96293 ( 6960) *********************** 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 721 residues out of total 4700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 640 time to evaluate : 1.622 Fit side-chains REVERT: A 80 HIS cc_start: 0.6632 (m-70) cc_final: 0.6135 (m170) REVERT: A 166 LYS cc_start: 0.7248 (tttm) cc_final: 0.6961 (ttmm) REVERT: A 284 GLN cc_start: 0.7685 (mm-40) cc_final: 0.7400 (mt0) REVERT: A 368 ASN cc_start: 0.7941 (m-40) cc_final: 0.7699 (m110) REVERT: A 395 GLU cc_start: 0.6926 (tt0) cc_final: 0.6572 (mt-10) REVERT: A 502 GLU cc_start: 0.6909 (tt0) cc_final: 0.6442 (mt-10) REVERT: A 663 LYS cc_start: 0.7505 (mmpt) cc_final: 0.6944 (mtmt) REVERT: A 666 GLU cc_start: 0.7582 (tt0) cc_final: 0.7306 (tt0) REVERT: A 686 GLU cc_start: 0.7376 (tt0) cc_final: 0.6707 (tp30) REVERT: A 691 LYS cc_start: 0.8107 (mttt) cc_final: 0.7895 (mttp) REVERT: A 706 ASP cc_start: 0.7979 (m-30) cc_final: 0.7759 (m-30) REVERT: A 797 LYS cc_start: 0.6754 (mttt) cc_final: 0.6395 (mtpm) REVERT: A 923 ASN cc_start: 0.8160 (m110) cc_final: 0.7896 (m110) REVERT: A 969 ARG cc_start: 0.8130 (mtp-110) cc_final: 0.7514 (mtp85) REVERT: A 1000 ASP cc_start: 0.8179 (m-30) cc_final: 0.7963 (m-30) REVERT: A 1107 ARG cc_start: 0.6462 (ttp-110) cc_final: 0.5747 (ptm-80) REVERT: A 1122 ARG cc_start: 0.6586 (mtm110) cc_final: 0.5956 (ttp80) REVERT: A 1123 ARG cc_start: 0.7276 (ttp80) cc_final: 0.7054 (ttp80) REVERT: A 1128 ARG cc_start: 0.6907 (OUTLIER) cc_final: 0.6392 (ttp-110) REVERT: A 1157 MET cc_start: 0.8545 (mmm) cc_final: 0.8293 (mmm) REVERT: A 1365 MET cc_start: 0.8687 (ptm) cc_final: 0.8424 (ptm) REVERT: D 78 ARG cc_start: 0.6837 (ptp-170) cc_final: 0.6615 (ptp-170) REVERT: D 80 HIS cc_start: 0.6596 (m-70) cc_final: 0.6074 (m170) REVERT: D 166 LYS cc_start: 0.7243 (tttm) cc_final: 0.6959 (ttmm) REVERT: D 284 GLN cc_start: 0.7679 (mm-40) cc_final: 0.7399 (mt0) REVERT: D 335 MET cc_start: 0.9136 (mtp) cc_final: 0.8925 (mtp) REVERT: D 368 ASN cc_start: 0.7935 (m-40) cc_final: 0.7700 (m110) REVERT: D 395 GLU cc_start: 0.6907 (tt0) cc_final: 0.6620 (mt-10) REVERT: D 502 GLU cc_start: 0.6959 (tt0) cc_final: 0.6461 (mt-10) REVERT: D 595 ARG cc_start: 0.6784 (mtt180) cc_final: 0.6537 (mtt180) REVERT: D 663 LYS cc_start: 0.7479 (mmpt) cc_final: 0.6981 (mtmt) REVERT: D 666 GLU cc_start: 0.7573 (tt0) cc_final: 0.7271 (tt0) REVERT: D 667 GLU cc_start: 0.7966 (mt-10) cc_final: 0.7525 (mm-30) REVERT: D 675 GLU cc_start: 0.7971 (tp30) cc_final: 0.7554 (tp30) REVERT: D 686 GLU cc_start: 0.7269 (tt0) cc_final: 0.6595 (tp30) REVERT: D 691 LYS cc_start: 0.8062 (mttt) cc_final: 0.7843 (mttp) REVERT: D 706 ASP cc_start: 0.7969 (m-30) cc_final: 0.7675 (m-30) REVERT: D 708 LYS cc_start: 0.7844 (mttp) cc_final: 0.7528 (mttm) REVERT: D 797 LYS cc_start: 0.6746 (mttt) cc_final: 0.6397 (mtpm) REVERT: D 930 MET cc_start: 0.8290 (tpp) cc_final: 0.8090 (tpp) REVERT: D 969 ARG cc_start: 0.8119 (mtp-110) cc_final: 0.7501 (mtp85) REVERT: D 1000 ASP cc_start: 0.8159 (m-30) cc_final: 0.7944 (m-30) REVERT: D 1065 ASP cc_start: 0.7989 (t70) cc_final: 0.7728 (t0) REVERT: D 1107 ARG cc_start: 0.6546 (ttp-110) cc_final: 0.5818 (ptm-80) REVERT: D 1122 ARG cc_start: 0.6594 (mtm110) cc_final: 0.5787 (ttp80) REVERT: D 1123 ARG cc_start: 0.7328 (ttp80) cc_final: 0.7109 (ttp80) REVERT: D 1128 ARG cc_start: 0.6807 (OUTLIER) cc_final: 0.6260 (ttp-110) REVERT: D 1365 MET cc_start: 0.8679 (ptm) cc_final: 0.8401 (ptm) REVERT: B 78 ARG cc_start: 0.6838 (ptp-170) cc_final: 0.6619 (ptp-170) REVERT: B 80 HIS cc_start: 0.6604 (m-70) cc_final: 0.6082 (m170) REVERT: B 166 LYS cc_start: 0.7236 (tttm) cc_final: 0.6952 (ttmm) REVERT: B 284 GLN cc_start: 0.7679 (mm-40) cc_final: 0.7395 (mt0) REVERT: B 335 MET cc_start: 0.9142 (mtp) cc_final: 0.8931 (mtp) REVERT: B 368 ASN cc_start: 0.7952 (m-40) cc_final: 0.7707 (m110) REVERT: B 395 GLU cc_start: 0.6906 (tt0) cc_final: 0.6623 (mt-10) REVERT: B 502 GLU cc_start: 0.6963 (tt0) cc_final: 0.6467 (mt-10) REVERT: B 595 ARG cc_start: 0.6807 (mtt180) cc_final: 0.6561 (mtt180) REVERT: B 663 LYS cc_start: 0.7513 (mmpt) cc_final: 0.7008 (mtmt) REVERT: B 666 GLU cc_start: 0.7543 (tt0) cc_final: 0.7292 (tt0) REVERT: B 667 GLU cc_start: 0.7962 (mt-10) cc_final: 0.7520 (mm-30) REVERT: B 675 GLU cc_start: 0.7975 (tp30) cc_final: 0.7563 (tp30) REVERT: B 686 GLU cc_start: 0.7269 (tt0) cc_final: 0.6595 (tp30) REVERT: B 691 LYS cc_start: 0.8065 (mttt) cc_final: 0.7845 (mttp) REVERT: B 706 ASP cc_start: 0.7968 (m-30) cc_final: 0.7680 (m-30) REVERT: B 708 LYS cc_start: 0.7850 (mttp) cc_final: 0.7536 (mttm) REVERT: B 797 LYS cc_start: 0.6743 (mttt) cc_final: 0.6395 (mtpm) REVERT: B 923 ASN cc_start: 0.8155 (m110) cc_final: 0.7893 (m110) REVERT: B 969 ARG cc_start: 0.8118 (mtp-110) cc_final: 0.7496 (mtp85) REVERT: B 1000 ASP cc_start: 0.8174 (m-30) cc_final: 0.7960 (m-30) REVERT: B 1107 ARG cc_start: 0.6551 (ttp-110) cc_final: 0.5823 (ptm-80) REVERT: B 1122 ARG cc_start: 0.6593 (mtm110) cc_final: 0.5786 (ttp80) REVERT: B 1123 ARG cc_start: 0.7327 (ttp80) cc_final: 0.7108 (ttp80) REVERT: B 1128 ARG cc_start: 0.6822 (OUTLIER) cc_final: 0.6271 (ttp-110) REVERT: B 1160 PHE cc_start: 0.7622 (m-10) cc_final: 0.7282 (t80) REVERT: B 1365 MET cc_start: 0.8675 (ptm) cc_final: 0.8398 (ptm) REVERT: C 80 HIS cc_start: 0.6629 (m-70) cc_final: 0.6132 (m170) REVERT: C 166 LYS cc_start: 0.7240 (tttm) cc_final: 0.6958 (ttmm) REVERT: C 284 GLN cc_start: 0.7681 (mm-40) cc_final: 0.7396 (mt0) REVERT: C 335 MET cc_start: 0.9132 (mtp) cc_final: 0.8922 (mtp) REVERT: C 368 ASN cc_start: 0.7949 (m-40) cc_final: 0.7709 (m110) REVERT: C 395 GLU cc_start: 0.6915 (tt0) cc_final: 0.6616 (mt-10) REVERT: C 502 GLU cc_start: 0.6968 (tt0) cc_final: 0.6477 (mt-10) REVERT: C 595 ARG cc_start: 0.6809 (mtt180) cc_final: 0.6562 (mtt180) REVERT: C 663 LYS cc_start: 0.7516 (mmpt) cc_final: 0.7018 (mtmt) REVERT: C 666 GLU cc_start: 0.7551 (tt0) cc_final: 0.7287 (tt0) REVERT: C 667 GLU cc_start: 0.7962 (mt-10) cc_final: 0.7516 (mm-30) REVERT: C 675 GLU cc_start: 0.7978 (tp30) cc_final: 0.7561 (tp30) REVERT: C 686 GLU cc_start: 0.7275 (tt0) cc_final: 0.6604 (tp30) REVERT: C 691 LYS cc_start: 0.8077 (mttt) cc_final: 0.7858 (mttp) REVERT: C 706 ASP cc_start: 0.7979 (m-30) cc_final: 0.7687 (m-30) REVERT: C 708 LYS cc_start: 0.7853 (mttp) cc_final: 0.7540 (mttm) REVERT: C 797 LYS cc_start: 0.6750 (mttt) cc_final: 0.6402 (mtpm) REVERT: C 969 ARG cc_start: 0.8123 (mtp-110) cc_final: 0.7507 (mtp85) REVERT: C 1000 ASP cc_start: 0.8160 (m-30) cc_final: 0.7944 (m-30) REVERT: C 1107 ARG cc_start: 0.6535 (ttp-110) cc_final: 0.5807 (ptm-80) REVERT: C 1122 ARG cc_start: 0.6623 (mtm110) cc_final: 0.5813 (ttp80) REVERT: C 1123 ARG cc_start: 0.7352 (ttp80) cc_final: 0.7131 (ttp80) REVERT: C 1128 ARG cc_start: 0.6834 (OUTLIER) cc_final: 0.6284 (ttp-110) REVERT: C 1150 MET cc_start: 0.8048 (OUTLIER) cc_final: 0.6669 (mmt) REVERT: C 1365 MET cc_start: 0.8685 (ptm) cc_final: 0.8449 (ptm) REVERT: C 1394 MET cc_start: 0.8592 (mtm) cc_final: 0.8267 (mtp) outliers start: 81 outliers final: 24 residues processed: 658 average time/residue: 0.9307 time to fit residues: 723.7048 Evaluate side-chains 587 residues out of total 4700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 558 time to evaluate : 1.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 357 THR 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 1229 VAL Chi-restraints excluded: chain A residue 1243 ILE Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 357 THR 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 1229 VAL Chi-restraints excluded: chain D residue 1243 ILE Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 357 THR 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 1229 VAL Chi-restraints excluded: chain B residue 1243 ILE Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 357 THR 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 1150 MET Chi-restraints excluded: chain C residue 1229 VAL Chi-restraints excluded: chain C residue 1243 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 548 random chunks: chunk 142 optimal weight: 3.9990 chunk 371 optimal weight: 0.9990 chunk 285 optimal weight: 1.9990 chunk 99 optimal weight: 10.0000 chunk 174 optimal weight: 6.9990 chunk 243 optimal weight: 6.9990 chunk 384 optimal weight: 0.9990 chunk 112 optimal weight: 1.9990 chunk 156 optimal weight: 0.0170 chunk 532 optimal weight: 2.9990 chunk 225 optimal weight: 0.8980 overall best weight: 0.9824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 61 ASN D 659 GLN D1282 ASN B 61 ASN B 659 GLN B1282 ASN C 659 GLN C1282 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.167247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.121831 restraints weight = 51667.066| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 1.91 r_work: 0.3282 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.3640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 43764 Z= 0.134 Angle : 0.489 6.784 59548 Z= 0.259 Chirality : 0.039 0.167 6772 Planarity : 0.004 0.043 7540 Dihedral : 8.227 89.865 7084 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.82 % Allowed : 11.96 % Favored : 86.