Starting phenix.real_space_refine on Thu Feb 5 20:50:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ldk_63003/02_2026/9ldk_63003.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ldk_63003/02_2026/9ldk_63003.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ldk_63003/02_2026/9ldk_63003.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ldk_63003/02_2026/9ldk_63003.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ldk_63003/02_2026/9ldk_63003.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ldk_63003/02_2026/9ldk_63003.map" } resolution = 2.79 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= 0.001 sd= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 92 5.16 5 C 12492 2.51 5 N 3350 2.21 5 O 3712 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 97 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19646 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 864, 6568 Classifications: {'peptide': 864} Link IDs: {'PTRANS': 39, 'TRANS': 824} Chain breaks: 3 Chain: "B" Number of atoms: 6568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 864, 6568 Classifications: {'peptide': 864} Link IDs: {'PTRANS': 39, 'TRANS': 824} Chain breaks: 3 Chain: "C" Number of atoms: 3255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3255 Classifications: {'peptide': 420} Link IDs: {'PTRANS': 20, 'TRANS': 399} Chain: "F" Number of atoms: 3255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3255 Classifications: {'peptide': 420} Link IDs: {'PTRANS': 20, 'TRANS': 399} Time building chain proxies: 4.53, per 1000 atoms: 0.23 Number of scatterers: 19646 At special positions: 0 Unit cell: (122.57, 147.29, 114.33, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 92 16.00 O 3712 8.00 N 3350 7.00 C 12492 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=0, symmetry=0 Time building additional restraints: 1.57 Conformation dependent library (CDL) restraints added in 910.2 milliseconds 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4792 Finding SS restraints... Secondary structure from input PDB file: 105 helices and 18 sheets defined 47.3% alpha, 9.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.89 Creating SS restraints... Processing helix chain 'A' and resid 5 through 24 removed outlier: 4.027A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N GLU A 14 " --> pdb=" O ASN A 10 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG A 15 " --> pdb=" O ALA A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 27 through 45 removed outlier: 3.862A pdb=" N LYS A 33 " --> pdb=" O GLU A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 52 removed outlier: 4.057A pdb=" N LEU A 49 " --> pdb=" O ALA A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 80 removed outlier: 3.804A pdb=" N LYS A 65 " --> pdb=" O ILE A 61 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ILE A 67 " --> pdb=" O GLU A 63 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ILE A 76 " --> pdb=" O ALA A 72 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N TYR A 77 " --> pdb=" O SER A 73 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA A 79 " --> pdb=" O TYR A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 128 removed outlier: 3.572A pdb=" N PHE A 122 " --> pdb=" O SER A 118 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LEU A 128 " --> pdb=" O SER A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 159 removed outlier: 3.568A pdb=" N THR A 146 " --> pdb=" O ALA A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 183 Processing helix chain 'A' and resid 198 through 204 Processing helix chain 'A' and resid 226 through 239 removed outlier: 3.858A pdb=" N VAL A 231 " --> pdb=" O ILE A 227 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N ALA A 232 " --> pdb=" O LYS A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 244 Processing helix chain 'A' and resid 258 through 270 removed outlier: 3.718A pdb=" N GLU A 264 " --> pdb=" O ASP A 260 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ARG A 265 " --> pdb=" O ALA A 261 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA A 267 " --> pdb=" O ARG A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 286 removed outlier: 4.153A pdb=" N LYS A 280 " --> pdb=" O GLY A 276 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE A 286 " --> pdb=" O VAL A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 309 removed outlier: 3.911A pdb=" N ILE A 304 " --> pdb=" O PRO A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 363 removed outlier: 3.503A pdb=" N GLU A 354 " --> pdb=" O GLU A 350 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LYS A 358 " --> pdb=" O GLU A 354 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LEU A 359 " --> pdb=" O LYS A 355 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLY A 363 " --> pdb=" O LEU A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 387 removed outlier: 4.318A pdb=" N VAL A 382 " --> pdb=" O GLN A 378 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER A 383 " --> pdb=" O PRO A 379 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLN A 387 " --> pdb=" O SER A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 477 removed outlier: 3.513A pdb=" N GLU A 473 " --> pdb=" O ILE A 469 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N VAL A 474 " --> pdb=" O ALA A 470 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE A 475 " --> pdb=" O LEU A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 492 removed outlier: 3.611A pdb=" N ASN A 492 " --> pdb=" O PHE A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 507 removed outlier: 4.751A pdb=" N VAL A 502 " --> pdb=" O GLN A 498 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ALA A 506 " --> pdb=" O VAL A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 533 Processing helix chain 'A' and resid 546 through 561 removed outlier: 3.843A pdb=" N LYS A 553 " --> pdb=" O MET A 549 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE A 554 " --> pdb=" O ASP A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 573 removed outlier: 3.793A pdb=" N LEU A 569 " --> pdb=" O HIS A 565 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N LEU A 571 " --> pdb=" O GLU A 567 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ARG A 572 " --> pdb=" O GLU A 568 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N PHE A 573 " --> pdb=" O LEU A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 643 through 663 removed outlier: 3.525A pdb=" N ALA A 648 " --> pdb=" O LYS A 644 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASP A 653 " --> pdb=" O PHE A 649 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA A 661 " --> pdb=" O HIS A 657 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N VAL A 663 " --> pdb=" O MET A 659 " (cutoff:3.500A) Processing helix chain 'A' and resid 669 through 682 removed outlier: 4.352A pdb=" N GLY A 673 " --> pdb=" O GLU A 669 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N GLN A 674 " --> pdb=" O PHE A 670 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA A 675 " --> pdb=" O SER A 671 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU A 679 " --> pdb=" O ALA A 675 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU A 682 " --> pdb=" O ALA A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 685 through 692 Processing helix chain 'A' and resid 697 through 715 removed outlier: 3.768A pdb=" N GLU A 701 " --> pdb=" O PRO A 697 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG A 702 " --> pdb=" O VAL A 698 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA A 706 " --> pdb=" O ARG A 702 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N THR A 708 " --> pdb=" O HIS A 704 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA A 713 " --> pdb=" O ILE A 709 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 733 removed outlier: 3.515A pdb=" N MET A 725 " --> pdb=" O VAL A 721 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N HIS A 727 " --> pdb=" O HIS A 723 " (cutoff:3.500A) Processing helix chain 'A' and resid 744 through 749 Processing helix chain 'A' and resid 750 through 753 removed outlier: 3.696A pdb=" N ALA A 753 " --> pdb=" O ARG A 750 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 750 through 753' Processing helix chain 'A' and resid 771 through 782 removed outlier: 3.702A pdb=" N ILE A 778 " --> pdb=" O ARG A 774 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA A 779 " --> pdb=" O TYR A 775 