Starting phenix.real_space_refine on Thu Nov 20 03:06:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6bqv_7133/11_2025/6bqv_7133_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6bqv_7133/11_2025/6bqv_7133.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6bqv_7133/11_2025/6bqv_7133_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6bqv_7133/11_2025/6bqv_7133_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6bqv_7133/11_2025/6bqv_7133.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6bqv_7133/11_2025/6bqv_7133.map" } resolution = 3.1 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= 0.000 sd= 1.000 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: 5 Type Number sf(0) Gaussians Ca 4 9.91 5 S 152 5.16 5 C 19268 2.51 5 N 5148 2.21 5 O 5144 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 72 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29716 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 7323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 932, 7323 Classifications: {'peptide': 932} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 37, 'TRANS': 894} Chain breaks: 10 Unresolved non-hydrogen bonds: 93 Unresolved non-hydrogen angles: 121 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'ARG:plan': 5, 'HIS:plan': 3, 'ASN:plan1': 1, 'PHE:plan': 2, 'ASP:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 60 Chain: "A" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 106 Unusual residues: {' CA': 1, 'Y01': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Restraints were copied for chains: B, C, D Time building chain proxies: 8.45, per 1000 atoms: 0.28 Number of scatterers: 29716 At special positions: 0 Unit cell: (139.118, 139.118, 160.038, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 4 19.99 S 152 16.00 O 5144 8.00 N 5148 7.00 C 19268 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.49 Conformation dependent library (CDL) restraints added in 1.3 seconds 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6896 Finding SS restraints... Secondary structure from input PDB file: 184 helices and 16 sheets defined 67.1% alpha, 3.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.03 Creating SS restraints... Processing helix chain 'A' and resid 99 through 108 removed outlier: 3.804A pdb=" N TYR A 103 " --> pdb=" O PRO A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 140 Processing helix chain 'A' and resid 141 through 150 removed outlier: 3.722A pdb=" N ALA A 145 " --> pdb=" O GLY A 141 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR A 149 " --> pdb=" O ALA A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 177 removed outlier: 4.109A pdb=" N HIS A 165 " --> pdb=" O GLY A 161 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N MET A 175 " --> pdb=" O ARG A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 260 removed outlier: 4.431A pdb=" N ARG A 248 " --> pdb=" O GLY A 244 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N PHE A 249 " --> pdb=" O GLY A 245 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TYR A 256 " --> pdb=" O ARG A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 294 removed outlier: 3.601A pdb=" N LEU A 285 " --> pdb=" O ASP A 281 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N THR A 286 " --> pdb=" O GLU A 282 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ASN A 290 " --> pdb=" O THR A 286 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA A 291 " --> pdb=" O ARG A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 316 removed outlier: 4.017A pdb=" N THR A 314 " --> pdb=" O CYS A 310 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU A 316 " --> pdb=" O ALA A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 339 removed outlier: 3.590A pdb=" N ILE A 335 " --> pdb=" O ALA A 331 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ARG A 336 " --> pdb=" O ARG A 332 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N PHE A 338 " --> pdb=" O ARG A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 358 removed outlier: 3.687A pdb=" N LEU A 347 " --> pdb=" O ASP A 343 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N VAL A 351 " --> pdb=" O LEU A 347 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLU A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ARG A 353 " --> pdb=" O ALA A 349 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ARG A 357 " --> pdb=" O ARG A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 386 removed outlier: 3.504A pdb=" N LEU A 381 " --> pdb=" O VAL A 377 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL A 382 " --> pdb=" O LEU A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 403 Processing helix chain 'A' and resid 405 through 415 removed outlier: 3.747A pdb=" N ALA A 409 " --> pdb=" O ARG A 405 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER A 411 " --> pdb=" O ASP A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 435 removed outlier: 3.588A pdb=" N LEU A 425 " --> pdb=" O ARG A 421 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA A 427 " --> pdb=" O PHE A 423 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N SER A 428 " --> pdb=" O HIS A 424 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASP A 431 " --> pdb=" O ALA A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 447 removed outlier: 3.764A pdb=" N VAL A 441 " --> pdb=" O ARG A 437 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU A 443 " --> pdb=" O GLU A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 466 removed outlier: 3.613A pdb=" N ALA A 466 " --> pdb=" O GLN A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 481 Processing helix chain 'A' and resid 504 through 510 Processing helix chain 'A' and resid 559 through 569 Processing helix chain 'A' and resid 571 through 579 Processing helix chain 'A' and resid 584 through 602 removed outlier: 3.576A pdb=" N ARG A 601 " --> pdb=" O ARG A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 634 removed outlier: 4.069A pdb=" N ARG A 611 " --> pdb=" O GLU A 607 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA A 616 " --> pdb=" O ARG A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 643 removed outlier: 3.688A pdb=" N LEU A 641 " --> pdb=" O ARG A 637 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LEU A 642 " --> pdb=" O ALA A 638 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU A 643 " --> pdb=" O ALA A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 661 Processing helix chain 'A' and resid 663 through 668 Processing helix chain 'A' and resid 669 through 681 removed outlier: 3.523A pdb=" N GLN A 678 " --> pdb=" O SER A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 689 through 698 removed outlier: 3.796A pdb=" N LEU A 693 " --> pdb=" O PRO A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 699 through 705 removed outlier: 3.524A pdb=" N TYR A 704 " --> pdb=" O PRO A 701 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N THR A 705 " --> pdb=" O LEU A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 777 removed outlier: 3.756A pdb=" N PHE A 775 " --> pdb=" O ARG A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 778 through 804 Processing helix chain 'A' and resid 811 through 830 removed outlier: 3.518A pdb=" N ARG A 830 " --> pdb=" O CYS A 826 " (cutoff:3.500A) Processing helix chain 'A' and resid 851 through 860 removed outlier: 3.533A pdb=" N ARG A 855 " --> pdb=" O SER A 851 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ARG A 857 " --> pdb=" O SER A 853 " (cutoff:3.500A) Processing helix chain 'A' and resid 862 through 884 removed outlier: 3.567A pdb=" N THR A 884 " --> pdb=" O GLY A 880 " (cutoff:3.500A) Processing helix chain 'A' and resid 887 through 910 removed outlier: 3.954A pdb=" N LEU A 906 " --> pdb=" O PHE A 902 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N LEU A 907 " --> pdb=" O THR A 903 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N HIS A 908 " --> pdb=" O VAL A 904 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 921 Processing helix chain 'A' and resid 926 through 952 removed outlier: 3.524A pdb=" N PHE A 932 " --> pdb=" O LYS A 928 " (cutoff:3.500A) Processing helix chain 'A' and resid 958 through 966 Processing helix chain 'A' and resid 967 through 973 removed outlier: 3.514A pdb=" N GLN A 973 " --> pdb=" O ARG A 969 " (cutoff:3.500A) Processing helix chain 'A' and resid 974 through 976 No H-bonds generated for 'chain 'A' and resid 974 through 976' Processing helix chain 'A' and resid 979 through 984 Processing helix chain 'A' and resid 985 through 988 Processing helix chain 'A' and resid 1016 through 1031 Processing helix chain 'A' and resid 1033 through 1071 removed outlier: 3.506A pdb=" N GLY A1048 " --> pdb=" O SER A1044 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N GLY A1052 " --> pdb=" O GLY A1048 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ASN A1053 " --> pdb=" O LYS A1049 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA A1060 " --> pdb=" O LEU A1056 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N TYR A1063 " --> pdb=" O LYS A1059 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ARG A1064 " --> pdb=" O ALA A1060 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU A1068 " --> pdb=" O ARG A1064 " (cutoff:3.500A) Processing helix chain 'A' and resid 1086 through 1094 removed outlier: 3.527A pdb=" N GLN A1091 " --> pdb=" O LEU A1087 " (cutoff:3.500A) Processing helix chain 'A' and resid 1114 through 1142 removed outlier: 3.562A pdb=" N ALA A1135 " --> pdb=" O ASN A1131 " (cutoff:3.500A) Processing helix chain 'A' and resid 1143 through 1167 removed outlier: 3.958A pdb=" N HIS A1164 " --> pdb=" O LYS A1160 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE A1165 " --> pdb=" O GLN A1161 " (cutoff:3.500A) Processing helix chain 'A' and resid 1167 through 1175 removed outlier: 3.595A pdb=" N LEU A1175 " --> pdb=" O ARG A1171 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 108 removed outlier: 3.804A pdb=" N TYR B 103 " --> pdb=" O PRO B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 140 Processing helix chain 'B' and resid 141 through 150 removed outlier: 3.722A pdb=" N ALA B 145 " --> pdb=" O GLY B 141 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR B 149 " --> pdb=" O ALA B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 177 removed outlier: 4.109A pdb=" N HIS B 165 " --> pdb=" O GLY B 161 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N MET B 175 " --> pdb=" O ARG B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 260 removed outlier: 4.430A pdb=" N ARG B 248 " --> pdb=" O GLY B 244 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N PHE B 249 " --> pdb=" O GLY B 245 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TYR B 256 " --> pdb=" O ARG B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 294 removed outlier: 3.601A pdb=" N LEU B 285 " --> pdb=" O ASP B 281 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N THR B 286 " --> pdb=" O GLU B 282 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ASN B 290 " --> pdb=" O THR B 286 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ALA B 291 " --> pdb=" O ARG B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 316 removed outlier: 4.017A pdb=" N THR B 314 " --> pdb=" O CYS B 310 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU B 316 " --> pdb=" O ALA B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 339 removed outlier: 3.590A pdb=" N ILE B 335 " --> pdb=" O ALA B 331 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ARG B 336 " --> pdb=" O ARG B 332 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N PHE B 338 " --> pdb=" O ARG B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 358 removed outlier: 3.686A pdb=" N LEU B 347 " --> pdb=" O ASP B 343 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N VAL B 351 " --> pdb=" O LEU B 347 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLU B 352 " --> pdb=" O GLN B 348 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ARG B 353 " --> pdb=" O ALA B 349 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ARG B 357 " --> pdb=" O ARG B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 386 removed outlier: 3.505A pdb=" N LEU B 381 " --> pdb=" O VAL B 377 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL B 382 " --> pdb=" O LEU B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 397 through 403 Processing helix chain 'B' and resid 405 through 415 removed outlier: 3.747A pdb=" N ALA B 409 " --> pdb=" O ARG B 405 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER B 411 " --> pdb=" O ASP B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 435 removed outlier: 3.587A pdb=" N LEU B 425 " --> pdb=" O ARG B 421 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA B 427 " --> pdb=" O PHE B 423 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N SER B 428 " --> pdb=" O HIS B 424 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASP B 431 " --> pdb=" O ALA B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 447 removed outlier: 3.765A pdb=" N VAL B 441 " --> pdb=" O ARG B 437 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU B 443 " --> pdb=" O GLU B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 466 removed outlier: 3.612A pdb=" N ALA B 466 " --> pdb=" O GLN B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 481 Processing helix chain 'B' and resid 504 through 510 Processing helix chain 'B' and resid 559 through 569 Processing helix chain 'B' and resid 571 through 579 Processing helix chain 'B' and resid 584 through 602 removed outlier: 3.576A pdb=" N ARG B 601 " --> pdb=" O ARG B 597 " (cutoff:3.500A) Processing helix chain 'B' and resid 607 through 634 removed outlier: 4.069A pdb=" N ARG B 611 " --> pdb=" O GLU B 607 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA B 616 " --> pdb=" O ARG B 612 " (cutoff:3.500A) Processing helix chain 'B' and resid 634 through 643 removed outlier: 3.688A pdb=" N LEU B 641 " --> pdb=" O ARG B 637 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LEU B 642 " --> pdb=" O ALA B 638 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU B 643 " --> pdb=" O ALA B 639 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 661 Processing helix chain 'B' and resid 663 through 668 Processing helix chain 'B' and resid 669 through 681 removed outlier: 3.524A pdb=" N GLN B 678 " --> pdb=" O SER B 674 " (cutoff:3.500A) Processing helix chain 'B' and resid 689 through 698 removed outlier: 3.797A pdb=" N LEU B 693 " --> pdb=" O PRO B 689 " (cutoff:3.500A) Processing helix chain 'B' and resid 699 through 705 removed outlier: 3.525A pdb=" N TYR B 704 " --> pdb=" O PRO B 701 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N THR B 705 " --> pdb=" O LEU B 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 768 through 777 removed outlier: 3.756A pdb=" N PHE B 775 " --> pdb=" O ARG B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 778 through 804 Processing helix chain 'B' and resid 811 through 830 removed outlier: 3.519A pdb=" N ARG B 830 " --> pdb=" O CYS B 826 " (cutoff:3.500A) Processing helix chain 'B' and resid 851 through 860 removed outlier: 3.533A pdb=" N ARG B 855 " --> pdb=" O SER B 851 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ARG B 857 " --> pdb=" O SER B 853 " (cutoff:3.500A) Processing helix chain 'B' and resid 862 through 884 removed outlier: 3.567A pdb=" N THR B 884 " --> pdb=" O GLY B 880 " (cutoff:3.500A) Processing helix chain 'B' and resid 887 through 910 removed outlier: 3.954A pdb=" N LEU B 906 " --> pdb=" O PHE B 902 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N LEU B 907 " --> pdb=" O THR B 903 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N HIS B 908 " --> pdb=" O VAL B 904 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 916 through 921 Processing helix chain 'B' and resid 926 through 952 removed outlier: 3.524A pdb=" N PHE B 932 " --> pdb=" O LYS B 928 " (cutoff:3.500A) Processing helix chain 'B' and resid 958 through 966 Processing helix chain 'B' and resid 967 through 973 removed outlier: 3.514A pdb=" N GLN B 973 " --> pdb=" O ARG B 969 " (cutoff:3.500A) Processing helix chain 'B' and resid 974 through 976 No H-bonds generated for 'chain 'B' and resid 974 through 976' Processing helix chain 'B' and resid 979 through 984 Processing helix chain 'B' and resid 985 through 988 Processing helix chain 'B' and resid 1016 through 1031 Processing helix chain 'B' and resid 1033 through 1071 removed outlier: 3.505A pdb=" N GLY B1048 " --> pdb=" O SER B1044 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N GLY B1052 " --> pdb=" O GLY B1048 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ASN B1053 " --> pdb=" O LYS B1049 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA B1060 " --> pdb=" O LEU B1056 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N TYR B1063 " --> pdb=" O LYS B1059 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ARG B1064 " --> pdb=" O ALA B1060 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU B1068 " --> pdb=" O ARG B1064 " (cutoff:3.500A) Processing helix chain 'B' and resid 1086 through 1094 removed outlier: 3.527A pdb=" N GLN B1091 " --> pdb=" O LEU B1087 " (cutoff:3.500A) Processing helix chain 'B' and resid 1114 through 1142 removed outlier: 3.561A pdb=" N ALA B1135 " --> pdb=" O ASN B1131 " (cutoff:3.500A) Processing helix chain 'B' and resid 1143 through 1167 removed outlier: 3.958A pdb=" N HIS B1164 " --> pdb=" O LYS B1160 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE B1165 " --> pdb=" O GLN B1161 " (cutoff:3.500A) Processing helix chain 'B' and resid 1167 through 1175 removed outlier: 3.595A pdb=" N LEU B1175 " --> pdb=" O ARG B1171 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 108 removed outlier: 3.804A pdb=" N TYR C 103 " --> pdb=" O PRO C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 140 Processing helix chain 'C' and resid 141 through 150 removed outlier: 3.722A pdb=" N ALA C 145 " --> pdb=" O GLY C 141 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N THR C 149 " --> pdb=" O ALA C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 161 through 177 removed outlier: 4.109A pdb=" N HIS C 165 " --> pdb=" O GLY C 161 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N MET C 175 " --> pdb=" O ARG C 171 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 260 removed outlier: 4.431A pdb=" N ARG C 248 " --> pdb=" O GLY C 244 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N PHE C 249 " --> pdb=" O GLY C 245 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TYR C 256 " --> pdb=" O ARG C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 294 removed outlier: 3.602A pdb=" N LEU C 285 " --> pdb=" O ASP C 281 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N THR C 286 " --> pdb=" O GLU C 282 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ASN C 290 " --> pdb=" O THR C 286 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA C 291 " --> pdb=" O ARG C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 307 through 316 removed outlier: 4.017A pdb=" N THR C 314 " --> pdb=" O CYS C 310 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU C 316 " --> pdb=" O ALA C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 339 removed outlier: 3.591A pdb=" N ILE C 335 " --> pdb=" O ALA C 331 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ARG C 336 " --> pdb=" O ARG C 332 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N PHE C 338 " --> pdb=" O ARG C 334 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 358 removed outlier: 3.687A pdb=" N LEU C 347 " --> pdb=" O ASP C 343 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N VAL C 351 " --> pdb=" O LEU C 347 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLU C 352 " --> pdb=" O GLN C 348 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ARG C 353 " --> pdb=" O ALA C 349 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ARG C 357 " --> pdb=" O ARG C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 372 through 386 removed outlier: 3.504A pdb=" N LEU C 381 " --> pdb=" O VAL C 377 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL C 382 " --> pdb=" O LEU C 378 " (cutoff:3.500A) Processing helix chain 'C' and resid 397 through 403 Processing helix chain 'C' and resid 405 through 415 removed outlier: 3.747A pdb=" N ALA C 409 " --> pdb=" O ARG C 405 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER C 411 " --> pdb=" O ASP C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 421 through 435 removed outlier: 3.587A pdb=" N LEU C 425 " --> pdb=" O ARG C 421 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA C 427 " --> pdb=" O PHE C 423 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N SER C 428 " --> pdb=" O HIS C 424 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASP C 431 " --> pdb=" O ALA C 427 " (cutoff:3.500A) Processing helix chain 'C' and resid 437 through 447 removed outlier: 3.765A pdb=" N VAL C 441 " --> pdb=" O ARG C 437 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU C 443 " --> pdb=" O GLU C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 456 through 466 removed outlier: 3.613A pdb=" N ALA C 466 " --> pdb=" O GLN C 462 " (cutoff:3.500A) Processing helix chain 'C' and resid 473 through 481 Processing helix chain 'C' and resid 504 through 510 Processing helix chain 'C' and resid 559 through 569 Processing helix chain 'C' and resid 571 through 579 Processing helix chain 'C' and resid 584 through 602 removed outlier: 3.576A pdb=" N ARG C 601 " --> pdb=" O ARG C 597 " (cutoff:3.500A) Processing helix chain 'C' and resid 607 through 634 removed outlier: 4.069A pdb=" N ARG C 611 " --> pdb=" O GLU C 607 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA C 616 " --> pdb=" O ARG C 612 " (cutoff:3.500A) Processing helix chain 'C' and resid 634 through 643 removed outlier: 3.689A pdb=" N LEU C 641 " --> pdb=" O ARG C 637 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LEU C 642 " --> pdb=" O ALA C 638 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU C 643 " --> pdb=" O ALA C 639 " (cutoff:3.500A) Processing helix chain 'C' and resid 653 through 661 Processing helix chain 'C' and resid 663 through 668 Processing helix chain 'C' and resid 669 through 681 removed outlier: 3.523A pdb=" N GLN C 678 " --> pdb=" O SER C 674 " (cutoff:3.500A) Processing helix chain 'C' and resid 689 through 698 removed outlier: 3.796A pdb=" N LEU C 693 " --> pdb=" O PRO C 689 " (cutoff:3.500A) Processing helix chain 'C' and resid 699 through 705 removed outlier: 3.524A pdb=" N TYR C 704 " --> pdb=" O PRO C 701 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N THR C 705 " --> pdb=" O LEU C 702 " (cutoff:3.500A) Processing helix chain 'C' and resid 768 through 777 removed outlier: 3.756A pdb=" N PHE C 775 " --> pdb=" O ARG C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 778 through 804 Processing helix chain 'C' and resid 811 through 830 removed outlier: 3.519A pdb=" N ARG C 830 " --> pdb=" O CYS C 826 " (cutoff:3.500A) Processing helix chain 'C' and resid 851 through 860 removed outlier: 3.533A pdb=" N ARG C 855 " --> pdb=" O SER C 851 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ARG C 857 " --> pdb=" O SER C 853 " (cutoff:3.500A) Processing helix chain 'C' and resid 862 through 884 removed outlier: 3.567A pdb=" N THR C 884 " --> pdb=" O GLY C 880 " (cutoff:3.500A) Processing helix chain 'C' and resid 887 through 910 removed outlier: 3.954A pdb=" N LEU C 906 " --> pdb=" O PHE C 902 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N LEU C 907 " --> pdb=" O THR C 903 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N HIS C 908 " --> pdb=" O VAL C 904 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 916 through 921 Processing helix chain 'C' and resid 926 through 952 removed outlier: 3.523A pdb=" N PHE C 932 " --> pdb=" O LYS C 928 " (cutoff:3.500A) Processing helix chain 'C' and resid 958 through 966 Processing helix chain 'C' and resid 967 through 973 removed outlier: 3.514A pdb=" N GLN C 973 " --> pdb=" O ARG C 969 " (cutoff:3.500A) Processing helix chain 'C' and resid 974 through 976 No H-bonds generated for 'chain 'C' and resid 974 through 976' Processing helix chain 'C' and resid 979 through 984 Processing helix chain 'C' and resid 985 through 988 Processing helix chain 'C' and resid 1016 through 1031 Processing helix chain 'C' and resid 1033 through 1071 removed outlier: 3.506A pdb=" N GLY C1048 " --> pdb=" O SER C1044 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N GLY C1052 " --> pdb=" O GLY C1048 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ASN C1053 " --> pdb=" O LYS C1049 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA C1060 " --> pdb=" O LEU C1056 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N TYR C1063 " --> pdb=" O LYS C1059 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ARG C1064 " --> pdb=" O ALA C1060 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU C1068 " --> pdb=" O ARG C1064 " (cutoff:3.500A) Processing helix chain 'C' and resid 1086 through 1094 removed outlier: 3.528A pdb=" N GLN C1091 " --> pdb=" O LEU C1087 " (cutoff:3.500A) Processing helix chain 'C' and resid 1114 through 1142 removed outlier: 3.561A pdb=" N ALA C1135 " --> pdb=" O ASN C1131 " (cutoff:3.500A) Processing helix chain 'C' and resid 1143 through 1167 removed outlier: 3.958A pdb=" N HIS C1164 " --> pdb=" O LYS C1160 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE C1165 " --> pdb=" O GLN C1161 " (cutoff:3.500A) Processing helix chain 'C' and resid 1167 through 1175 removed outlier: 3.595A pdb=" N LEU C1175 " --> pdb=" O ARG C1171 " (cutoff:3.500A) Processing helix chain 'D' and resid 99 through 108 removed outlier: 3.804A pdb=" N TYR D 103 " --> pdb=" O PRO D 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 140 Processing helix chain 'D' and resid 141 through 150 removed outlier: 3.723A pdb=" N ALA D 145 " --> pdb=" O GLY D 141 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR D 149 " --> pdb=" O ALA D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 177 removed outlier: 4.109A pdb=" N HIS D 165 " --> pdb=" O GLY D 161 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N MET D 175 " --> pdb=" O ARG D 171 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 260 removed outlier: 4.430A pdb=" N ARG D 248 " --> pdb=" O GLY D 244 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N PHE D 249 " --> pdb=" O GLY D 245 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TYR D 256 " --> pdb=" O ARG D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 294 removed outlier: 3.601A pdb=" N LEU D 285 " --> pdb=" O ASP D 281 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N THR D 286 " --> pdb=" O GLU D 282 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ASN D 290 " --> pdb=" O THR D 286 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA D 291 " --> pdb=" O ARG D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 307 through 316 removed outlier: 4.018A pdb=" N THR D 314 " --> pdb=" O CYS D 310 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU D 316 " --> pdb=" O ALA D 312 " (cutoff:3.500A) Processing helix chain 'D' and resid 330 through 339 removed outlier: 3.590A pdb=" N ILE D 335 " --> pdb=" O ALA D 331 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ARG D 336 " --> pdb=" O ARG D 332 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N PHE D 338 " --> pdb=" O ARG D 334 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 358 removed outlier: 3.686A pdb=" N LEU D 347 " --> pdb=" O ASP D 343 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N VAL D 351 " --> pdb=" O LEU D 347 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLU D 352 " --> pdb=" O GLN D 348 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ARG D 353 " --> pdb=" O ALA D 349 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ARG D 357 " --> pdb=" O ARG D 353 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 386 removed outlier: 3.504A pdb=" N LEU D 381 " --> pdb=" O VAL D 377 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL D 382 " --> pdb=" O LEU D 378 " (cutoff:3.500A) Processing helix chain 'D' and resid 397 through 403 Processing helix chain 'D' and resid 405 through 415 removed outlier: 3.747A pdb=" N ALA D 409 " --> pdb=" O ARG D 405 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER D 411 " --> pdb=" O ASP D 407 " (cutoff:3.500A) Processing helix chain 'D' and resid 421 through 435 removed outlier: 3.587A pdb=" N LEU D 425 " --> pdb=" O ARG D 421 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA D 427 " --> pdb=" O PHE D 423 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N SER D 428 " --> pdb=" O HIS D 424 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASP D 431 " --> pdb=" O ALA D 427 " (cutoff:3.500A) Processing helix chain 'D' and resid 437 through 447 removed outlier: 3.765A pdb=" N VAL D 441 " --> pdb=" O ARG D 437 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU D 443 " --> pdb=" O GLU D 439 " (cutoff:3.500A) Processing helix chain 'D' and resid 456 through 466 removed outlier: 3.612A pdb=" N ALA D 466 " --> pdb=" O GLN D 462 " (cutoff:3.500A) Processing helix chain 'D' and resid 473 through 481 Processing helix chain 'D' and resid 504 through 510 Processing helix chain 'D' and resid 559 through 569 Processing helix chain 'D' and resid 571 through 579 Processing helix chain 'D' and resid 584 through 602 removed outlier: 3.577A pdb=" N ARG D 601 " --> pdb=" O ARG D 597 " (cutoff:3.500A) Processing helix chain 'D' and resid 607 through 634 removed outlier: 4.069A pdb=" N ARG D 611 " --> pdb=" O GLU D 607 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA D 616 " --> pdb=" O ARG D 612 " (cutoff:3.500A) Processing helix chain 'D' and resid 634 through 643 removed outlier: 3.688A pdb=" N LEU D 641 " --> pdb=" O ARG D 637 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LEU D 642 " --> pdb=" O ALA D 638 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU D 643 " --> pdb=" O ALA D 639 " (cutoff:3.500A) Processing helix chain 'D' and resid 653 through 661 Processing helix chain 'D' and resid 663 through 668 Processing helix chain 'D' and resid 669 through 681 removed outlier: 3.523A pdb=" N GLN D 678 " --> pdb=" O SER D 674 " (cutoff:3.500A) Processing helix chain 'D' and resid 689 through 698 removed outlier: 3.795A pdb=" N LEU D 693 " --> pdb=" O PRO D 689 " (cutoff:3.500A) Processing helix chain 'D' and resid 699 through 705 removed outlier: 3.525A pdb=" N TYR D 704 " --> pdb=" O PRO D 701 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N THR D 705 " --> pdb=" O LEU D 702 " (cutoff:3.500A) Processing helix chain 'D' and resid 768 through 777 removed outlier: 3.756A pdb=" N PHE D 775 " --> pdb=" O ARG D 771 " (cutoff:3.500A) Processing helix chain 'D' and resid 778 through 804 Processing helix chain 'D' and resid 811 through 830 removed outlier: 3.518A pdb=" N ARG D 830 " --> pdb=" O CYS D 826 " (cutoff:3.500A) Processing helix chain 'D' and resid 851 through 860 removed outlier: 3.533A pdb=" N ARG D 855 " --> pdb=" O SER D 851 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ARG D 857 " --> pdb=" O SER D 853 " (cutoff:3.500A) Processing helix chain 'D' and resid 862 through 884 removed outlier: 3.566A pdb=" N THR D 884 " --> pdb=" O GLY D 880 " (cutoff:3.500A) Processing helix chain 'D' and resid 887 through 910 removed outlier: 3.955A pdb=" N LEU D 906 " --> pdb=" O PHE D 902 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N LEU D 907 " --> pdb=" O THR D 903 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N HIS D 908 " --> pdb=" O VAL D 904 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE D 909 " --> pdb=" O ARG D 905 " (cutoff:3.500A) Processing helix chain 'D' and resid 916 through 921 Processing helix chain 'D' and resid 926 through 952 removed outlier: 3.524A pdb=" N PHE D 932 " --> pdb=" O LYS D 928 " (cutoff:3.500A) Processing helix chain 'D' and resid 958 through 966 Processing helix chain 'D' and resid 967 through 973 removed outlier: 3.514A pdb=" N GLN D 973 " --> pdb=" O ARG D 969 " (cutoff:3.500A) Processing helix chain 'D' and resid 974 through 976 No H-bonds generated for 'chain 'D' and resid 974 through 976' Processing helix chain 'D' and resid 979 through 984 Processing helix chain 'D' and resid 985 through 988 Processing helix chain 'D' and resid 1016 through 1031 Processing helix chain 'D' and resid 1033 through 1071 removed outlier: 3.506A pdb=" N GLY D1048 " --> pdb=" O SER D1044 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N GLY D1052 " --> pdb=" O GLY D1048 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ASN D1053 " --> pdb=" O LYS D1049 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA D1060 " --> pdb=" O LEU D1056 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N TYR D1063 " --> pdb=" O LYS D1059 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ARG D1064 " --> pdb=" O ALA D1060 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU D1068 " --> pdb=" O ARG D1064 " (cutoff:3.500A) Processing helix chain 'D' and resid 1086 through 1094 removed outlier: 3.528A pdb=" N GLN D1091 " --> pdb=" O LEU D1087 " (cutoff:3.500A) Processing helix chain 'D' and resid 1114 through 1142 removed outlier: 3.561A pdb=" N ALA D1135 " --> pdb=" O ASN D1131 " (cutoff:3.500A) Processing helix chain 'D' and resid 1143 through 1167 removed outlier: 3.957A pdb=" N HIS D1164 " --> pdb=" O LYS D1160 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE D1165 " --> pdb=" O GLN D1161 " (cutoff:3.500A) Processing helix chain 'D' and resid 1167 through 1175 removed outlier: 3.595A pdb=" N LEU D1175 " --> pdb=" O ARG D1171 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 89 through 93 removed outlier: 6.933A pdb=" N ASN A 89 " --> pdb=" O PHE A 232 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N LEU A 234 " --> pdb=" O ASN A 89 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N LEU A 91 " --> pdb=" O LEU A 234 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 185 through 187 removed outlier: 3.582A pdb=" N VAL A 119 " --> pdb=" O TRP A 152 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N VAL A 118 " --> pdb=" O LEU A 274 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N LEU A 276 " --> pdb=" O VAL A 118 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N SER A 120 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N LEU A 299 " --> pdb=" O VAL A 273 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N LEU A 275 " --> pdb=" O LEU A 299 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N VAL A 301 " --> pdb=" O LEU A 275 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N LEU A 277 " --> pdb=" O VAL A 301 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N CYS A 298 " --> pdb=" O THR A 362 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N TYR A 364 " --> pdb=" O CYS A 298 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N LEU A 300 " --> pdb=" O TYR A 364 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 261 through 262 Processing sheet with id=AA4, first strand: chain 'A' and resid 1000 through 1001 Processing sheet with id=AA5, first strand: chain 'B' and resid 89 through 93 removed outlier: 6.934A pdb=" N ASN B 89 " --> pdb=" O PHE B 232 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N LEU B 234 " --> pdb=" O ASN B 89 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N LEU B 91 " --> pdb=" O LEU B 234 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 185 through 187 removed outlier: 3.581A pdb=" N VAL B 119 " --> pdb=" O TRP B 152 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N VAL B 118 " --> pdb=" O LEU B 274 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N LEU B 276 " --> pdb=" O VAL B 118 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N SER B 120 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N LEU B 299 " --> pdb=" O VAL B 273 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N LEU B 275 " --> pdb=" O LEU B 299 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N VAL B 301 " --> pdb=" O LEU B 275 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N LEU B 277 " --> pdb=" O VAL B 301 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N CYS B 298 " --> pdb=" O THR B 362 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N TYR B 364 " --> pdb=" O CYS B 298 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N LEU B 300 " --> pdb=" O TYR B 364 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 261 through 262 Processing sheet with id=AA8, first strand: chain 'B' and resid 1000 through 1001 Processing sheet with id=AA9, first strand: chain 'C' and resid 89 through 93 removed outlier: 6.933A pdb=" N ASN C 89 " --> pdb=" O PHE C 232 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N LEU C 234 " --> pdb=" O ASN C 89 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N LEU C 91 " --> pdb=" O LEU C 234 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'C' and resid 185 through 187 removed outlier: 3.581A pdb=" N VAL C 119 " --> pdb=" O TRP C 152 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N VAL C 118 " --> pdb=" O LEU C 274 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N LEU C 276 " --> pdb=" O VAL C 118 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N SER C 120 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N LEU C 299 " --> pdb=" O VAL C 273 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N LEU C 275 " --> pdb=" O LEU C 299 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N VAL C 301 " --> pdb=" O LEU C 275 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N LEU C 277 " --> pdb=" O VAL C 301 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N CYS C 298 " --> pdb=" O THR C 362 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N TYR C 364 " --> pdb=" O CYS C 298 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N LEU C 300 " --> pdb=" O TYR C 364 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 261 through 262 Processing sheet with id=AB3, first strand: chain 'C' and resid 1000 through 1001 Processing sheet with id=AB4, first strand: chain 'D' and resid 89 through 93 removed outlier: 6.933A pdb=" N ASN D 89 " --> pdb=" O PHE D 232 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N LEU D 234 " --> pdb=" O ASN D 89 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N LEU D 91 " --> pdb=" O LEU D 234 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'D' and resid 185 through 187 removed outlier: 3.581A pdb=" N VAL D 119 " --> pdb=" O TRP D 152 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N VAL D 118 " --> pdb=" O LEU D 274 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N LEU D 276 " --> pdb=" O VAL D 118 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N SER D 120 " --> pdb=" O LEU D 276 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N LEU D 299 " --> pdb=" O VAL D 273 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N LEU D 275 " --> pdb=" O LEU D 299 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N VAL D 301 " --> pdb=" O LEU D 275 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N LEU D 277 " --> pdb=" O VAL D 301 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N CYS D 298 " --> pdb=" O THR D 362 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N TYR D 364 " --> pdb=" O CYS D 298 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N LEU D 300 " --> pdb=" O TYR D 364 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 261 through 262 Processing sheet with id=AB7, first strand: chain 'D' and resid 1000 through 1001 1544 hydrogen bonds defined for protein. 