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.49 (0.11), residues: 5476 helix: 2.14 (0.09), residues: 3040 sheet: -1.15 (0.21), residues: 428 loop : -0.27 (0.14), residues: 2008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 152 TYR 0.025 0.002 TYR A 420 PHE 0.016 0.001 PHE C 879 TRP 0.009 0.001 TRP B1366 HIS 0.003 0.001 HIS B1207 Details of bonding type rmsd covalent geometry : bond 0.00292 (43760) covalent geometry : angle 0.48897 (59540) SS BOND : bond 0.00112 ( 4) SS BOND : angle 0.43640 ( 8) hydrogen bonds : bond 0.04225 ( 2364) hydrogen bonds : angle 3.75091 ( 6960) *********************** 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 665 residues out of total 4700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 588 time to evaluate : 1.722 Fit side-chains REVERT: A 80 HIS cc_start: 0.6559 (m-70) cc_final: 0.6095 (m170) REVERT: A 166 LYS cc_start: 0.7168 (tttm) cc_final: 0.6860 (ttmm) REVERT: A 284 GLN cc_start: 0.7645 (mm-40) cc_final: 0.7380 (mt0) REVERT: A 368 ASN cc_start: 0.7950 (m-40) cc_final: 0.7717 (m110) REVERT: A 395 GLU cc_start: 0.6979 (tt0) cc_final: 0.6527 (pt0) REVERT: A 502 GLU cc_start: 0.6943 (tt0) cc_final: 0.6477 (mt-10) REVERT: A 517 ARG cc_start: 0.6296 (ttm110) cc_final: 0.5898 (ttp-110) REVERT: A 592 GLN cc_start: 0.6688 (tm-30) cc_final: 0.6063 (tp40) REVERT: A 595 ARG cc_start: 0.6695 (mtt180) cc_final: 0.6491 (mtt180) REVERT: A 663 LYS cc_start: 0.7595 (mmpt) cc_final: 0.7046 (mtmt) REVERT: A 666 GLU cc_start: 0.7548 (tt0) cc_final: 0.7295 (tt0) REVERT: A 686 GLU cc_start: 0.7379 (tt0) cc_final: 0.6769 (tp30) REVERT: A 691 LYS cc_start: 0.8140 (mttt) cc_final: 0.7895 (mttt) REVERT: A 694 MET cc_start: 0.6620 (OUTLIER) cc_final: 0.6134 (ttp) REVERT: A 706 ASP cc_start: 0.7920 (m-30) cc_final: 0.7603 (m-30) REVERT: A 797 LYS cc_start: 0.6761 (mttt) cc_final: 0.6421 (mtpm) REVERT: A 923 ASN cc_start: 0.8135 (m110) cc_final: 0.7881 (m110) REVERT: A 932 MET cc_start: 0.7809 (mmt) cc_final: 0.7467 (mmm) REVERT: A 933 GLU cc_start: 0.8054 (mm-30) cc_final: 0.7772 (mm-30) REVERT: A 969 ARG cc_start: 0.8118 (mtp-110) cc_final: 0.7496 (mtp85) REVERT: A 1000 ASP cc_start: 0.8223 (m-30) cc_final: 0.8012 (m-30) REVERT: A 1005 GLU cc_start: 0.8013 (mt-10) cc_final: 0.7762 (mt-10) REVERT: A 1107 ARG cc_start: 0.6573 (ttp-110) cc_final: 0.5837 (ptm-80) REVERT: A 1122 ARG cc_start: 0.6542 (mtm110) cc_final: 0.5911 (ttp80) REVERT: A 1123 ARG cc_start: 0.7281 (ttp80) cc_final: 0.7054 (ttp80) REVERT: A 1128 ARG cc_start: 0.6941 (OUTLIER) cc_final: 0.6443 (ttp-110) REVERT: A 1151 ASP cc_start: 0.8008 (m-30) cc_final: 0.7747 (m-30) REVERT: A 1160 PHE cc_start: 0.7548 (m-10) cc_final: 0.7258 (t80) REVERT: D 80 HIS cc_start: 0.6606 (m-70) cc_final: 0.6140 (m170) REVERT: D 166 LYS cc_start: 0.7202 (tttm) cc_final: 0.6887 (ttmm) REVERT: D 284 GLN cc_start: 0.7652 (mm-40) cc_final: 0.7367 (mt0) REVERT: D 368 ASN cc_start: 0.7931 (m-40) cc_final: 0.7699 (m110) REVERT: D 395 GLU cc_start: 0.6964 (tt0) cc_final: 0.6515 (pt0) REVERT: D 502 GLU cc_start: 0.6966 (tt0) cc_final: 0.6437 (mt-10) REVERT: D 517 ARG cc_start: 0.6297 (ttm110) cc_final: 0.6085 (ttp-110) REVERT: D 595 ARG cc_start: 0.6794 (mtt180) cc_final: 0.6591 (mtt180) REVERT: D 663 LYS cc_start: 0.7555 (mmpt) cc_final: 0.7014 (mtmt) REVERT: D 666 GLU cc_start: 0.7541 (tt0) cc_final: 0.7241 (tt0) REVERT: D 686 GLU cc_start: 0.7389 (tt0) cc_final: 0.6758 (tp30) REVERT: D 691 LYS cc_start: 0.8149 (mttt) cc_final: 0.7903 (mttt) REVERT: D 694 MET cc_start: 0.6590 (OUTLIER) cc_final: 0.6111 (ttp) REVERT: D 706 ASP cc_start: 0.7949 (m-30) cc_final: 0.7697 (m-30) REVERT: D 708 LYS cc_start: 0.7819 (mttp) cc_final: 0.7500 (mttm) REVERT: D 797 LYS cc_start: 0.6755 (mttt) cc_final: 0.6366 (mtpm) REVERT: D 933 GLU cc_start: 0.8041 (mm-30) cc_final: 0.7772 (mm-30) REVERT: D 969 ARG cc_start: 0.8106 (mtp-110) cc_final: 0.7502 (mtp85) REVERT: D 1000 ASP cc_start: 0.8219 (m-30) cc_final: 0.7993 (m-30) REVERT: D 1005 GLU cc_start: 0.8013 (mt-10) cc_final: 0.7702 (mt-10) REVERT: D 1065 ASP cc_start: 0.8035 (t70) cc_final: 0.7760 (t0) REVERT: D 1080 HIS cc_start: 0.6790 (t-90) cc_final: 0.6538 (t-90) REVERT: D 1107 ARG cc_start: 0.6603 (ttp-110) cc_final: 0.5852 (ptm-80) REVERT: D 1108 LYS cc_start: 0.7276 (ttmt) cc_final: 0.6661 (ttpp) REVERT: D 1122 ARG cc_start: 0.6508 (mtm110) cc_final: 0.5756 (ttp80) REVERT: D 1123 ARG cc_start: 0.7260 (ttp80) cc_final: 0.7048 (ttp80) REVERT: D 1128 ARG cc_start: 0.6878 (OUTLIER) cc_final: 0.6360 (ttp-110) REVERT: D 1151 ASP cc_start: 0.7941 (m-30) cc_final: 0.7691 (m-30) REVERT: B 80 HIS cc_start: 0.6618 (m-70) cc_final: 0.6152 (m170) REVERT: B 166 LYS cc_start: 0.7199 (tttm) cc_final: 0.6884 (ttmm) REVERT: B 284 GLN cc_start: 0.7642 (mm-40) cc_final: 0.7365 (mt0) REVERT: B 368 ASN cc_start: 0.7961 (m-40) cc_final: 0.7725 (m110) REVERT: B 395 GLU cc_start: 0.6957 (tt0) cc_final: 0.6509 (pt0) REVERT: B 502 GLU cc_start: 0.6964 (tt0) cc_final: 0.6436 (mt-10) REVERT: B 517 ARG cc_start: 0.6312 (ttm110) cc_final: 0.5905 (ttp-110) REVERT: B 595 ARG cc_start: 0.6819 (mtt180) cc_final: 0.6618 (mtt180) REVERT: B 663 LYS cc_start: 0.7561 (mmpt) cc_final: 0.7022 (mtmt) REVERT: B 666 GLU cc_start: 0.7572 (tt0) cc_final: 0.7241 (tt0) REVERT: B 686 GLU cc_start: 0.7393 (tt0) cc_final: 0.6757 (tp30) REVERT: B 691 LYS cc_start: 0.8137 (mttt) cc_final: 0.7891 (mttt) REVERT: B 694 MET cc_start: 0.6586 (OUTLIER) cc_final: 0.6099 (ttp) REVERT: B 706 ASP cc_start: 0.7940 (m-30) cc_final: 0.7657 (m-30) REVERT: B 708 LYS cc_start: 0.7825 (mttp) cc_final: 0.7502 (mttm) REVERT: B 797 LYS cc_start: 0.6761 (mttt) cc_final: 0.6430 (mtpm) REVERT: B 923 ASN cc_start: 0.8130 (m110) cc_final: 0.7877 (m110) REVERT: B 932 MET cc_start: 0.7634 (mmt) cc_final: 0.7247 (mmm) REVERT: B 933 GLU cc_start: 0.8025 (mm-30) cc_final: 0.7759 (mm-30) REVERT: B 969 ARG cc_start: 0.8101 (mtp-110) cc_final: 0.7496 (mtp85) REVERT: B 1000 ASP cc_start: 0.8222 (m-30) cc_final: 0.7998 (m-30) REVERT: B 1005 GLU cc_start: 0.8016 (mt-10) cc_final: 0.7705 (mt-10) REVERT: B 1080 HIS cc_start: 0.6793 (t-90) cc_final: 0.6552 (t-90) REVERT: B 1107 ARG cc_start: 0.6604 (ttp-110) cc_final: 0.5854 (ptm-80) REVERT: B 1108 LYS cc_start: 0.7270 (ttmt) cc_final: 0.6656 (ttpp) REVERT: B 1122 ARG cc_start: 0.6515 (mtm110) cc_final: 0.5762 (ttp80) REVERT: B 1123 ARG cc_start: 0.7267 (ttp80) cc_final: 0.7052 (ttp80) REVERT: B 1128 ARG cc_start: 0.6875 (OUTLIER) cc_final: 0.6357 (ttp-110) REVERT: B 1150 MET cc_start: 0.8171 (OUTLIER) cc_final: 0.7331 (mpp) REVERT: B 1151 ASP cc_start: 0.8000 (m-30) cc_final: 0.7739 (m-30) REVERT: C 80 HIS cc_start: 0.6565 (m-70) cc_final: 0.6102 (m170) REVERT: C 166 LYS cc_start: 0.7208 (tttm) cc_final: 0.6893 (ttmm) REVERT: C 284 GLN cc_start: 0.7648 (mm-40) cc_final: 0.7365 (mt0) REVERT: C 368 ASN cc_start: 0.7952 (m-40) cc_final: 0.7720 (m110) REVERT: C 395 GLU cc_start: 0.6969 (tt0) cc_final: 0.6524 (pt0) REVERT: C 502 GLU cc_start: 0.6956 (tt0) cc_final: 0.6423 (mt-10) REVERT: C 517 ARG cc_start: 0.6319 (ttm110) cc_final: 0.5913 (ttp-110) REVERT: C 595 ARG cc_start: 0.6812 (mtt180) cc_final: 0.6611 (mtt180) REVERT: C 663 LYS cc_start: 0.7567 (mmpt) cc_final: 0.7029 (mtmt) REVERT: C 666 GLU cc_start: 0.7564 (tt0) cc_final: 0.7280 (tt0) REVERT: C 686 GLU cc_start: 0.7379 (tt0) cc_final: 0.6748 (tp30) REVERT: C 691 LYS cc_start: 0.8139 (mttt) cc_final: 0.7894 (mttt) REVERT: C 694 MET cc_start: 0.6588 (OUTLIER) cc_final: 0.6103 (ttp) REVERT: C 706 ASP cc_start: 0.7935 (m-30) cc_final: 0.7687 (m-30) REVERT: C 708 LYS cc_start: 0.7812 (mttp) cc_final: 0.7490 (mttm) REVERT: C 797 LYS cc_start: 0.6752 (mttt) cc_final: 0.6361 (mtpm) REVERT: C 932 MET cc_start: 0.7633 (mmt) cc_final: 0.7251 (mmm) REVERT: C 969 ARG cc_start: 0.8111 (mtp-110) cc_final: 0.7484 (mtp85) REVERT: C 1000 ASP cc_start: 0.8224 (m-30) cc_final: 0.7997 (m-30) REVERT: C 1005 GLU cc_start: 0.8019 (mt-10) cc_final: 0.7708 (mt-10) REVERT: C 1080 HIS cc_start: 0.6795 (t-90) cc_final: 0.6549 (t-90) REVERT: C 1107 ARG cc_start: 0.6585 (ttp-110) cc_final: 0.5833 (ptm-80) REVERT: C 1108 LYS cc_start: 0.7253 (ttmt) cc_final: 0.6634 (ttpp) REVERT: C 1122 ARG cc_start: 0.6530 (mtm110) cc_final: 0.5774 (ttp80) REVERT: C 1123 ARG cc_start: 0.7288 (ttp80) cc_final: 0.7073 (ttp80) REVERT: C 1128 ARG cc_start: 0.6887 (OUTLIER) cc_final: 0.6371 (ttp-110) REVERT: C 1151 ASP cc_start: 0.7973 (m-30) cc_final: 0.7753 (m-30) REVERT: C 1160 PHE cc_start: 0.7582 (m-10) cc_final: 0.7235 (t80) outliers start: 77 outliers final: 35 residues processed: 606 average time/residue: 0.9003 time to fit residues: 649.8559 Evaluate side-chains 601 residues out of total 4700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 557 time to evaluate : 1.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 LEU 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 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 615 MET Chi-restraints excluded: chain D residue 683 MET Chi-restraints excluded: chain D residue 687 MET Chi-restraints excluded: chain D residue 694 MET 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 111 LEU Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 615 MET Chi-restraints excluded: chain B residue 683 MET Chi-restraints excluded: chain B residue 687 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 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 111 LEU Chi-restraints excluded: chain C residue 615 MET Chi-restraints excluded: chain C residue 683 MET Chi-restraints excluded: chain C residue 687 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 548 random chunks: chunk 283 optimal weight: 6.9990 chunk 497 optimal weight: 5.9990 chunk 37 optimal weight: 7.9990 chunk 213 optimal weight: 5.9990 chunk 484 optimal weight: 1.9990 chunk 371 optimal weight: 2.9990 chunk 285 optimal weight: 8.9990 chunk 250 optimal weight: 3.9990 chunk 135 optimal weight: 1.9990 chunk 142 optimal weight: 0.1980 chunk 67 optimal weight: 5.9990 overall best weight: 2.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN A 450 ASN A 659 GLN D 61 ASN D 450 ASN B 61 ASN B 450 ASN C 61 ASN C 450 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.166010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.119887 restraints weight = 51170.735| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 1.90 r_work: 0.3231 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.4079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 43764 Z= 0.230 Angle : 0.594 7.475 59548 Z= 0.312 Chirality : 0.043 0.214 6772 Planarity : 0.005 0.044 7540 Dihedral : 8.548 89.508 7084 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.27 % Allowed : 12.10 % Favored : 85.