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASP A 780 " --> pdb=" O ALA A 776 " (cutoff:3.500A) Processing helix chain 'A' and resid 790 through 810 removed outlier: 3.842A pdb=" N GLU A 796 " --> pdb=" O ALA A 792 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS A 797 " --> pdb=" O ALA A 793 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU A 798 " --> pdb=" O LYS A 794 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LYS A 806 " --> pdb=" O LEU A 802 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA A 807 " --> pdb=" O GLU A 803 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N GLU A 808 " --> pdb=" O THR A 804 " (cutoff:3.500A) Processing helix chain 'A' and resid 828 through 837 removed outlier: 3.555A pdb=" N ALA A 836 " --> pdb=" O LEU A 832 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N PHE A 837 " --> pdb=" O SER A 833 " (cutoff:3.500A) Processing helix chain 'A' and resid 850 through 854 Processing helix chain 'A' and resid 855 through 863 removed outlier: 3.540A pdb=" N TYR A 862 " --> pdb=" O LEU A 858 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N TYR A 863 " --> pdb=" O LEU A 859 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 24 removed outlier: 3.968A pdb=" N ALA B 11 " --> pdb=" O ALA B 7 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLU B 14 " --> pdb=" O ASN B 10 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG B 15 " --> pdb=" O ALA B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 45 removed outlier: 3.905A pdb=" N LYS B 33 " --> pdb=" O GLU B 29 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA B 41 " --> pdb=" O ALA B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 80 removed outlier: 3.557A pdb=" N LYS B 65 " --> pdb=" O ILE B 61 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ILE B 67 " --> pdb=" O GLU B 63 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ILE B 76 " --> pdb=" O ALA B 72 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N TYR B 77 " --> pdb=" O SER B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 128 removed outlier: 3.514A pdb=" N PHE B 122 " --> pdb=" O SER B 118 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LEU B 128 " --> pdb=" O SER B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 159 removed outlier: 3.603A pdb=" N THR B 146 " --> pdb=" O ALA B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 183 Processing helix chain 'B' and resid 198 through 204 removed outlier: 3.619A pdb=" N SER B 204 " --> pdb=" O LYS B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 239 removed outlier: 4.646A pdb=" N ALA B 232 " --> pdb=" O LYS B 228 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL B 234 " --> pdb=" O ALA B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 244 Processing helix chain 'B' and resid 256 through 270 removed outlier: 4.814A pdb=" N ASP B 260 " --> pdb=" O ASP B 256 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N ALA B 261 " --> pdb=" O SER B 257 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLU B 264 " --> pdb=" O ASP B 260 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ARG B 265 " --> pdb=" O ALA B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 287 removed outlier: 3.697A pdb=" N VAL B 282 " --> pdb=" O GLU B 278 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N GLN B 283 " --> pdb=" O LEU B 279 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N ASP B 284 " --> pdb=" O LYS B 280 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU B 287 " --> pdb=" O GLN B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 309 removed outlier: 3.887A pdb=" N ILE B 304 " --> pdb=" O PRO B 300 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA B 305 " --> pdb=" O ALA B 301 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLU B 306 " --> pdb=" O TYR B 302 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU B 307 " --> pdb=" O LYS B 303 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA B 308 " --> pdb=" O ILE B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 364 removed outlier: 3.516A pdb=" N GLU B 354 " --> pdb=" O GLU B 350 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LYS B 358 " --> pdb=" O GLU B 354 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LEU B 359 " --> pdb=" O LYS B 355 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY B 364 " --> pdb=" O VAL B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 378 through 387 removed outlier: 4.244A pdb=" N VAL B 382 " --> pdb=" O GLN B 378 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER B 383 " --> pdb=" O PRO B 379 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLN B 387 " --> pdb=" O SER B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 466 through 477 removed outlier: 3.506A pdb=" N GLU B 473 " --> pdb=" O ILE B 469 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N VAL B 474 " --> pdb=" O ALA B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 507 removed outlier: 4.804A pdb=" N VAL B 502 " --> pdb=" O GLN B 498 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ALA B 506 " --> pdb=" O VAL B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 534 Processing helix chain 'B' and resid 546 through 561 removed outlier: 3.655A pdb=" N ALA B 552 " --> pdb=" O PRO B 548 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LYS B 553 " --> pdb=" O MET B 549 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ILE B 554 " --> pdb=" O ASP B 550 " (cutoff:3.500A) Processing helix chain 'B' and resid 565 through 573 removed outlier: 3.811A pdb=" N LEU B 569 " --> pdb=" O HIS B 565 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N LEU B 571 " --> pdb=" O GLU B 567 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ARG B 572 " --> pdb=" O GLU B 568 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE B 573 " --> pdb=" O LEU B 569 " (cutoff:3.500A) Processing helix chain 'B' and resid 643 through 663 removed outlier: 4.246A pdb=" N ALA B 648 " --> pdb=" O LYS B 644 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N PHE B 649 " --> pdb=" O SER B 645 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLY B 650 " --> pdb=" O LEU B 646 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ASP B 653 " --> pdb=" O PHE B 649 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA B 661 " --> pdb=" O HIS B 657 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N VAL B 663 " --> pdb=" O MET B 659 " (cutoff:3.500A) Processing helix chain 'B' and resid 671 through 683 removed outlier: 4.020A pdb=" N LEU B 679 " --> pdb=" O ALA B 675 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU B 681 " --> pdb=" O GLN B 677 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU B 682 " --> pdb=" O ALA B 678 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LYS B 683 " --> pdb=" O LEU B 679 " (cutoff:3.500A) Processing helix chain 'B' and resid 685 through 692 Processing helix chain 'B' and resid 696 through 715 removed outlier: 3.813A pdb=" N ARG B 700 " --> pdb=" O ASN B 696 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA B 706 " --> pdb=" O ARG B 702 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N THR B 708 " --> pdb=" O HIS B 704 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA B 713 " --> pdb=" O ILE B 709 " (cutoff:3.500A) Processing helix chain 'B' and resid 721 through 730 removed outlier: 3.948A pdb=" N HIS B 727 " --> pdb=" O HIS B 723 " (cutoff:3.500A) Processing helix chain 'B' and resid 744 through 749 removed outlier: 3.564A pdb=" N ILE B 749 " --> pdb=" O ILE B 745 " (cutoff:3.500A) Processing helix chain 'B' and resid 750 through 753 removed outlier: 3.628A pdb=" N ALA B 753 " --> pdb=" O ARG B 750 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 750 through 753' Processing helix chain 'B' and resid 771 through 782 removed outlier: 3.675A pdb=" N ILE B 778 " --> pdb=" O ARG B 774 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA B 779 " --> pdb=" O TYR B 775 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASP B 780 " --> pdb=" O ALA B 776 " (cutoff:3.500A) Processing helix chain 'B' and resid 790 through 810 removed outlier: 3.884A pdb=" N GLU B 796 " --> pdb=" O ALA B 792 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LYS B 797 " --> pdb=" O ALA B 793 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU B 798 " --> pdb=" O LYS B 794 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LYS B 806 " --> pdb=" O LEU B 802 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA B 807 " --> pdb=" O GLU B 803 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N GLU B 808 " --> pdb=" O THR B 804 " (cutoff:3.500A) Processing helix chain 'B' and resid 815 through 819 Processing helix chain 'B' and resid 822 through 827 removed outlier: 3.681A pdb=" N LEU B 826 " --> pdb=" O GLU B 822 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ALA B 827 " --> pdb=" O ALA B 823 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 822 through 827' Processing helix chain 'B' and resid 828 through 834 removed outlier: 4.103A pdb=" N GLU B 834 " --> pdb=" O ASP B 830 " (cutoff:3.500A) Processing helix chain 'B' and resid 835 through 839 removed outlier: 3.929A pdb=" N ASP B 839 " --> pdb=" O ALA B 836 " (cutoff:3.500A) Processing helix chain 'B' and resid 850 through 855 Processing helix chain 'B' and resid 855 through 861 Processing helix chain 'C' and resid 466 through 477 removed outlier: 3.647A pdb=" N GLU C 473 " --> pdb=" O ILE C 469 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL C 474 " --> pdb=" O ALA C 470 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE C 475 " --> pdb=" O LEU C 471 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ASP C 477 " --> pdb=" O GLU C 473 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 493 removed outlier: 3.652A pdb=" N ASN C 493 " --> pdb=" O PHE C 489 " (cutoff:3.500A) Processing helix chain 'C' and resid 497 through 507 removed outlier: 3.764A pdb=" N ALA C 506 " --> pdb=" O VAL C 502 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLY C 507 " --> pdb=" O LEU C 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 523 through 533 Processing helix chain 'C' and resid 546 through 561 removed outlier: 3.726A pdb=" N ALA C 552 " --> pdb=" O PRO C 548 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LYS C 553 " --> pdb=" O MET C 549 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ILE C 554 " --> pdb=" O ASP C 550 " (cutoff:3.500A) Processing helix chain 'C' and resid 565 through 573 removed outlier: 4.059A pdb=" N LEU C 569 " --> pdb=" O HIS C 565 " (cutoff:3.500A) Processing helix chain 'C' and resid 625 through 628 Processing helix chain 'C' and resid 646 through 660 removed outlier: 3.733A pdb=" N LEU C 652 " --> pdb=" O ALA C 648 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLU C 660 " --> pdb=" O THR C 656 " (cutoff:3.500A) Processing helix chain 'C' and resid 671 through 683 removed outlier: 3.936A pdb=" N GLN C 677 " --> pdb=" O GLY C 673 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU C 679 " --> pdb=" O ALA C 675 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LYS C 680 " --> pdb=" O LEU C 676 " (cutoff:3.500A) Processing helix chain 'C' and resid 686 through 690 Processing helix chain 'C' and resid 692 through 695 Processing helix chain 'C' and resid 696 through 717 removed outlier: 3.685A pdb=" N ARG C 700 " --> pdb=" O ASN C 696 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N THR C 708 " --> pdb=" O HIS C 704 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE C 709 " --> pdb=" O SER C 705 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ASN C 716 " --> pdb=" O ILE C 712 " (cutoff:3.500A) Processing helix chain 'C' and resid 721 through 733 removed outlier: 3.676A pdb=" N ALA C 726 " --> pdb=" O CYS C 722 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N HIS C 727 " --> pdb=" O HIS C 723 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N SER C 731 " --> pdb=" O HIS C 727 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N PHE C 733 " --> pdb=" O LEU C 729 " (cutoff:3.500A) Processing helix chain 'C' and resid 739 through 744 removed outlier: 4.180A pdb=" N LEU C 744 " --> pdb=" O ALA C 740 " (cutoff:3.500A) Processing helix chain 'C' and resid 744 through 752 removed outlier: 3.699A pdb=" N ILE C 749 " --> pdb=" O ILE C 745 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ARG C 750 " --> pdb=" O CYS C 746 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASN C 752 " --> pdb=" O VAL C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 771 through 782 removed outlier: 3.625A pdb=" N ALA C 776 " --> pdb=" O ARG C 772 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE C 778 " --> pdb=" O ARG C 774 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASP C 780 " --> pdb=" O ALA C 776 " (cutoff:3.500A) Processing helix chain 'C' and resid 790 through 809 Processing helix chain 'C' and resid 815 through 819 removed outlier: 3.784A pdb=" N GLY C 819 " --> pdb=" O ARG C 816 " (cutoff:3.500A) Processing helix chain 'C' and resid 828 through 837 removed outlier: 4.199A pdb=" N ASP C 835 " --> pdb=" O LYS C 831 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA C 836 " --> pdb=" O LEU C 832 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N PHE C 837 " --> pdb=" O SER C 833 " (cutoff:3.500A) Processing helix chain 'C' and resid 850 through 862 removed outlier: 4.311A pdb=" N GLN C 856 " --> pdb=" O SER C 852 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ILE C 857 " --> pdb=" O GLU C 853 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU C 858 " --> pdb=" O LEU C 854 " (cutoff:3.500A) Processing helix chain 'F' and resid 466 through 477 removed outlier: 3.544A pdb=" N GLU F 473 " --> pdb=" O ILE F 469 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL F 474 " --> pdb=" O ALA F 470 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE F 475 " --> pdb=" O LEU F 471 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ASP F 477 " --> pdb=" O GLU F 473 " (cutoff:3.500A) Processing helix chain 'F' and resid 488 through 493 removed outlier: 3.516A pdb=" N ASN F 492 " --> pdb=" O ARG F 488 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ASN F 493 " --> pdb=" O PHE F 489 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 488 through 493' Processing helix chain 'F' and resid 496 through 507 removed outlier: 3.668A pdb=" N THR F 500 " --> pdb=" O ALA F 496 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA F 506 " --> pdb=" O VAL F 502 " (cutoff:3.500A) Processing helix chain 'F' and resid 526 through 534 removed outlier: 3.916A pdb=" N GLU F 530 " --> pdb=" O ARG F 526 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LEU F 531 " --> pdb=" O LYS F 527 " (cutoff:3.500A) Processing helix chain 'F' and resid 546 through 561 removed outlier: 3.581A pdb=" N VAL F 557 " --> pdb=" O LYS F 553 " (cutoff:3.500A) Processing helix chain 'F' and resid 565 through 573 removed outlier: 4.364A pdb=" N LEU F 569 " --> pdb=" O HIS F 565 " (cutoff:3.500A) Processing helix chain 'F' and resid 646 through 660 removed outlier: 3.559A pdb=" N LEU F 652 " --> pdb=" O ALA F 648 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU F 660 " --> pdb=" O THR F 656 " (cutoff:3.500A) Processing helix chain 'F' and resid 671 through 683 removed outlier: 3.719A pdb=" N LEU F 679 " --> pdb=" O ALA F 675 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYS F 680 " --> pdb=" O LEU F 676 " (cutoff:3.500A) Processing helix chain 'F' and resid 686 through 690 Processing helix chain 'F' and resid 692 through 695 Processing helix chain 'F' and resid 696 through 716 removed outlier: 3.517A pdb=" N ARG F 700 " --> pdb=" O ASN F 696 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N THR F 708 " --> pdb=" O HIS F 704 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASN F 716 " --> pdb=" O ILE F 712 " (cutoff:3.500A) Processing helix chain 'F' and resid 721 through 733 removed outlier: 3.741A pdb=" N HIS F 727 " --> pdb=" O HIS F 723 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LYS F 728 " --> pdb=" O SER F 724 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N PHE F 733 " --> pdb=" O LEU F 729 " (cutoff:3.500A) Processing helix chain 'F' and resid 744 through 752 removed outlier: 3.801A pdb=" N ARG F 750 " --> pdb=" O CYS F 746 " (cutoff:3.500A) Processing helix chain 'F' and resid 772 through 782 removed outlier: 3.797A pdb=" N ALA F 776 " --> pdb=" O ARG F 772 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ILE F 778 " --> pdb=" O ARG F 774 " (cutoff:3.500A) Processing helix chain 'F' and resid 790 through 809 removed outlier: 3.604A pdb=" N ILE F 795 " --> pdb=" O THR F 791 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLU F 796 " --> pdb=" O ALA F 792 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LYS F 797 " --> pdb=" O ALA F 793 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU F 798 " --> pdb=" O LYS F 794 