4572 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: 6.11 Time building geometry restraints manager: 3.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 4666 1.31 - 1.43: 8280 1.43 - 1.56: 17050 1.56 - 1.69: 148 1.69 - 1.81: 248 Bond restraints: 30392 Sorted by residual: bond pdb=" CAI Y01 A1302 " pdb=" CAZ Y01 A1302 " ideal model delta sigma weight residual 1.332 1.679 -0.347 2.00e-02 2.50e+03 3.02e+02 bond pdb=" CAI Y01 D1302 " pdb=" CAZ Y01 D1302 " ideal model delta sigma weight residual 1.332 1.679 -0.347 2.00e-02 2.50e+03 3.01e+02 bond pdb=" CAI Y01 B1302 " pdb=" CAZ Y01 B1302 " ideal model delta sigma weight residual 1.332 1.679 -0.347 2.00e-02 2.50e+03 3.00e+02 bond pdb=" CAI Y01 C1302 " pdb=" CAZ Y01 C1302 " ideal model delta sigma weight residual 1.332 1.678 -0.346 2.00e-02 2.50e+03 3.00e+02 bond pdb=" CAI Y01 D1301 " pdb=" CAZ Y01 D1301 " ideal model delta sigma weight residual 1.332 1.675 -0.343 2.00e-02 2.50e+03 2.94e+02 ... (remaining 30387 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.83: 40234 3.83 - 7.66: 833 7.66 - 11.50: 153 11.50 - 15.33: 8 15.33 - 19.16: 8 Bond angle restraints: 41236 Sorted by residual: angle pdb=" C ALA A1076 " pdb=" N PRO A1077 " pdb=" CA PRO A1077 " ideal model delta sigma weight residual 120.38 133.32 -12.94 1.03e+00 9.43e-01 1.58e+02 angle pdb=" C ALA C1076 " pdb=" N PRO C1077 " pdb=" CA PRO C1077 " ideal model delta sigma weight residual 120.38 133.31 -12.93 1.03e+00 9.43e-01 1.58e+02 angle pdb=" C ALA D1076 " pdb=" N PRO D1077 " pdb=" CA PRO D1077 " ideal model delta sigma weight residual 120.38 133.30 -12.92 1.03e+00 9.43e-01 1.57e+02 angle pdb=" C ALA B1076 " pdb=" N PRO B1077 " pdb=" CA PRO B1077 " ideal model delta sigma weight residual 120.38 133.30 -12.92 1.03e+00 9.43e-01 1.57e+02 angle pdb=" N PRO D1077 " pdb=" CA PRO D1077 " pdb=" C PRO D1077 " ideal model delta sigma weight residual 110.70 119.19 -8.49 1.22e+00 6.72e-01 4.84e+01 ... (remaining 41231 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.35: 16833 17.35 - 34.69: 1255 34.69 - 52.04: 352 52.04 - 69.38: 68 69.38 - 86.73: 32 Dihedral angle restraints: 18540 sinusoidal: 7864 harmonic: 10676 Sorted by residual: dihedral pdb=" CA LEU D 707 " pdb=" C LEU D 707 " pdb=" N ILE D 708 " pdb=" CA ILE D 708 " ideal model delta harmonic sigma weight residual 180.00 -131.35 -48.65 0 5.00e+00 4.00e-02 9.47e+01 dihedral pdb=" CA LEU B 707 " pdb=" C LEU B 707 " pdb=" N ILE B 708 " pdb=" CA ILE B 708 " ideal model delta harmonic sigma weight residual 180.00 -131.40 -48.60 0 5.00e+00 4.00e-02 9.45e+01 dihedral pdb=" CA LEU A 707 " pdb=" C LEU A 707 " pdb=" N ILE A 708 " pdb=" CA ILE A 708 " ideal model delta harmonic sigma weight residual -180.00 -131.41 -48.59 0 5.00e+00 4.00e-02 9.44e+01 ... (remaining 18537 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 4263 0.103 - 0.205: 334 0.205 - 0.308: 39 0.308 - 0.411: 16 0.411 - 0.514: 8 Chirality restraints: 4660 Sorted by residual: chirality pdb=" CBI Y01 C1303 " pdb=" CAU Y01 C1303 " pdb=" CBE Y01 C1303 " pdb=" CBG Y01 C1303 " both_signs ideal model delta sigma weight residual False 2.94 2.42 0.51 2.00e-01 2.50e+01 6.60e+00 chirality pdb=" CBI Y01 A1303 " pdb=" CAU Y01 A1303 " pdb=" CBE Y01 A1303 " pdb=" CBG Y01 A1303 " both_signs ideal model delta sigma weight residual False 2.94 2.42 0.51 2.00e-01 2.50e+01 6.58e+00 chirality pdb=" CBI Y01 B1303 " pdb=" CAU Y01 B1303 " pdb=" CBE Y01 B1303 " pdb=" CBG Y01 B1303 " both_signs ideal model delta sigma weight residual False 2.94 2.42 0.51 2.00e-01 2.50e+01 6.55e+00 ... (remaining 4657 not shown) Planarity restraints: 5152 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 152 " 0.043 2.00e-02 2.50e+03 2.85e-02 2.03e+01 pdb=" CG TRP C 152 " -0.075 2.00e-02 2.50e+03 pdb=" CD1 TRP C 152 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 TRP C 152 " -0.006 2.00e-02 2.50e+03 pdb=" NE1 TRP C 152 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP C 152 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP C 152 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 152 " 0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 152 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP C 152 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 152 " -0.043 2.00e-02 2.50e+03 2.84e-02 2.02e+01 pdb=" CG TRP A 152 " 0.075 2.00e-02 2.50e+03 pdb=" CD1 TRP A 152 " -0.023 2.00e-02 2.50e+03 pdb=" CD2 TRP A 152 " 0.006 2.00e-02 2.50e+03 pdb=" NE1 TRP A 152 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 152 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 152 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 152 " -0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 152 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 152 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 152 " 0.043 2.00e-02 2.50e+03 2.84e-02 2.01e+01 pdb=" CG TRP D 152 " -0.075 2.00e-02 2.50e+03 pdb=" CD1 TRP D 152 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 TRP D 152 " -0.006 2.00e-02 2.50e+03 pdb=" NE1 TRP D 152 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP D 152 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP D 152 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 152 " 0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 152 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP D 152 " 0.009 2.00e-02 2.50e+03 ... (remaining 5149 not shown) Histogram of nonbonded interaction distances: 1.46 - 2.15: 67 2.15 - 2.84: 9784 2.84 - 3.52: 41306 3.52 - 4.21: 73228 4.21 - 4.90: 121080 Nonbonded interactions: 245465 Sorted by model distance: nonbonded pdb=" OD2 ASP B 172 " pdb=" CZ PHE D 414 " model vdw 1.462 3.340 nonbonded pdb=" CZ PHE A 414 " pdb=" OD2 ASP C 172 " model vdw 1.475 3.340 nonbonded pdb=" CD1 LEU A 472 " pdb=" CD PRO A 604 " model vdw 1.479 3.860 nonbonded pdb=" CD1 LEU B 472 " pdb=" CD PRO B 604 " model vdw 1.479 3.860 nonbonded pdb=" CD1 LEU D 472 " pdb=" CD PRO D 604 " model vdw 1.479 3.860 ... (remaining 245460 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: 0.09 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.500 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 28.780 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 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: 0.000 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 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 : 0.014 0.347 30396 Z= 0.671 Angle : 1.370 19.159 41236 Z= 0.701 Chirality : 0.068 0.514 4660 Planarity : 0.008 0.075 5152 Dihedral : 14.129 86.727 11644 Min Nonbonded Distance : 1.462 Molprobity Statistics. All-atom Clashscore : 21.09 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.57 % Favored : 91.21 % Rotamer: Outliers : 3.54 % Allowed : 8.58 % Favored : 87.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: -5.79 (0.09), residues: 3640 helix: -3.64 (0.06), residues: 2340 sheet: -4.91 (0.20), residues: 216 loop : -3.43 (0.15), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG C 964 TYR 0.033 0.003 TYR A 227 PHE 0.035 0.004 PHE C 710 TRP 0.075 0.004 TRP C 152 HIS 0.018 0.003 HIS C 774 Details of bonding type rmsd covalent geometry : bond 0.01381 (30392) covalent geometry : angle 1.37032 (41236) hydrogen bonds : bond 0.27110 ( 1544) hydrogen bonds : angle 9.87036 ( 4572) Misc. bond : bond 0.15120 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 872 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 764 time to evaluate : 1.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 251 LEU cc_start: 0.6386 (OUTLIER) cc_final: 0.6176 (tm) REVERT: A 254 GLU cc_start: 0.7119 (mt-10) cc_final: 0.6883 (mt-10) REVERT: A 355 MET cc_start: 0.4310 (tpp) cc_final: 0.3947 (mmm) REVERT: A 462 GLN cc_start: 0.8528 (tp40) cc_final: 0.8264 (tp-100) REVERT: A 559 TRP cc_start: 0.8305 (m100) cc_final: 0.7900 (m100) REVERT: A 588 SER cc_start: 0.9171 (m) cc_final: 0.8958 (m) REVERT: A 620 GLU cc_start: 0.8739 (mm-30) cc_final: 0.7656 (tt0) REVERT: A 629 GLU cc_start: 0.7718 (mm-30) cc_final: 0.7361 (mm-30) REVERT: A 635 GLU cc_start: 0.8193 (mt-10) cc_final: 0.7807 (mp0) REVERT: A 659 MET cc_start: 0.7429 (ttm) cc_final: 0.7037 (ttp) REVERT: A 856 LEU cc_start: 0.8130 (mp) cc_final: 0.7891 (mp) REVERT: A 877 LEU cc_start: 0.8777 (mp) cc_final: 0.8126 (tt) REVERT: A 983 MET cc_start: 0.8868 (mtm) cc_final: 0.8508 (mtm) REVERT: A 984 ASP cc_start: 0.8819 (t0) cc_final: 0.8532 (t0) REVERT: A 1032 ASN cc_start: 0.8902 (OUTLIER) cc_final: 0.8523 (m110) REVERT: A 1056 LEU cc_start: 0.8396 (OUTLIER) cc_final: 0.8076 (mp) REVERT: A 1063 TYR cc_start: 0.8837 (t80) cc_final: 0.8532 (t80) REVERT: A 1067 ARG cc_start: 0.7912 (ptm-80) cc_final: 0.7603 (ptm-80) REVERT: A 1118 GLU cc_start: 0.8339 (tm-30) cc_final: 0.7934 (tm-30) REVERT: A 1140 LYS cc_start: 0.8702 (tttt) cc_final: 0.8396 (tttp) REVERT: A 1154 LYS cc_start: 0.8135 (mttt) cc_final: 0.7908 (mtmt) REVERT: A 1168 TYR cc_start: 0.6689 (OUTLIER) cc_final: 0.6101 (m-10) REVERT: B 355 MET cc_start: 0.4497 (tpp) cc_final: 0.4171 (mmm) REVERT: B 436 ASP cc_start: 0.7549 (t70) cc_final: 0.7317 (t70) REVERT: B 462 GLN cc_start: 0.8551 (tp40) cc_final: 0.8324 (tp-100) REVERT: B 588 SER cc_start: 0.9242 (m) cc_final: 0.9018 (m) REVERT: B 608 GLU cc_start: 0.6934 (tp30) cc_final: 0.5450 (mm-30) REVERT: B 620 GLU cc_start: 0.8697 (mm-30) cc_final: 0.7446 (tt0) REVERT: B 629 GLU cc_start: 0.7683 (mm-30) cc_final: 0.7425 (mm-30) REVERT: B 635 GLU cc_start: 0.8138 (mt-10) cc_final: 0.7693 (mp0) REVERT: B 659 MET cc_start: 0.7470 (ttm) cc_final: 0.7152 (ttp) REVERT: B 711 ARG cc_start: 0.6607 (mpt-90) cc_final: 0.6006 (ptm-80) REVERT: B 852 LEU cc_start: 0.7014 (mm) cc_final: 0.6748 (mt) REVERT: B 856 LEU cc_start: 0.8105 (mp) cc_final: 0.7819 (mp) REVERT: B 877 LEU cc_start: 0.8788 (mp) cc_final: 0.8156 (tt) REVERT: B 915 GLN cc_start: 0.7882 (tt0) cc_final: 0.7573 (mp10) REVERT: B 983 MET cc_start: 0.8901 (mtm) cc_final: 0.8625 (mtm) REVERT: B 1032 ASN cc_start: 0.8901 (OUTLIER) cc_final: 0.8498 (m110) REVERT: B 1056 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.8034 (mp) REVERT: B 1063 TYR cc_start: 0.8949 (t80) cc_final: 0.8740 (t80) REVERT: B 1067 ARG cc_start: 0.8031 (ptm-80) cc_final: 0.7735 (ptm-80) REVERT: B 1080 ILE cc_start: 0.8528 (tt) cc_final: 0.8328 (tt) REVERT: B 1115 LYS cc_start: 0.7952 (tppp) cc_final: 0.7649 (mmtt) REVERT: B 1140 LYS cc_start: 0.8677 (tttt) cc_final: 0.8418 (tttp) REVERT: B 1149 LYS cc_start: 0.8762 (mtpp) cc_final: 0.8376 (mtpt) REVERT: B 1154 LYS cc_start: 0.8107 (mttt) cc_final: 0.7867 (mtmt) REVERT: B 1168 TYR cc_start: 0.6662 (OUTLIER) cc_final: 0.6182 (m-10) REVERT: C 251 LEU cc_start: 0.6385 (OUTLIER) cc_final: 0.6176 (tm) REVERT: C 254 GLU cc_start: 0.7148 (mt-10) cc_final: 0.6913 (mt-10) REVERT: C 355 MET cc_start: 0.4313 (tpp) cc_final: 0.3950 (mmm) REVERT: C 405 ARG cc_start: 0.7492 (tpt-90) cc_final: 0.7281 (ttt90) REVERT: C 436 ASP cc_start: 0.7373 (t70) cc_final: 0.7172 (t70) REVERT: C 462 GLN cc_start: 0.8547 (tp40) cc_final: 0.8285 (tp-100) REVERT: C 559 TRP cc_start: 0.8309 (m100) cc_final: 0.7886 (m100) REVERT: C 588 SER cc_start: 0.9171 (m) cc_final: 0.8956 (m) REVERT: C 608 GLU cc_start: 0.6968 (tp30) cc_final: 0.5690 (mm-30) REVERT: C 620 GLU cc_start: 0.8736 (mm-30) cc_final: 0.7654 (tt0) REVERT: C 629 GLU cc_start: 0.7701 (mm-30) cc_final: 0.7351 (mm-30) REVERT: C 635 GLU cc_start: 0.8193 (mt-10) cc_final: 0.7800 (mp0) REVERT: C 659 MET cc_start: 0.7469 (ttm) cc_final: 0.7059 (ttp) REVERT: C 711 ARG cc_start: 0.6566 (mpt-90) cc_final: 0.5977 (ptm-80) REVERT: C 856 LEU cc_start: 0.8126 (mp) cc_final: 0.7906 (mp) REVERT: C 877 LEU cc_start: 0.8778 (mp) cc_final: 0.8122 (tt) REVERT: C 915 GLN cc_start: 0.7969 (tt0) cc_final: 0.7594 (mp10) REVERT: C 983 MET cc_start: 0.8846 (mtm) cc_final: 0.8481 (mtm) REVERT: C 1032 ASN cc_start: 0.8893 (OUTLIER) cc_final: 0.8500 (m110) REVERT: C 1056 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.8080 (mp) REVERT: C 1063 TYR cc_start: 0.8844 (t80) cc_final: 0.8547 (t80) REVERT: C 1067 ARG cc_start: 0.7905 (ptm-80) cc_final: 0.7595 (ptm-80) REVERT: C 1115 LYS cc_start: 0.8032 (tppp) cc_final: 0.7734 (mmtt) REVERT: C 1140 LYS cc_start: 0.8708 (tttt) cc_final: 0.8406 (tttp) REVERT: C 1154 LYS cc_start: 0.8109 (mttt) cc_final: 0.7891 (mtmt) REVERT: C 1168 TYR cc_start: 0.6775 (OUTLIER) cc_final: 0.6175 (m-10) REVERT: D 251 LEU cc_start: 0.6303 (OUTLIER) cc_final: 0.6058 (tm) REVERT: D 254 GLU cc_start: 0.7029 (mt-10) cc_final: 0.6818 (mt-10) REVERT: D 355 MET cc_start: 0.4191 (tpp) cc_final: 0.3955 (mmm) REVERT: D 405 ARG cc_start: 0.7507 (tpt-90) cc_final: 0.7288 (ttt90) REVERT: D 462 GLN cc_start: 0.8480 (tp40) cc_final: 0.8097 (tp-100) REVERT: D 559 TRP cc_start: 0.8294 (m100) cc_final: 0.7870 (m100) REVERT: D 588 SER cc_start: 0.9130 (m) cc_final: 0.8915 (m) REVERT: D 612 ARG cc_start: 0.8483 (tpp80) cc_final: 0.8249 (tpp-160) REVERT: D 620 GLU cc_start: 0.8733 (mm-30) cc_final: 0.7614 (tt0) REVERT: D 629 GLU cc_start: 0.7770 (mm-30) cc_final: 0.7392 (mm-30) REVERT: D 635 GLU cc_start: 0.8159 (mt-10) cc_final: 0.7788 (mp0) REVERT: D 659 MET cc_start: 0.7408 (ttm) cc_final: 0.6989 (ttp) REVERT: D 711 ARG cc_start: 0.6384 (mpt-90) cc_final: 0.5864 (ptm-80) REVERT: D 856 LEU cc_start: 0.8127 (mp) cc_final: 0.7893 (mp) REVERT: D 877 LEU cc_start: 0.8779 (mp) cc_final: 0.8143 (tt) REVERT: D 983 MET cc_start: 0.8867 (mtm) cc_final: 0.8506 (mtm) REVERT: D 1032 ASN cc_start: 0.8915 (OUTLIER) cc_final: 0.8540 (m110) REVERT: D 1045 TYR cc_start: 0.8707 (t80) cc_final: 0.8500 (t80) REVERT: D 1056 LEU cc_start: 0.8354 (OUTLIER) cc_final: 0.8063 (mp) REVERT: D 1063 TYR cc_start: 0.8855 (t80) cc_final: 0.8523 (t80) REVERT: D 1067 ARG cc_start: 0.7860 (ptm-80) cc_final: 0.7561 (ptm-80) REVERT: D 1118 GLU cc_start: 0.8389 (tm-30) cc_final: 0.7909 (tm-30) REVERT: D 1140 LYS cc_start: 0.8682 (tttt) cc_final: 0.8385 (tttp) REVERT: D 1154 LYS cc_start: 0.8043 (mttt) cc_final: 0.7830 (mtmt) REVERT: D 1168 TYR cc_start: 0.6648 (OUTLIER) cc_final: 0.6110 (m-10) outliers start: 108 outliers final: 47 residues processed: 849 average time/residue: 0.2440 time to fit residues: 305.2299 Evaluate side-chains 578 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 516 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 688 THR Chi-restraints excluded: chain A residue 690 ILE Chi-restraints excluded: chain A residue 703 ILE Chi-restraints excluded: chain A residue 824 LEU Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 830 ARG Chi-restraints excluded: chain A residue 906 LEU Chi-restraints excluded: chain A residue 1032 ASN Chi-restraints excluded: chain A residue 1056 LEU Chi-restraints excluded: chain A residue 1075 LEU Chi-restraints excluded: chain A residue 1166 ARG Chi-restraints excluded: chain A residue 1168 TYR Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 615 LEU Chi-restraints excluded: chain B residue 688 THR Chi-restraints excluded: chain B residue 690 ILE Chi-restraints excluded: chain B residue 703 ILE Chi-restraints excluded: chain B residue 824 LEU Chi-restraints excluded: chain B residue 827 GLU Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 906 LEU Chi-restraints excluded: chain B residue 1032 ASN Chi-restraints excluded: chain B residue 1056 LEU Chi-restraints excluded: chain B residue 1166 ARG Chi-restraints excluded: chain B residue 1168 TYR Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 472 LEU Chi-restraints excluded: chain C residue 615 LEU Chi-restraints excluded: chain C residue 688 THR Chi-restraints excluded: chain C residue 690 ILE Chi-restraints excluded: chain C residue 703 ILE Chi-restraints excluded: chain C residue 824 LEU Chi-restraints excluded: chain C residue 829 LEU Chi-restraints excluded: chain C residue 830 ARG Chi-restraints excluded: chain C residue 906 LEU Chi-restraints excluded: chain C residue 1032 ASN Chi-restraints excluded: chain C residue 1056 LEU Chi-restraints excluded: chain C residue 1075 LEU Chi-restraints excluded: chain C residue 1166 ARG Chi-restraints excluded: chain C residue 1168 TYR Chi-restraints excluded: chain D residue 251 LEU Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain D residue 472 LEU Chi-restraints excluded: chain D residue 615 LEU Chi-restraints excluded: chain D residue 688 THR Chi-restraints excluded: chain D residue 690 ILE Chi-restraints excluded: chain D residue 703 ILE Chi-restraints excluded: chain D residue 824 LEU Chi-restraints excluded: chain D residue 829 LEU Chi-restraints excluded: chain D residue 830 ARG Chi-restraints excluded: chain D residue 906 LEU Chi-restraints excluded: chain D residue 1032 ASN Chi-restraints excluded: chain D residue 1056 LEU Chi-restraints excluded: chain D residue 1075 LEU Chi-restraints excluded: chain D residue 1166 ARG Chi-restraints excluded: chain D residue 1168 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 0.9980 chunk 298 optimal weight: 2.