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.11), residues: 5476 helix: 1.92 (0.09), residues: 3040 sheet: -1.05 (0.21), residues: 436 loop : -0.43 (0.14), residues: 2000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 506 TYR 0.021 0.003 TYR A1063 PHE 0.026 0.002 PHE A 496 TRP 0.011 0.002 TRP C1366 HIS 0.005 0.001 HIS C 254 Details of bonding type rmsd covalent geometry : bond 0.00529 (43760) covalent geometry : angle 0.59358 (59540) SS BOND : bond 0.00079 ( 4) SS BOND : angle 0.52991 ( 8) hydrogen bonds : bond 0.05182 ( 2364) hydrogen bonds : angle 4.00386 ( 6960) *********************** 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 686 residues out of total 4700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 590 time to evaluate : 1.608 Fit side-chains REVERT: A 166 LYS cc_start: 0.7281 (tttm) cc_final: 0.6947 (ttmm) REVERT: A 284 GLN cc_start: 0.7652 (mm-40) cc_final: 0.7341 (mt0) REVERT: A 395 GLU cc_start: 0.6953 (tt0) cc_final: 0.6517 (pt0) REVERT: A 477 LYS cc_start: 0.6965 (mptt) cc_final: 0.6280 (mmtp) REVERT: A 502 GLU cc_start: 0.6960 (tt0) cc_final: 0.6668 (mt-10) REVERT: A 507 GLU cc_start: 0.6793 (tp30) cc_final: 0.6374 (tp30) REVERT: A 592 GLN cc_start: 0.6687 (OUTLIER) cc_final: 0.6072 (tp40) REVERT: A 663 LYS cc_start: 0.7526 (mmpt) cc_final: 0.7044 (mtmt) REVERT: A 666 GLU cc_start: 0.7637 (tt0) cc_final: 0.7353 (tt0) REVERT: A 686 GLU cc_start: 0.7395 (tt0) cc_final: 0.6770 (tp30) REVERT: A 706 ASP cc_start: 0.7988 (m-30) cc_final: 0.7731 (m-30) REVERT: A 797 LYS cc_start: 0.6792 (mttt) cc_final: 0.6385 (mtpm) REVERT: A 932 MET cc_start: 0.7897 (mmt) cc_final: 0.7571 (mmm) REVERT: A 969 ARG cc_start: 0.8149 (mtp-110) cc_final: 0.7646 (mtp85) REVERT: A 1005 GLU cc_start: 0.8032 (mt-10) cc_final: 0.7796 (mt-10) REVERT: A 1107 ARG cc_start: 0.6594 (ttp-110) cc_final: 0.5849 (ptm-80) REVERT: A 1108 LYS cc_start: 0.7296 (OUTLIER) cc_final: 0.6790 (ttpp) REVERT: A 1122 ARG cc_start: 0.6614 (mtm110) cc_final: 0.5790 (ttp80) REVERT: A 1123 ARG cc_start: 0.7314 (ttp80) cc_final: 0.7058 (ttp80) REVERT: A 1128 ARG cc_start: 0.7019 (OUTLIER) cc_final: 0.6543 (ttp-110) REVERT: A 1151 ASP cc_start: 0.8025 (m-30) cc_final: 0.7798 (m-30) REVERT: A 1222 GLU cc_start: 0.8354 (tt0) cc_final: 0.8144 (tt0) REVERT: A 1348 ASP cc_start: 0.8336 (t70) cc_final: 0.8128 (t70) REVERT: D 166 LYS cc_start: 0.7267 (tttm) cc_final: 0.6931 (ttmm) REVERT: D 284 GLN cc_start: 0.7648 (mm-40) cc_final: 0.7337 (mt0) REVERT: D 395 GLU cc_start: 0.7001 (tt0) cc_final: 0.6539 (pt0) REVERT: D 477 LYS cc_start: 0.6977 (mptt) cc_final: 0.6288 (mmtp) REVERT: D 502 GLU cc_start: 0.6893 (tt0) cc_final: 0.6578 (mt-10) REVERT: D 507 GLU cc_start: 0.6809 (tp30) cc_final: 0.6369 (tp30) REVERT: D 663 LYS cc_start: 0.7512 (mmpt) cc_final: 0.7072 (mtmt) REVERT: D 666 GLU cc_start: 0.7660 (tt0) cc_final: 0.7364 (tt0) REVERT: D 667 GLU cc_start: 0.7919 (mt-10) cc_final: 0.7501 (mm-30) REVERT: D 686 GLU cc_start: 0.7382 (tt0) cc_final: 0.6754 (tp30) REVERT: D 691 LYS cc_start: 0.8107 (mttt) cc_final: 0.7901 (mttt) REVERT: D 706 ASP cc_start: 0.7992 (m-30) cc_final: 0.7689 (m-30) REVERT: D 708 LYS cc_start: 0.7896 (mttp) cc_final: 0.7545 (mttm) REVERT: D 797 LYS cc_start: 0.6803 (mttt) cc_final: 0.6383 (mtpm) REVERT: D 932 MET cc_start: 0.7866 (mmt) cc_final: 0.7530 (mmm) REVERT: D 969 ARG cc_start: 0.8144 (mtp-110) cc_final: 0.7489 (mtp85) REVERT: D 1005 GLU cc_start: 0.8012 (mt-10) cc_final: 0.7687 (mt-10) REVERT: D 1065 ASP cc_start: 0.8150 (t70) cc_final: 0.7850 (t0) REVERT: D 1107 ARG cc_start: 0.6636 (ttp-110) cc_final: 0.5871 (ptm-80) REVERT: D 1108 LYS cc_start: 0.7243 (ttmt) cc_final: 0.6677 (ttpp) REVERT: D 1122 ARG cc_start: 0.6648 (mtm110) cc_final: 0.5976 (ttp80) REVERT: D 1123 ARG cc_start: 0.7271 (ttp80) cc_final: 0.7027 (ttp80) REVERT: D 1128 ARG cc_start: 0.6962 (OUTLIER) cc_final: 0.6442 (ttp-110) REVERT: D 1151 ASP cc_start: 0.7996 (m-30) cc_final: 0.7787 (m-30) REVERT: D 1222 GLU cc_start: 0.8365 (tt0) cc_final: 0.8152 (tt0) REVERT: D 1348 ASP cc_start: 0.8333 (t70) cc_final: 0.8127 (t70) REVERT: B 166 LYS cc_start: 0.7274 (tttm) cc_final: 0.6941 (ttmm) REVERT: B 284 GLN cc_start: 0.7658 (mm-40) cc_final: 0.7344 (mt0) REVERT: B 395 GLU cc_start: 0.6960 (tt0) cc_final: 0.6519 (pt0) REVERT: B 477 LYS cc_start: 0.6977 (mptt) cc_final: 0.6282 (mmtp) REVERT: B 502 GLU cc_start: 0.6900 (tt0) cc_final: 0.6585 (mt-10) REVERT: B 507 GLU cc_start: 0.6811 (tp30) cc_final: 0.6370 (tp30) REVERT: B 663 LYS cc_start: 0.7525 (mmpt) cc_final: 0.7086 (mtmt) REVERT: B 666 GLU cc_start: 0.7624 (tt0) cc_final: 0.7354 (tt0) REVERT: B 667 GLU cc_start: 0.7924 (mt-10) cc_final: 0.7533 (mm-30) REVERT: B 686 GLU cc_start: 0.7409 (tt0) cc_final: 0.6784 (tp30) REVERT: B 706 ASP cc_start: 0.7995 (m-30) cc_final: 0.7722 (m-30) REVERT: B 708 LYS cc_start: 0.7905 (mttp) cc_final: 0.7553 (mttm) REVERT: B 797 LYS cc_start: 0.6801 (mttt) cc_final: 0.6382 (mtpm) REVERT: B 969 ARG cc_start: 0.8152 (mtp-110) cc_final: 0.7650 (mtp85) REVERT: B 1005 GLU cc_start: 0.8021 (mt-10) cc_final: 0.7692 (mt-10) REVERT: B 1085 ARG cc_start: 0.5152 (tpp80) cc_final: 0.4949 (mmt90) REVERT: B 1107 ARG cc_start: 0.6631 (ttp-110) cc_final: 0.5872 (ptm-80) REVERT: B 1108 LYS cc_start: 0.7252 (ttmt) cc_final: 0.6687 (ttpp) REVERT: B 1122 ARG cc_start: 0.6640 (mtm110) cc_final: 0.5970 (ttp80) REVERT: B 1123 ARG cc_start: 0.7267 (ttp80) cc_final: 0.7024 (ttp80) REVERT: B 1128 ARG cc_start: 0.6954 (OUTLIER) cc_final: 0.6430 (ttp-110) REVERT: B 1151 ASP cc_start: 0.8019 (m-30) cc_final: 0.7697 (m-30) REVERT: B 1222 GLU cc_start: 0.8356 (tt0) cc_final: 0.8153 (tt0) REVERT: B 1348 ASP cc_start: 0.8336 (t70) cc_final: 0.8129 (t0) REVERT: C 166 LYS cc_start: 0.7262 (tttm) cc_final: 0.6926 (ttmm) REVERT: C 284 GLN cc_start: 0.7647 (mm-40) cc_final: 0.7336 (mt0) REVERT: C 395 GLU cc_start: 0.6964 (tt0) cc_final: 0.6524 (pt0) REVERT: C 477 LYS cc_start: 0.6972 (mptt) cc_final: 0.6284 (mmtp) REVERT: C 502 GLU cc_start: 0.6909 (tt0) cc_final: 0.6627 (mt-10) REVERT: C 507 GLU cc_start: 0.6813 (tp30) cc_final: 0.6374 (tp30) REVERT: C 663 LYS cc_start: 0.7535 (mmpt) cc_final: 0.7096 (mtmt) REVERT: C 666 GLU cc_start: 0.7626 (tt0) cc_final: 0.7358 (tt0) REVERT: C 667 GLU cc_start: 0.7936 (mt-10) cc_final: 0.7531 (mm-30) REVERT: C 686 GLU cc_start: 0.7389 (tt0) cc_final: 0.6757 (tp30) REVERT: C 706 ASP cc_start: 0.8005 (m-30) cc_final: 0.7710 (m-30) REVERT: C 708 LYS cc_start: 0.7898 (mttp) cc_final: 0.7550 (mttm) REVERT: C 797 LYS cc_start: 0.6799 (mttt) cc_final: 0.6380 (mtpm) REVERT: C 969 ARG cc_start: 0.8150 (mtp-110) cc_final: 0.7647 (mtp85) REVERT: C 1005 GLU cc_start: 0.8020 (mt-10) cc_final: 0.7690 (mt-10) REVERT: C 1080 HIS cc_start: 0.6947 (t-90) cc_final: 0.6743 (t-90) REVERT: C 1085 ARG cc_start: 0.5122 (tpp80) cc_final: 0.4920 (mmt90) REVERT: C 1107 ARG cc_start: 0.6633 (ttp-110) cc_final: 0.5868 (ptm-80) REVERT: C 1108 LYS cc_start: 0.7244 (ttmt) cc_final: 0.6678 (ttpp) REVERT: C 1122 ARG cc_start: 0.6661 (mtm110) cc_final: 0.5988 (ttp80) REVERT: C 1123 ARG cc_start: 0.7376 (ttp80) cc_final: 0.7135 (ttp80) REVERT: C 1128 ARG cc_start: 0.6961 (OUTLIER) cc_final: 0.6440 (ttp-110) REVERT: C 1151 ASP cc_start: 0.8047 (m-30) cc_final: 0.7751 (m-30) REVERT: C 1222 GLU cc_start: 0.8355 (tt0) cc_final: 0.8152 (tt0) REVERT: C 1348 ASP cc_start: 0.8328 (t70) cc_final: 0.8126 (t70) outliers start: 96 outliers final: 40 residues processed: 626 average time/residue: 0.8917 time to fit residues: 663.6972 Evaluate side-chains 610 residues out of total 4700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 564 time to evaluate : 1.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 MET Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 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 1108 LYS Chi-restraints excluded: chain A residue 1128 ARG Chi-restraints excluded: chain A residue 1150 MET Chi-restraints excluded: chain A residue 1229 VAL Chi-restraints excluded: chain A residue 1243 ILE Chi-restraints excluded: chain D residue 111 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 1082 LEU Chi-restraints excluded: chain D residue 1128 ARG Chi-restraints excluded: chain D residue 1229 VAL Chi-restraints excluded: chain D residue 1243 ILE 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 357 THR 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 1243 ILE Chi-restraints excluded: chain C residue 70 MET Chi-restraints excluded: chain C residue 111 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 1229 VAL 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 101 optimal weight: 1.9990 chunk 236 optimal weight: 10.0000 chunk 472 optimal weight: 2.9990 chunk 516 optimal weight: 0.9980 chunk 369 optimal weight: 0.8980 chunk 537 optimal weight: 2.9990 chunk 252 optimal weight: 0.0270 chunk 258 optimal weight: 1.9990 chunk 244 optimal weight: 10.0000 chunk 543 optimal weight: 0.7980 chunk 7 optimal weight: 0.6980 overall best weight: 0.6838 ------------------------------------------------------------------------------- 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 C 61 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.168794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.123459 restraints weight = 51332.746| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 1.91 r_work: 0.3302 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.4023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 43764 Z= 0.115 Angle : 0.472 6.520 59548 Z= 0.249 Chirality : 0.038 0.166 6772 Planarity : 0.004 0.045 7540 Dihedral : 8.102 88.719 7084 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.65 % Allowed : 13.00 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.48 (0.11), residues: 5476 helix: 2.16 (0.09), residues: 3040 sheet: -1.20 (0.22), residues: 412 loop : -0.33 (0.14), residues: 2024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 152 TYR 0.019 0.002 TYR C 420 PHE 0.023 0.001 PHE A 496 TRP 0.012 0.001 TRP A1124 HIS 0.004 0.001 HIS B 240 Details of bonding type rmsd covalent geometry : bond 0.00248 (43760) covalent geometry : angle 0.47164 (59540) SS BOND : bond 0.00065 ( 4) SS BOND : angle 0.41838 ( 8) hydrogen bonds : bond 0.04010 ( 2364) hydrogen bonds : angle 3.72753 ( 6960) *********************** 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 666 residues out of total 4700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 596 time to evaluate : 2.096 Fit side-chains REVERT: A 80 HIS cc_start: 0.6633 (m-70) cc_final: 0.6147 (m170) REVERT: A 166 LYS cc_start: 0.7303 (tttm) cc_final: 0.6959 (ttmm) REVERT: A 284 GLN cc_start: 0.7606 (mm-40) cc_final: 0.7327 (mt0) REVERT: A 368 ASN cc_start: 0.7896 (m-40) cc_final: 0.7639 (m110) REVERT: A 395 GLU cc_start: 0.6961 (tt0) cc_final: 0.6592 (mt-10) REVERT: A 456 MET cc_start: 0.6216 (ttm) cc_final: 0.5531 (ttp) REVERT: A 477 LYS cc_start: 0.7008 (mptt) cc_final: 0.6284 (mmtp) REVERT: A 502 GLU cc_start: 0.7006 (tt0) cc_final: 0.6755 (mt-10) REVERT: A 507 GLU cc_start: 0.6762 (tp30) cc_final: 0.6353 (tp30) REVERT: A 663 LYS cc_start: 0.7597 (mmpt) cc_final: 0.7094 (mtmt) REVERT: A 666 GLU cc_start: 0.7543 (tt0) cc_final: 0.7204 (tt0) REVERT: A 686 GLU cc_start: 0.7278 (tt0) cc_final: 0.6689 (tp30) REVERT: A 694 MET cc_start: 0.6555 (OUTLIER) cc_final: 0.6204 (ttp) REVERT: A 706 ASP cc_start: 0.7980 (m-30) cc_final: 0.7691 (m-30) REVERT: A 725 ASP cc_start: 0.8027 (m-30) cc_final: 0.7662 (m-30) REVERT: A 797 LYS cc_start: 0.6733 (mttt) cc_final: 0.6324 (mtpm) REVERT: A 923 ASN cc_start: 0.8095 (m110) cc_final: 0.7836 (m110) REVERT: A 932 MET cc_start: 0.7909 (mmt) cc_final: 0.7552 (mmm) REVERT: A 933 GLU cc_start: 0.8036 (mm-30) cc_final: 0.7753 (mm-30) REVERT: A 969 ARG cc_start: 0.8188 (mtp-110) cc_final: 0.7511 (mtp85) REVERT: A 1005 GLU cc_start: 0.8101 (mt-10) cc_final: 0.7774 (mt-10) REVERT: A 1107 ARG cc_start: 0.6641 (ttp-110) cc_final: 0.5844 (ptm-80) REVERT: A 1122 ARG cc_start: 0.6597 (mtm110) cc_final: 0.5803 (ttp80) REVERT: A 1123 ARG cc_start: 0.7270 (ttp80) cc_final: 0.6990 (ttp80) REVERT: A 1128 ARG cc_start: 0.7026 (OUTLIER) cc_final: 0.6573 (ttp-110) REVERT: A 1151 ASP cc_start: 0.7975 (m-30) cc_final: 0.7683 (m-30) REVERT: A 1160 PHE cc_start: 0.7544 (m-10) cc_final: 0.7339 (t80) REVERT: A 1252 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.8097 (tp30) REVERT: D 80 HIS cc_start: 0.6618 (m-70) cc_final: 0.6116 (m170) REVERT: D 166 LYS cc_start: 0.7278 (tttm) cc_final: 0.6930 (ttmm) REVERT: D 284 GLN cc_start: 0.7605 (mm-40) cc_final: 0.7300 (mt0) REVERT: D 368 ASN cc_start: 0.7906 (m-40) cc_final: 0.7657 (m110) REVERT: D 395 GLU cc_start: 0.6949 (tt0) cc_final: 0.6480 (pt0) REVERT: D 477 LYS cc_start: 0.7044 (mptt) cc_final: 0.6310 (mmtp) REVERT: D 502 GLU cc_start: 0.6944 (tt0) cc_final: 0.6690 (mt-10) REVERT: D 507 GLU cc_start: 0.6707 (tp30) cc_final: 0.6271 (tp30) REVERT: D 663 LYS cc_start: 0.7578 (mmpt) cc_final: 0.7051 (mtmt) REVERT: D 666 GLU cc_start: 0.7540 (tt0) cc_final: 0.7262 (tt0) REVERT: D 686 GLU cc_start: 0.7296 (tt0) cc_final: 0.6703 (tp30) REVERT: D 706 ASP cc_start: 0.7952 (m-30) cc_final: 0.7656 (m-30) REVERT: D 708 LYS cc_start: 0.7771 (mttp) cc_final: 0.7425 (mttm) REVERT: D 797 LYS cc_start: 0.6729 (mttt) cc_final: 0.6325 (mtpm) REVERT: D 923 ASN cc_start: 0.8088 (m110) cc_final: 0.7831 (m110) REVERT: D 932 MET cc_start: 0.7880 (mmt) cc_final: 0.7520 (mmm) REVERT: D 933 GLU cc_start: 0.7978 (mm-30) cc_final: 0.7711 (mm-30) REVERT: D 969 ARG cc_start: 0.8185 (mtp-110) cc_final: 0.7509 (mtp85) REVERT: D 1005 GLU cc_start: 0.8109 (mt-10) cc_final: 0.7780 (mt-10) REVERT: D 1065 ASP cc_start: 0.8123 (t70) cc_final: 0.7807 (t0) REVERT: D 1107 ARG cc_start: 0.6596 (ttp-110) cc_final: 0.5841 (ptm-80) REVERT: D 1108 LYS cc_start: 0.7263 (ttmt) cc_final: 0.6683 (ttpp) REVERT: D 1122 ARG cc_start: 0.6573 (mtm110) cc_final: 0.5799 (ttp80) REVERT: D 1123 ARG cc_start: 0.7302 (ttp80) cc_final: 0.7028 (ttp80) REVERT: D 1128 ARG cc_start: 0.6905 (OUTLIER) cc_final: 0.6468 (ttp-110) REVERT: D 1151 ASP cc_start: 0.7986 (m-30) cc_final: 0.7729 (m-30) REVERT: D 1252 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.8076 (tp30) REVERT: B 80 HIS cc_start: 0.6644 (m-70) cc_final: 0.6133 (m170) REVERT: B 166 LYS cc_start: 0.7304 (tttm) cc_final: 0.6961 (ttmm) REVERT: B 284 GLN cc_start: 0.7594 (mm-40) cc_final: 0.7298 (mt0) REVERT: B 368 ASN cc_start: 0.7896 (m-40) cc_final: 0.7639 (m110) REVERT: B 395 GLU cc_start: 0.6923 (tt0) cc_final: 0.6461 (pt0) REVERT: B 477 LYS cc_start: 0.7032 (mptt) cc_final: 0.6296 (mmtp) REVERT: B 502 GLU cc_start: 0.6947 (tt0) cc_final: 0.6713 (mt-10) REVERT: B 507 GLU cc_start: 0.6706 (tp30) cc_final: 0.6262 (tp30) REVERT: B 663 LYS cc_start: 0.7590 (mmpt) cc_final: 0.7066 (mtmt) REVERT: B 666 GLU cc_start: 0.7597 (tt0) cc_final: 0.7280 (tt0) REVERT: B 686 GLU cc_start: 0.7297 (tt0) cc_final: 0.6699 (tp30) REVERT: B 706 ASP cc_start: 0.8010 (m-30) cc_final: 0.7755 (m-30) REVERT: B 708 LYS cc_start: 0.7780 (mttp) cc_final: 0.7435 (mttm) REVERT: B 797 LYS cc_start: 0.6719 (mttt) cc_final: 0.6317 (mtpm) REVERT: B 923 ASN cc_start: 0.8093 (m110) cc_final: 0.7829 (m110) REVERT: B 932 MET cc_start: 0.7801 (mmt) cc_final: 0.7420 (mmm) REVERT: B 933 GLU cc_start: 0.7988 (mm-30) cc_final: 0.7724 (mm-30) REVERT: B 969 ARG cc_start: 0.8195 (mtp-110) cc_final: 0.7519 (mtp85) REVERT: B 1005 GLU cc_start: 0.8103 (mt-10) cc_final: 0.7775 (mt-10) REVERT: B 1085 ARG cc_start: 0.5166 (tpp80) cc_final: 0.4244 (tmt170) REVERT: B 1107 ARG cc_start: 0.6628 (ttp-110) cc_final: 0.5864 (ptm-80) REVERT: B 1108 LYS cc_start: 0.7268 (ttmt) cc_final: 0.6688 (ttpp) REVERT: B 1122 ARG cc_start: 0.6594 (mtm110) cc_final: 0.5823 (ttp80) REVERT: B 1123 ARG cc_start: 0.7319 (ttp80) cc_final: 0.7048 (ttp80) REVERT: B 1128 ARG cc_start: 0.6923 (OUTLIER) cc_final: 0.6471 (ttp-110) REVERT: B 1151 ASP cc_start: 0.8066 (m-30) cc_final: 0.7698 (m-30) REVERT: B 1157 MET cc_start: 0.8569 (mmt) cc_final: 0.7992 (mmm) REVERT: B 1252 GLU cc_start: 0.8295 (OUTLIER) cc_final: 0.8081 (tp30) REVERT: C 80 HIS cc_start: 0.6624 (m-70) cc_final: 0.6122 (m170) REVERT: C 166 LYS cc_start: 0.7297 (tttm) cc_final: 0.6952 (ttmm) REVERT: C 284 GLN cc_start: 0.7607 (mm-40) cc_final: 0.7300 (mt0) REVERT: C 368 ASN cc_start: 0.7901 (m-40) cc_final: 0.7647 (m110) REVERT: C 395 GLU cc_start: 0.6936 (tt0) cc_final: 0.6569 (mt-10) REVERT: C 477 LYS cc_start: 0.7062 (mptt) cc_final: 0.6334 (mmtp) REVERT: C 502 GLU cc_start: 0.6955 (tt0) cc_final: 0.6709 (mt-10) REVERT: C 507 GLU cc_start: 0.6801 (tp30) cc_final: 0.6368 (tp30) REVERT: C 663 LYS cc_start: 0.7601 (mmpt) cc_final: 0.7082 (mtmt) REVERT: C 666 GLU cc_start: 0.7592 (tt0) cc_final: 0.7275 (tt0) REVERT: C 686 GLU cc_start: 0.7311 (tt0) cc_final: 0.6711 (tp30) REVERT: C 706 ASP cc_start: 0.7973 (m-30) cc_final: 0.7676 (m-30) REVERT: C 708 LYS cc_start: 0.7776 (mttp) cc_final: 0.7429 (mttm) REVERT: C 797 LYS cc_start: 0.6728 (mttt) cc_final: 0.6324 (mtpm) REVERT: C 923 ASN cc_start: 0.8097 (m110) cc_final: 0.7839 (m110) REVERT: C 932 MET cc_start: 0.7790 (mmt) cc_final: 0.7410 (mmm) REVERT: C 933 GLU cc_start: 0.8017 (mm-30) cc_final: 0.7756 (mm-30) REVERT: C 969 ARG cc_start: 0.8192 (mtp-110) cc_final: 0.7514 (mtp85) REVERT: C 1005 GLU cc_start: 0.8140 (mt-10) cc_final: 0.7811 (mt-10) REVERT: C 1085 ARG cc_start: 0.5177 (tpp80) cc_final: 0.4254 (tmt170) REVERT: C 1107 ARG cc_start: 0.6606 (ttp-110) cc_final: 0.5840 (ptm-80) REVERT: C 1108 LYS cc_start: 0.7253 (ttmt) cc_final: 0.6673 (ttpp) REVERT: C 1122 ARG cc_start: 0.6558 (mtm110) cc_final: 0.5799 (ttp80) REVERT: C 1123 ARG cc_start: 0.7308 (ttp80) cc_final: 0.7035 (ttp80) REVERT: C 1128 ARG cc_start: 0.6910 (OUTLIER) cc_final: 0.6475 (ttp-110) REVERT: C 1151 ASP cc_start: 0.8014 (m-30) cc_final: 0.7678 (m-30) REVERT: C 1252 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.8079 (tp30) outliers start: 70 outliers final: 40 residues processed: 623 average time/residue: 0.9384 time to fit residues: 693.1725 Evaluate side-chains 615 residues out of total 4700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 566 time to evaluate : 1.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 THR 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 1150 MET 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 94 THR 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 687 MET Chi-restraints excluded: chain D residue 694 MET 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 D residue 1252 GLU Chi-restraints excluded: chain B residue 94 THR 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 687 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 B residue 1252 GLU Chi-restraints excluded: chain C residue 94 THR 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 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 447 optimal weight: 7.9990 chunk 450 optimal weight: 10.0000 chunk 435 optimal weight: 0.0470 chunk 458 optimal weight: 9.9990 chunk 270 optimal weight: 4.9990 chunk 523 optimal weight: 0.9980 chunk 378 optimal weight: 5.9990 chunk 296 optimal weight: 3.9990 chunk 511 optimal weight: 10.0000 chunk 419 optimal weight: 0.4980 chunk 230 optimal weight: 4.9990 overall best weight: 2.1082 ------------------------------------------------------------------------------- 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 A1152 GLN D 61 ASN D 82 HIS D1152 GLN B 61 ASN B 82 HIS B1152 GLN C 61 ASN C 82 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.165368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.119329 restraints weight = 50716.480| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 1.91 r_work: 0.3243 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.4255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 43764 Z= 0.215 Angle : 0.583 7.142 59548 Z= 0.304 Chirality : 0.042 0.166 6772 Planarity : 0.004 0.046 7540 Dihedral : 8.453 89.176 7084 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.89 % Allowed : 13.30 % Favored : 84.