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N TRP F 801 " --> pdb=" O LYS F 797 " (cutoff:3.500A) Processing helix chain 'F' and resid 815 through 819 removed outlier: 3.721A pdb=" N GLY F 819 " --> pdb=" O ARG F 816 " (cutoff:3.500A) Processing helix chain 'F' and resid 827 through 834 removed outlier: 4.195A pdb=" N LYS F 831 " --> pdb=" O ALA F 827 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLU F 834 " --> pdb=" O ASP F 830 " (cutoff:3.500A) Processing helix chain 'F' and resid 850 through 861 removed outlier: 4.763A pdb=" N GLN F 856 " --> pdb=" O SER F 852 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE F 857 " --> pdb=" O GLU F 853 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU F 858 " --> pdb=" O LEU F 854 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 91 through 92 removed outlier: 6.252A pdb=" N SER B 369 " --> pdb=" O LEU B 395 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N TYR B 372 " --> pdb=" O PRO B 218 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N VAL B 220 " --> pdb=" O TYR B 372 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N THR B 217 " --> pdb=" O SER B 251 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N VAL B 253 " --> pdb=" O THR B 217 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N VAL B 219 " --> pdb=" O VAL B 253 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N VAL B 255 " --> pdb=" O VAL B 219 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N ILE B 221 " --> pdb=" O VAL B 255 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N GLN B 250 " --> pdb=" O THR B 340 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA B 342 " --> pdb=" O GLN B 250 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL B 254 " --> pdb=" O TYR B 344 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N LEU B 319 " --> pdb=" O LEU B 341 " (cutoff:3.500A) removed outlier: 8.141A pdb=" N MET B 343 " --> pdb=" O LEU B 319 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N GLY B 321 " --> pdb=" O MET B 343 " (cutoff:3.500A) removed outlier: 8.464A pdb=" N ARG B 345 " --> pdb=" O GLY B 321 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N TYR B 272 " --> pdb=" O ILE B 320 " (cutoff:3.500A) removed outlier: 8.179A pdb=" N GLU B 322 " --> pdb=" O TYR B 272 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N LEU B 274 " --> pdb=" O GLU B 322 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 101 through 103 Processing sheet with id=AA3, first strand: chain 'A' and resid 167 through 169 removed outlier: 6.601A pdb=" N ILE A 107 " --> pdb=" O ILE A 135 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N CYS A 108 " --> pdb=" O LEU A 191 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N THR A 193 " --> pdb=" O CYS A 108 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N ILE A 190 " --> pdb=" O ILE A 210 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N VAL A 212 " --> pdb=" O ILE A 190 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N ALA A 192 " --> pdb=" O VAL A 212 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 271 through 274 removed outlier: 6.106A pdb=" N TYR A 272 " --> pdb=" O ILE A 320 " (cutoff:3.500A) removed outlier: 8.215A pdb=" N GLU A 322 " --> pdb=" O TYR A 272 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N LEU A 274 " --> pdb=" O GLU A 322 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N LEU A 319 " --> pdb=" O LEU A 341 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N MET A 343 " --> pdb=" O LEU A 319 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N GLY A 321 " --> pdb=" O MET A 343 " (cutoff:3.500A) removed outlier: 8.332A pdb=" N ARG A 345 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N GLN A 250 " --> pdb=" O THR A 340 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ALA A 342 " --> pdb=" O GLN A 250 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL A 254 " --> pdb=" O TYR A 344 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N THR A 217 " --> pdb=" O SER A 251 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N VAL A 253 " --> pdb=" O THR A 217 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N VAL A 219 " --> pdb=" O VAL A 253 " (cutoff:3.500A) removed outlier: 8.191A pdb=" N VAL A 255 " --> pdb=" O VAL A 219 " (cutoff:3.500A) removed outlier: 8.310A pdb=" N ILE A 221 " --> pdb=" O VAL A 255 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N TYR A 372 " --> pdb=" O PRO A 218 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N VAL A 220 " --> pdb=" O TYR A 372 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 365 through 366 Processing sheet with id=AA6, first strand: chain 'A' and resid 419 through 420 Processing sheet with id=AA7, first strand: chain 'A' and resid 452 through 453 removed outlier: 3.800A pdb=" N LEU A 452 " --> pdb=" O PHE F 462 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N PHE F 462 " --> pdb=" O LEU A 452 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N SER F 459 " --> pdb=" O ALA F 632 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N VAL F 634 " --> pdb=" O SER F 459 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N TYR F 461 " --> pdb=" O VAL F 634 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N MET F 592 " --> pdb=" O MET F 631 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N ILE F 633 " --> pdb=" O MET F 592 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ALA F 594 " --> pdb=" O ILE F 633 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N ASP F 635 " --> pdb=" O ALA F 594 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N ILE F 540 " --> pdb=" O ILE F 593 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N VAL F 595 " --> pdb=" O ILE F 540 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ALA F 542 " --> pdb=" O VAL F 595 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ARG F 481 " --> pdb=" O VAL F 539 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N ILE F 541 " --> pdb=" O ARG F 481 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N LEU F 483 " --> pdb=" O ILE F 541 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLU F 511 " --> pdb=" O ALA F 482 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLU F 515 " --> pdb=" O THR F 486 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 509 through 514 removed outlier: 4.179A pdb=" N GLU A 511 " --> pdb=" O ALA A 482 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ILE A 484 " --> pdb=" O GLU A 511 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N PHE A 513 " --> pdb=" O ILE A 484 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR A 486 " --> pdb=" O PHE A 513 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ARG A 481 " --> pdb=" O VAL A 539 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N ILE A 541 " --> pdb=" O ARG A 481 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N LEU A 483 " --> pdb=" O ILE A 541 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ILE A 540 " --> pdb=" O ILE A 593 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N VAL A 595 " --> pdb=" O ILE A 540 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ALA A 542 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N MET A 592 " --> pdb=" O MET A 631 " (cutoff:3.500A) removed outlier: 8.240A pdb=" N ILE A 633 " --> pdb=" O MET A 592 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ALA A 594 " --> pdb=" O ILE A 633 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N ASP A 635 " --> pdb=" O ALA A 594 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N SER A 459 " --> pdb=" O ALA A 632 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N VAL A 634 " --> pdb=" O SER A 459 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N TYR A 461 " --> pdb=" O VAL A 634 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N PHE A 462 " --> pdb=" O LEU F 452 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LEU F 452 " --> pdb=" O PHE A 462 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 608 through 612 removed outlier: 3.526A pdb=" N VAL A 611 " --> pdb=" O TYR A 620 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 101 through 103 Processing sheet with id=AB2, first strand: chain 'B' and resid 167 through 169 removed outlier: 6.380A pdb=" N ILE B 134 " --> pdb=" O GLY B 168 " (cutoff:3.500A) removed outlier: 8.443A pdb=" N LEU B 191 " --> pdb=" O ILE B 106 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N CYS B 108 " --> pdb=" O LEU