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 ASN ** A 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 173 HIS ** A 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 260 GLN A 419 GLN ** A 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 673 GLN A 977 GLN A1084 HIS A1128 HIS B 165 HIS B 173 HIS ** B 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 419 GLN ** B 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 673 GLN B1084 HIS B1128 HIS B1161 GLN C 116 ASN C 165 HIS C 173 HIS ** C 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 260 GLN C 419 GLN ** C 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 673 GLN C 977 GLN C1014 GLN C1084 HIS C1128 HIS C1131 ASN C1161 GLN D 116 ASN D 165 HIS D 173 HIS ** D 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 260 GLN D 419 GLN ** D 447 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 673 GLN D 786 ASN D 977 GLN D1014 GLN D1037 ASN D1084 HIS D1128 HIS D1161 GLN Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.215985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.143784 restraints weight = 34956.066| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 2.61 r_work: 0.3122 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.2918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 30396 Z= 0.265 Angle : 0.831 10.045 41236 Z= 0.410 Chirality : 0.045 0.250 4660 Planarity : 0.008 0.107 5152 Dihedral : 9.790 59.631 5055 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.75 % Favored : 92.14 % Rotamer: Outliers : 5.87 % Allowed : 13.14 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -3.68 (0.12), residues: 3640 helix: -1.76 (0.09), residues: 2388 sheet: -4.73 (0.20), residues: 208 loop : -3.17 (0.16), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 474 TYR 0.018 0.002 TYR A 464 PHE 0.031 0.003 PHE A 797 TRP 0.034 0.003 TRP A 152 HIS 0.008 0.002 HIS B 774 Details of bonding type rmsd covalent geometry : bond 0.00618 (30392) covalent geometry : angle 0.83056 (41236) hydrogen bonds : bond 0.04422 ( 1544) hydrogen bonds : angle 5.33835 ( 4572) Misc. bond : bond 0.00036 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 744 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 179 poor density : 565 time to evaluate : 1.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 ARG cc_start: 0.7189 (ttp80) cc_final: 0.6801 (ttp80) REVERT: A 260 GLN cc_start: 0.7652 (OUTLIER) cc_final: 0.6993 (mt0) REVERT: A 355 MET cc_start: 0.4376 (tpp) cc_final: 0.4075 (mmm) REVERT: A 410 GLN cc_start: 0.7610 (OUTLIER) cc_final: 0.7258 (mp10) REVERT: A 578 PHE cc_start: 0.9378 (m-10) cc_final: 0.9104 (m-80) REVERT: A 588 SER cc_start: 0.9190 (m) cc_final: 0.8917 (m) REVERT: A 659 MET cc_start: 0.7935 (ttm) cc_final: 0.7545 (ttp) REVERT: A 711 ARG cc_start: 0.6257 (mpt-90) cc_final: 0.5825 (ptm-80) REVERT: A 819 PHE cc_start: 0.8881 (t80) cc_final: 0.8620 (t80) REVERT: A 827 GLU cc_start: 0.8097 (tp30) cc_final: 0.7487 (tp30) REVERT: A 852 LEU cc_start: 0.7335 (mm) cc_final: 0.7035 (mt) REVERT: A 877 LEU cc_start: 0.8912 (mp) cc_final: 0.8432 (tt) REVERT: A 983 MET cc_start: 0.9068 (mtm) cc_final: 0.8860 (mtp) REVERT: A 1015 TYR cc_start: 0.8710 (t80) cc_final: 0.8246 (t80) REVERT: A 1032 ASN cc_start: 0.9148 (OUTLIER) cc_final: 0.8827 (m110) REVERT: A 1063 TYR cc_start: 0.9249 (t80) cc_final: 0.8819 (t80) REVERT: A 1067 ARG cc_start: 0.8555 (ptm-80) cc_final: 0.8067 (ptm-80) REVERT: A 1075 LEU cc_start: 0.8417 (OUTLIER) cc_final: 0.8142 (mt) REVERT: A 1080 ILE cc_start: 0.8719 (tt) cc_final: 0.8496 (tt) REVERT: A 1154 LYS cc_start: 0.8295 (mttt) cc_final: 0.8057 (mtpt) REVERT: A 1166 ARG cc_start: 0.7639 (OUTLIER) cc_final: 0.7352 (tpt-90) REVERT: B 355 MET cc_start: 0.4197 (tpp) cc_final: 0.3744 (mmm) REVERT: B 398 ARG cc_start: 0.7238 (ttt-90) cc_final: 0.6918 (ttt-90) REVERT: B 410 GLN cc_start: 0.7533 (OUTLIER) cc_final: 0.7193 (mp10) REVERT: B 462 GLN cc_start: 0.8371 (tp40) cc_final: 0.8169 (tp-100) REVERT: B 588 SER cc_start: 0.9223 (m) cc_final: 0.8934 (m) REVERT: B 599 MET cc_start: 0.8131 (ptm) cc_final: 0.7683 (ptm) REVERT: B 615 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8617 (tp) REVERT: B 659 MET cc_start: 0.7954 (ttm) cc_final: 0.7409 (ttp) REVERT: B 711 ARG cc_start: 0.6371 (mpt-90) cc_final: 0.6071 (ptm-80) REVERT: B 819 PHE cc_start: 0.8878 (t80) cc_final: 0.8609 (t80) REVERT: B 827 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7828 (tp30) REVERT: B 852 LEU cc_start: 0.7392 (mm) cc_final: 0.7104 (mt) REVERT: B 877 LEU cc_start: 0.8933 (mp) cc_final: 0.8425 (tt) REVERT: B 915 GLN cc_start: 0.8635 (tt0) cc_final: 0.8192 (mp10) REVERT: B 983 MET cc_start: 0.9078 (mtm) cc_final: 0.8854 (mtp) REVERT: B 1015 TYR cc_start: 0.8714 (t80) cc_final: 0.8250 (t80) REVERT: B 1032 ASN cc_start: 0.9155 (OUTLIER) cc_final: 0.8838 (m110) REVERT: B 1063 TYR cc_start: 0.9276 (t80) cc_final: 0.8831 (t80) REVERT: B 1067 ARG cc_start: 0.8572 (ptm-80) cc_final: 0.8021 (ptm-80) REVERT: B 1080 ILE cc_start: 0.8700 (tt) cc_final: 0.8350 (tt) REVERT: B 1154 LYS cc_start: 0.8293 (mttt) cc_final: 0.8081 (mtpt) REVERT: B 1166 ARG cc_start: 0.7629 (OUTLIER) cc_final: 0.7339 (tpt-90) REVERT: C 260 GLN cc_start: 0.7645 (OUTLIER) cc_final: 0.6980 (mt0) REVERT: C 355 MET cc_start: 0.4353 (tpp) cc_final: 0.3678 (mmm) REVERT: C 410 GLN cc_start: 0.7554 (OUTLIER) cc_final: 0.7196 (mp10) REVERT: C 588 SER cc_start: 0.9187 (m) cc_final: 0.8917 (m) REVERT: C 611 ARG cc_start: 0.8038 (mtm110) cc_final: 0.7735 (mtm110) REVERT: C 659 MET cc_start: 0.7930 (ttm) cc_final: 0.7352 (ttp) REVERT: C 711 ARG cc_start: 0.6402 (mpt-90) cc_final: 0.6065 (ptm-80) REVERT: C 819 PHE cc_start: 0.8877 (t80) cc_final: 0.8614 (t80) REVERT: C 827 GLU cc_start: 0.8113 (tp30) cc_final: 0.7493 (tp30) REVERT: C 852 LEU cc_start: 0.7339 (mm) cc_final: 0.7041 (mt) REVERT: C 877 LEU cc_start: 0.8934 (mp) cc_final: 0.8451 (tt) REVERT: C 915 GLN cc_start: 0.8612 (tt0) cc_final: 0.8158 (mp10) REVERT: C 983 MET cc_start: 0.9070 (mtm) cc_final: 0.8850 (mtp) REVERT: C 1015 TYR cc_start: 0.8714 (t80) cc_final: 0.8255 (t80) REVERT: C 1032 ASN cc_start: 0.9148 (OUTLIER) cc_final: 0.8831 (m110) REVERT: C 1063 TYR cc_start: 0.9241 (t80) cc_final: 0.8787 (t80) REVERT: C 1067 ARG cc_start: 0.8547 (ptm-80) cc_final: 0.8029 (ptm-80) REVERT: C 1075 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.8166 (mt) REVERT: C 1080 ILE cc_start: 0.8726 (tt) cc_final: 0.8495 (tt) REVERT: C 1154 LYS cc_start: 0.8286 (mttt) cc_final: 0.8069 (mtpt) REVERT: C 1166 ARG cc_start: 0.7508 (OUTLIER) cc_final: 0.7120 (tpt-90) REVERT: D 260 GLN cc_start: 0.7624 (OUTLIER) cc_final: 0.6979 (mt0) REVERT: D 355 MET cc_start: 0.4533 (tpp) cc_final: 0.4277 (mmm) REVERT: D 410 GLN cc_start: 0.7636 (OUTLIER) cc_final: 0.7314 (mp10) REVERT: D 578 PHE cc_start: 0.9392 (m-10) cc_final: 0.9107 (m-80) REVERT: D 588 SER cc_start: 0.9189 (m) cc_final: 0.8906 (m) REVERT: D 659 MET cc_start: 0.7938 (ttm) cc_final: 0.7550 (ttp) REVERT: D 711 ARG cc_start: 0.6411 (mpt-90) cc_final: 0.6100 (ptm-80) REVERT: D 819 PHE cc_start: 0.8887 (t80) cc_final: 0.8627 (t80) REVERT: D 827 GLU cc_start: 0.8045 (tp30) cc_final: 0.7832 (tp30) REVERT: D 852 LEU cc_start: 0.7315 (mm) cc_final: 0.7016 (mt) REVERT: D 877 LEU cc_start: 0.8929 (mp) cc_final: 0.8402 (tt) REVERT: D 983 MET cc_start: 0.9083 (mtm) cc_final: 0.8864 (mtp) REVERT: D 1015 TYR cc_start: 0.8710 (t80) cc_final: 0.8241 (t80) REVERT: D 1032 ASN cc_start: 0.9142 (OUTLIER) cc_final: 0.8817 (m110) REVERT: D 1056 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.8308 (mp) REVERT: D 1063 TYR cc_start: 0.9247 (t80) cc_final: 0.8806 (t80) REVERT: D 1067 ARG cc_start: 0.8528 (ptm-80) cc_final: 0.8029 (ptm-80) REVERT: D 1075 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.8153 (mt) REVERT: D 1080 ILE cc_start: 0.8765 (tt) cc_final: 0.8564 (tt) REVERT: D 1154 LYS cc_start: 0.8276 (mttt) cc_final: 0.8075 (mtpt) REVERT: D 1166 ARG cc_start: 0.7441 (OUTLIER) cc_final: 0.7071 (tpt-90) outliers start: 179 outliers final: 70 residues processed: 704 average time/residue: 0.2209 time to fit residues: 239.8698 Evaluate side-chains 602 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 511 time to evaluate : 1.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 260 GLN Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 410 GLN Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 474 ARG Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 587 SER Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 690 ILE Chi-restraints excluded: chain A residue 699 CYS Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 812 SER Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 904 VAL Chi-restraints excluded: chain A residue 993 CYS Chi-restraints excluded: chain A residue 1017 ASN Chi-restraints excluded: chain A residue 1032 ASN Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1054 SER Chi-restraints excluded: chain A residue 1075 LEU Chi-restraints excluded: chain A residue 1166 ARG Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 410 GLN Chi-restraints excluded: chain B residue 474 ARG Chi-restraints excluded: chain B residue 564 LEU Chi-restraints excluded: chain B residue 587 SER Chi-restraints excluded: chain B residue 615 LEU Chi-restraints excluded: chain B residue 643 LEU Chi-restraints excluded: chain B residue 690 ILE Chi-restraints excluded: chain B residue 709 THR Chi-restraints excluded: chain B residue 812 SER Chi-restraints excluded: chain B residue 827 GLU Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 904 VAL Chi-restraints excluded: chain B residue 972 LEU Chi-restraints excluded: chain B residue 993 CYS Chi-restraints excluded: chain B residue 1017 ASN Chi-restraints excluded: chain B residue 1032 ASN Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1166 ARG Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 260 GLN Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 407 ASP Chi-restraints excluded: chain C residue 410 GLN Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 474 ARG Chi-restraints excluded: chain C residue 564 LEU Chi-restraints excluded: chain C residue 587 SER Chi-restraints excluded: chain C residue 643 LEU Chi-restraints excluded: chain C residue 690 ILE Chi-restraints excluded: chain C residue 709 THR Chi-restraints excluded: chain C residue 812 SER Chi-restraints excluded: chain C residue 876 LEU Chi-restraints excluded: chain C residue 883 LEU Chi-restraints excluded: chain C residue 904 VAL Chi-restraints excluded: chain C residue 972 LEU Chi-restraints excluded: chain C residue 993 CYS Chi-restraints excluded: chain C residue 1032 ASN Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain C residue 1054 SER Chi-restraints excluded: chain C residue 1075 LEU Chi-restraints excluded: chain C residue 1166 ARG Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 260 GLN Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 315 LEU Chi-restraints excluded: chain D residue 407 ASP Chi-restraints excluded: chain D residue 410 GLN Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 474 ARG Chi-restraints excluded: chain D residue 564 LEU Chi-restraints excluded: chain D residue 587 SER Chi-restraints excluded: chain D residue 690 ILE Chi-restraints excluded: chain D residue 699 CYS Chi-restraints excluded: chain D residue 709 THR Chi-restraints excluded: chain D residue 812 SER Chi-restraints excluded: chain D residue 825 LEU Chi-restraints excluded: chain D residue 876 LEU Chi-restraints excluded: chain D residue 883 LEU Chi-restraints excluded: chain D residue 904 VAL Chi-restraints excluded: chain D residue 972 LEU Chi-restraints excluded: chain D residue 993 CYS Chi-restraints excluded: chain D residue 1032 ASN Chi-restraints excluded: chain D residue 1034 LEU Chi-restraints excluded: chain D residue 1054 SER Chi-restraints excluded: chain D residue 1056 LEU Chi-restraints excluded: chain D residue 1075 LEU Chi-restraints excluded: chain D residue 1166 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 335 optimal weight: 0.5980 chunk 157 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 chunk 180 optimal weight: 2.9990 chunk 272 optimal weight: 0.0870 chunk 118 optimal weight: 0.5980 chunk 69 optimal weight: 0.2980 chunk 6 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 chunk 303 optimal weight: 10.0000 chunk 30 optimal weight: 1.9990 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 HIS A1061 GLN A1084 HIS A1161 GLN B 116 ASN B1037 ASN B1061 GLN B1084 HIS C 165 HIS C 260 GLN C1061 GLN C1084 HIS D 165 HIS ** D 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1061 GLN D1084 HIS D1170 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.214966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.143836 restraints weight = 34943.264| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 2.34 r_work: 0.3211 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.3585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 30396 Z= 0.138 Angle : 0.688 9.863 41236 Z= 0.335 Chirality : 0.041 0.263 4660 Planarity : 0.006 0.081 5152 Dihedral : 8.187 58.890 4965 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 4.91 % Allowed : 14.91 % Favored : 80.18 % 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: -2.27 (0.13), residues: 3640 helix: -0.53 (0.10), residues: 2384 sheet: -4.47 (0.22), residues: 184 loop : -3.02 (0.16), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 474 TYR 0.016 0.001 TYR A 256 PHE 0.023 0.001 PHE D 414 TRP 0.028 0.002 TRP D 152 HIS 0.005 0.001 HIS C 774 Details of bonding type rmsd covalent geometry : bond 0.00309 (30392) covalent geometry : angle 0.68831 (41236) hydrogen bonds : bond 0.03721 ( 1544) hydrogen bonds : angle 4.63406 ( 4572) Misc. bond : bond 0.00034 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 737 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 587 time to evaluate : 1.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 257 ILE cc_start: 0.6942 (OUTLIER) cc_final: 0.6632 (tp) REVERT: A 410 GLN cc_start: 0.7469 (OUTLIER) cc_final: 0.7121 (mp10) REVERT: A 454 PHE cc_start: 0.8241 (t80) cc_final: 0.7973 (t80) REVERT: A 629 GLU cc_start: 0.8263 (mm-30) cc_final: 0.7923 (mm-30) REVERT: A 659 MET cc_start: 0.7954 (ttm) cc_final: 0.7589 (ttp) REVERT: A 770 ARG cc_start: 0.7880 (mtp85) cc_final: 0.6704 (ttp80) REVERT: A 819 PHE cc_start: 0.8822 (t80) cc_final: 0.8551 (t80) REVERT: A 852 LEU cc_start: 0.7499 (OUTLIER) cc_final: 0.7222 (mt) REVERT: A 911 THR cc_start: 0.9248 (t) cc_final: 0.8670 (m) REVERT: A 972 LEU cc_start: 0.9384 (OUTLIER) cc_final: 0.9138 (mp) REVERT: A 983 MET cc_start: 0.9159 (mtm) cc_final: 0.8910 (mtp) REVERT: A 1015 TYR cc_start: 0.8679 (t80) cc_final: 0.8158 (t80) REVERT: A 1032 ASN cc_start: 0.9135 (OUTLIER) cc_final: 0.8856 (m110) REVERT: A 1042 MET cc_start: 0.9328 (mtp) cc_final: 0.9092 (mtm) REVERT: A 1063 TYR cc_start: 0.9271 (t80) cc_final: 0.8822 (t80) REVERT: A 1067 ARG cc_start: 0.8561 (ptm-80) cc_final: 0.7900 (ptm-80) REVERT: A 1075 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.8068 (mt) REVERT: A 1154 LYS cc_start: 0.8477 (mttt) cc_final: 0.8236 (mtpt) REVERT: B 142 LEU cc_start: 0.8337 (tp) cc_final: 0.8104 (tp) REVERT: B 355 MET cc_start: 0.4731 (tpp) cc_final: 0.4048 (mmm) REVERT: B 398 ARG cc_start: 0.7411 (ttt-90) cc_final: 0.7123 (ttt180) REVERT: B 410 GLN cc_start: 0.7572 (OUTLIER) cc_final: 0.7215 (mp10) REVERT: B 578 PHE cc_start: 0.9381 (m-80) cc_final: 0.9161 (m-80) REVERT: B 588 SER cc_start: 0.9200 (m) cc_final: 0.8961 (m) REVERT: B 599 MET cc_start: 0.7922 (ptm) cc_final: 0.7598 (ptm) REVERT: B 611 ARG cc_start: 0.8250 (mtm110) cc_final: 0.7943 (mtm110) REVERT: B 629 GLU cc_start: 0.8167 (mm-30) cc_final: 0.7858 (mm-30) REVERT: B 659 MET cc_start: 0.8022 (ttm) cc_final: 0.7627 (ttp) REVERT: B 770 ARG cc_start: 0.7736 (mtp85) cc_final: 0.6629 (ttp80) REVERT: B 819 PHE cc_start: 0.8833 (t80) cc_final: 0.8554 (t80) REVERT: B 852 LEU cc_start: 0.7458 (OUTLIER) cc_final: 0.7218 (mt) REVERT: B 915 GLN cc_start: 0.8748 (tt0) cc_final: 0.8198 (mp10) REVERT: B 1015 TYR cc_start: 0.8668 (t80) cc_final: 0.8136 (t80) REVERT: B 1032 ASN cc_start: 0.9144 (OUTLIER) cc_final: 0.8871 (m110) REVERT: B 1042 MET cc_start: 0.9270 (mtp) cc_final: 0.9031 (mtm) REVERT: B 1063 TYR cc_start: 0.9292 (t80) cc_final: 0.8785 (t80) REVERT: B 1067 ARG cc_start: 0.8624 (ptm-80) cc_final: 0.7956 (ptm-80) REVERT: B 1080 ILE cc_start: 0.8582 (tt) cc_final: 0.8198 (tt) REVERT: B 1154 LYS cc_start: 0.8502 (mttt) cc_final: 0.8292 (mtpt) REVERT: C 144 ARG cc_start: 0.7171 (ttp80) cc_final: 0.6806 (ptm-80) REVERT: C 257 ILE cc_start: 0.6918 (OUTLIER) cc_final: 0.6644 (tp) REVERT: C 260 GLN cc_start: 0.7462 (OUTLIER) cc_final: 0.7063 (mt0) REVERT: C 410 GLN cc_start: 0.7519 (OUTLIER) cc_final: 0.7189 (mp10) REVERT: C 629 GLU cc_start: 0.8236 (mm-30) cc_final: 0.7910 (mm-30) REVERT: C 659 MET cc_start: 0.7948 (ttm) cc_final: 0.7553 (ttp) REVERT: C 770 ARG cc_start: 0.7838 (mtp85) cc_final: 0.6659 (ttp80) REVERT: C 819 PHE cc_start: 0.8826 (t80) cc_final: 0.8550 (t80) REVERT: C 852 LEU cc_start: 0.7480 (OUTLIER) cc_final: 0.7211 (mt) REVERT: C 911 THR cc_start: 0.9263 (t) cc_final: 0.8677 (m) REVERT: C 915 GLN cc_start: 0.8744 (tt0) cc_final: 0.8201 (mp10) REVERT: C 1015 TYR cc_start: 0.8686 (t80) cc_final: 0.8158 (t80) REVERT: C 1032 ASN cc_start: 0.9144 (OUTLIER) cc_final: 0.8864 (m110) REVERT: C 1042 MET cc_start: 0.9306 (mtp) cc_final: 0.9074 (mtm) REVERT: C 1063 TYR cc_start: 0.9267 (t80) cc_final: 0.8808 (t80) REVERT: C 1067 ARG cc_start: 0.8562 (ptm-80) cc_final: 0.7911 (ptm-80) REVERT: C 1075 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.8074 (mt) REVERT: C 1154 LYS cc_start: 0.8484 (mttt) cc_final: 0.8243 (mtpt) REVERT: D 144 ARG cc_start: 0.7173 (ttp80) cc_final: 0.6807 (ptm-80) REVERT: D 410 GLN cc_start: 0.7495 (OUTLIER) cc_final: 0.7120 (mp10) REVERT: D 454 PHE cc_start: 0.8232 (t80) cc_final: 0.8029 (t80) REVERT: D 588 SER cc_start: 0.9170 (m) cc_final: 0.8929 (m) REVERT: D 629 GLU cc_start: 0.8269 (mm-30) cc_final: 0.7998 (mm-30) REVERT: D 659 MET cc_start: 0.7936 (ttm) cc_final: 0.7552 (ttp) REVERT: D 770 ARG cc_start: 0.7850 (mtp85) cc_final: 0.6684 (ttp80) REVERT: D 819 PHE cc_start: 0.8831 (t80) cc_final: 0.8569 (t80) REVERT: D 827 GLU cc_start: 0.8046 (tp30) cc_final: 0.7798 (tp30) REVERT: D 852 LEU cc_start: 0.7445 (OUTLIER) cc_final: 0.7189 (mt) REVERT: D 1015 TYR cc_start: 0.8669 (t80) cc_final: 0.8136 (t80) REVERT: D 1032 ASN cc_start: 0.9149 (OUTLIER) cc_final: 0.8872 (m110) REVERT: D 1056 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8330 (mp) REVERT: D 1063 TYR cc_start: 0.9266 (t80) cc_final: 0.8801 (t80) REVERT: D 1067 ARG cc_start: 0.8572 (ptm-80) cc_final: 0.7930 (ptm-80) REVERT: D 1075 LEU cc_start: 0.8345 (OUTLIER) cc_final: 0.8083 (mt) REVERT: D 1129 LYS cc_start: 0.9090 (ttpt) cc_final: 0.8827 (ttmt) outliers start: 150 outliers final: 51 residues processed: 678 average time/residue: 0.2269 time to fit residues: 235.3318 Evaluate side-chains 568 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 497 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 410 GLN Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 690 ILE Chi-restraints excluded: chain A residue 794 LEU Chi-restraints excluded: chain A residue 812 SER Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 904 VAL Chi-restraints excluded: chain A residue 972 LEU Chi-restraints excluded: chain A residue 1032 ASN Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1054 SER Chi-restraints excluded: chain A residue 1075 LEU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 410 GLN Chi-restraints excluded: chain B residue 509 MET Chi-restraints excluded: chain B residue 587 SER Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 690 ILE Chi-restraints excluded: chain B residue 812 SER Chi-restraints excluded: chain B residue 827 GLU Chi-restraints excluded: chain B residue 852 LEU Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 904 VAL Chi-restraints excluded: chain B residue 1032 ASN Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1166 ARG Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 257 ILE Chi-restraints excluded: chain C residue 260 GLN Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 407 ASP Chi-restraints excluded: chain C residue 410 GLN Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 509 MET Chi-restraints excluded: chain C residue 595 LEU Chi-restraints excluded: chain C residue 626 LEU Chi-restraints excluded: chain C residue 690 ILE Chi-restraints excluded: chain C residue 794 LEU Chi-restraints excluded: chain C residue 812 SER Chi-restraints excluded: chain C residue 852 LEU Chi-restraints excluded: chain C residue 876 LEU Chi-restraints excluded: chain C residue 904 VAL Chi-restraints excluded: chain C residue 1032 ASN Chi-restraints excluded: chain C residue 1054 SER Chi-restraints excluded: chain C residue 1075 LEU Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 407 ASP Chi-restraints excluded: chain D residue 410 GLN Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 587 SER Chi-restraints excluded: chain D residue 595 LEU Chi-restraints excluded: chain D residue 690 ILE Chi-restraints excluded: chain D residue 789 SER Chi-restraints excluded: chain D residue 812 SER Chi-restraints excluded: chain D residue 852 LEU Chi-restraints excluded: chain D residue 876 LEU Chi-restraints excluded: chain D residue 904 VAL Chi-restraints excluded: chain D residue 1032 ASN Chi-restraints excluded: chain D residue 1034 LEU Chi-restraints excluded: chain D residue 1054 SER Chi-restraints excluded: chain D residue 1056 LEU Chi-restraints excluded: chain D residue 1075 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 263 optimal weight: 5.9990 chunk 228 optimal weight: 3.9990 chunk 244 optimal weight: 0.7980 chunk 54 optimal weight: 0.6980 chunk 214 optimal weight: 9.9990 chunk 365 optimal weight: 0.6980 chunk 113 optimal weight: 3.9990 chunk 198 optimal weight: 9.9990 chunk 112 optimal weight: 6.9990 chunk 105 optimal weight: 20.0000 chunk 118 optimal weight: 8.9990 overall best weight: 2.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 HIS A 260 GLN A 786 ASN A 915 GLN A1061 GLN A1128 HIS A1161 GLN B1161 GLN C 786 ASN C1061 GLN C1161 GLN D 260 GLN D 915 GLN D1061 GLN D1128 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.209551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.134302 restraints weight = 34416.571| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 2.14 r_work: 0.3054 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.4266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.080 30396 Z= 0.288 Angle : 0.797 12.507 41236 Z= 0.386 Chirality : 0.046 0.249 4660 Planarity : 0.006 0.126 5152 Dihedral : 8.390 59.468 4951 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.16 % Favored : 91.84 % Rotamer: Outliers : 6.26 % Allowed : 15.10 % Favored : 78.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -1.91 (0.13), residues: 3640 helix: -0.24 (0.10), residues: 2384 sheet: -4.13 (0.28), residues: 192 loop : -2.95 (0.16), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 113 TYR 0.014 0.002 TYR C 256 PHE 0.023 0.002 PHE B 797 TRP 0.023 0.002 TRP D 152 HIS 0.009 0.002 HIS D 908 Details of bonding type rmsd covalent geometry : bond 0.00678 (30392) covalent geometry : angle 0.79715 (41236) hydrogen bonds : bond 0.04329 ( 1544) hydrogen bonds : angle 4.83120 ( 4572) Misc. bond : bond 0.00364 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 725 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 191 poor density : 534 time to evaluate : 1.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 410 GLN cc_start: 0.7499 (OUTLIER) cc_final: 0.7122 (mp10) REVERT: A 412 GLU cc_start: 0.7210 (tp30) cc_final: 0.6982 (tm-30) REVERT: A 433 LEU cc_start: 0.9011 (mt) cc_final: 0.8787 (mt) REVERT: A 711 ARG cc_start: 0.6465 (mmm-85) cc_final: 0.5843 (ptm-80) REVERT: A 770 ARG cc_start: 0.7956 (mtp85) cc_final: 0.6741 (ttp80) REVERT: A 852 LEU cc_start: 0.7528 (OUTLIER) cc_final: 0.7281 (mt) REVERT: A 877 LEU cc_start: 0.8971 (mp) cc_final: 0.8524 (tt) REVERT: A 900 MET cc_start: 0.9384 (mtp) cc_final: 0.9093 (mtp) REVERT: A 972 LEU cc_start: 0.9367 (OUTLIER) cc_final: 0.9000 (mp) REVERT: A 983 MET cc_start: 0.9306 (mtm) cc_final: 0.9077 (mtp) REVERT: A 1015 TYR cc_start: 0.8893 (t80) cc_final: 0.8412 (t80) REVERT: A 1067 ARG cc_start: 0.8695 (ptm-80) cc_final: 0.8198 (ptm-80) REVERT: A 1075 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8136 (mt) REVERT: A 1154 LYS cc_start: 0.8570 (mttt) cc_final: 0.8276 (mtpt) REVERT: B 142 LEU cc_start: 0.8500 (tp) cc_final: 0.8250 (tp) REVERT: B 355 MET cc_start: 0.4581 (tpp) cc_final: 0.4053 (mmm) REVERT: B 410 GLN cc_start: 0.7470 (OUTLIER) cc_final: 0.7198 (mp10) REVERT: B 578 PHE cc_start: 0.9367 (m-80) cc_final: 0.9081 (m-80) REVERT: B 588 SER cc_start: 0.9259 (m) cc_final: 0.9015 (m) REVERT: B 711 ARG cc_start: 0.8012 (OUTLIER) cc_final: 0.7802 (ptm-80) REVERT: B 770 ARG cc_start: 0.7901 (mtp85) cc_final: 0.6647 (ttp80) REVERT: B 877 LEU cc_start: 0.8959 (mp) cc_final: 0.8501 (tt) REVERT: B 900 MET cc_start: 0.9371 (mtp) cc_final: 0.9082 (mtp) REVERT: B 915 GLN cc_start: 0.8788 (tt0) cc_final: 0.8170 (mp10) REVERT: B 1015 TYR cc_start: 0.8881 (t80) cc_final: 0.8251 (t80) REVERT: B 1067 ARG cc_start: 0.8704 (ptm-80) cc_final: 0.8197 (ptm-80) REVERT: B 1080 ILE cc_start: 0.8633 (tt) cc_final: 0.8280 (tt) REVERT: B 1119 ARG cc_start: 0.7971 (ptm-80) cc_final: 0.7757 (ptm160) REVERT: B 1128 HIS cc_start: 0.8855 (OUTLIER) cc_final: 0.8199 (m-70) REVERT: B 1134 LEU cc_start: 0.9038 (mt) cc_final: 0.8772 (mm) REVERT: B 1149 LYS cc_start: 0.8920 (mtpp) cc_final: 0.8693 (mtpt) REVERT: C 410 GLN cc_start: 0.7572 (OUTLIER) cc_final: 0.7232 (mp10) REVERT: C 447 HIS cc_start: 0.7122 (OUTLIER) cc_final: 0.6883 (m170) REVERT: C 570 ASN cc_start: 0.9042 (t0) cc_final: 0.8837 (t0) REVERT: C 711 ARG cc_start: 0.8025 (OUTLIER) cc_final: 0.7792 (ptm-80) REVERT: C 770 ARG cc_start: 0.7921 (mtp85) cc_final: 0.6709 (ttp80) REVERT: C 827 GLU cc_start: 0.8261 (tp30) cc_final: 0.7968 (tp30) REVERT: C 852 LEU cc_start: 0.7532 (OUTLIER) cc_final: 0.7315 (mt) REVERT: C 877 LEU cc_start: 0.8979 (mp) cc_final: 0.8530 (tt) REVERT: C 900 MET cc_start: 0.9368 (mtp) cc_final: 0.9070 (mtp) REVERT: C 915 GLN cc_start: 0.8827 (tt0) cc_final: 0.8206 (mp10) REVERT: C 1015 TYR cc_start: 0.8886 (t80) cc_final: 0.8264 (t80) REVERT: C 1067 ARG cc_start: 0.8706 (ptm-80) cc_final: 0.8207 (ptm-80) REVERT: C 1075 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8153 (mt) REVERT: C 1119 ARG cc_start: 0.7983 (ptm-80) cc_final: 0.7770 (ptm160) REVERT: C 1128 HIS cc_start: 0.8896 (OUTLIER) cc_final: 0.8205 (m-70) REVERT: C 1154 LYS cc_start: 0.8574 (mttt) cc_final: 0.8363 (mtpt) REVERT: D 284 MET cc_start: 0.6196 (OUTLIER) cc_final: 0.5995 (mtt) REVERT: D 410 GLN cc_start: 0.7427 (OUTLIER) cc_final: 0.7127 (mp10) REVERT: D 474 ARG cc_start: 0.6202 (OUTLIER) cc_final: 0.5330 (tpp-160) REVERT: D 588 SER cc_start: 0.9255 (m) cc_final: 0.9008 (m) REVERT: D 611 ARG cc_start: 0.8215 (mtm180) cc_final: 0.7949 (mtm180) REVERT: D 711 ARG cc_start: 0.7979 (OUTLIER) cc_final: 0.7722 (ptm-80) REVERT: D 770 ARG cc_start: 0.7950 (mtp85) cc_final: 0.6714 (ttp80) REVERT: D 827 GLU cc_start: 0.8200 (tp30) cc_final: 0.7717 (tp30) REVERT: D 852 LEU cc_start: 0.7510 (OUTLIER) cc_final: 0.7261 (mt) REVERT: D 877 LEU cc_start: 0.8931 (mp) cc_final: 0.8496 (tt) REVERT: D 900 MET cc_start: 0.9381 (mtp) cc_final: 0.9092 (mtp) REVERT: D 972 LEU cc_start: 0.9362 (OUTLIER) cc_final: 0.8989 (mp) REVERT: D 1015 TYR cc_start: 0.8876 (t80) cc_final: 0.8247 (t80) REVERT: D 1067 ARG cc_start: 0.8703 (ptm-80) cc_final: 0.8203 (ptm-80) REVERT: D 1075 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.8140 (mt) REVERT: D 1119 ARG cc_start: 0.8006 (ptm-80) cc_final: 0.7797 (ptm160) outliers start: 191 outliers final: 103 residues processed: 659 average time/residue: 0.2180 time to fit residues: 222.0167 Evaluate side-chains 625 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 502 time to evaluate : 1.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 260 GLN Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 410 GLN Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 509 MET Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 690 ILE Chi-restraints excluded: chain A residue 699 CYS Chi-restraints excluded: chain A residue 708 ILE Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 794 LEU Chi-restraints excluded: chain A residue 812 SER Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 883 LEU Chi-restraints excluded: chain A residue 904 VAL Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 972 LEU Chi-restraints excluded: chain A residue 993 CYS Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1054 SER Chi-restraints excluded: chain A residue 1075 LEU Chi-restraints excluded: chain A residue 1122 LEU Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 407 ASP Chi-restraints excluded: chain B residue 410 GLN Chi-restraints excluded: chain B residue 474 ARG Chi-restraints excluded: chain B residue 509 MET Chi-restraints excluded: chain B residue 560 SER Chi-restraints excluded: chain B residue 587 SER Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 690 ILE Chi-restraints excluded: chain B residue 708 ILE Chi-restraints excluded: chain B residue 709 THR Chi-restraints excluded: chain B residue 711 ARG Chi-restraints excluded: chain B residue 812 SER Chi-restraints excluded: chain B residue 827 GLU Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 904 VAL Chi-restraints excluded: chain B residue 911 THR Chi-restraints excluded: chain B residue 963 LEU Chi-restraints excluded: chain B residue 972 LEU Chi-restraints excluded: chain B residue 993 CYS Chi-restraints excluded: chain B residue 1017 ASN Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1054 SER Chi-restraints excluded: chain B residue 1122 LEU Chi-restraints excluded: chain B residue 1128 HIS Chi-restraints excluded: chain B residue 1166 ARG Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 407 ASP Chi-restraints excluded: chain C residue 410 GLN Chi-restraints excluded: chain C residue 447 HIS Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 509 MET Chi-restraints excluded: chain C residue 595 LEU Chi-restraints excluded: chain C residue 611 ARG Chi-restraints excluded: chain C residue 626 LEU Chi-restraints excluded: chain C residue 690 ILE Chi-restraints excluded: chain C residue 708 ILE Chi-restraints excluded: chain C residue 709 THR Chi-restraints excluded: chain C residue 711 ARG Chi-restraints excluded: chain C residue 794 LEU Chi-restraints excluded: chain C residue 812 SER Chi-restraints excluded: chain C residue 852 LEU Chi-restraints excluded: chain C residue 869 LEU Chi-restraints excluded: chain C residue 876 LEU Chi-restraints excluded: chain C residue 883 LEU Chi-restraints excluded: chain C residue 904 VAL Chi-restraints excluded: chain C residue 912 VAL Chi-restraints excluded: chain C residue 963 LEU Chi-restraints excluded: chain C residue 972 LEU Chi-restraints excluded: chain C residue 993 CYS Chi-restraints excluded: chain C residue 1017 ASN Chi-restraints excluded: chain C residue 1054 SER Chi-restraints excluded: chain C residue 1075 LEU Chi-restraints excluded: chain C residue 1122 LEU Chi-restraints excluded: chain C residue 1128 HIS Chi-restraints excluded: chain D residue 260 GLN Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain D residue 284 MET Chi-restraints excluded: chain D residue 407 ASP Chi-restraints excluded: chain D residue 410 GLN Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 474 ARG Chi-restraints excluded: chain D residue 509 MET Chi-restraints excluded: chain D residue 560 SER Chi-restraints excluded: chain D residue 587 SER Chi-restraints excluded: chain D residue 595 LEU Chi-restraints excluded: chain D residue 626 LEU Chi-restraints excluded: chain D residue 690 ILE Chi-restraints excluded: chain D residue 699 CYS Chi-restraints excluded: chain D residue 708 ILE Chi-restraints excluded: chain D residue 709 THR Chi-restraints excluded: chain D residue 711 ARG Chi-restraints excluded: chain D residue 789 SER Chi-restraints excluded: chain D residue 794 LEU Chi-restraints excluded: chain D residue 812 SER Chi-restraints excluded: chain D residue 852 LEU Chi-restraints excluded: chain D residue 869 LEU Chi-restraints excluded: chain D residue 876 LEU Chi-restraints excluded: chain D residue 883 LEU Chi-restraints excluded: chain D residue 904 VAL Chi-restraints excluded: chain D residue 912 VAL Chi-restraints excluded: chain D residue 963 LEU Chi-restraints excluded: chain D residue 972 LEU Chi-restraints excluded: chain D residue 993 CYS Chi-restraints excluded: chain D residue 1034 LEU Chi-restraints excluded: chain D residue 1054 SER Chi-restraints excluded: chain D residue 1075 LEU Chi-restraints excluded: chain D residue 1122 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 56 optimal weight: 0.5980 chunk 154 optimal weight: 0.7980 chunk 86 optimal weight: 10.0000 chunk 71 optimal weight: 0.6980 chunk 244 optimal weight: 1.9990 chunk 257 optimal weight: 0.6980 chunk 24 optimal weight: 0.5980 chunk 273 optimal weight: 0.8980 chunk 348 optimal weight: 0.9980 chunk 136 optimal weight: 4.9990 chunk 146 optimal weight: 0.0970 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 889 HIS A1061 GLN A1128 HIS B 419 GLN B 889 HIS C 419 GLN C 889 HIS C1061 GLN D 419 GLN D 889 HIS D1128 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.216410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.145556 restraints weight = 34376.644| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 2.11 r_work: 0.3171 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.4561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 30396 Z= 0.134 Angle : 0.668 10.093 41236 Z= 0.320 Chirality : 0.040 0.228 4660 Planarity : 0.005 0.097 5152 Dihedral : 7.306 59.909 4941 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 4.98 % Allowed : 16.58 % Favored : 78.44 % 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: -1.19 (0.14), residues: 3640 helix: 0.34 (0.10), residues: 2392 sheet: -3.49 (0.36), residues: 144 loop : -2.90 (0.16), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 612 TYR 0.007 0.001 TYR A1015 PHE 0.019 0.001 PHE A 414 TRP 0.029 0.002 TRP A 152 HIS 0.003 0.001 HIS C 774 Details of bonding type rmsd covalent geometry : bond 0.00300 (30392) covalent geometry : angle 0.66752 (41236) hydrogen bonds : bond 0.03514 ( 1544) hydrogen bonds : angle 4.37285 ( 4572) Misc. bond : bond 0.00305 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 693 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 541 time to evaluate : 0.