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.11), residues: 5476 helix: 2.01 (0.09), residues: 3032 sheet: -1.23 (0.21), residues: 436 loop : -0.47 (0.14), residues: 2008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 152 TYR 0.022 0.002 TYR C1063 PHE 0.022 0.002 PHE C 879 TRP 0.011 0.002 TRP A1124 HIS 0.005 0.001 HIS A1156 Details of bonding type rmsd covalent geometry : bond 0.00492 (43760) covalent geometry : angle 0.58272 (59540) SS BOND : bond 0.00035 ( 4) SS BOND : angle 0.62237 ( 8) hydrogen bonds : bond 0.05031 ( 2364) hydrogen bonds : angle 3.92905 ( 6960) *********************** 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 643 residues out of total 4700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 563 time to evaluate : 1.521 Fit side-chains REVERT: A 166 LYS cc_start: 0.7367 (tttm) cc_final: 0.6776 (ttmm) REVERT: A 170 LEU cc_start: 0.7964 (OUTLIER) cc_final: 0.7423 (mm) REVERT: A 284 GLN cc_start: 0.7661 (mm-40) cc_final: 0.7391 (mt0) REVERT: A 395 GLU cc_start: 0.7057 (tt0) cc_final: 0.6632 (mt-10) REVERT: A 456 MET cc_start: 0.6289 (ttm) cc_final: 0.5636 (ttp) REVERT: A 477 LYS cc_start: 0.7089 (mptt) cc_final: 0.6381 (mmtp) REVERT: A 507 GLU cc_start: 0.6819 (tp30) cc_final: 0.6376 (tp30) REVERT: A 592 GLN cc_start: 0.6736 (OUTLIER) cc_final: 0.6520 (tm-30) REVERT: A 663 LYS cc_start: 0.7495 (mmpt) cc_final: 0.7000 (mtmt) REVERT: A 666 GLU cc_start: 0.7628 (tt0) cc_final: 0.7346 (tt0) REVERT: A 686 GLU cc_start: 0.7362 (tt0) cc_final: 0.6739 (tp30) REVERT: A 706 ASP cc_start: 0.7976 (m-30) cc_final: 0.7716 (m-30) REVERT: A 969 ARG cc_start: 0.8121 (mtp-110) cc_final: 0.7474 (mtp85) REVERT: A 1005 GLU cc_start: 0.8017 (mt-10) cc_final: 0.7705 (mt-10) REVERT: A 1107 ARG cc_start: 0.6653 (ttp-110) cc_final: 0.5894 (ptm-80) REVERT: A 1108 LYS cc_start: 0.7266 (OUTLIER) cc_final: 0.6757 (ttpp) REVERT: A 1122 ARG cc_start: 0.6714 (mtm110) cc_final: 0.5838 (ttp80) REVERT: A 1123 ARG cc_start: 0.7347 (ttp80) cc_final: 0.7070 (ttp80) REVERT: A 1128 ARG cc_start: 0.7060 (OUTLIER) cc_final: 0.6614 (ttp-110) REVERT: A 1151 ASP cc_start: 0.8032 (m-30) cc_final: 0.7766 (m-30) REVERT: A 1160 PHE cc_start: 0.7563 (m-10) cc_final: 0.7299 (t80) REVERT: D 166 LYS cc_start: 0.7355 (tttm) cc_final: 0.6764 (ttmm) REVERT: D 170 LEU cc_start: 0.7967 (OUTLIER) cc_final: 0.7424 (mm) REVERT: D 284 GLN cc_start: 0.7670 (mm-40) cc_final: 0.7366 (mt0) REVERT: D 335 MET cc_start: 0.9141 (mtp) cc_final: 0.8874 (mtp) REVERT: D 395 GLU cc_start: 0.7042 (tt0) cc_final: 0.6616 (mt-10) REVERT: D 477 LYS cc_start: 0.7078 (mptt) cc_final: 0.6374 (mmtp) REVERT: D 507 GLU cc_start: 0.6750 (tp30) cc_final: 0.6326 (tp30) REVERT: D 663 LYS cc_start: 0.7529 (mmpt) cc_final: 0.7009 (mtmt) REVERT: D 666 GLU cc_start: 0.7557 (tt0) cc_final: 0.7246 (tt0) REVERT: D 686 GLU cc_start: 0.7355 (tt0) cc_final: 0.6748 (tp30) REVERT: D 706 ASP cc_start: 0.7985 (m-30) cc_final: 0.7699 (m-30) REVERT: D 708 LYS cc_start: 0.7863 (mttp) cc_final: 0.7489 (mttm) REVERT: D 969 ARG cc_start: 0.8097 (mtp-110) cc_final: 0.7448 (mtp85) REVERT: D 1005 GLU cc_start: 0.8017 (mt-10) cc_final: 0.7713 (mt-10) REVERT: D 1065 ASP cc_start: 0.8101 (t70) cc_final: 0.7796 (t0) REVERT: D 1107 ARG cc_start: 0.6680 (ttp-110) cc_final: 0.5893 (ptm-80) REVERT: D 1108 LYS cc_start: 0.7225 (ttmt) cc_final: 0.6672 (ttpp) REVERT: D 1119 LYS cc_start: 0.7271 (mtpt) cc_final: 0.6613 (mtmt) REVERT: D 1122 ARG cc_start: 0.6746 (mtm110) cc_final: 0.6036 (ttp80) REVERT: D 1123 ARG cc_start: 0.7391 (ttp80) cc_final: 0.7178 (ttp80) REVERT: D 1128 ARG cc_start: 0.6989 (OUTLIER) cc_final: 0.6501 (ttp-110) REVERT: D 1151 ASP cc_start: 0.7940 (m-30) cc_final: 0.7713 (m-30) REVERT: B 80 HIS cc_start: 0.6645 (m-70) cc_final: 0.6091 (m170) REVERT: B 166 LYS cc_start: 0.7350 (tttm) cc_final: 0.6830 (ttmm) REVERT: B 170 LEU cc_start: 0.7969 (OUTLIER) cc_final: 0.7424 (mm) REVERT: B 284 GLN cc_start: 0.7678 (mm-40) cc_final: 0.7365 (mt0) REVERT: B 335 MET cc_start: 0.9133 (mtp) cc_final: 0.8867 (mtp) REVERT: B 395 GLU cc_start: 0.7038 (tt0) cc_final: 0.6612 (mt-10) REVERT: B 477 LYS cc_start: 0.7112 (mptt) cc_final: 0.6398 (mmtp) REVERT: B 507 GLU cc_start: 0.6797 (tp30) cc_final: 0.6367 (tp30) REVERT: B 663 LYS cc_start: 0.7532 (mmpt) cc_final: 0.7011 (mtmt) REVERT: B 666 GLU cc_start: 0.7553 (tt0) cc_final: 0.7290 (tt0) REVERT: B 686 GLU cc_start: 0.7368 (tt0) cc_final: 0.6758 (tp30) REVERT: B 706 ASP cc_start: 0.8088 (m-30) cc_final: 0.7782 (m-30) REVERT: B 708 LYS cc_start: 0.7873 (mttp) cc_final: 0.7496 (mttm) REVERT: B 969 ARG cc_start: 0.8103 (mtp-110) cc_final: 0.7454 (mtp85) REVERT: B 1005 GLU cc_start: 0.8024 (mt-10) cc_final: 0.7719 (mt-10) REVERT: B 1107 ARG cc_start: 0.6690 (ttp-110) cc_final: 0.5903 (ptm-80) REVERT: B 1108 LYS cc_start: 0.7233 (ttmt) cc_final: 0.6679 (ttpp) REVERT: B 1119 LYS cc_start: 0.7285 (mtpt) cc_final: 0.6636 (mtmt) REVERT: B 1122 ARG cc_start: 0.6748 (mtm110) cc_final: 0.6039 (ttp80) REVERT: B 1123 ARG cc_start: 0.7392 (ttp80) cc_final: 0.7183 (ttp80) REVERT: B 1128 ARG cc_start: 0.6975 (OUTLIER) cc_final: 0.6521 (ttp-110) REVERT: B 1151 ASP cc_start: 0.8066 (m-30) cc_final: 0.7695 (m-30) REVERT: C 166 LYS cc_start: 0.7347 (tttm) cc_final: 0.6755 (ttmm) REVERT: C 170 LEU cc_start: 0.7954 (OUTLIER) cc_final: 0.7415 (mm) REVERT: C 284 GLN cc_start: 0.7678 (mm-40) cc_final: 0.7372 (mt0) REVERT: C 335 MET cc_start: 0.9132 (mtp) cc_final: 0.8863 (mtp) REVERT: C 395 GLU cc_start: 0.7065 (tt0) cc_final: 0.6642 (mt-10) REVERT: C 477 LYS cc_start: 0.7107 (mptt) cc_final: 0.6407 (mmtp) REVERT: C 507 GLU cc_start: 0.6802 (tp30) cc_final: 0.6373 (tp30) REVERT: C 663 LYS cc_start: 0.7565 (mmpt) cc_final: 0.7046 (mtmt) REVERT: C 666 GLU cc_start: 0.7595 (tt0) cc_final: 0.7337 (tt0) REVERT: C 686 GLU cc_start: 0.7390 (tt0) cc_final: 0.6786 (tp30) REVERT: C 706 ASP cc_start: 0.8078 (m-30) cc_final: 0.7784 (m-30) REVERT: C 708 LYS cc_start: 0.7870 (mttp) cc_final: 0.7495 (mttm) REVERT: C 969 ARG cc_start: 0.8112 (mtp-110) cc_final: 0.7464 (mtp85) REVERT: C 1005 GLU cc_start: 0.8031 (mt-10) cc_final: 0.7721 (mt-10) REVERT: C 1085 ARG cc_start: 0.5116 (tpp80) cc_final: 0.4208 (tmt170) REVERT: C 1107 ARG cc_start: 0.6669 (ttp-110) cc_final: 0.5889 (ptm-80) REVERT: C 1108 LYS cc_start: 0.7221 (ttmt) cc_final: 0.6662 (ttpp) REVERT: C 1119 LYS cc_start: 0.7291 (mtpt) cc_final: 0.6637 (mtmt) REVERT: C 1122 ARG cc_start: 0.6730 (mtm110) cc_final: 0.6019 (ttp80) REVERT: C 1123 ARG cc_start: 0.7444 (ttp80) cc_final: 0.7236 (ttp80) REVERT: C 1128 ARG cc_start: 0.6980 (OUTLIER) cc_final: 0.6496 (ttp-110) REVERT: C 1147 MET cc_start: 0.8166 (mmm) cc_final: 0.7884 (mtm) REVERT: C 1151 ASP cc_start: 0.8036 (m-30) cc_final: 0.7674 (m-30) outliers start: 80 outliers final: 44 residues processed: 593 average time/residue: 0.8706 time to fit residues: 614.9248 Evaluate side-chains 598 residues out of total 4700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 544 time to evaluate : 1.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 574 VAL Chi-restraints excluded: chain A residue 592 GLN 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 1011 VAL Chi-restraints excluded: chain A residue 1075 LEU Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1108 LYS Chi-restraints excluded: chain A residue 1128 ARG Chi-restraints excluded: chain A residue 1150 MET 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 170 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 694 MET Chi-restraints excluded: chain D residue 1011 VAL 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 1243 ILE Chi-restraints excluded: chain B residue 94 THR 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 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 1243 ILE Chi-restraints excluded: chain C residue 170 LEU 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 548 random chunks: chunk 333 optimal weight: 7.9990 chunk 299 optimal weight: 5.9990 chunk 413 optimal weight: 1.9990 chunk 427 optimal weight: 2.9990 chunk 547 optimal weight: 0.9980 chunk 125 optimal weight: 0.9990 chunk 468 optimal weight: 2.9990 chunk 519 optimal weight: 0.0370 chunk 371 optimal weight: 3.9990 chunk 153 optimal weight: 2.9990 chunk 60 optimal weight: 6.9990 overall best weight: 1.4064 ------------------------------------------------------------------------------- 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 C 61 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.166290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.120554 restraints weight = 51006.409| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 1.90 r_work: 0.3243 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.4267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 43764 Z= 0.162 Angle : 0.530 8.413 59548 Z= 0.277 Chirality : 0.040 0.168 6772 Planarity : 0.004 0.045 7540 Dihedral : 8.277 88.857 7084 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.94 % Allowed : 13.49 % Favored : 84.