B 191 " (cutoff:3.500A) removed outlier: 8.273A pdb=" N THR B 193 " --> pdb=" O CYS B 108 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ILE B 190 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N VAL B 212 " --> pdb=" O ILE B 190 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ALA B 192 " --> pdb=" O VAL B 212 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 365 through 366 Processing sheet with id=AB4, first strand: chain 'B' and resid 419 through 420 Processing sheet with id=AB5, first strand: chain 'B' and resid 452 through 453 removed outlier: 6.379A pdb=" N SER C 459 " --> pdb=" O ALA C 632 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N VAL C 634 " --> pdb=" O SER C 459 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N TYR C 461 " --> pdb=" O VAL C 634 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N MET C 592 " --> pdb=" O MET C 631 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N ILE C 633 " --> pdb=" O MET C 592 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ALA C 594 " --> pdb=" O ILE C 633 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N ASP C 635 " --> pdb=" O ALA C 594 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N ILE C 540 " --> pdb=" O ILE C 593 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N VAL C 595 " --> pdb=" O ILE C 540 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N ALA C 542 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ARG C 481 " --> pdb=" O VAL C 539 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N ILE C 541 " --> pdb=" O ARG C 481 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N LEU C 483 " --> pdb=" O ILE C 541 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLU C 511 " --> pdb=" O ALA C 482 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLU C 515 " --> pdb=" O THR C 486 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 509 through 514 removed outlier: 3.935A pdb=" N GLU B 511 " --> pdb=" O ALA B 482 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ILE B 484 " --> pdb=" O GLU B 511 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N PHE B 513 " --> pdb=" O ILE B 484 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ARG B 481 " --> pdb=" O VAL B 539 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N ILE B 541 " --> pdb=" O ARG B 481 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N LEU B 483 " --> pdb=" O ILE B 541 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N MET B 592 " --> pdb=" O MET B 631 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N ILE B 633 " --> pdb=" O MET B 592 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ALA B 594 " --> pdb=" O ILE B 633 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N ASP B 635 " --> pdb=" O ALA B 594 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N SER B 459 " --> pdb=" O ALA B 632 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N VAL B 634 " --> pdb=" O SER B 459 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N TYR B 461 " --> pdb=" O VAL B 634 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU C 452 " --> pdb=" O PHE B 462 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 608 through 612 removed outlier: 3.544A pdb=" N VAL B 611 " --> pdb=" O TYR B 620 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 608 through 612 Processing sheet with id=AB9, first strand: chain 'F' and resid 608 through 612 661 hydrogen bonds defined for protein. 1911 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: 3.75 Time building geometry restraints manager: 2.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6483 1.34 - 1.46: 4115 1.46 - 1.58: 9277 1.58 - 1.70: 1 1.70 - 1.82: 158 Bond restraints: 20034 Sorted by residual: bond pdb=" N ASP C 624 " pdb=" CA ASP C 624 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.20e-02 6.94e+03 8.98e+00 bond pdb=" N VAL A 325 " pdb=" CA VAL A 325 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.22e-02 6.72e+03 8.69e+00 bond pdb=" N ASP B 839 " pdb=" CA ASP B 839 " ideal model delta sigma weight residual 1.457 1.494 -0.036 1.29e-02 6.01e+03 7.99e+00 bond pdb=" N ILE A 47 " pdb=" CA ILE A 47 " ideal model delta sigma weight residual 1.461 1.495 -0.034 1.23e-02 6.61e+03 7.68e+00 bond pdb=" N ASP C 487 " pdb=" CA ASP C 487 " ideal model delta sigma weight residual 1.454 1.486 -0.032 1.16e-02 7.43e+03 7.56e+00 ... (remaining 20029 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.63: 26698 2.63 - 5.27: 396 5.27 - 7.90: 48 7.90 - 10.53: 16 10.53 - 13.16: 2 Bond angle restraints: 27160 Sorted by residual: angle pdb=" N ALA C 626 " pdb=" CA ALA C 626 " pdb=" C ALA C 626 " ideal model delta sigma weight residual 112.87 125.77 -12.90 1.20e+00 6.94e-01 1.16e+02 angle pdb=" C TYR C 625 " pdb=" CA TYR C 625 " pdb=" CB TYR C 625 " ideal model delta sigma weight residual 110.46 120.73 -10.27 1.94e+00 2.66e-01 2.80e+01 angle pdb=" CA ASP A 327 " pdb=" CB ASP A 327 " pdb=" CG ASP A 327 " ideal model delta sigma weight residual 112.60 117.15 -4.55 1.00e+00 1.00e+00 2.07e+01 angle pdb=" N GLY F 843 " pdb=" CA GLY F 843 " pdb=" C GLY F 843 " ideal model delta sigma weight residual 115.61 107.96 7.65 1.74e+00 3.30e-01 1.93e+01 angle pdb=" CB MET C 640 " pdb=" CG MET C 640 " pdb=" SD MET C 640 " ideal model delta sigma weight residual 112.70 125.86 -13.16 3.00e+00 1.11e-01 1.93e+01 ... (remaining 27155 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.57: 10254 17.57 - 35.15: 1452 35.15 - 52.72: 336 52.72 - 70.30: 67 70.30 - 87.87: 15 Dihedral angle restraints: 12124 sinusoidal: 4686 harmonic: 7438 Sorted by residual: dihedral pdb=" CD ARG A 46 " pdb=" NE ARG A 46 " pdb=" CZ ARG A 46 " pdb=" NH1 ARG A 46 " ideal model delta sinusoidal sigma weight residual 0.00 -71.01 71.01 1 1.00e+01 1.00e-02 6.48e+01 dihedral pdb=" CA ILE B 47 " pdb=" C ILE B 47 " pdb=" N PRO B 48 " pdb=" CA PRO B 48 " ideal model delta harmonic sigma weight residual 180.00 150.10 29.90 0 5.00e+00 4.00e-02 3.57e+01 dihedral pdb=" C TYR C 625 " pdb=" N TYR C 625 " pdb=" CA TYR C 625 " pdb=" CB TYR C 625 " ideal model delta harmonic sigma weight residual -122.60 -134.44 11.84 0 2.50e+00 1.60e-01 2.24e+01 ... (remaining 12121 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 2917 0.092 - 0.184: 180 0.184 - 0.276: 6 0.276 - 0.368: 2 0.368 - 0.461: 1 Chirality restraints: 3106 Sorted by residual: chirality pdb=" CA ALA C 626 " pdb=" N ALA C 626 " pdb=" C ALA C 626 " pdb=" CB ALA C 626 " both_signs ideal model delta sigma weight residual False 2.48 2.02 0.46 2.00e-01 2.50e+01 5.30e+00 chirality pdb=" CA ALA B 844 " pdb=" N ALA B 844 " pdb=" C ALA B 844 " pdb=" CB ALA B 844 " both_signs ideal model delta sigma weight residual False 2.48 2.82 -0.33 2.00e-01 2.50e+01 2.73e+00 chirality pdb=" CA TYR C 625 " pdb=" N TYR C 625 " pdb=" C TYR C 625 " pdb=" CB TYR C 625 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.35e+00 ... (remaining 3103 not shown) Planarity restraints: 3512 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 46 " -1.050 9.50e-02 1.11e+02 4.71e-01 1.34e+02 pdb=" NE ARG A 46 " 0.062 2.00e-02 2.50e+03 pdb=" CZ ARG A 46 " 0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG A 46 " -0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG A 46 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY B 195 " -0.064 5.00e-02 4.00e+02 9.70e-02 1.51e+01 pdb=" N PRO B 196 " 0.168 5.00e-02 4.00e+02 pdb=" CA PRO B 196 " -0.053 5.00e-02 4.00e+02 pdb=" CD PRO B 196 " -0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 195 " -0.061 5.00e-02 4.00e+02 9.30e-02 1.38e+01 pdb=" N PRO A 196 " 0.161 5.00e-02 4.00e+02 pdb=" CA PRO A 196 " -0.050 5.00e-02 4.00e+02 pdb=" CD PRO A 196 " -0.050 5.00e-02 4.00e+02 ... (remaining 3509 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 224 2.54 - 3.13: 15474 3.13 - 3.72: 31892 3.72 - 4.31: 42201 4.31 - 4.90: 69381 Nonbonded interactions: 159172 Sorted by model distance: nonbonded pdb=" O ALA B 844 " pdb=" OD1 ASN B 845 " model vdw 1.952 3.040 nonbonded pdb=" N GLU F 517 " pdb=" OE1 GLU F 517 " model vdw 2.176 3.120 nonbonded pdb=" O LYS B 831 " pdb=" NZ LYS B 831 " model vdw 2.191 3.120 nonbonded pdb=" N GLU C 517 " pdb=" OE1 GLU C 517 " model vdw 2.191 3.120 nonbonded pdb=" OD2 ASP C 672 " pdb=" NH2 ARG C 774 " model vdw 2.193 3.120 ... (remaining 159167 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'F' } 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: 1.210 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: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 18.600 Find NCS groups from input model: 0.260 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:7.