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 410 GLN cc_start: 0.7573 (OUTLIER) cc_final: 0.7134 (mp10) REVERT: A 433 LEU cc_start: 0.8955 (mt) cc_final: 0.8721 (mp) REVERT: A 629 GLU cc_start: 0.8176 (mm-30) cc_final: 0.7917 (mm-30) REVERT: A 711 ARG cc_start: 0.6226 (mmm-85) cc_final: 0.5829 (ptm-80) REVERT: A 770 ARG cc_start: 0.7834 (mtp85) cc_final: 0.6726 (ttp80) REVERT: A 827 GLU cc_start: 0.8136 (tp30) cc_final: 0.7792 (tp30) REVERT: A 911 THR cc_start: 0.9208 (t) cc_final: 0.8624 (m) REVERT: A 972 LEU cc_start: 0.9365 (OUTLIER) cc_final: 0.9147 (mp) REVERT: A 1015 TYR cc_start: 0.8650 (t80) cc_final: 0.8087 (t80) REVERT: A 1042 MET cc_start: 0.9333 (mtp) cc_final: 0.9105 (mtm) REVERT: A 1063 TYR cc_start: 0.9259 (t80) cc_final: 0.8828 (t80) REVERT: A 1067 ARG cc_start: 0.8496 (ptm-80) cc_final: 0.7982 (ptm-80) REVERT: A 1075 LEU cc_start: 0.8342 (OUTLIER) cc_final: 0.8084 (mt) REVERT: B 142 LEU cc_start: 0.8558 (tp) cc_final: 0.8287 (tp) REVERT: B 186 MET cc_start: 0.7418 (mpt) cc_final: 0.6975 (mpt) REVERT: B 355 MET cc_start: 0.4906 (tpp) cc_final: 0.4440 (mmm) REVERT: B 410 GLN cc_start: 0.7591 (OUTLIER) cc_final: 0.7239 (mp10) REVERT: B 581 MET cc_start: 0.8869 (mmt) cc_final: 0.8588 (tpp) REVERT: B 588 SER cc_start: 0.9119 (m) cc_final: 0.8862 (m) REVERT: B 629 GLU cc_start: 0.8147 (mm-30) cc_final: 0.7913 (mm-30) REVERT: B 640 ARG cc_start: 0.8688 (mtp180) cc_final: 0.8312 (mtp180) REVERT: B 711 ARG cc_start: 0.7883 (OUTLIER) cc_final: 0.7670 (ptm-80) REVERT: B 770 ARG cc_start: 0.7814 (mtp85) cc_final: 0.6685 (ttp80) REVERT: B 827 GLU cc_start: 0.8338 (tm-30) cc_final: 0.8024 (tp30) REVERT: B 830 ARG cc_start: 0.7944 (ttp80) cc_final: 0.7654 (tmm-80) REVERT: B 915 GLN cc_start: 0.8681 (tt0) cc_final: 0.8128 (mp10) REVERT: B 1015 TYR cc_start: 0.8651 (t80) cc_final: 0.7992 (t80) REVERT: B 1042 MET cc_start: 0.9327 (mtp) cc_final: 0.9107 (mtm) REVERT: B 1063 TYR cc_start: 0.9288 (t80) cc_final: 0.8817 (t80) REVERT: B 1067 ARG cc_start: 0.8591 (ptm-80) cc_final: 0.8053 (ptm-80) REVERT: B 1080 ILE cc_start: 0.8559 (tt) cc_final: 0.8190 (tt) REVERT: B 1128 HIS cc_start: 0.8823 (OUTLIER) cc_final: 0.8347 (m-70) REVERT: B 1149 LYS cc_start: 0.8899 (mtpp) cc_final: 0.8671 (mtpt) REVERT: C 410 GLN cc_start: 0.7578 (OUTLIER) cc_final: 0.7144 (mp10) REVERT: C 433 LEU cc_start: 0.8948 (mt) cc_final: 0.8729 (mp) REVERT: C 570 ASN cc_start: 0.9020 (t0) cc_final: 0.8711 (t0) REVERT: C 629 GLU cc_start: 0.8237 (mm-30) cc_final: 0.7987 (mm-30) REVERT: C 640 ARG cc_start: 0.8710 (mtp180) cc_final: 0.8348 (mtp180) REVERT: C 711 ARG cc_start: 0.7793 (OUTLIER) cc_final: 0.7554 (ptm-80) REVERT: C 770 ARG cc_start: 0.7789 (mtp85) cc_final: 0.6663 (ttp80) REVERT: C 827 GLU cc_start: 0.8115 (tp30) cc_final: 0.7773 (tp30) REVERT: C 911 THR cc_start: 0.9202 (t) cc_final: 0.8623 (m) REVERT: C 915 GLN cc_start: 0.8708 (tt0) cc_final: 0.8178 (mp10) REVERT: C 941 LEU cc_start: 0.9300 (OUTLIER) cc_final: 0.9098 (mt) REVERT: C 1015 TYR cc_start: 0.8631 (t80) cc_final: 0.7966 (t80) REVERT: C 1042 MET cc_start: 0.9301 (mtp) cc_final: 0.9073 (mtm) REVERT: C 1063 TYR cc_start: 0.9267 (t80) cc_final: 0.8836 (t80) REVERT: C 1067 ARG cc_start: 0.8545 (ptm-80) cc_final: 0.8033 (ptm-80) REVERT: C 1075 LEU cc_start: 0.8382 (OUTLIER) cc_final: 0.8112 (mt) REVERT: C 1128 HIS cc_start: 0.8797 (OUTLIER) cc_final: 0.8303 (m-70) REVERT: C 1130 GLU cc_start: 0.8580 (mt-10) cc_final: 0.8239 (mm-30) REVERT: C 1154 LYS cc_start: 0.8555 (mttt) cc_final: 0.8209 (mtpt) REVERT: D 334 ARG cc_start: 0.3672 (mmt-90) cc_final: 0.3174 (mmm-85) REVERT: D 410 GLN cc_start: 0.7615 (OUTLIER) cc_final: 0.7213 (mp10) REVERT: D 474 ARG cc_start: 0.6311 (OUTLIER) cc_final: 0.5391 (tpp-160) REVERT: D 581 MET cc_start: 0.8899 (mmt) cc_final: 0.8599 (tpp) REVERT: D 588 SER cc_start: 0.9141 (m) cc_final: 0.8895 (m) REVERT: D 640 ARG cc_start: 0.8699 (mtp180) cc_final: 0.8327 (mtp180) REVERT: D 770 ARG cc_start: 0.7849 (mtp85) cc_final: 0.6699 (ttp80) REVERT: D 827 GLU cc_start: 0.8116 (tp30) cc_final: 0.7641 (tp30) REVERT: D 985 VAL cc_start: 0.9000 (t) cc_final: 0.8780 (m) REVERT: D 1015 TYR cc_start: 0.8610 (t80) cc_final: 0.7929 (t80) REVERT: D 1034 LEU cc_start: 0.9201 (OUTLIER) cc_final: 0.8957 (tp) REVERT: D 1063 TYR cc_start: 0.9277 (t80) cc_final: 0.8807 (t80) REVERT: D 1067 ARG cc_start: 0.8599 (ptm-80) cc_final: 0.8099 (ptm-80) REVERT: D 1075 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.8166 (mt) outliers start: 152 outliers final: 86 residues processed: 634 average time/residue: 0.2129 time to fit residues: 212.8834 Evaluate side-chains 594 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 493 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 410 GLN Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 690 ILE Chi-restraints excluded: chain A residue 708 ILE Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 812 SER Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 898 ASP Chi-restraints excluded: chain A residue 904 VAL Chi-restraints excluded: chain A residue 922 ILE Chi-restraints excluded: chain A residue 972 LEU Chi-restraints excluded: chain A residue 1054 SER Chi-restraints excluded: chain A residue 1075 LEU Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 410 GLN Chi-restraints excluded: chain B residue 474 ARG Chi-restraints excluded: chain B residue 560 SER Chi-restraints excluded: chain B residue 587 SER Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 690 ILE Chi-restraints excluded: chain B residue 708 ILE Chi-restraints excluded: chain B residue 709 THR Chi-restraints excluded: chain B residue 711 ARG Chi-restraints excluded: chain B residue 812 SER Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 898 ASP Chi-restraints excluded: chain B residue 904 VAL Chi-restraints excluded: chain B residue 911 THR Chi-restraints excluded: chain B residue 922 ILE Chi-restraints excluded: chain B residue 963 LEU Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1054 SER Chi-restraints excluded: chain B residue 1128 HIS Chi-restraints excluded: chain B residue 1166 ARG Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 407 ASP Chi-restraints excluded: chain C residue 410 GLN Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain C residue 473 ILE Chi-restraints excluded: chain C residue 595 LEU Chi-restraints excluded: chain C residue 626 LEU Chi-restraints excluded: chain C residue 690 ILE Chi-restraints excluded: chain C residue 708 ILE Chi-restraints excluded: chain C residue 709 THR Chi-restraints excluded: chain C residue 711 ARG Chi-restraints excluded: chain C residue 794 LEU Chi-restraints excluded: chain C residue 812 SER Chi-restraints excluded: chain C residue 829 LEU Chi-restraints excluded: chain C residue 876 LEU Chi-restraints excluded: chain C residue 883 LEU Chi-restraints excluded: chain C residue 898 ASP Chi-restraints excluded: chain C residue 904 VAL Chi-restraints excluded: chain C residue 922 ILE Chi-restraints excluded: chain C residue 941 LEU Chi-restraints excluded: chain C residue 1054 SER Chi-restraints excluded: chain C residue 1075 LEU Chi-restraints excluded: chain C residue 1128 HIS Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 407 ASP Chi-restraints excluded: chain D residue 410 GLN Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 474 ARG Chi-restraints excluded: chain D residue 560 SER Chi-restraints excluded: chain D residue 587 SER Chi-restraints excluded: chain D residue 595 LEU Chi-restraints excluded: chain D residue 626 LEU Chi-restraints excluded: chain D residue 690 ILE Chi-restraints excluded: chain D residue 708 ILE Chi-restraints excluded: chain D residue 709 THR Chi-restraints excluded: chain D residue 789 SER Chi-restraints excluded: chain D residue 812 SER Chi-restraints excluded: chain D residue 829 LEU Chi-restraints excluded: chain D residue 876 LEU Chi-restraints excluded: chain D residue 883 LEU Chi-restraints excluded: chain D residue 904 VAL Chi-restraints excluded: chain D residue 922 ILE Chi-restraints excluded: chain D residue 1034 LEU Chi-restraints excluded: chain D residue 1054 SER Chi-restraints excluded: chain D residue 1075 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 296 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 354 optimal weight: 2.9990 chunk 6 optimal weight: 8.9990 chunk 32 optimal weight: 0.9990 chunk 116 optimal weight: 0.0980 chunk 50 optimal weight: 1.9990 chunk 7 optimal weight: 10.0000 chunk 224 optimal weight: 6.9990 chunk 332 optimal weight: 0.6980 chunk 122 optimal weight: 6.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1128 HIS D 419 GLN D1128 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.213704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.141460 restraints weight = 34137.041| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 2.12 r_work: 0.3107 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.4800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 30396 Z= 0.189 Angle : 0.697 10.128 41236 Z= 0.334 Chirality : 0.042 0.248 4660 Planarity : 0.005 0.101 5152 Dihedral : 7.305 59.115 4938 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % Rotamer: Outliers : 5.18 % Allowed : 17.23 % Favored : 77.59 % 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: -0.94 (0.14), residues: 3640 helix: 0.47 (0.11), residues: 2408 sheet: -3.26 (0.39), residues: 144 loop : -2.68 (0.17), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 612 TYR 0.009 0.001 TYR C 968 PHE 0.017 0.002 PHE B 578 TRP 0.029 0.002 TRP A 691 HIS 0.005 0.001 HIS B 908 Details of bonding type rmsd covalent geometry : bond 0.00442 (30392) covalent geometry : angle 0.69688 (41236) hydrogen bonds : bond 0.03824 ( 1544) hydrogen bonds : angle 4.47727 ( 4572) Misc. bond : bond 0.00254 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 675 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 517 time to evaluate : 1.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 MET cc_start: 0.7350 (mpt) cc_final: 0.7029 (mpt) REVERT: A 410 GLN cc_start: 0.7507 (OUTLIER) cc_final: 0.7111 (mp10) REVERT: A 433 LEU cc_start: 0.9046 (mt) cc_final: 0.8843 (mp) REVERT: A 629 GLU cc_start: 0.8165 (mm-30) cc_final: 0.7926 (mm-30) REVERT: A 711 ARG cc_start: 0.6387 (mmm-85) cc_final: 0.5880 (ptm-80) REVERT: A 770 ARG cc_start: 0.7893 (mtp85) cc_final: 0.6710 (ttp80) REVERT: A 827 GLU cc_start: 0.8158 (tp30) cc_final: 0.7822 (tp30) REVERT: A 1015 TYR cc_start: 0.8787 (t80) cc_final: 0.8278 (t80) REVERT: A 1063 TYR cc_start: 0.9288 (t80) cc_final: 0.8885 (t80) REVERT: A 1067 ARG cc_start: 0.8624 (ptm-80) cc_final: 0.8117 (ptm-80) REVERT: A 1072 ARG cc_start: 0.8779 (ttm170) cc_final: 0.8398 (mtt180) REVERT: A 1075 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.8158 (mt) REVERT: A 1130 GLU cc_start: 0.8591 (mt-10) cc_final: 0.8250 (mm-30) REVERT: B 142 LEU cc_start: 0.8571 (tp) cc_final: 0.8354 (tp) REVERT: B 186 MET cc_start: 0.7339 (mpt) cc_final: 0.6912 (mpt) REVERT: B 248 ARG cc_start: 0.5801 (ttp80) cc_final: 0.5460 (ptp90) REVERT: B 355 MET cc_start: 0.4764 (tpp) cc_final: 0.4201 (mmm) REVERT: B 410 GLN cc_start: 0.7569 (OUTLIER) cc_final: 0.7183 (mp10) REVERT: B 433 LEU cc_start: 0.9015 (OUTLIER) cc_final: 0.8498 (mp) REVERT: B 578 PHE cc_start: 0.9350 (m-80) cc_final: 0.9123 (m-80) REVERT: B 588 SER cc_start: 0.9155 (m) cc_final: 0.8903 (m) REVERT: B 629 GLU cc_start: 0.8188 (mm-30) cc_final: 0.7952 (mm-30) REVERT: B 640 ARG cc_start: 0.8713 (mtp180) cc_final: 0.8291 (mtp180) REVERT: B 770 ARG cc_start: 0.7848 (mtp85) cc_final: 0.6710 (ttp80) REVERT: B 827 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.7948 (tp30) REVERT: B 830 ARG cc_start: 0.7997 (ttp80) cc_final: 0.7673 (tmm-80) REVERT: B 915 GLN cc_start: 0.8736 (tt0) cc_final: 0.8169 (mp10) REVERT: B 1015 TYR cc_start: 0.8761 (t80) cc_final: 0.8105 (t80) REVERT: B 1063 TYR cc_start: 0.9303 (t80) cc_final: 0.8869 (t80) REVERT: B 1067 ARG cc_start: 0.8627 (ptm-80) cc_final: 0.8097 (ptm-80) REVERT: B 1080 ILE cc_start: 0.8597 (tt) cc_final: 0.8246 (tt) REVERT: B 1128 HIS cc_start: 0.8891 (OUTLIER) cc_final: 0.8348 (m-70) REVERT: B 1130 GLU cc_start: 0.8605 (mt-10) cc_final: 0.8221 (mm-30) REVERT: B 1136 ARG cc_start: 0.8337 (mtm110) cc_final: 0.8083 (mtm110) REVERT: B 1149 LYS cc_start: 0.8898 (mtpp) cc_final: 0.8653 (mtpt) REVERT: C 186 MET cc_start: 0.7353 (mpt) cc_final: 0.6978 (mpt) REVERT: C 410 GLN cc_start: 0.7700 (OUTLIER) cc_final: 0.7274 (mp10) REVERT: C 442 ARG cc_start: 0.8184 (ttm110) cc_final: 0.7937 (ttm170) REVERT: C 570 ASN cc_start: 0.9097 (t0) cc_final: 0.8727 (t0) REVERT: C 611 ARG cc_start: 0.8234 (OUTLIER) cc_final: 0.7801 (mtm110) REVERT: C 629 GLU cc_start: 0.8215 (mm-30) cc_final: 0.7974 (mm-30) REVERT: C 640 ARG cc_start: 0.8755 (mtp180) cc_final: 0.8337 (mtp180) REVERT: C 711 ARG cc_start: 0.8017 (OUTLIER) cc_final: 0.7794 (ptm-80) REVERT: C 770 ARG cc_start: 0.7822 (mtp85) cc_final: 0.6690 (ttp80) REVERT: C 827 GLU cc_start: 0.8156 (tp30) cc_final: 0.7832 (tp30) REVERT: C 915 GLN cc_start: 0.8767 (tt0) cc_final: 0.8208 (mp10) REVERT: C 1015 TYR cc_start: 0.8734 (t80) cc_final: 0.8034 (t80) REVERT: C 1063 TYR cc_start: 0.9281 (t80) cc_final: 0.8881 (t80) REVERT: C 1067 ARG cc_start: 0.8625 (ptm-80) cc_final: 0.8111 (ptm-80) REVERT: C 1072 ARG cc_start: 0.8793 (ttm170) cc_final: 0.8411 (mtt180) REVERT: C 1075 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8176 (mt) REVERT: C 1128 HIS cc_start: 0.8854 (OUTLIER) cc_final: 0.8297 (m-70) REVERT: C 1130 GLU cc_start: 0.8595 (mt-10) cc_final: 0.8256 (mm-30) REVERT: C 1154 LYS cc_start: 0.8540 (mttt) cc_final: 0.8231 (mtpt) REVERT: D 410 GLN cc_start: 0.7642 (OUTLIER) cc_final: 0.7306 (mp10) REVERT: D 474 ARG cc_start: 0.6316 (OUTLIER) cc_final: 0.5450 (tpp-160) REVERT: D 578 PHE cc_start: 0.9303 (m-80) cc_final: 0.9097 (m-80) REVERT: D 588 SER cc_start: 0.9165 (m) cc_final: 0.8911 (m) REVERT: D 640 ARG cc_start: 0.8749 (mtp180) cc_final: 0.8325 (mtp180) REVERT: D 770 ARG cc_start: 0.7863 (mtp85) cc_final: 0.6681 (ttp80) REVERT: D 827 GLU cc_start: 0.8163 (tp30) cc_final: 0.7839 (tp30) REVERT: D 1015 TYR cc_start: 0.8706 (t80) cc_final: 0.8004 (t80) REVERT: D 1063 TYR cc_start: 0.9304 (t80) cc_final: 0.8850 (t80) REVERT: D 1067 ARG cc_start: 0.8638 (ptm-80) cc_final: 0.8124 (ptm-80) REVERT: D 1075 LEU cc_start: 0.8441 (OUTLIER) cc_final: 0.8237 (mt) REVERT: D 1130 GLU cc_start: 0.8592 (mt-10) cc_final: 0.8257 (mm-30) outliers start: 158 outliers final: 110 residues processed: 613 average time/residue: 0.2223 time to fit residues: 210.1103 Evaluate side-chains 628 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 504 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 284 MET Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 410 GLN Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 637 ARG Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 690 ILE Chi-restraints excluded: chain A residue 699 CYS Chi-restraints excluded: chain A residue 708 ILE Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 794 LEU Chi-restraints excluded: chain A residue 812 SER Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 898 ASP Chi-restraints excluded: chain A residue 904 VAL Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 922 ILE Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 972 LEU Chi-restraints excluded: chain A residue 993 CYS Chi-restraints excluded: chain A residue 1054 SER Chi-restraints excluded: chain A residue 1075 LEU Chi-restraints excluded: chain A residue 1122 LEU Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 410 GLN Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 474 ARG Chi-restraints excluded: chain B residue 560 SER Chi-restraints excluded: chain B residue 587 SER Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain B residue 611 ARG Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 637 ARG Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 690 ILE Chi-restraints excluded: chain B residue 708 ILE Chi-restraints excluded: chain B residue 709 THR Chi-restraints excluded: chain B residue 812 SER Chi-restraints excluded: chain B residue 827 GLU Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 898 ASP Chi-restraints excluded: chain B residue 904 VAL Chi-restraints excluded: chain B residue 911 THR Chi-restraints excluded: chain B residue 922 ILE Chi-restraints excluded: chain B residue 963 LEU Chi-restraints excluded: chain B residue 993 CYS Chi-restraints excluded: chain B residue 1054 SER Chi-restraints excluded: chain B residue 1122 LEU Chi-restraints excluded: chain B residue 1128 HIS Chi-restraints excluded: chain B residue 1166 ARG Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 284 MET Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 410 GLN Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain C residue 473 ILE Chi-restraints excluded: chain C residue 595 LEU Chi-restraints excluded: chain C residue 611 ARG Chi-restraints excluded: chain C residue 626 LEU Chi-restraints excluded: chain C residue 675 LEU Chi-restraints excluded: chain C residue 690 ILE Chi-restraints excluded: chain C residue 708 ILE Chi-restraints excluded: chain C residue 709 THR Chi-restraints excluded: chain C residue 711 ARG Chi-restraints excluded: chain C residue 794 LEU Chi-restraints excluded: chain C residue 812 SER Chi-restraints excluded: chain C residue 876 LEU Chi-restraints excluded: chain C residue 883 LEU Chi-restraints excluded: chain C residue 898 ASP Chi-restraints excluded: chain C residue 904 VAL Chi-restraints excluded: chain C residue 912 VAL Chi-restraints excluded: chain C residue 922 ILE Chi-restraints excluded: chain C residue 963 LEU Chi-restraints excluded: chain C residue 993 CYS Chi-restraints excluded: chain C residue 1049 LYS Chi-restraints excluded: chain C residue 1054 SER Chi-restraints excluded: chain C residue 1075 LEU Chi-restraints excluded: chain C residue 1122 LEU Chi-restraints excluded: chain C residue 1128 HIS Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 410 GLN Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 463 LEU Chi-restraints excluded: chain D residue 474 ARG Chi-restraints excluded: chain D residue 560 SER Chi-restraints excluded: chain D residue 587 SER Chi-restraints excluded: chain D residue 595 LEU Chi-restraints excluded: chain D residue 626 LEU Chi-restraints excluded: chain D residue 675 LEU Chi-restraints excluded: chain D residue 690 ILE Chi-restraints excluded: chain D residue 699 CYS Chi-restraints excluded: chain D residue 708 ILE Chi-restraints excluded: chain D residue 709 THR Chi-restraints excluded: chain D residue 789 SER Chi-restraints excluded: chain D residue 794 LEU Chi-restraints excluded: chain D residue 812 SER Chi-restraints excluded: chain D residue 829 LEU Chi-restraints excluded: chain D residue 876 LEU Chi-restraints excluded: chain D residue 883 LEU Chi-restraints excluded: chain D residue 904 VAL Chi-restraints excluded: chain D residue 912 VAL Chi-restraints excluded: chain D residue 922 ILE Chi-restraints excluded: chain D residue 963 LEU Chi-restraints excluded: chain D residue 993 CYS Chi-restraints excluded: chain D residue 1049 LYS Chi-restraints excluded: chain D residue 1054 SER Chi-restraints excluded: chain D residue 1075 LEU Chi-restraints excluded: chain D residue 1122 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 271 optimal weight: 8.9990 chunk 118 optimal weight: 0.0670 chunk 305 optimal weight: 8.9990 chunk 113 optimal weight: 9.9990 chunk 333 optimal weight: 4.9990 chunk 65 optimal weight: 0.6980 chunk 44 optimal weight: 0.9980 chunk 193 optimal weight: 7.9990 chunk 5 optimal weight: 4.9990 chunk 213 optimal weight: 1.9990 chunk 251 optimal weight: 0.5980 overall best weight: 0.8720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1128 HIS D 419 GLN D 505 HIS D1128 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.209609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.134004 restraints weight = 34479.391| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 2.31 r_work: 0.3103 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.5011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 30396 Z= 0.157 Angle : 0.660 10.702 41236 Z= 0.318 Chirality : 0.041 0.200 4660 Planarity : 0.005 0.096 5152 Dihedral : 6.997 58.276 4938 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 5.01 % Allowed : 17.69 % Favored : 77.29 % 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: -0.66 (0.14), residues: 3640 helix: 0.70 (0.11), residues: 2404 sheet: -3.42 (0.33), residues: 192 loop : -2.49 (0.18), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1166 TYR 0.009 0.001 TYR B 103 PHE 0.018 0.001 PHE A 578 TRP 0.033 0.002 TRP A 691 HIS 0.003 0.001 HIS D 908 Details of bonding type rmsd covalent geometry : bond 0.00364 (30392) covalent geometry : angle 0.66014 (41236) hydrogen bonds : bond 0.03588 ( 1544) hydrogen bonds : angle 4.36584 ( 4572) Misc. bond : bond 0.00253 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 668 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 515 time to evaluate : 1.130 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 410 GLN cc_start: 0.7537 (OUTLIER) cc_final: 0.7089 (mp10) REVERT: A 629 GLU cc_start: 0.7989 (mm-30) cc_final: 0.7741 (mm-30) REVERT: A 711 ARG cc_start: 0.6326 (mmm-85) cc_final: 0.5857 (ptm-80) REVERT: A 770 ARG cc_start: 0.7775 (mtp85) cc_final: 0.6709 (ttp80) REVERT: A 