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.33 (0.11), residues: 5476 helix: 2.08 (0.09), residues: 3032 sheet: -1.24 (0.21), residues: 436 loop : -0.45 (0.14), residues: 2008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 152 TYR 0.017 0.002 TYR C1063 PHE 0.020 0.002 PHE C 879 TRP 0.014 0.001 TRP A1124 HIS 0.004 0.001 HIS B1156 Details of bonding type rmsd covalent geometry : bond 0.00366 (43760) covalent geometry : angle 0.53020 (59540) SS BOND : bond 0.00048 ( 4) SS BOND : angle 0.48856 ( 8) hydrogen bonds : bond 0.04557 ( 2364) hydrogen bonds : angle 3.83720 ( 6960) *********************** 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 643 residues out of total 4700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 561 time to evaluate : 1.354 Fit side-chains REVERT: A 166 LYS cc_start: 0.7358 (tttm) cc_final: 0.6839 (ttmm) REVERT: A 170 LEU cc_start: 0.7946 (OUTLIER) cc_final: 0.7397 (mm) REVERT: A 284 GLN cc_start: 0.7641 (mm-40) cc_final: 0.7369 (mt0) REVERT: A 395 GLU cc_start: 0.7041 (tt0) cc_final: 0.6597 (mt-10) REVERT: A 456 MET cc_start: 0.6249 (ttm) cc_final: 0.5582 (ttp) REVERT: A 477 LYS cc_start: 0.7105 (mptt) cc_final: 0.6406 (mmtp) REVERT: A 507 GLU cc_start: 0.6879 (tp30) cc_final: 0.6391 (tp30) REVERT: A 592 GLN cc_start: 0.6681 (OUTLIER) cc_final: 0.6455 (tm-30) REVERT: A 663 LYS cc_start: 0.7529 (mmpt) cc_final: 0.6988 (mtmt) REVERT: A 666 GLU cc_start: 0.7579 (tt0) cc_final: 0.7223 (tt0) REVERT: A 686 GLU cc_start: 0.7381 (tt0) cc_final: 0.6768 (tp30) REVERT: A 706 ASP cc_start: 0.7968 (m-30) cc_final: 0.7718 (m-30) REVERT: A 923 ASN cc_start: 0.8113 (m110) cc_final: 0.7839 (m110) REVERT: A 932 MET cc_start: 0.7680 (mmt) cc_final: 0.7291 (mmm) REVERT: A 933 GLU cc_start: 0.8049 (mm-30) cc_final: 0.7766 (mm-30) REVERT: A 969 ARG cc_start: 0.8160 (mtp-110) cc_final: 0.7470 (mtp85) REVERT: A 1005 GLU cc_start: 0.8037 (mt-10) cc_final: 0.7754 (mt-10) REVERT: A 1107 ARG cc_start: 0.6735 (ttp-110) cc_final: 0.5930 (ptm-80) REVERT: A 1108 LYS cc_start: 0.7273 (OUTLIER) cc_final: 0.6785 (ttpp) REVERT: A 1122 ARG cc_start: 0.6740 (mtm110) cc_final: 0.5857 (ttp80) REVERT: A 1128 ARG cc_start: 0.7069 (OUTLIER) cc_final: 0.6644 (ttp-110) REVERT: A 1151 ASP cc_start: 0.8028 (m-30) cc_final: 0.7754 (m-30) REVERT: A 1160 PHE cc_start: 0.7623 (m-10) cc_final: 0.7292 (t80) REVERT: D 82 HIS cc_start: 0.6483 (m-70) cc_final: 0.6121 (m90) REVERT: D 166 LYS cc_start: 0.7345 (tttm) cc_final: 0.6826 (ttmm) REVERT: D 170 LEU cc_start: 0.7962 (OUTLIER) cc_final: 0.7414 (mm) REVERT: D 284 GLN cc_start: 0.7643 (mm-40) cc_final: 0.7339 (mt0) REVERT: D 395 GLU cc_start: 0.7064 (tt0) cc_final: 0.6597 (mt-10) REVERT: D 477 LYS cc_start: 0.7085 (mptt) cc_final: 0.6380 (mmtp) REVERT: D 507 GLU cc_start: 0.6788 (tp30) cc_final: 0.6195 (tp30) REVERT: D 663 LYS cc_start: 0.7502 (mmpt) cc_final: 0.6982 (mtmt) REVERT: D 666 GLU cc_start: 0.7506 (tt0) cc_final: 0.7144 (tt0) REVERT: D 686 GLU cc_start: 0.7324 (tt0) cc_final: 0.6703 (tp30) REVERT: D 706 ASP cc_start: 0.8060 (m-30) cc_final: 0.7759 (m-30) REVERT: D 708 LYS cc_start: 0.7869 (mttp) cc_final: 0.7502 (mttm) REVERT: D 923 ASN cc_start: 0.8136 (m110) cc_final: 0.7862 (m110) REVERT: D 932 MET cc_start: 0.7680 (mmt) cc_final: 0.7293 (mmm) REVERT: D 964 GLU cc_start: 0.7707 (tt0) cc_final: 0.7408 (pt0) REVERT: D 969 ARG cc_start: 0.8143 (mtp-110) cc_final: 0.7453 (mtp85) REVERT: D 1005 GLU cc_start: 0.8047 (mt-10) cc_final: 0.7729 (mt-10) REVERT: D 1065 ASP cc_start: 0.8067 (t70) cc_final: 0.7760 (t0) REVERT: D 1085 ARG cc_start: 0.5066 (tpp80) cc_final: 0.4199 (tmt170) REVERT: D 1107 ARG cc_start: 0.6652 (ttp-110) cc_final: 0.5905 (ptm-80) REVERT: D 1108 LYS cc_start: 0.7256 (ttmt) cc_final: 0.6703 (ttpp) REVERT: D 1119 LYS cc_start: 0.7230 (mtpt) cc_final: 0.6509 (mtmt) REVERT: D 1122 ARG cc_start: 0.6738 (mtm110) cc_final: 0.6028 (ttp80) REVERT: D 1123 ARG cc_start: 0.7395 (ttp80) cc_final: 0.7172 (ttp80) REVERT: D 1128 ARG cc_start: 0.6969 (OUTLIER) cc_final: 0.6533 (ttp-110) REVERT: D 1151 ASP cc_start: 0.7972 (m-30) cc_final: 0.7728 (m-30) REVERT: D 1157 MET cc_start: 0.8548 (OUTLIER) cc_final: 0.8060 (mmt) REVERT: B 80 HIS cc_start: 0.6666 (m-70) cc_final: 0.6144 (m170) REVERT: B 166 LYS cc_start: 0.7340 (tttm) cc_final: 0.6822 (ttmm) REVERT: B 170 LEU cc_start: 0.7959 (OUTLIER) cc_final: 0.7412 (mm) REVERT: B 284 GLN cc_start: 0.7646 (mm-40) cc_final: 0.7340 (mt0) REVERT: B 395 GLU cc_start: 0.7050 (tt0) cc_final: 0.6585 (mt-10) REVERT: B 477 LYS cc_start: 0.7096 (mptt) cc_final: 0.6391 (mmtp) REVERT: B 507 GLU cc_start: 0.6807 (tp30) cc_final: 0.6293 (tp30) REVERT: B 663 LYS cc_start: 0.7512 (mmpt) cc_final: 0.6996 (mtmt) REVERT: B 666 GLU cc_start: 0.7587 (tt0) cc_final: 0.7321 (tt0) REVERT: B 686 GLU cc_start: 0.7343 (tt0) cc_final: 0.6723 (tp30) REVERT: B 706 ASP cc_start: 0.8106 (m-30) cc_final: 0.7824 (m-30) REVERT: B 708 LYS cc_start: 0.7869 (mttp) cc_final: 0.7500 (mttm) REVERT: B 923 ASN cc_start: 0.8177 (m110) cc_final: 0.7905 (m110) REVERT: B 932 MET cc_start: 0.7819 (mmt) cc_final: 0.7477 (mmm) REVERT: B 969 ARG cc_start: 0.8145 (mtp-110) cc_final: 0.7455 (mtp85) REVERT: B 1005 GLU cc_start: 0.8045 (mt-10) cc_final: 0.7725 (mt-10) REVERT: B 1085 ARG cc_start: 0.5082 (tpp80) cc_final: 0.4212 (tmt170) REVERT: B 1107 ARG cc_start: 0.6657 (ttp-110) cc_final: 0.5910 (ptm-80) REVERT: B 1108 LYS cc_start: 0.7255 (ttmt) cc_final: 0.6700 (ttpp) REVERT: B 1119 LYS cc_start: 0.7258 (mtpt) cc_final: 0.6547 (mtmt) REVERT: B 1122 ARG cc_start: 0.6750 (mtm110) cc_final: 0.6040 (ttp80) REVERT: B 1123 ARG cc_start: 0.7401 (ttp80) cc_final: 0.7176 (ttp80) REVERT: B 1128 ARG cc_start: 0.6994 (OUTLIER) cc_final: 0.6544 (ttp-110) REVERT: B 1151 ASP cc_start: 0.8037 (m-30) cc_final: 0.7627 (m-30) REVERT: B 1157 MET cc_start: 0.8218 (mmm) cc_final: 0.7723 (mmt) REVERT: C 166 LYS cc_start: 0.7337 (tttm) cc_final: 0.6819 (ttmm) REVERT: C 170 LEU cc_start: 0.7945 (OUTLIER) cc_final: 0.7401 (mm) REVERT: C 284 GLN cc_start: 0.7650 (mm-40) cc_final: 0.7373 (mt0) REVERT: C 395 GLU cc_start: 0.7088 (tt0) cc_final: 0.6614 (mt-10) REVERT: C 477 LYS cc_start: 0.7104 (mptt) cc_final: 0.6403 (mmtp) REVERT: C 507 GLU cc_start: 0.6755 (tp30) cc_final: 0.6276 (tp30) REVERT: C 663 LYS cc_start: 0.7531 (mmpt) cc_final: 0.7017 (mtmt) REVERT: C 666 GLU cc_start: 0.7626 (tt0) cc_final: 0.7364 (tt0) REVERT: C 686 GLU cc_start: 0.7365 (tt0) cc_final: 0.6748 (tp30) REVERT: C 706 ASP cc_start: 0.8084 (m-30) cc_final: 0.7806 (m-30) REVERT: C 708 LYS cc_start: 0.7860 (mttp) cc_final: 0.7490 (mttm) REVERT: C 923 ASN cc_start: 0.8106 (m110) cc_final: 0.7832 (m110) REVERT: C 932 MET cc_start: 0.7838 (mmt) cc_final: 0.7500 (mmm) REVERT: C 969 ARG cc_start: 0.8152 (mtp-110) cc_final: 0.7460 (mtp85) REVERT: C 1005 GLU cc_start: 0.8067 (mt-10) cc_final: 0.7752 (mt-10) REVERT: C 1085 ARG cc_start: 0.5091 (tpp80) cc_final: 0.4186 (tmt170) REVERT: C 1107 ARG cc_start: 0.6652 (ttp-110) cc_final: 0.5906 (ptm-80) REVERT: C 1108 LYS cc_start: 0.7252 (ttmt) cc_final: 0.6695 (ttpp) REVERT: C 1119 LYS cc_start: 0.7255 (mtpt) cc_final: 0.6539 (mtmt) REVERT: C 1122 ARG cc_start: 0.6744 (mtm110) cc_final: 0.6036 (ttp80) REVERT: C 1123 ARG cc_start: 0.7465 (ttp80) cc_final: 0.7240 (ttp80) REVERT: C 1128 ARG cc_start: 0.6977 (OUTLIER) cc_final: 0.6548 (ttp-110) REVERT: C 1147 MET cc_start: 0.8153 (mmm) cc_final: 0.7886 (mtm) REVERT: C 1151 ASP cc_start: 0.8078 (m-30) cc_final: 0.7689 (m-30) outliers start: 82 outliers final: 43 residues processed: 592 average time/residue: 0.8202 time to fit residues: 582.5044 Evaluate side-chains 606 residues out of total 4700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 552 time to evaluate : 1.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 574 VAL 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 1011 VAL Chi-restraints excluded: chain A residue 1075 LEU Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1108 LYS Chi-restraints excluded: chain A residue 1128 ARG Chi-restraints excluded: chain A residue 1150 MET 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 D residue 170 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 694 MET Chi-restraints excluded: chain D residue 1011 VAL 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 1157 MET Chi-restraints excluded: chain D residue 1229 VAL Chi-restraints excluded: chain D residue 1243 ILE Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 357 THR 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 C residue 170 LEU Chi-restraints excluded: chain C residue 357 THR 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 1243 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 548 random chunks: chunk 76 optimal weight: 1.9990 chunk 404 optimal weight: 0.4980 chunk 381 optimal weight: 10.0000 chunk 433 optimal weight: 5.9990 chunk 43 optimal weight: 0.5980 chunk 126 optimal weight: 4.9990 chunk 531 optimal weight: 1.9990 chunk 419 optimal weight: 0.0470 chunk 484 optimal weight: 0.0020 chunk 391 optimal weight: 0.3980 chunk 110 optimal weight: 0.4980 overall best weight: 0.2886 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN A 813 HIS D 61 ASN D 813 HIS B 61 ASN B 813 HIS C 61 ASN C 813 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.169450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.124462 restraints weight = 50917.637| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 1.90 r_work: 0.3297 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3164 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.4200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 43764 Z= 0.099 Angle : 0.469 8.258 59548 Z= 0.245 Chirality : 0.038 0.164 6772 Planarity : 0.004 0.045 7540 Dihedral : 7.920 89.406 7084 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.23 % Allowed : 14.56 % Favored : 84.