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 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 : 0.004 0.051 20034 Z= 0.182 Angle : 0.784 13.163 27160 Z= 0.428 Chirality : 0.047 0.461 3106 Planarity : 0.010 0.471 3512 Dihedral : 17.179 87.874 7332 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 14.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 4.12 % Allowed : 36.19 % Favored : 59.69 % Cbeta Deviations : 0.04 % 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: -2.15 (0.16), residues: 2548 helix: -1.64 (0.15), residues: 1098 sheet: -0.32 (0.29), residues: 316 loop : -1.39 (0.19), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG F 790 TYR 0.017 0.001 TYR B 581 PHE 0.033 0.002 PHE F 489 TRP 0.017 0.001 TRP B 424 HIS 0.003 0.001 HIS A 479 Details of bonding type rmsd covalent geometry : bond 0.00358 (20034) covalent geometry : angle 0.78370 (27160) hydrogen bonds : bond 0.28310 ( 661) hydrogen bonds : angle 8.51762 ( 1911) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 218 time to evaluate : 0.779 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 319 LEU cc_start: 0.9168 (OUTLIER) cc_final: 0.8910 (pp) REVERT: A 432 ASN cc_start: 0.8824 (p0) cc_final: 0.8488 (p0) REVERT: A 763 PHE cc_start: 0.8954 (OUTLIER) cc_final: 0.8747 (m-80) REVERT: A 839 ASP cc_start: 0.8058 (t70) cc_final: 0.7260 (t0) REVERT: B 1 MET cc_start: 0.7025 (ppp) cc_final: 0.6143 (pmm) REVERT: B 59 MET cc_start: 0.9349 (ptm) cc_final: 0.8763 (ptp) REVERT: B 74 GLU cc_start: 0.8643 (pt0) cc_final: 0.8130 (pp20) REVERT: C 519 ASP cc_start: 0.7970 (t70) cc_final: 0.7698 (t0) REVERT: C 766 TYR cc_start: 0.6400 (OUTLIER) cc_final: 0.5548 (m-10) REVERT: C 796 GLU cc_start: 0.8947 (mm-30) cc_final: 0.8674 (mm-30) REVERT: C 839 ASP cc_start: 0.7418 (t0) cc_final: 0.7033 (t0) REVERT: C 840 GLN cc_start: 0.4193 (OUTLIER) cc_final: 0.3950 (pp30) REVERT: F 519 ASP cc_start: 0.7757 (t0) cc_final: 0.7543 (t0) outliers start: 85 outliers final: 59 residues processed: 288 average time/residue: 0.5028 time to fit residues: 168.1657 Evaluate side-chains 268 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 205 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 SER Chi-restraints excluded: chain A residue 132 ASN Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 224 THR Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 580 ILE Chi-restraints excluded: chain A residue 649 PHE Chi-restraints excluded: chain A residue 665 VAL Chi-restraints excluded: chain A residue 723 HIS Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 763 PHE Chi-restraints excluded: chain A residue 814 SER Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 64 ASP Chi-restraints excluded: chain B residue 132 ASN Chi-restraints excluded: chain B residue 137 SER Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 329 SER Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain B residue 463 ARG Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 508 VAL Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 811 ILE Chi-restraints excluded: chain B residue 814 SER Chi-restraints excluded: chain B residue 835 ASP Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 483 LEU Chi-restraints excluded: chain C residue 499 ILE Chi-restraints excluded: chain C residue 510 THR Chi-restraints excluded: chain C residue 616 THR Chi-restraints excluded: chain C residue 630 ASP Chi-restraints excluded: chain C residue 727 HIS Chi-restraints excluded: chain C residue 766 TYR Chi-restraints excluded: chain C residue 830 ASP Chi-restraints excluded: chain C residue 840 GLN Chi-restraints excluded: chain C residue 857 ILE Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 497 ASP Chi-restraints excluded: chain F residue 499 ILE Chi-restraints excluded: chain F residue 508 VAL Chi-restraints excluded: chain F residue 525 VAL Chi-restraints excluded: chain F residue 543 LEU Chi-restraints excluded: chain F residue 569 LEU Chi-restraints excluded: chain F residue 741 ASN Chi-restraints excluded: chain F residue 754 ASN Chi-restraints excluded: chain F residue 767 ASP Chi-restraints excluded: chain F residue 784 LEU Chi-restraints excluded: chain F residue 826 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 1.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 0.3980 chunk 183 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 overall best weight: 1.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 78 ASN A 172 GLN A 377 ASN ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 756 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 139 HIS ** C 454 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 781 HIS C 840 GLN F 565 HIS F 756 ASN F 765 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.091500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.070718 restraints weight = 49437.642| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 3.96 r_work: 0.2996 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.1439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 20034 Z= 0.139 Angle : 0.661 9.808 27160 Z= 0.334 Chirality : 0.046 0.181 3106 Planarity : 0.005 0.075 3512 Dihedral : 7.014 59.042 2848 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 7.12 % Allowed : 28.73 % Favored : 64.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.85 % 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: -2.06 (0.16), residues: 2548 helix: -1.27 (0.14), residues: 1176 sheet: -0.49 (0.27), residues: 344 loop : -1.62 (0.19), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 790 TYR 0.013 0.001 TYR B 766 PHE 0.021 0.002 PHE C 489 TRP 0.010 0.001 TRP B 424 HIS 0.006 0.001 HIS A 704 Details of bonding type rmsd covalent geometry : bond 0.00317 (20034) covalent geometry : angle 0.66060 (27160) hydrogen bonds : bond 0.04299 ( 661) hydrogen bonds : angle 4.83189 ( 1911) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 232 time to evaluate : 0.497 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 219 VAL cc_start: 0.9517 (OUTLIER) cc_final: 0.8901 (t) REVERT: A 387 GLN cc_start: 0.8440 (mp10) cc_final: 0.8183 (mp10) REVERT: A 432 ASN cc_start: 0.8981 (p0) cc_final: 0.8767 (p0) REVERT: A 592 MET cc_start: 0.9055 (OUTLIER) cc_final: 0.8600 (tmm) REVERT: A 714 PHE cc_start: 0.9486 (OUTLIER) cc_final: 0.9239 (p90) REVERT: A 814 SER cc_start: 0.8307 (OUTLIER) cc_final: 0.8038 (p) REVERT: A 839 ASP cc_start: 0.7787 (t70) cc_final: 0.6863 (t0) REVERT: B 1 MET cc_start: 0.7336 (ppp) cc_final: 0.6817 (pmm) REVERT: B 59 MET cc_start: 0.9385 (ptm) cc_final: 0.8892 (ptt) REVERT: B 74 GLU cc_start: 0.8915 (OUTLIER) cc_final: 0.8436 (pp20) REVERT: B 91 GLU cc_start: 0.7592 (tm-30) cc_final: 0.7377 (tm-30) REVERT: B 319 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8926 (pp) REVERT: B 432 ASN cc_start: 0.9011 (p0) cc_final: 0.8791 (p0) REVERT: B 463 ARG cc_start: 0.9065 (OUTLIER) cc_final: 0.8805 (mmt180) REVERT: B 714 PHE cc_start: 0.9445 (OUTLIER) cc_final: 0.9194 (p90) REVERT: B 733 PHE cc_start: 0.8924 (m-80) cc_final: 0.8721 (m-10) REVERT: B 865 ARG cc_start: 0.6750 (OUTLIER) cc_final: 0.6517 (ptp-170) REVERT: C 473 GLU cc_start: 0.9181 (tt0) cc_final: 0.8912 (tt0) REVERT: C 565 HIS cc_start: 0.8324 (t70) cc_final: 0.8069 (t70) REVERT: C 568 GLU cc_start: 0.8686 (mp0) cc_final: 0.8455 (mp0) REVERT: C 834 GLU cc_start: 0.8405 (OUTLIER) cc_final: 0.8102 (pm20) REVERT: C 839 ASP cc_start: 0.7408 (t0) cc_final: 0.6914 (t0) REVERT: F 463 ARG cc_start: 0.8303 (OUTLIER) cc_final: 0.7980 (mmp-170) REVERT: F 565 HIS cc_start: 0.7090 (OUTLIER) cc_final: 0.6772 (p90) REVERT: F 660 GLU cc_start: 0.8719 (pp20) cc_final: 0.8483 (pp20) REVERT: F 760 GLN cc_start: 0.7581 (OUTLIER) cc_final: 0.7222 (pp30) outliers start: 147 outliers final: 52 residues processed: 348 average time/residue: 0.4900 time to fit residues: 195.5666 Evaluate side-chains 268 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 203 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 132 ASN Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 592 MET Chi-restraints excluded: chain A residue 598 THR Chi-restraints excluded: chain A residue 601 THR Chi-restraints excluded: chain A residue 647 CYS Chi-restraints excluded: chain A residue 714 PHE Chi-restraints excluded: chain A residue 721 VAL Chi-restraints