827 GLU cc_start: 0.8028 (tp30) cc_final: 0.7749 (tp30) REVERT: A 972 LEU cc_start: 0.9354 (OUTLIER) cc_final: 0.9120 (mp) REVERT: A 1015 TYR cc_start: 0.8655 (t80) cc_final: 0.8136 (t80) REVERT: A 1063 TYR cc_start: 0.9242 (t80) cc_final: 0.8790 (t80) REVERT: A 1067 ARG cc_start: 0.8472 (ptm-80) cc_final: 0.7912 (ptm-80) REVERT: A 1075 LEU cc_start: 0.8250 (OUTLIER) cc_final: 0.8045 (mt) REVERT: A 1130 GLU cc_start: 0.8367 (mt-10) cc_final: 0.8086 (mm-30) REVERT: A 1156 ASP cc_start: 0.8352 (m-30) cc_final: 0.8121 (m-30) REVERT: B 186 MET cc_start: 0.7422 (mpt) cc_final: 0.6945 (mpt) REVERT: B 248 ARG cc_start: 0.5597 (ttp80) cc_final: 0.5329 (ptp90) REVERT: B 355 MET cc_start: 0.4758 (tpp) cc_final: 0.4278 (mmm) REVERT: B 410 GLN cc_start: 0.7564 (OUTLIER) cc_final: 0.7169 (mp10) REVERT: B 433 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8329 (mp) REVERT: B 588 SER cc_start: 0.9062 (m) cc_final: 0.8792 (m) REVERT: B 629 GLU cc_start: 0.7989 (mm-30) cc_final: 0.7728 (mm-30) REVERT: B 770 ARG cc_start: 0.7746 (mtp85) cc_final: 0.6688 (ttp80) REVERT: B 830 ARG cc_start: 0.7846 (ttp80) cc_final: 0.7640 (ttt-90) REVERT: B 915 GLN cc_start: 0.8615 (tt0) cc_final: 0.8128 (mp10) REVERT: B 1015 TYR cc_start: 0.8617 (t80) cc_final: 0.8007 (t80) REVERT: B 1063 TYR cc_start: 0.9250 (t80) cc_final: 0.8797 (t80) REVERT: B 1067 ARG cc_start: 0.8495 (ptm-80) cc_final: 0.7941 (ptm-80) REVERT: B 1080 ILE cc_start: 0.8474 (tt) cc_final: 0.8134 (tt) REVERT: B 1128 HIS cc_start: 0.8801 (OUTLIER) cc_final: 0.8268 (m-70) REVERT: B 1130 GLU cc_start: 0.8367 (mt-10) cc_final: 0.8100 (mm-30) REVERT: B 1136 ARG cc_start: 0.8225 (mtm110) cc_final: 0.7953 (mtm110) REVERT: B 1149 LYS cc_start: 0.8796 (mtpp) cc_final: 0.8542 (mtpt) REVERT: B 1156 ASP cc_start: 0.8571 (m-30) cc_final: 0.8234 (m-30) REVERT: C 410 GLN cc_start: 0.7673 (OUTLIER) cc_final: 0.7231 (mp10) REVERT: C 570 ASN cc_start: 0.9012 (t0) cc_final: 0.8634 (t0) REVERT: C 611 ARG cc_start: 0.8132 (OUTLIER) cc_final: 0.7702 (mtm110) REVERT: C 629 GLU cc_start: 0.8086 (mm-30) cc_final: 0.7837 (mm-30) REVERT: C 711 ARG cc_start: 0.8001 (OUTLIER) cc_final: 0.7799 (ptm-80) REVERT: C 770 ARG cc_start: 0.7742 (mtp85) cc_final: 0.6683 (ttp80) REVERT: C 827 GLU cc_start: 0.8034 (tp30) cc_final: 0.7760 (tp30) REVERT: C 915 GLN cc_start: 0.8582 (tt0) cc_final: 0.8111 (mp10) REVERT: C 1015 TYR cc_start: 0.8554 (t80) cc_final: 0.7810 (t80) REVERT: C 1063 TYR cc_start: 0.9233 (t80) cc_final: 0.8835 (t80) REVERT: C 1067 ARG cc_start: 0.8472 (ptm-80) cc_final: 0.7926 (ptm-80) REVERT: C 1128 HIS cc_start: 0.8760 (OUTLIER) cc_final: 0.8216 (m-70) REVERT: C 1156 ASP cc_start: 0.8367 (m-30) cc_final: 0.8136 (m-30) REVERT: D 410 GLN cc_start: 0.7686 (OUTLIER) cc_final: 0.7265 (mp10) REVERT: D 474 ARG cc_start: 0.6311 (tpp-160) cc_final: 0.5515 (tpp-160) REVERT: D 588 SER cc_start: 0.9084 (m) cc_final: 0.8812 (m) REVERT: D 640 ARG cc_start: 0.8693 (mtp180) cc_final: 0.8261 (mtp180) REVERT: D 770 ARG cc_start: 0.7769 (mtp85) cc_final: 0.6686 (ttp80) REVERT: D 827 GLU cc_start: 0.7969 (tp30) cc_final: 0.7627 (tp30) REVERT: D 830 ARG cc_start: 0.7839 (tmm-80) cc_final: 0.7493 (tmm-80) REVERT: D 1015 TYR cc_start: 0.8522 (t80) cc_final: 0.7783 (t80) REVERT: D 1063 TYR cc_start: 0.9252 (t80) cc_final: 0.8838 (t80) REVERT: D 1067 ARG cc_start: 0.8504 (ptm-80) cc_final: 0.7977 (ptm-80) REVERT: D 1156 ASP cc_start: 0.8281 (m-30) cc_final: 0.8064 (m-30) outliers start: 153 outliers final: 116 residues processed: 603 average time/residue: 0.2210 time to fit residues: 205.7781 Evaluate side-chains 619 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 492 time to evaluate : 1.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 284 MET Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 410 GLN Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 690 ILE Chi-restraints excluded: chain A residue 699 CYS Chi-restraints excluded: chain A residue 708 ILE Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 794 LEU Chi-restraints excluded: chain A residue 812 SER Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 898 ASP Chi-restraints excluded: chain A residue 904 VAL Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 922 ILE Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 972 LEU Chi-restraints excluded: chain A residue 993 CYS Chi-restraints excluded: chain A residue 1049 LYS Chi-restraints excluded: chain A residue 1054 SER Chi-restraints excluded: chain A residue 1075 LEU Chi-restraints excluded: chain A residue 1122 LEU Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 410 GLN Chi-restraints excluded: chain B residue 426 GLU Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 447 HIS Chi-restraints excluded: chain B residue 474 ARG Chi-restraints excluded: chain B residue 560 SER Chi-restraints excluded: chain B residue 587 SER Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain B residue 611 ARG Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 637 ARG Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 690 ILE Chi-restraints excluded: chain B residue 708 ILE Chi-restraints excluded: chain B residue 709 THR Chi-restraints excluded: chain B residue 812 SER Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 898 ASP Chi-restraints excluded: chain B residue 904 VAL Chi-restraints excluded: chain B residue 911 THR Chi-restraints excluded: chain B residue 922 ILE Chi-restraints excluded: chain B residue 963 LEU Chi-restraints excluded: chain B residue 1049 LYS Chi-restraints excluded: chain B residue 1054 SER Chi-restraints excluded: chain B residue 1122 LEU Chi-restraints excluded: chain B residue 1128 HIS Chi-restraints excluded: chain B residue 1166 ARG Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 284 MET Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 410 GLN Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain C residue 595 LEU Chi-restraints excluded: chain C residue 611 ARG Chi-restraints excluded: chain C residue 626 LEU Chi-restraints excluded: chain C residue 637 ARG Chi-restraints excluded: chain C residue 675 LEU Chi-restraints excluded: chain C residue 690 ILE Chi-restraints excluded: chain C residue 708 ILE Chi-restraints excluded: chain C residue 709 THR Chi-restraints excluded: chain C residue 711 ARG Chi-restraints excluded: chain C residue 794 LEU Chi-restraints excluded: chain C residue 812 SER Chi-restraints excluded: chain C residue 829 LEU Chi-restraints excluded: chain C residue 876 LEU Chi-restraints excluded: chain C residue 883 LEU Chi-restraints excluded: chain C residue 898 ASP Chi-restraints excluded: chain C residue 904 VAL Chi-restraints excluded: chain C residue 912 VAL Chi-restraints excluded: chain C residue 922 ILE Chi-restraints excluded: chain C residue 963 LEU Chi-restraints excluded: chain C residue 1049 LYS Chi-restraints excluded: chain C residue 1054 SER Chi-restraints excluded: chain C residue 1122 LEU Chi-restraints excluded: chain C residue 1128 HIS Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain D residue 284 MET Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 410 GLN Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 463 LEU Chi-restraints excluded: chain D residue 560 SER Chi-restraints excluded: chain D residue 587 SER Chi-restraints excluded: chain D residue 595 LEU Chi-restraints excluded: chain D residue 626 LEU Chi-restraints excluded: chain D residue 637 ARG Chi-restraints excluded: chain D residue 675 LEU Chi-restraints excluded: chain D residue 690 ILE Chi-restraints excluded: chain D residue 708 ILE Chi-restraints excluded: chain D residue 709 THR Chi-restraints excluded: chain D residue 789 SER Chi-restraints excluded: chain D residue 794 LEU Chi-restraints excluded: chain D residue 812 SER Chi-restraints excluded: chain D residue 829 LEU Chi-restraints excluded: chain D residue 876 LEU Chi-restraints excluded: chain D residue 883 LEU Chi-restraints excluded: chain D residue 904 VAL Chi-restraints excluded: chain D residue 912 VAL Chi-restraints excluded: chain D residue 922 ILE Chi-restraints excluded: chain D residue 963 LEU Chi-restraints excluded: chain D residue 1054 SER Chi-restraints excluded: chain D residue 1122 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 40 optimal weight: 0.5980 chunk 130 optimal weight: 6.9990 chunk 34 optimal weight: 0.0270 chunk 114 optimal weight: 20.0000 chunk 15 optimal weight: 0.8980 chunk 87 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 260 optimal weight: 0.5980 chunk 268 optimal weight: 1.9990 chunk 267 optimal weight: 0.5980 chunk 321 optimal weight: 4.9990 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 419 GLN A1128 HIS D1128 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.210698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.137812 restraints weight = 34761.566| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 2.53 r_work: 0.3116 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.5186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 30396 Z= 0.128 Angle : 0.661 14.911 41236 Z= 0.311 Chirality : 0.041 0.422 4660 Planarity : 0.005 0.088 5152 Dihedral : 6.606 59.149 4934 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 4.52 % Allowed : 18.45 % Favored : 77.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.14), residues: 3640 helix: 0.85 (0.11), residues: 2412 sheet: -3.43 (0.33), residues: 192 loop : -2.55 (0.18), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D1166 TYR 0.012 0.001 TYR B 818 PHE 0.025 0.001 PHE C 578 TRP 0.036 0.002 TRP A 691 HIS 0.003 0.001 HIS D 447 Details of bonding type rmsd covalent geometry : bond 0.00289 (30392) covalent geometry : angle 0.66140 (41236) hydrogen bonds : bond 0.03397 ( 1544) hydrogen bonds : angle 4.24761 ( 4572) Misc. bond : bond 0.00251 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 657 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 519 time to evaluate : 1.063 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 MET cc_start: 0.7238 (mpt) cc_final: 0.6662 (mpt) REVERT: A 410 GLN cc_start: 0.7494 (OUTLIER) cc_final: 0.7247 (mp10) REVERT: A 629 GLU cc_start: 0.7969 (mm-30) cc_final: 0.7711 (mm-30) REVERT: A 711 ARG cc_start: 0.6219 (mmm-85) cc_final: 0.5813 (ptm-80) REVERT: A 770 ARG cc_start: 0.7774 (mtp85) cc_final: 0.6683 (ttp80) REVERT: A 827 GLU cc_start: 0.8034 (tp30) cc_final: 0.7737 (tp30) REVERT: A 1015 TYR cc_start: 0.8617 (t80) cc_final: 0.8059 (t80) REVERT: A 1042 MET cc_start: 0.9241 (mtp) cc_final: 0.9028 (mtm) REVERT: A 1063 TYR cc_start: 0.9222 (t80) cc_final: 0.8771 (t80) REVERT: A 1067 ARG cc_start: 0.8441 (ptm-80) cc_final: 0.7875 (ptm-80) REVERT: A 1130 GLU cc_start: 0.8361 (mt-10) cc_final: 0.8128 (mm-30) REVERT: A 1156 ASP cc_start: 0.8280 (m-30) cc_final: 0.8033 (m-30) REVERT: B 186 MET cc_start: 0.7384 (mpt) cc_final: 0.6856 (mpt) REVERT: B 248 ARG cc_start: 0.5560 (ttp80) cc_final: 0.5299 (ptp90) REVERT: B 274 LEU cc_start: 0.7057 (OUTLIER) cc_final: 0.6824 (tp) REVERT: B 355 MET cc_start: 0.4612 (tpp) cc_final: 0.4181 (mmm) REVERT: B 410 GLN cc_start: 0.7566 (OUTLIER) cc_final: 0.7133 (mp10) REVERT: B 433 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8295 (mp) REVERT: B 588 SER cc_start: 0.9022 (m) cc_final: 0.8748 (m) REVERT: B 629 GLU cc_start: 0.7962 (mm-30) cc_final: 0.7702 (mm-30) REVERT: B 770 ARG cc_start: 0.7733 (mtp85) cc_final: 0.6627 (ttp80) REVERT: B 915 GLN cc_start: 0.8609 (tt0) cc_final: 0.8098 (mp10) REVERT: B 1015 TYR cc_start: 0.8584 (t80) cc_final: 0.7953 (t80) REVERT: B 1063 TYR cc_start: 0.9247 (t80) cc_final: 0.8869 (t80) REVERT: B 1067 ARG cc_start: 0.8481 (ptm-80) cc_final: 0.7930 (ptm-80) REVERT: B 1080 ILE cc_start: 0.8494 (tt) cc_final: 0.8111 (tt) REVERT: B 1128 HIS cc_start: 0.8693 (OUTLIER) cc_final: 0.8127 (m-70) REVERT: B 1130 GLU cc_start: 0.8370 (mt-10) cc_final: 0.8129 (mm-30) REVERT: B 1136 ARG cc_start: 0.8211 (mtm110) cc_final: 0.7964 (mtm110) REVERT: B 1149 LYS cc_start: 0.8800 (mtpp) cc_final: 0.8554 (mtpt) REVERT: C 186 MET cc_start: 0.7252 (mpt) cc_final: 0.6621 (mpt) REVERT: C 254 GLU cc_start: 0.6972 (mt-10) cc_final: 0.6439 (tm-30) REVERT: C 410 GLN cc_start: 0.7660 (OUTLIER) cc_final: 0.7125 (mp10) REVERT: C 629 GLU cc_start: 0.8000 (mm-30) cc_final: 0.7771 (mm-30) REVERT: C 711 ARG cc_start: 0.7991 (OUTLIER) cc_final: 0.7755 (ptm-80) REVERT: C 770 ARG cc_start: 0.7719 (mtp85) cc_final: 0.6666 (ttp80) REVERT: C 827 GLU cc_start: 0.8082 (tp30) cc_final: 0.7792 (tp30) REVERT: C 915 GLN cc_start: 0.8613 (tt0) cc_final: 0.8113 (mp10) REVERT: C 1015 TYR cc_start: 0.8451 (t80) cc_final: 0.7831 (t80) REVERT: C 1063 TYR cc_start: 0.9224 (t80) cc_final: 0.8739 (t80) REVERT: C 1067 ARG cc_start: 0.8405 (ptm-80) cc_final: 0.7796 (ptm-80) REVERT: C 1156 ASP cc_start: 0.8318 (m-30) cc_final: 0.7948 (m-30) REVERT: D 186 MET cc_start: 0.7276 (mpt) cc_final: 0.6623 (mpt) REVERT: D 334 ARG cc_start: 0.3136 (mmt-90) cc_final: 0.2819 (mmm-85) REVERT: D 410 GLN cc_start: 0.7660 (OUTLIER) cc_final: 0.7200 (mp10) REVERT: D 474 ARG cc_start: 0.6233 (tpp-160) cc_final: 0.5501 (tpp-160) REVERT: D 588 SER cc_start: 0.9061 (m) cc_final: 0.8818 (m) REVERT: D 770 ARG cc_start: 0.7738 (mtp85) cc_final: 0.6664 (ttp80) REVERT: D 827 GLU cc_start: 0.7986 (tp30) cc_final: 0.7658 (tp30) REVERT: D 830 ARG cc_start: 0.7714 (tmm-80) cc_final: 0.7452 (tmm-80) REVERT: D 1015 TYR cc_start: 0.8461 (t80) cc_final: 0.7860 (t80) REVERT: D 1063 TYR cc_start: 0.9235 (t80) cc_final: 0.8772 (t80) REVERT: D 1067 ARG cc_start: 0.8473 (ptm-80) cc_final: 0.7909 (ptm-80) REVERT: D 1154 LYS cc_start: 0.8364 (mttt) cc_final: 0.8136 (mtmt) outliers start: 138 outliers final: 102 residues processed: 596 average time/residue: 0.2119 time to fit residues: 194.9366 Evaluate side-chains 613 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 503 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 410 GLN Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 690 ILE Chi-restraints excluded: chain A residue 699 CYS Chi-restraints excluded: chain A residue 708 ILE Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 794 LEU Chi-restraints excluded: chain A residue 812 SER Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 904 VAL Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 922 ILE Chi-restraints excluded: chain A residue 927 MET Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 993 CYS Chi-restraints excluded: chain A residue 1054 SER Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 410 GLN Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 447 HIS Chi-restraints excluded: chain B residue 587 SER Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain B residue 611 ARG Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 637 ARG Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 690 ILE Chi-restraints excluded: chain B residue 708 ILE Chi-restraints excluded: chain B residue 709 THR Chi-restraints excluded: chain B residue 812 SER Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 898 ASP Chi-restraints excluded: chain B residue 904 VAL Chi-restraints excluded: chain B residue 911 THR Chi-restraints excluded: chain B residue 922 ILE Chi-restraints excluded: chain B residue 963 LEU Chi-restraints excluded: chain B residue 993 CYS Chi-restraints excluded: chain B residue 1054 SER Chi-restraints excluded: chain B residue 1128 HIS Chi-restraints excluded: chain B residue 1166 ARG Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 410 GLN Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 447 HIS Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain C residue 595 LEU Chi-restraints excluded: chain C residue 626 LEU Chi-restraints excluded: chain C residue 637 ARG Chi-restraints excluded: chain C residue 675 LEU Chi-restraints excluded: chain C residue 690 ILE Chi-restraints excluded: chain C residue 708 ILE Chi-restraints excluded: chain C residue 709 THR Chi-restraints excluded: chain C residue 711 ARG Chi-restraints excluded: chain C residue 794 LEU Chi-restraints excluded: chain C residue 812 SER Chi-restraints excluded: chain C residue 876 LEU Chi-restraints excluded: chain C residue 883 LEU Chi-restraints excluded: chain C residue 904 VAL Chi-restraints excluded: chain C residue 912 VAL Chi-restraints excluded: chain C residue 922 ILE Chi-restraints excluded: chain C residue 963 LEU Chi-restraints excluded: chain C residue 993 CYS Chi-restraints excluded: chain C residue 1054 SER Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain D residue 410 GLN Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 463 LEU Chi-restraints excluded: chain D residue 560 SER Chi-restraints excluded: chain D residue 587 SER Chi-restraints excluded: chain D residue 595 LEU Chi-restraints excluded: chain D residue 626 LEU Chi-restraints excluded: chain D residue 637 ARG Chi-restraints excluded: chain D residue 675 LEU Chi-restraints excluded: chain D residue 690 ILE Chi-restraints excluded: chain D residue 699 CYS Chi-restraints excluded: chain D residue 708 ILE Chi-restraints excluded: chain D residue 709 THR Chi-restraints excluded: chain D residue 789 SER Chi-restraints excluded: chain D residue 794 LEU Chi-restraints excluded: chain D residue 812 SER Chi-restraints excluded: chain D residue 876 LEU Chi-restraints excluded: chain D residue 904 VAL Chi-restraints excluded: chain D residue 912 VAL Chi-restraints excluded: chain D residue 922 ILE Chi-restraints excluded: chain D residue 927 MET Chi-restraints excluded: chain D residue 963 LEU Chi-restraints excluded: chain D residue 993 CYS Chi-restraints excluded: chain D residue 1054 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 67 optimal weight: 0.9990 chunk 302 optimal weight: 6.9990 chunk 303 optimal weight: 7.9990 chunk 187 optimal weight: 6.9990 chunk 77 optimal weight: 1.9990 chunk 238 optimal weight: 3.9990 chunk 150 optimal weight: 1.9990 chunk 220 optimal weight: 0.9980 chunk 252 optimal weight: 0.5980 chunk 331 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 505 HIS A1128 HIS C 505 HIS C1128 HIS D1128 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.213077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.137887 restraints weight = 34151.773| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 1.59 r_work: 0.3145 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.5286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 30396 Z= 0.205 Angle : 0.728 15.558 41236 Z= 0.344 Chirality : 0.044 0.397 4660 Planarity : 0.005 0.101 5152 Dihedral : 6.893 59.182 4932 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % Rotamer: Outliers : 4.36 % Allowed : 18.64 % Favored : 77.00 % 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: -0.56 (0.14), residues: 3640 helix: 0.72 (0.11), residues: 2404 sheet: -3.04 (0.40), residues: 144 loop : -2.46 (0.18), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1166 TYR 0.011 0.001 TYR B 103 PHE 0.029 0.002 PHE C 578 TRP 0.042 0.002 TRP A 691 HIS 0.006 0.001 HIS A 908 Details of bonding type rmsd covalent geometry : bond 0.00480 (30392) covalent geometry : angle 0.72777 (41236) hydrogen bonds : bond 0.03851 ( 1544) hydrogen bonds : angle 4.51366 ( 4572) Misc. bond : bond 0.00246 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 635 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 502 time to evaluate : 1.