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.58 (0.11), residues: 5476 helix: 2.28 (0.09), residues: 3040 sheet: -1.21 (0.22), residues: 412 loop : -0.35 (0.14), residues: 2024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 152 TYR 0.019 0.001 TYR B 420 PHE 0.020 0.001 PHE A 496 TRP 0.017 0.001 TRP A1124 HIS 0.005 0.001 HIS C 82 Details of bonding type rmsd covalent geometry : bond 0.00203 (43760) covalent geometry : angle 0.46933 (59540) SS BOND : bond 0.00106 ( 4) SS BOND : angle 0.37392 ( 8) hydrogen bonds : bond 0.03700 ( 2364) hydrogen bonds : angle 3.64450 ( 6960) *********************** 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 631 residues out of total 4700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 579 time to evaluate : 1.015 Fit side-chains REVERT: A 166 LYS cc_start: 0.7400 (tttm) cc_final: 0.6838 (ttmm) REVERT: A 170 LEU cc_start: 0.7915 (OUTLIER) cc_final: 0.7369 (mm) REVERT: A 284 GLN cc_start: 0.7615 (mm-40) cc_final: 0.7358 (mt0) REVERT: A 368 ASN cc_start: 0.7890 (m-40) cc_final: 0.7652 (m110) REVERT: A 395 GLU cc_start: 0.7020 (tt0) cc_final: 0.6515 (pt0) REVERT: A 477 LYS cc_start: 0.7121 (mptt) cc_final: 0.6401 (mmtp) REVERT: A 507 GLU cc_start: 0.6864 (tp30) cc_final: 0.6514 (tp30) REVERT: A 569 SER cc_start: 0.6326 (t) cc_final: 0.5881 (m) REVERT: A 595 ARG cc_start: 0.6669 (mtp180) cc_final: 0.6325 (mtt180) REVERT: A 663 LYS cc_start: 0.7539 (mmpt) cc_final: 0.7011 (mtmt) REVERT: A 666 GLU cc_start: 0.7396 (tt0) cc_final: 0.7137 (tt0) REVERT: A 686 GLU cc_start: 0.7288 (tt0) cc_final: 0.6688 (tp30) REVERT: A 694 MET cc_start: 0.6592 (OUTLIER) cc_final: 0.6272 (ttp) REVERT: A 706 ASP cc_start: 0.7968 (m-30) cc_final: 0.7713 (m-30) REVERT: A 725 ASP cc_start: 0.8068 (m-30) cc_final: 0.7718 (m-30) REVERT: A 797 LYS cc_start: 0.6749 (mttt) cc_final: 0.6189 (mtpp) REVERT: A 923 ASN cc_start: 0.8108 (m110) cc_final: 0.7851 (m110) REVERT: A 932 MET cc_start: 0.7706 (mmt) cc_final: 0.7316 (mmm) REVERT: A 933 GLU cc_start: 0.8026 (mm-30) cc_final: 0.7757 (mm-30) REVERT: A 964 GLU cc_start: 0.7621 (OUTLIER) cc_final: 0.7288 (pt0) REVERT: A 969 ARG cc_start: 0.8160 (mtp-110) cc_final: 0.7477 (mtp85) REVERT: A 1005 GLU cc_start: 0.8161 (mt-10) cc_final: 0.7859 (mt-10) REVERT: A 1107 ARG cc_start: 0.6607 (ttp-110) cc_final: 0.5808 (ptm-80) REVERT: A 1122 ARG cc_start: 0.6623 (mtm110) cc_final: 0.5805 (ttp80) REVERT: A 1128 ARG cc_start: 0.6987 (OUTLIER) cc_final: 0.6632 (ttp-110) REVERT: A 1151 ASP cc_start: 0.8005 (m-30) cc_final: 0.7732 (m-30) REVERT: A 1160 PHE cc_start: 0.7616 (m-10) cc_final: 0.7333 (t80) REVERT: D 82 HIS cc_start: 0.6380 (m-70) cc_final: 0.6106 (m90) REVERT: D 166 LYS cc_start: 0.7395 (tttm) cc_final: 0.6836 (ttmm) REVERT: D 170 LEU cc_start: 0.7946 (OUTLIER) cc_final: 0.7397 (mm) REVERT: D 284 GLN cc_start: 0.7603 (mm-40) cc_final: 0.7343 (mt0) REVERT: D 368 ASN cc_start: 0.7835 (m-40) cc_final: 0.7619 (m110) REVERT: D 395 GLU cc_start: 0.6973 (tt0) cc_final: 0.6516 (pt0) REVERT: D 477 LYS cc_start: 0.7097 (mptt) cc_final: 0.6383 (mmtp) REVERT: D 507 GLU cc_start: 0.6868 (tp30) cc_final: 0.6475 (tp30) REVERT: D 569 SER cc_start: 0.6323 (t) cc_final: 0.5856 (m) REVERT: D 595 ARG cc_start: 0.6689 (mtp180) cc_final: 0.6367 (mtt180) REVERT: D 663 LYS cc_start: 0.7521 (mmpt) cc_final: 0.7027 (mtmt) REVERT: D 666 GLU cc_start: 0.7373 (tt0) cc_final: 0.7097 (tt0) REVERT: D 686 GLU cc_start: 0.7287 (tt0) cc_final: 0.6674 (tp30) REVERT: D 694 MET cc_start: 0.6595 (OUTLIER) cc_final: 0.6254 (ttp) REVERT: D 706 ASP cc_start: 0.7956 (m-30) cc_final: 0.7645 (m-30) REVERT: D 708 LYS cc_start: 0.7736 (mttp) cc_final: 0.7367 (mttm) REVERT: D 725 ASP cc_start: 0.8024 (m-30) cc_final: 0.7648 (m-30) REVERT: D 797 LYS cc_start: 0.6762 (mttt) cc_final: 0.6228 (mtpp) REVERT: D 923 ASN cc_start: 0.8115 (m110) cc_final: 0.7862 (m110) REVERT: D 932 MET cc_start: 0.7711 (mmt) cc_final: 0.7316 (mmm) REVERT: D 933 GLU cc_start: 0.7991 (mm-30) cc_final: 0.7747 (mm-30) REVERT: D 964 GLU cc_start: 0.7651 (tt0) cc_final: 0.7361 (pt0) REVERT: D 969 ARG cc_start: 0.8156 (mtp-110) cc_final: 0.7486 (mtp85) REVERT: D 1005 GLU cc_start: 0.8128 (mt-10) cc_final: 0.7769 (mt-10) REVERT: D 1065 ASP cc_start: 0.8073 (t70) cc_final: 0.7765 (t0) REVERT: D 1085 ARG cc_start: 0.5061 (tpp80) cc_final: 0.4198 (tmt170) REVERT: D 1107 ARG cc_start: 0.6541 (ttp-110) cc_final: 0.5792 (ptm-80) REVERT: D 1108 LYS cc_start: 0.7246 (ttmt) cc_final: 0.6695 (ttpp) REVERT: D 1122 ARG cc_start: 0.6693 (mtm110) cc_final: 0.6034 (ttp80) REVERT: D 1123 ARG cc_start: 0.7337 (ttp80) cc_final: 0.7112 (ttp80) REVERT: D 1128 ARG cc_start: 0.6872 (OUTLIER) cc_final: 0.6499 (ttp-110) REVERT: D 1151 ASP cc_start: 0.7993 (m-30) cc_final: 0.7727 (m-30) REVERT: D 1157 MET cc_start: 0.8460 (OUTLIER) cc_final: 0.7974 (mmt) REVERT: B 80 HIS cc_start: 0.6535 (m-70) cc_final: 0.6001 (m170) REVERT: B 166 LYS cc_start: 0.7386 (tttm) cc_final: 0.6825 (ttmm) REVERT: B 170 LEU cc_start: 0.7934 (OUTLIER) cc_final: 0.7385 (mm) REVERT: B 284 GLN cc_start: 0.7611 (mm-40) cc_final: 0.7343 (mt0) REVERT: B 368 ASN cc_start: 0.7836 (m-40) cc_final: 0.7623 (m110) REVERT: B 395 GLU cc_start: 0.6963 (tt0) cc_final: 0.6502 (pt0) REVERT: B 477 LYS cc_start: 0.7107 (mptt) cc_final: 0.6394 (mmtp) REVERT: B 507 GLU cc_start: 0.6863 (tp30) cc_final: 0.6477 (tp30) REVERT: B 569 SER cc_start: 0.6330 (t) cc_final: 0.5878 (m) REVERT: B 595 ARG cc_start: 0.6710 (mtp180) cc_final: 0.6392 (mtt180) REVERT: B 663 LYS cc_start: 0.7521 (mmpt) cc_final: 0.7027 (mtmt) REVERT: B 666 GLU cc_start: 0.7432 (tt0) cc_final: 0.7190 (tt0) REVERT: B 686 GLU cc_start: 0.7302 (tt0) cc_final: 0.6687 (tp30) REVERT: B 694 MET cc_start: 0.6612 (OUTLIER) cc_final: 0.6251 (ttp) REVERT: B 706 ASP cc_start: 0.8101 (m-30) cc_final: 0.7809 (m-30) REVERT: B 708 LYS cc_start: 0.7751 (mttp) cc_final: 0.7379 (mttm) REVERT: B 725 ASP cc_start: 0.8032 (m-30) cc_final: 0.7659 (m-30) REVERT: B 923 ASN cc_start: 0.8108 (m110) cc_final: 0.7858 (m110) REVERT: B 932 MET cc_start: 0.7844 (mmt) cc_final: 0.7501 (mmm) REVERT: B 933 GLU cc_start: 0.8008 (mm-30) cc_final: 0.7720 (mm-30) REVERT: B 964 GLU cc_start: 0.7635 (OUTLIER) cc_final: 0.7294 (pt0) REVERT: B 969 ARG cc_start: 0.8154 (mtp-110) cc_final: 0.7484 (mtp85) REVERT: B 1005 GLU cc_start: 0.8120 (mt-10) cc_final: 0.7778 (mt-10) REVERT: B 1085 ARG cc_start: 0.5021 (tpp80) cc_final: 0.4152 (tmt170) REVERT: B 1107 ARG cc_start: 0.6547 (ttp-110) cc_final: 0.5799 (ptm-80) REVERT: B 1108 LYS cc_start: 0.7255 (ttmt) cc_final: 0.6702 (ttpp) REVERT: B 1122 ARG cc_start: 0.6693 (mtm110) cc_final: 0.6027 (ttp80) REVERT: B 1123 ARG cc_start: 0.7343 (ttp80) cc_final: 0.7121 (ttp80) REVERT: B 1128 ARG cc_start: 0.6875 (OUTLIER) cc_final: 0.6489 (ttp-110) REVERT: B 1151 ASP cc_start: 0.8054 (m-30) cc_final: 0.7666 (m-30) REVERT: C 80 HIS cc_start: 0.6501 (m-70) cc_final: 0.6054 (m170) REVERT: C 166 LYS cc_start: 0.7383 (tttm) cc_final: 0.6820 (ttmm) REVERT: C 170 LEU cc_start: 0.7906 (OUTLIER) cc_final: 0.7364 (mm) REVERT: C 284 GLN cc_start: 0.7608 (mm-40) cc_final: 0.7353 (mt0) REVERT: C 368 ASN cc_start: 0.7900 (m-40) cc_final: 0.7654 (m110) REVERT: C 395 GLU cc_start: 0.7037 (tt0) cc_final: 0.6518 (pt0) REVERT: C 477 LYS cc_start: 0.7112 (mptt) cc_final: 0.6403 (mmtp) REVERT: C 507 GLU cc_start: 0.6898 (tp30) cc_final: 0.6515 (tp30) REVERT: C 569 SER cc_start: 0.6322 (t) cc_final: 0.5872 (m) REVERT: C 595 ARG cc_start: 0.6699 (mtp180) cc_final: 0.6385 (mtt180) REVERT: C 663 LYS cc_start: 0.7546 (mmpt) cc_final: 0.7050 (mtmt) REVERT: C 666 GLU cc_start: 0.7476 (tt0) cc_final: 0.7239 (tt0) REVERT: C 686 GLU cc_start: 0.7310 (tt0) cc_final: 0.6702 (tp30) REVERT: C 694 MET cc_start: 0.6620 (OUTLIER) cc_final: 0.6262 (ttp) REVERT: C 706 ASP cc_start: 0.7968 (m-30) cc_final: 0.7683 (m-30) REVERT: C 708 LYS cc_start: 0.7734 (mttp) cc_final: 0.7363 (mttm) REVERT: C 725 ASP cc_start: 0.8062 (m-30) cc_final: 0.7696 (m-30) REVERT: C 797 LYS cc_start: 0.6726 (mttt) cc_final: 0.6184 (mtpp) REVERT: C 923 ASN cc_start: 0.8094 (m110) cc_final: 0.7836 (m110) REVERT: C 932 MET cc_start: 0.7860 (mmt) cc_final: 0.7517 (mmm) REVERT: C 933 GLU cc_start: 0.8025 (mm-30) cc_final: 0.7764 (mm-30) REVERT: C 964 GLU cc_start: 0.7644 (OUTLIER) cc_final: 0.7305 (pt0) REVERT: C 969 ARG cc_start: 0.8158 (mtp-110) cc_final: 0.7484 (mtp85) REVERT: C 1005 GLU cc_start: 0.8168 (mt-10) cc_final: 0.7776 (mt-10) REVERT: C 1085 ARG cc_start: 0.5116 (tpp80) cc_final: 0.4191 (tmt170) REVERT: C 1107 ARG cc_start: 0.6530 (ttp-110) cc_final: 0.5776 (ptm-80) REVERT: C 1108 LYS cc_start: 0.7230 (ttmt) cc_final: 0.6673 (ttpp) REVERT: C 1122 ARG cc_start: 0.6714 (mtm110) cc_final: 0.6015 (ttp80) REVERT: C 1123 ARG cc_start: 0.7364 (ttp80) cc_final: 0.7147 (ttp80) REVERT: C 1128 ARG cc_start: 0.6883 (OUTLIER) cc_final: 0.6517 (ttp-110) REVERT: C 1147 MET cc_start: 0.8105 (mmm) cc_final: 0.7770 (mtm) REVERT: C 1151 ASP cc_start: 0.8085 (m-30) cc_final: 0.7679 (m-30) REVERT: C 1160 PHE cc_start: 0.8146 (t80) cc_final: 0.7052 (m-10) outliers start: 52 outliers final: 25 residues processed: 589 average time/residue: 0.6129 time to fit residues: 433.4973 Evaluate side-chains 591 residues out of total 4700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 550 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 LEU 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 964 GLU Chi-restraints excluded: chain A residue 1011 VAL 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 683 MET Chi-restraints excluded: chain D residue 694 MET Chi-restraints excluded: chain D residue 1011 VAL 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 1157 MET Chi-restraints excluded: chain D residue 1229 VAL Chi-restraints excluded: chain D residue 1243 ILE Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 683 MET Chi-restraints excluded: chain B residue 694 MET Chi-restraints excluded: chain B residue 964 GLU 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 683 MET Chi-restraints excluded: chain C residue 694 MET Chi-restraints excluded: chain C residue 964 GLU 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 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 524 optimal weight: 3.9990 chunk 373 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 235 optimal weight: 5.9990 chunk 452 optimal weight: 9.9990 chunk 128 optimal weight: 8.9990 chunk 195 optimal weight: 3.9990 chunk 507 optimal weight: 0.7980 chunk 94 optimal weight: 3.9990 chunk 240 optimal weight: 6.9990 chunk 407 optimal weight: 2.