excluded: chain A residue 723 HIS Chi-restraints excluded: chain A residue 746 CYS Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 814 SER Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 132 ASN Chi-restraints excluded: chain B residue 236 MET Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 332 PHE Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain B residue 463 ARG Chi-restraints excluded: chain B residue 508 VAL Chi-restraints excluded: chain B residue 601 THR Chi-restraints excluded: chain B residue 649 PHE Chi-restraints excluded: chain B residue 714 PHE Chi-restraints excluded: chain B residue 746 CYS Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 811 ILE Chi-restraints excluded: chain B residue 814 SER Chi-restraints excluded: chain B residue 835 ASP Chi-restraints excluded: chain B residue 865 ARG Chi-restraints excluded: chain C residue 463 ARG Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 499 ILE Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain C residue 525 VAL Chi-restraints excluded: chain C residue 727 HIS Chi-restraints excluded: chain C residue 830 ASP Chi-restraints excluded: chain C residue 834 GLU Chi-restraints excluded: chain C residue 845 ASN Chi-restraints excluded: chain F residue 463 ARG Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 499 ILE Chi-restraints excluded: chain F residue 508 VAL Chi-restraints excluded: chain F residue 525 VAL Chi-restraints excluded: chain F residue 565 HIS Chi-restraints excluded: chain F residue 722 CYS Chi-restraints excluded: chain F residue 746 CYS Chi-restraints excluded: chain F residue 758 THR Chi-restraints excluded: chain F residue 760 GLN Chi-restraints excluded: chain F residue 784 LEU Chi-restraints excluded: chain F residue 850 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 212 optimal weight: 0.7980 chunk 205 optimal weight: 4.9990 chunk 42 optimal weight: 10.0000 chunk 91 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 127 optimal weight: 8.9990 chunk 57 optimal weight: 7.9990 chunk 159 optimal weight: 0.6980 chunk 33 optimal weight: 9.9990 chunk 242 optimal weight: 0.0870 chunk 253 optimal weight: 8.9990 overall best weight: 1.7162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 HIS A 378 GLN ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 756 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 139 HIS ** C 454 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 565 HIS F 732 GLN F 765 GLN ** F 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.088194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.067633 restraints weight = 49500.469| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 3.92 r_work: 0.2931 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.2032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 20034 Z= 0.149 Angle : 0.625 8.885 27160 Z= 0.315 Chirality : 0.045 0.170 3106 Planarity : 0.004 0.067 3512 Dihedral : 5.979 50.847 2795 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 6.78 % Allowed : 28.78 % Favored : 64.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.85 % 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: -1.83 (0.16), residues: 2548 helix: -0.99 (0.14), residues: 1182 sheet: -0.75 (0.27), residues: 370 loop : -1.48 (0.20), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 263 TYR 0.021 0.001 TYR A 77 PHE 0.029 0.002 PHE B 514 TRP 0.016 0.001 TRP B 424 HIS 0.040 0.001 HIS F 565 Details of bonding type rmsd covalent geometry : bond 0.00339 (20034) covalent geometry : angle 0.62513 (27160) hydrogen bonds : bond 0.04080 ( 661) hydrogen bonds : angle 4.38848 ( 1911) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 208 time to evaluate : 0.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 432 ASN cc_start: 0.8986 (p0) cc_final: 0.8775 (p0) REVERT: A 592 MET cc_start: 0.9100 (OUTLIER) cc_final: 0.8633 (tmm) REVERT: A 839 ASP cc_start: 0.7938 (t70) cc_final: 0.7046 (t0) REVERT: B 1 MET cc_start: 0.7475 (ppp) cc_final: 0.7117 (pmm) REVERT: B 59 MET cc_start: 0.9432 (OUTLIER) cc_final: 0.8971 (ptt) REVERT: B 74 GLU cc_start: 0.9004 (OUTLIER) cc_final: 0.8502 (pp20) REVERT: B 91 GLU cc_start: 0.7432 (tm-30) cc_final: 0.7226 (tm-30) REVERT: B 164 LYS cc_start: 0.8882 (ttpp) cc_final: 0.8520 (ttpt) REVERT: B 432 ASN cc_start: 0.9005 (p0) cc_final: 0.8794 (p0) REVERT: B 463 ARG cc_start: 0.9073 (OUTLIER) cc_final: 0.8821 (mmt180) REVERT: B 681 LEU cc_start: 0.7598 (OUTLIER) cc_final: 0.7352 (pp) REVERT: B 733 PHE cc_start: 0.9054 (m-80) cc_final: 0.8787 (m-80) REVERT: B 865 ARG cc_start: 0.7152 (OUTLIER) cc_final: 0.6921 (ptt-90) REVERT: C 473 GLU cc_start: 0.9203 (tt0) cc_final: 0.8907 (tt0) REVERT: C 509 GLU cc_start: 0.8686 (OUTLIER) cc_final: 0.8355 (pm20) REVERT: C 519 ASP cc_start: 0.8646 (t0) cc_final: 0.8138 (t0) REVERT: C 565 HIS cc_start: 0.8345 (t70) cc_final: 0.8009 (t70) REVERT: C 766 TYR cc_start: 0.6164 (OUTLIER) cc_final: 0.5360 (m-10) REVERT: C 839 ASP cc_start: 0.7503 (t0) cc_final: 0.7064 (t0) REVERT: F 463 ARG cc_start: 0.8293 (OUTLIER) cc_final: 0.7951 (mmp-170) REVERT: F 473 GLU cc_start: 0.9066 (tt0) cc_final: 0.8846 (tt0) REVERT: F 509 GLU cc_start: 0.8834 (mp0) cc_final: 0.8221 (pm20) REVERT: F 565 HIS cc_start: 0.7203 (OUTLIER) cc_final: 0.6488 (p90) REVERT: F 567 GLU cc_start: 0.8984 (mp0) cc_final: 0.8301 (pt0) REVERT: F 765 GLN cc_start: 0.7437 (OUTLIER) cc_final: 0.7169 (mp10) outliers start: 140 outliers final: 54 residues processed: 318 average time/residue: 0.5072 time to fit residues: 184.5652 Evaluate side-chains 245 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 180 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 132 ASN Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 332 PHE Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 592 MET Chi-restraints excluded: chain A residue 723 HIS Chi-restraints excluded: chain A residue 746 CYS Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain B residue 59 MET Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 132 ASN Chi-restraints excluded: chain B residue 236 MET Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 332 PHE Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain B residue 463 ARG Chi-restraints excluded: chain B residue 508 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 665 VAL Chi-restraints excluded: chain B residue 681 LEU Chi-restraints excluded: chain B residue 746 CYS Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 811 ILE Chi-restraints excluded: chain B residue 814 SER Chi-restraints excluded: chain B residue 835 ASP Chi-restraints excluded: chain B residue 865 ARG Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 497 ASP Chi-restraints excluded: chain C residue 499 ILE Chi-restraints excluded: chain C residue 509 GLU Chi-restraints excluded: chain C residue 516 VAL Chi-restraints excluded: chain C residue 525 VAL Chi-restraints excluded: chain C residue 669 GLU Chi-restraints excluded: chain C residue 727 HIS Chi-restraints excluded: chain C residue 766 TYR Chi-restraints excluded: chain C residue 830 ASP Chi-restraints excluded: chain C residue 834 GLU Chi-restraints excluded: chain C residue 845 ASN Chi-restraints excluded: chain F residue 463 ARG Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 497 ASP Chi-restraints excluded: chain F residue 499 ILE Chi-restraints excluded: chain F residue 508 VAL Chi-restraints excluded: chain F residue 543 LEU Chi-restraints excluded: chain F residue 557 VAL Chi-restraints excluded: chain F residue 565 HIS Chi-restraints excluded: chain F residue 631 MET Chi-restraints excluded: chain F residue 647 CYS Chi-restraints excluded: chain F residue 719 LEU Chi-restraints excluded: chain F residue 723 HIS Chi-restraints excluded: chain F residue 746 CYS Chi-restraints excluded: chain F residue 758 THR Chi-restraints excluded: chain F residue 765 GLN Chi-restraints excluded: chain F residue 859 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 176 optimal weight: 0.1980 chunk 169 optimal weight: 3.9990 chunk 68 optimal weight: 7.9990 chunk 232 optimal weight: 0.8980 chunk 215 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 187 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 chunk 87 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 172 GLN A 289 ASN A 377 ASN ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 756 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 139 HIS B 377 ASN ** C 454 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 533 ASN F 565 HIS ** F 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.088746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.068456 restraints weight = 49705.356| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 3.89 r_work: 0.2941 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.2437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 20034 Z= 0.119 Angle : 0.608 9.555 27160 Z= 0.303 Chirality : 0.044 0.160 3106 Planarity : 0.004 0.068 3512 Dihedral : 5.699 51.350 2788 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 6.20 % Allowed : 29.80 % Favored : 64.