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 MET cc_start: 0.7398 (mpt) cc_final: 0.6783 (mpt) REVERT: A 410 GLN cc_start: 0.7676 (OUTLIER) cc_final: 0.7223 (mp10) REVERT: A 442 ARG cc_start: 0.8189 (ttm110) cc_final: 0.7978 (ttm170) REVERT: A 711 ARG cc_start: 0.6266 (mmm-85) cc_final: 0.5788 (ptm-80) REVERT: A 770 ARG cc_start: 0.7866 (mtp85) cc_final: 0.6726 (ttp80) REVERT: A 1015 TYR cc_start: 0.8777 (t80) cc_final: 0.8223 (t80) REVERT: A 1063 TYR cc_start: 0.9276 (t80) cc_final: 0.8832 (t80) REVERT: A 1067 ARG cc_start: 0.8549 (ptm-80) cc_final: 0.8013 (ptm-80) REVERT: A 1136 ARG cc_start: 0.8290 (mtm110) cc_final: 0.8058 (ttp-170) REVERT: B 186 MET cc_start: 0.7343 (mpt) cc_final: 0.6775 (mpt) REVERT: B 248 ARG cc_start: 0.5623 (ttp80) cc_final: 0.5341 (ptp90) REVERT: B 355 MET cc_start: 0.4687 (tpp) cc_final: 0.4365 (mmm) REVERT: B 403 TRP cc_start: 0.8989 (m-10) cc_final: 0.8760 (m-10) REVERT: B 410 GLN cc_start: 0.7582 (OUTLIER) cc_final: 0.7104 (mp10) REVERT: B 433 LEU cc_start: 0.8996 (OUTLIER) cc_final: 0.8487 (mp) REVERT: B 588 SER cc_start: 0.9126 (m) cc_final: 0.8867 (m) REVERT: B 629 GLU cc_start: 0.8057 (mm-30) cc_final: 0.7804 (mm-30) REVERT: B 770 ARG cc_start: 0.7820 (mtp85) cc_final: 0.6688 (ttp80) REVERT: B 915 GLN cc_start: 0.8705 (tt0) cc_final: 0.8163 (mp10) REVERT: B 1015 TYR cc_start: 0.8723 (t80) cc_final: 0.8075 (t80) REVERT: B 1063 TYR cc_start: 0.9279 (t80) cc_final: 0.8840 (t80) REVERT: B 1067 ARG cc_start: 0.8571 (ptm-80) cc_final: 0.8017 (ptm-80) REVERT: B 1080 ILE cc_start: 0.8587 (tt) cc_final: 0.8243 (tt) REVERT: B 1128 HIS cc_start: 0.8867 (OUTLIER) cc_final: 0.8255 (m-70) REVERT: B 1136 ARG cc_start: 0.8274 (mtm110) cc_final: 0.8025 (mtm110) REVERT: B 1149 LYS cc_start: 0.8843 (mtpp) cc_final: 0.8580 (mtpt) REVERT: B 1154 LYS cc_start: 0.8362 (mttt) cc_final: 0.8149 (mtpt) REVERT: B 1156 ASP cc_start: 0.8660 (m-30) cc_final: 0.8377 (m-30) REVERT: C 186 MET cc_start: 0.7408 (mpt) cc_final: 0.6740 (mpt) REVERT: C 410 GLN cc_start: 0.7576 (OUTLIER) cc_final: 0.7131 (mp10) REVERT: C 570 ASN cc_start: 0.8996 (t0) cc_final: 0.8689 (t0) REVERT: C 611 ARG cc_start: 0.8344 (mtm180) cc_final: 0.8067 (ptm160) REVERT: C 629 GLU cc_start: 0.8119 (mm-30) cc_final: 0.7888 (mm-30) REVERT: C 770 ARG cc_start: 0.7810 (mtp85) cc_final: 0.6696 (ttp80) REVERT: C 915 GLN cc_start: 0.8706 (tt0) cc_final: 0.8177 (mp10) REVERT: C 1015 TYR cc_start: 0.8685 (t80) cc_final: 0.7947 (t80) REVERT: C 1063 TYR cc_start: 0.9276 (t80) cc_final: 0.8837 (t80) REVERT: C 1067 ARG cc_start: 0.8551 (ptm-80) cc_final: 0.7990 (ptm-80) REVERT: C 1156 ASP cc_start: 0.8372 (m-30) cc_final: 0.8170 (m-30) REVERT: D 410 GLN cc_start: 0.7673 (OUTLIER) cc_final: 0.7179 (mp10) REVERT: D 474 ARG cc_start: 0.6447 (tpp-160) cc_final: 0.5851 (tpp-160) REVERT: D 581 MET cc_start: 0.8815 (mmt) cc_final: 0.8509 (tpp) REVERT: D 588 SER cc_start: 0.9140 (m) cc_final: 0.8876 (m) REVERT: D 632 ARG cc_start: 0.8688 (ttm110) cc_final: 0.8398 (ttm110) REVERT: D 770 ARG cc_start: 0.7801 (mtp85) cc_final: 0.6699 (ttp80) REVERT: D 827 GLU cc_start: 0.8072 (tp30) cc_final: 0.7755 (tp30) REVERT: D 1015 TYR cc_start: 0.8678 (t80) cc_final: 0.7954 (t80) REVERT: D 1063 TYR cc_start: 0.9281 (t80) cc_final: 0.8888 (t80) REVERT: D 1067 ARG cc_start: 0.8579 (ptm-80) cc_final: 0.8045 (ptm-80) outliers start: 133 outliers final: 108 residues processed: 584 average time/residue: 0.2214 time to fit residues: 199.1628 Evaluate side-chains 602 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 488 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 410 GLN Chi-restraints excluded: chain A residue 447 HIS Chi-restraints excluded: chain A residue 460 LEU Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 637 ARG Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 690 ILE Chi-restraints excluded: chain A residue 699 CYS Chi-restraints excluded: chain A residue 708 ILE Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 794 LEU Chi-restraints excluded: chain A residue 812 SER Chi-restraints excluded: chain A residue 829 LEU Chi-restraints excluded: chain A residue 863 SER Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 904 VAL Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 922 ILE Chi-restraints excluded: chain A residue 927 MET Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 993 CYS Chi-restraints excluded: chain A residue 1054 SER Chi-restraints excluded: chain A residue 1122 LEU Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 410 GLN Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 473 ILE Chi-restraints excluded: chain B residue 560 SER Chi-restraints excluded: chain B residue 587 SER Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain B residue 611 ARG Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 637 ARG Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 690 ILE Chi-restraints excluded: chain B residue 708 ILE Chi-restraints excluded: chain B residue 709 THR Chi-restraints excluded: chain B residue 812 SER Chi-restraints excluded: chain B residue 829 LEU Chi-restraints excluded: chain B residue 863 SER Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 898 ASP Chi-restraints excluded: chain B residue 904 VAL Chi-restraints excluded: chain B residue 911 THR Chi-restraints excluded: chain B residue 922 ILE Chi-restraints excluded: chain B residue 963 LEU Chi-restraints excluded: chain B residue 993 CYS Chi-restraints excluded: chain B residue 1054 SER Chi-restraints excluded: chain B residue 1122 LEU Chi-restraints excluded: chain B residue 1128 HIS Chi-restraints excluded: chain B residue 1166 ARG Chi-restraints excluded: chain C residue 275 LEU Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 410 GLN Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain C residue 473 ILE Chi-restraints excluded: chain C residue 595 LEU Chi-restraints excluded: chain C residue 598 VAL Chi-restraints excluded: chain C residue 626 LEU Chi-restraints excluded: chain C residue 637 ARG Chi-restraints excluded: chain C residue 675 LEU Chi-restraints excluded: chain C residue 690 ILE Chi-restraints excluded: chain C residue 708 ILE Chi-restraints excluded: chain C residue 709 THR Chi-restraints excluded: chain C residue 794 LEU Chi-restraints excluded: chain C residue 812 SER Chi-restraints excluded: chain C residue 829 LEU Chi-restraints excluded: chain C residue 876 LEU Chi-restraints excluded: chain C residue 883 LEU Chi-restraints excluded: chain C residue 904 VAL Chi-restraints excluded: chain C residue 912 VAL Chi-restraints excluded: chain C residue 922 ILE Chi-restraints excluded: chain C residue 963 LEU Chi-restraints excluded: chain C residue 993 CYS Chi-restraints excluded: chain C residue 1049 LYS Chi-restraints excluded: chain C residue 1054 SER Chi-restraints excluded: chain C residue 1122 LEU Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 410 GLN Chi-restraints excluded: chain D residue 460 LEU Chi-restraints excluded: chain D residue 587 SER Chi-restraints excluded: chain D residue 595 LEU Chi-restraints excluded: chain D residue 626 LEU Chi-restraints excluded: chain D residue 637 ARG Chi-restraints excluded: chain D residue 675 LEU Chi-restraints excluded: chain D residue 690 ILE Chi-restraints excluded: chain D residue 699 CYS Chi-restraints excluded: chain D residue 708 ILE Chi-restraints excluded: chain D residue 709 THR Chi-restraints excluded: chain D residue 789 SER Chi-restraints excluded: chain D residue 794 LEU Chi-restraints excluded: chain D residue 812 SER Chi-restraints excluded: chain D residue 829 LEU Chi-restraints excluded: chain D residue 876 LEU Chi-restraints excluded: chain D residue 904 VAL Chi-restraints excluded: chain D residue 912 VAL Chi-restraints excluded: chain D residue 922 ILE Chi-restraints excluded: chain D residue 963 LEU Chi-restraints excluded: chain D residue 993 CYS Chi-restraints excluded: chain D residue 1054 SER Chi-restraints excluded: chain D residue 1122 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 77 optimal weight: 0.9990 chunk 103 optimal weight: 30.0000 chunk 78 optimal weight: 0.7980 chunk 56 optimal weight: 0.5980 chunk 354 optimal weight: 0.5980 chunk 306 optimal weight: 4.9990 chunk 249 optimal weight: 1.9990 chunk 184 optimal weight: 0.6980 chunk 17 optimal weight: 0.0040 chunk 338 optimal weight: 0.0980 chunk 189 optimal weight: 0.9990 overall best weight: 0.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1128 HIS B 505 HIS C1128 HIS D1128 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.212362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.135579 restraints weight = 34584.120| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 2.08 r_work: 0.3189 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.5495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 30396 Z= 0.122 Angle : 0.667 14.348 41236 Z= 0.314 Chirality : 0.041 0.382 4660 Planarity : 0.005 0.085 5152 Dihedral : 6.376 59.810 4932 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.31 % Favored : 92.69 % Rotamer: Outliers : 3.08 % Allowed : 20.02 % Favored : 76.90 % 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: -0.37 (0.14), residues: 3640 helix: 0.93 (0.11), residues: 2416 sheet: -3.31 (0.33), residues: 192 loop : -2.43 (0.19), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 612 TYR 0.007 0.001 TYR B 103 PHE 0.035 0.001 PHE B 578 TRP 0.045 0.002 TRP A 691 HIS 0.004 0.001 HIS C 447 Details of bonding type rmsd covalent geometry : bond 0.00273 (30392) covalent geometry : angle 0.66661 (41236) hydrogen bonds : bond 0.03348 ( 1544) hydrogen bonds : angle 4.27718 ( 4572) Misc. bond : bond 0.00247 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7280 Ramachandran restraints generated. 3640 Oldfield, 0 Emsley, 3640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 607 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 513 time to evaluate : 1.042 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 MET cc_start: 0.7277 (mpt) cc_final: 0.6630 (mpt) REVERT: A 410 GLN cc_start: 0.7571 (OUTLIER) cc_final: 0.7033 (mp10) REVERT: A 629 GLU cc_start: 0.8052 (mm-30) cc_final: 0.7814 (mm-30) REVERT: A 711 ARG cc_start: 0.6034 (mmm-85) cc_final: 0.5674 (ptm-80) REVERT: A 770 ARG cc_start: 0.7814 (mtp85) cc_final: 0.6688 (ttp80) REVERT: A 1015 TYR cc_start: 0.8663 (t80) cc_final: 0.8155 (t80) REVERT: A 1063 TYR cc_start: 0.9251 (t80) cc_final: 0.8831 (t80) REVERT: A 1067 ARG cc_start: 0.8511 (ptm-80) cc_final: 0.7978 (ptm-80) REVERT: A 1136 ARG cc_start: 0.8373 (mtm110) cc_final: 0.7999 (ttp-170) REVERT: A 1154 LYS cc_start: 0.8304 (mttt) cc_final: 0.8065 (mtpt) REVERT: B 186 MET cc_start: 0.7372 (mpt) cc_final: 0.6694 (mpt) REVERT: B 248 ARG cc_start: 0.5517 (ttp80) cc_final: 0.5285 (ptp90) REVERT: B 355 MET cc_start: 0.4607 (tpp) cc_final: 0.4287 (mmm) REVERT: B 403 TRP cc_start: 0.8952 (m-10) cc_final: 0.8715 (m-10) REVERT: B 410 GLN cc_start: 0.7468 (OUTLIER) cc_final: 0.7035 (mp10) REVERT: B 433 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8395 (mp) REVERT: B 588 SER cc_start: 0.9051 (m) cc_final: 0.8796 (m) REVERT: B 629 GLU cc_start: 0.8046 (mm-30) cc_final: 0.7797 (mm-30) REVERT: B 770 ARG cc_start: 0.7760 (mtp85) cc_final: 0.6603 (ttp80) REVERT: B 915 GLN cc_start: 0.8733 (tt0) cc_final: 0.8147 (mp10) REVERT: B 1015 TYR cc_start: 0.8641 (t80) cc_final: 0.8062 (t80) REVERT: B 1042 MET cc_start: 0.9267 (mtp) cc_final: 0.9024 (mtm) REVERT: B 1063 TYR cc_start: 0.9267 (t80) cc_final: 0.8892 (t80) REVERT: B 1067 ARG cc_start: 0.8571 (ptm-80) cc_final: 0.8027 (ptm-80) REVERT: B 1080 ILE cc_start: 0.8502 (tt) cc_final: 0.8118 (tt) REVERT: B 1128 HIS cc_start: 0.8725 (OUTLIER) cc_final: 0.8160 (m-70) REVERT: B 1149 LYS cc_start: 0.8868 (mtpp) cc_final: 0.8622 (mtpt) REVERT: B 1156 ASP cc_start: 0.8674 (m-30) cc_final: 0.8347 (m-30) REVERT: C 186 MET cc_start: 0.7320 (mpt) cc_final: 0.6694 (mpt) REVERT: C 410 GLN cc_start: 0.7510 (OUTLIER) cc_final: 0.7018 (mp10) REVERT: C 629 GLU cc_start: 0.8049 (mm-30) cc_final: 0.7829 (mm-30) REVERT: C 770 ARG cc_start: 0.7783 (mtp85) cc_final: 0.6659 (ttp80) REVERT: C 827 GLU cc_start: 0.8338 (tp30) cc_final: 0.7811 (tp30) REVERT: C 915 GLN cc_start: 0.8696 (tt0) cc_final: 0.8138 (mp10) REVERT: C 1015 TYR cc_start: 0.8522 (t80) cc_final: 0.7988 (t80) REVERT: C 1063 TYR cc_start: 0.9242 (t80) cc_final: 0.8884 (t80) REVERT: C 1067 ARG cc_start: 0.8534 (ptm-80) cc_final: 0.8002 (ptm-80) REVERT: D 410 GLN cc_start: 0.7565 (OUTLIER) cc_final: 0.7145 (mp10) REVERT: D 474 ARG cc_start: 0.6386 (tpp-160) cc_final: 0.5776 (tpp-160) REVERT: D 588 SER cc_start: 0.9096 (m) cc_final: 0.8866 (m) REVERT: D 632 ARG cc_start: 0.8584 (ttm110) cc_final: 0.8224 (ttm110) REVERT: D 770 ARG cc_start: 0.7796 (mtp85) cc_final: 0.6666 (ttp80) REVERT: D 827 GLU cc_start: 0.8182 (tp30) cc_final: 0.7864 (tp30) REVERT: D 1015 TYR cc_start: 0.8493 (t80) cc_final: 0.7960 (t80) REVERT: D 1063 TYR cc_start: 0.9265 (t80) cc_final: 0.8864 (t80) REVERT: D 1067 ARG cc_start: 0.8551 (ptm-80) cc_final: 0.8027 (ptm-80) outliers start: 94 outliers final: 74 residues processed: 573 average time/residue: 0.2177 time to fit residues: 192.9862 Evaluate side-chains 566 residues out of total 3136 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 486 time to evaluate : 1.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 LEU Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 410 GLN Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 473 ILE Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 675 LEU Chi-restraints excluded: chain A residue 708 ILE Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 794 LEU Chi-restraints excluded: chain A residue 812 SER Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 922 ILE Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 993 CYS Chi-restraints excluded: chain A residue 1054 SER Chi-restraints excluded: chain B residue 276 LEU Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 410 GLN Chi-restraints excluded: chain B residue 433 LEU Chi-restraints excluded: chain B residue 587 SER Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain B residue 611 ARG Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 637 ARG Chi-restraints excluded: chain B residue 675 LEU Chi-restraints excluded: chain B residue 708 ILE Chi-restraints excluded: chain B residue 709 THR Chi-restraints excluded: chain B residue 812 SER Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 898 ASP Chi-restraints excluded: chain B residue 922 ILE Chi-restraints excluded: chain B residue 993 CYS Chi-restraints excluded: chain B residue 1054 SER Chi-restraints excluded: chain B residue 1128 HIS Chi-restraints excluded: chain B residue 1166 ARG Chi-restraints excluded: chain C residue 276 LEU Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 410 GLN Chi-restraints excluded: chain C residue 463 LEU Chi-restraints excluded: chain C residue 595 LEU Chi-restraints excluded: chain C residue 626 LEU Chi-restraints excluded: chain C residue 637 ARG Chi-restraints excluded: chain C residue 675 LEU Chi-restraints excluded: chain C residue 690 ILE Chi-restraints excluded: chain C residue 708 ILE Chi-restraints excluded: chain C residue 709 THR Chi-restraints excluded: chain C residue 794 LEU Chi-restraints excluded: chain C residue 812 SER Chi-restraints excluded: chain C residue 876 LEU Chi-restraints excluded: chain C residue 883 LEU Chi-restraints excluded: chain C residue 922 ILE Chi-restraints excluded: chain C residue 963 LEU Chi-restraints excluded: chain C residue 993 CYS Chi-restraints excluded: chain C residue 1054 SER Chi-restraints excluded: chain D residue 275 LEU Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 410 GLN Chi-restraints excluded: chain D residue 560 SER Chi-restraints excluded: chain D residue 587 SER Chi-restraints excluded: chain D residue 595 LEU Chi-restraints excluded: chain D residue 626 LEU Chi-restraints excluded: chain D residue 637 ARG Chi-restraints excluded: chain D residue 690 ILE Chi-restraints excluded: chain D residue 708 ILE Chi-restraints excluded: chain D residue 709 THR Chi-restraints excluded: chain D residue 789 SER Chi-restraints excluded: chain D residue 794 LEU Chi-restraints excluded: chain D residue 812 SER Chi-restraints excluded: chain D residue 876 LEU Chi-restraints excluded: chain D residue 912 VAL Chi-restraints excluded: chain D residue 922 ILE Chi-restraints excluded: chain D residue 963 LEU Chi-restraints excluded: chain D residue 993 CYS Chi-restraints excluded: chain D residue 1054 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 209 optimal weight: 10.0000 chunk 263 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 264 optimal weight: 0.7980 chunk 75 optimal weight: 0.6980 chunk 235 optimal weight: 0.8980 chunk 84 optimal weight: 0.5980 chunk 37 optimal weight: 8.9990 chunk 336 optimal weight: 1.9990 chunk 271 optimal weight: 0.4980 chunk 60 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1128 HIS C1128 HIS D1128 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.211635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.137730 restraints weight = 34755.725| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 2.26 r_work: 0.3146 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.5549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 30396 Z= 0.145 Angle : 0.691 14.570 41236 Z= 0.326 Chirality : 0.042 0.386 4660 Planarity : 0.005 0.087 5152 Dihedral : 6.434 59.762 4928 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.61 % Favored : 92.39 % Rotamer: Outliers : 3.15 % Allowed : 20.38 % Favored : 76.47 % 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: -0.26 (0.14), residues: 3640 helix: 0.96 (0.11), residues: 2396 sheet: -2.94 (0.40), residues: 144 loop : -2.31 (0.18), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D1166 TYR 0.013 0.001 TYR A 818 PHE 0.039 0.001 PHE B 578 TRP 0.043 0.002 TRP A 691 HIS 0.007 0.001 HIS D 447 Details of bonding type rmsd covalent geometry : bond 0.00335 (30392) covalent geometry : angle 0.69092 (41236) hydrogen bonds : bond 0.03488 ( 1544) hydrogen bonds : angle 4.34338 ( 4572) Misc. bond : bond 0.00242 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11021.37 seconds wall clock time: 188 minutes 1.34 seconds (11281.34 seconds total)