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN A1156 HIS D 61 ASN B 61 ASN C 61 ASN C1152 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.165378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.119475 restraints weight = 50781.964| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 1.90 r_work: 0.3246 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.4387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 43764 Z= 0.218 Angle : 0.593 7.862 59548 Z= 0.307 Chirality : 0.042 0.165 6772 Planarity : 0.004 0.046 7540 Dihedral : 8.377 89.596 7084 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.49 % Allowed : 13.97 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.35 (0.11), residues: 5476 helix: 2.09 (0.09), residues: 3036 sheet: -1.22 (0.21), residues: 436 loop : -0.44 (0.14), residues: 2004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B1126 TYR 0.043 0.003 TYR D 420 PHE 0.021 0.002 PHE D 879 TRP 0.014 0.002 TRP D1124 HIS 0.005 0.001 HIS A 254 Details of bonding type rmsd covalent geometry : bond 0.00501 (43760) covalent geometry : angle 0.59263 (59540) SS BOND : bond 0.00071 ( 4) SS BOND : angle 0.57759 ( 8) hydrogen bonds : bond 0.04957 ( 2364) hydrogen bonds : angle 3.90722 ( 6960) ********************** 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 605 residues out of total 4700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 542 time to evaluate : 1.074 Fit side-chains REVERT: A 80 HIS cc_start: 0.6722 (m-70) cc_final: 0.6188 (m170) REVERT: A 166 LYS cc_start: 0.7414 (tttm) cc_final: 0.6814 (ttmm) REVERT: A 170 LEU cc_start: 0.7963 (OUTLIER) cc_final: 0.7418 (mm) REVERT: A 284 GLN cc_start: 0.7671 (mm-40) cc_final: 0.7385 (mt0) REVERT: A 477 LYS cc_start: 0.7163 (mptt) cc_final: 0.6455 (mmtp) REVERT: A 507 GLU cc_start: 0.6881 (tp30) cc_final: 0.6460 (tp30) REVERT: A 663 LYS cc_start: 0.7504 (mmpt) cc_final: 0.7019 (mtmt) REVERT: A 666 GLU cc_start: 0.7570 (tt0) cc_final: 0.7277 (tt0) REVERT: A 686 GLU cc_start: 0.7361 (tt0) cc_final: 0.6747 (tp30) REVERT: A 706 ASP cc_start: 0.7969 (m-30) cc_final: 0.7715 (m-30) REVERT: A 964 GLU cc_start: 0.7738 (OUTLIER) cc_final: 0.7477 (pt0) REVERT: A 969 ARG cc_start: 0.8170 (mtp-110) cc_final: 0.7487 (mtp85) REVERT: A 1005 GLU cc_start: 0.8005 (mt-10) cc_final: 0.7657 (mt-10) REVERT: A 1085 ARG cc_start: 0.5127 (tpp80) cc_final: 0.4248 (tmt170) REVERT: A 1107 ARG cc_start: 0.6701 (ttp-110) cc_final: 0.5929 (ptm-80) REVERT: A 1108 LYS cc_start: 0.7275 (OUTLIER) cc_final: 0.6791 (ttpp) REVERT: A 1119 LYS cc_start: 0.7257 (mtpt) cc_final: 0.6544 (mtmt) REVERT: A 1122 ARG cc_start: 0.6741 (mtm110) cc_final: 0.5800 (ttp80) REVERT: A 1128 ARG cc_start: 0.7090 (OUTLIER) cc_final: 0.6721 (ttp-110) REVERT: A 1151 ASP cc_start: 0.8013 (m-30) cc_final: 0.7758 (m-30) REVERT: A 1160 PHE cc_start: 0.7665 (m-10) cc_final: 0.7372 (t80) REVERT: D 80 HIS cc_start: 0.6640 (m-70) cc_final: 0.6162 (m170) REVERT: D 82 HIS cc_start: 0.6467 (m-70) cc_final: 0.6257 (m170) REVERT: D 166 LYS cc_start: 0.7403 (tttm) cc_final: 0.6802 (ttmm) REVERT: D 170 LEU cc_start: 0.7960 (OUTLIER) cc_final: 0.7411 (mm) REVERT: D 284 GLN cc_start: 0.7667 (mm-40) cc_final: 0.7376 (mt0) REVERT: D 477 LYS cc_start: 0.7083 (mptt) cc_final: 0.6363 (mmtp) REVERT: D 507 GLU cc_start: 0.6717 (tp30) cc_final: 0.6294 (tp30) REVERT: D 663 LYS cc_start: 0.7511 (mmpt) cc_final: 0.6996 (mtmt) REVERT: D 666 GLU cc_start: 0.7499 (tt0) cc_final: 0.7120 (tt0) REVERT: D 686 GLU cc_start: 0.7343 (tt0) cc_final: 0.6738 (tp30) REVERT: D 706 ASP cc_start: 0.8000 (m-30) cc_final: 0.7709 (m-30) REVERT: D 708 LYS cc_start: 0.7870 (mttp) cc_final: 0.7480 (mttm) REVERT: D 964 GLU cc_start: 0.7738 (OUTLIER) cc_final: 0.7478 (pt0) REVERT: D 969 ARG cc_start: 0.8152 (mtp-110) cc_final: 0.7469 (mtp85) REVERT: D 1005 GLU cc_start: 0.8031 (mt-10) cc_final: 0.7701 (mt-10) REVERT: D 1065 ASP cc_start: 0.8099 (t70) cc_final: 0.7787 (t0) REVERT: D 1085 ARG cc_start: 0.5149 (tpp80) cc_final: 0.4254 (tmt170) REVERT: D 1107 ARG cc_start: 0.6666 (ttp-110) cc_final: 0.5902 (ptm-80) REVERT: D 1108 LYS cc_start: 0.7251 (ttmt) cc_final: 0.6704 (ttpp) REVERT: D 1119 LYS cc_start: 0.7261 (mtpt) cc_final: 0.6540 (mttt) REVERT: D 1122 ARG cc_start: 0.6762 (mtm110) cc_final: 0.5991 (ttp80) REVERT: D 1128 ARG cc_start: 0.6976 (OUTLIER) cc_final: 0.6598 (ttp-110) REVERT: D 1151 ASP cc_start: 0.8006 (m-30) cc_final: 0.7761 (m-30) REVERT: B 80 HIS cc_start: 0.6651 (m-70) cc_final: 0.6151 (m170) REVERT: B 166 LYS cc_start: 0.7396 (tttm) cc_final: 0.6794 (ttmm) REVERT: B 170 LEU cc_start: 0.7975 (OUTLIER) cc_final: 0.7431 (mm) REVERT: B 284 GLN cc_start: 0.7659 (mm-40) cc_final: 0.7365 (mt0) REVERT: B 477 LYS cc_start: 0.7124 (mptt) cc_final: 0.6426 (mmtp) REVERT: B 507 GLU cc_start: 0.6839 (tp30) cc_final: 0.6389 (tp30) REVERT: B 663 LYS cc_start: 0.7517 (mmpt) cc_final: 0.6999 (mtmt) REVERT: B 666 GLU cc_start: 0.7513 (tt0) cc_final: 0.7244 (tt0) REVERT: B 686 GLU cc_start: 0.7346 (tt0) cc_final: 0.6738 (tp30) REVERT: B 706 ASP cc_start: 0.8110 (m-30) cc_final: 0.7795 (m-30) REVERT: B 708 LYS cc_start: 0.7862 (mttp) cc_final: 0.7478 (mttm) REVERT: B 923 ASN cc_start: 0.8185 (m110) cc_final: 0.7907 (m110) REVERT: B 964 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.7487 (pt0) REVERT: B 969 ARG cc_start: 0.8159 (mtp-110) cc_final: 0.7476 (mtp85) REVERT: B 1005 GLU cc_start: 0.8034 (mt-10) cc_final: 0.7704 (mt-10) REVERT: B 1085 ARG cc_start: 0.5161 (tpp80) cc_final: 0.4264 (tmt170) REVERT: B 1107 ARG cc_start: 0.6670 (ttp-110) cc_final: 0.5907 (ptm-80) REVERT: B 1108 LYS cc_start: 0.7254 (ttmt) cc_final: 0.6707 (ttpp) REVERT: B 1119 LYS cc_start: 0.7270 (mtpt) cc_final: 0.6574 (mttt) REVERT: B 1122 ARG cc_start: 0.6767 (mtm110) cc_final: 0.5996 (ttp80) REVERT: B 1128 ARG cc_start: 0.6965 (OUTLIER) cc_final: 0.6584 (ttp-110) REVERT: B 1151 ASP cc_start: 0.8020 (m-30) cc_final: 0.7617 (m-30) REVERT: C 80 HIS cc_start: 0.6711 (m-70) cc_final: 0.6184 (m170) REVERT: C 166 LYS cc_start: 0.7395 (tttm) cc_final: 0.6791 (ttmm) REVERT: C 170 LEU cc_start: 0.7957 (OUTLIER) cc_final: 0.7410 (mm) REVERT: C 284 GLN cc_start: 0.7666 (mm-40) cc_final: 0.7375 (mt0) REVERT: C 477 LYS cc_start: 0.7148 (mptt) cc_final: 0.6449 (mmtp) REVERT: C 507 GLU cc_start: 0.6809 (tp30) cc_final: 0.6413 (tp30) REVERT: C 527 LEU cc_start: 0.7356 (OUTLIER) cc_final: 0.7048 (mm) REVERT: C 663 LYS cc_start: 0.7546 (mmpt) cc_final: 0.7027 (mtmt) REVERT: C 666 GLU cc_start: 0.7543 (tt0) cc_final: 0.7283 (tt0) REVERT: C 686 GLU cc_start: 0.7379 (tt0) cc_final: 0.6777 (tp30) REVERT: C 706 ASP cc_start: 0.8001 (m-30) cc_final: 0.7777 (m-30) REVERT: C 708 LYS cc_start: 0.7852 (mttp) cc_final: 0.7473 (mttm) REVERT: C 964 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.7492 (pt0) REVERT: C 969 ARG cc_start: 0.8163 (mtp-110) cc_final: 0.7478 (mtp85) REVERT: C 1005 GLU cc_start: 0.8041 (mt-10) cc_final: 0.7705 (mt-10) REVERT: C 1085 ARG cc_start: 0.5223 (tpp80) cc_final: 0.4261 (tmt170) REVERT: C 1107 ARG cc_start: 0.6672 (ttp-110) cc_final: 0.5909 (ptm-80) REVERT: C 1108 LYS cc_start: 0.7254 (ttmt) cc_final: 0.6701 (ttpp) REVERT: C 1119 LYS cc_start: 0.7299 (mtpt) cc_final: 0.6583 (mttt) REVERT: C 1122 ARG cc_start: 0.6767 (mtm110) cc_final: 0.5990 (ttp80) REVERT: C 1128 ARG cc_start: 0.6968 (OUTLIER) cc_final: 0.6598 (ttp-110) REVERT: C 1147 MET cc_start: 0.8157 (mmm) cc_final: 0.7887 (mtm) REVERT: C 1151 ASP cc_start: 0.8061 (m-30) cc_final: 0.7650 (m-30) outliers start: 63 outliers final: 36 residues processed: 563 average time/residue: 0.5468 time to fit residues: 370.4112 Evaluate side-chains 595 residues out of total 4700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 545 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 357 THR 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 964 GLU Chi-restraints excluded: chain A residue 1011 VAL Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1108 LYS Chi-restraints excluded: chain A residue 1128 ARG Chi-restraints excluded: chain A residue 1229 VAL Chi-restraints excluded: chain A residue 1243 ILE Chi-restraints excluded: chain D residue 170 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 694 MET Chi-restraints excluded: chain D residue 964 GLU Chi-restraints excluded: chain D residue 1011 VAL 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 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 694 MET Chi-restraints excluded: chain B residue 964 GLU 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 1243 ILE Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 527 LEU 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 694 MET Chi-restraints excluded: chain C residue 964 GLU 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 1229 VAL 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 72 optimal weight: 0.8980 chunk 198 optimal weight: 2.9990 chunk 366 optimal weight: 3.9990 chunk 445 optimal weight: 3.9990 chunk 175 optimal weight: 20.0000 chunk 74 optimal weight: 2.9990 chunk 265 optimal weight: 10.0000 chunk 469 optimal weight: 9.9990 chunk 196 optimal weight: 6.9990 chunk 154 optimal weight: 2.9990 chunk 455 optimal weight: 0.8980 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN A1301 ASN D 61 ASN D1301 ASN B 61 ASN B1156 HIS B1301 ASN C 61 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.164870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.119203 restraints weight = 51354.884| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 1.91 r_work: 0.3245 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.4519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 43764 Z= 0.218 Angle : 0.597 7.937 59548 Z= 0.311 Chirality : 0.042 0.172 6772 Planarity : 0.005 0.045 7540 Dihedral : 8.448 89.614 7084 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.42 % Allowed : 14.25 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.11), residues: 5476 helix: 1.95 (0.09), residues: 3036 sheet: -1.34 (0.21), residues: 436 loop : -0.51 (0.14), residues: 2004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 529 TYR 0.047 0.003 TYR D 420 PHE 0.022 0.002 PHE C 879 TRP 0.015 0.002 TRP A1124 HIS 0.007 0.001 HIS C1156 Details of bonding type rmsd covalent geometry : bond 0.00501 (43760) covalent geometry : angle 0.59696 (59540) SS BOND : bond 0.00040 ( 4) SS BOND : angle 0.60213 ( 8) hydrogen bonds : bond 0.05017 ( 2364) hydrogen bonds : angle 4.00386 ( 6960) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 21098.26 seconds wall clock time: 358 minutes 7.48 seconds (21487.48 seconds total)