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.85 % 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: -1.61 (0.16), residues: 2548 helix: -0.76 (0.15), residues: 1192 sheet: -0.66 (0.27), residues: 370 loop : -1.42 (0.20), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 773 TYR 0.028 0.001 TYR F 766 PHE 0.028 0.001 PHE A 714 TRP 0.009 0.001 TRP B 424 HIS 0.009 0.001 HIS F 565 Details of bonding type rmsd covalent geometry : bond 0.00284 (20034) covalent geometry : angle 0.60813 (27160) hydrogen bonds : bond 0.03438 ( 661) hydrogen bonds : angle 4.13416 ( 1911) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 202 time to evaluate : 0.777 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 LYS cc_start: 0.9610 (OUTLIER) cc_final: 0.9340 (tppp) REVERT: A 186 ASP cc_start: 0.9030 (OUTLIER) cc_final: 0.8603 (m-30) REVERT: A 351 ASP cc_start: 0.8119 (OUTLIER) cc_final: 0.7834 (p0) REVERT: A 592 MET cc_start: 0.9084 (OUTLIER) cc_final: 0.8584 (tmm) REVERT: A 839 ASP cc_start: 0.7849 (t70) cc_final: 0.7315 (t0) REVERT: B 59 MET cc_start: 0.9395 (ptm) cc_final: 0.8946 (ptt) REVERT: B 74 GLU cc_start: 0.8974 (OUTLIER) cc_final: 0.8499 (pp20) REVERT: B 343 MET cc_start: 0.9321 (OUTLIER) cc_final: 0.8954 (tpp) REVERT: B 638 LEU cc_start: 0.7824 (OUTLIER) cc_final: 0.7557 (pp) REVERT: B 865 ARG cc_start: 0.7229 (OUTLIER) cc_final: 0.6984 (ptt-90) REVERT: C 473 GLU cc_start: 0.9190 (tt0) cc_final: 0.8865 (tt0) REVERT: C 509 GLU cc_start: 0.8667 (OUTLIER) cc_final: 0.8358 (pm20) REVERT: C 519 ASP cc_start: 0.8305 (t0) cc_final: 0.8100 (t0) REVERT: C 565 HIS cc_start: 0.8434 (t70) cc_final: 0.8074 (t70) REVERT: C 766 TYR cc_start: 0.6140 (OUTLIER) cc_final: 0.5336 (m-10) REVERT: C 796 GLU cc_start: 0.9143 (mm-30) cc_final: 0.8756 (mm-30) REVERT: C 839 ASP cc_start: 0.7450 (t0) cc_final: 0.7053 (t70) REVERT: F 463 ARG cc_start: 0.8262 (OUTLIER) cc_final: 0.7963 (mmp-170) REVERT: F 473 GLU cc_start: 0.9058 (tt0) cc_final: 0.8824 (tt0) REVERT: F 509 GLU cc_start: 0.8885 (mp0) cc_final: 0.8238 (pm20) REVERT: F 519 ASP cc_start: 0.8248 (t0) cc_final: 0.7560 (t0) REVERT: F 555 MET cc_start: 0.8841 (OUTLIER) cc_final: 0.8323 (ptm) REVERT: F 565 HIS cc_start: 0.6819 (OUTLIER) cc_final: 0.5808 (p-80) REVERT: F 567 GLU cc_start: 0.8979 (mp0) cc_final: 0.8294 (pt0) REVERT: F 744 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8449 (pp) REVERT: F 780 ASP cc_start: 0.8594 (OUTLIER) cc_final: 0.8324 (p0) outliers start: 128 outliers final: 56 residues processed: 298 average time/residue: 0.5385 time to fit residues: 184.7817 Evaluate side-chains 254 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 183 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 132 ASN Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 332 PHE Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 351 ASP Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 493 ASN Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 592 MET Chi-restraints excluded: chain A residue 598 THR Chi-restraints excluded: chain A residue 723 HIS Chi-restraints excluded: chain A residue 733 PHE Chi-restraints excluded: chain A residue 746 CYS Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 857 ILE Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 132 ASN Chi-restraints excluded: chain B residue 236 MET Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 343 MET Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain B residue 508 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 514 PHE Chi-restraints excluded: chain B residue 638 LEU Chi-restraints excluded: chain B residue 665 VAL Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 746 CYS Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 811 ILE Chi-restraints excluded: chain B residue 814 SER Chi-restraints excluded: chain B residue 835 ASP Chi-restraints excluded: chain B residue 865 ARG Chi-restraints excluded: chain C residue 463 ARG Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 499 ILE Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain C residue 509 GLU Chi-restraints excluded: chain C residue 516 VAL Chi-restraints excluded: chain C residue 525 VAL Chi-restraints excluded: chain C residue 727 HIS Chi-restraints excluded: chain C residue 766 TYR Chi-restraints excluded: chain C residue 802 LEU Chi-restraints excluded: chain C residue 834 GLU Chi-restraints excluded: chain C residue 845 ASN Chi-restraints excluded: chain C residue 857 ILE Chi-restraints excluded: chain F residue 463 ARG Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 499 ILE Chi-restraints excluded: chain F residue 508 VAL Chi-restraints excluded: chain F residue 555 MET Chi-restraints excluded: chain F residue 557 VAL Chi-restraints excluded: chain F residue 558 MET Chi-restraints excluded: chain F residue 565 HIS Chi-restraints excluded: chain F residue 647 CYS Chi-restraints excluded: chain F residue 744 LEU Chi-restraints excluded: chain F residue 746 CYS Chi-restraints excluded: chain F residue 758 THR Chi-restraints excluded: chain F residue 780 ASP Chi-restraints excluded: chain F residue 802 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 64 optimal weight: 7.9990 chunk 198 optimal weight: 8.9990 chunk 72 optimal weight: 0.7980 chunk 71 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 145 optimal weight: 0.0370 chunk 179 optimal weight: 0.8980 chunk 168 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 63 optimal weight: 6.9990 chunk 15 optimal weight: 0.9980 overall best weight: 0.7460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 ASN A 377 ASN A 427 ASN A 432 ASN ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 756 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 139 HIS B 377 ASN B 432 ASN B 498 GLN ** C 454 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 565 HIS ** F 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.088984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.068723 restraints weight = 49317.437| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 3.88 r_work: 0.2949 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.2627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 20034 Z= 0.111 Angle : 0.601 9.259 27160 Z= 0.300 Chirality : 0.043 0.159 3106 Planarity : 0.004 0.067 3512 Dihedral : 5.423 55.595 2780 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 5.72 % Allowed : 30.28 % Favored : 64.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.85 % 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: -1.45 (0.16), residues: 2548 helix: -0.61 (0.15), residues: 1188 sheet: -0.60 (0.27), residues: 370 loop : -1.38 (0.20), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 488 TYR 0.011 0.001 TYR A 77 PHE 0.027 0.001 PHE B 714 TRP 0.011 0.001 TRP B 424 HIS 0.004 0.001 HIS A 704 Details of bonding type rmsd covalent geometry : bond 0.00263 (20034) covalent geometry : angle 0.60118 (27160) hydrogen bonds : bond 0.03233 ( 661) hydrogen bonds : angle 3.97923 ( 1911) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 197 time to evaluate : 0.735 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 LYS cc_start: 0.9608 (OUTLIER) cc_final: 0.9344 (tppp) REVERT: A 186 ASP cc_start: 0.9025 (OUTLIER) cc_final: 0.8604 (m-30) REVERT: A 351 ASP cc_start: 0.8158 (OUTLIER) cc_final: 0.7873 (p0) REVERT: A 592 MET cc_start: 0.9078 (OUTLIER) cc_final: 0.8595 (tmm) REVERT: A 839 ASP cc_start: 0.7901 (t70) cc_final: 0.7382 (t0) REVERT: B 1 MET cc_start: 0.7401 (ppp) cc_final: 0.6821 (pmm) REVERT: B 59 MET cc_start: 0.9385 (ptm) cc_final: 0.8852 (ptp) REVERT: B 74 GLU cc_start: 0.9023 (OUTLIER) cc_final: 0.8442 (pp20) REVERT: B 164 LYS cc_start: 0.9124 (ttpp) cc_final: 0.8829 (ttpp) REVERT: B 245 ILE cc_start: 0.9392 (tt) cc_final: 0.9106 (pp) REVERT: B 343 MET cc_start: 0.9313 (mmm) cc_final: 0.8971 (tpp) REVERT: B 865 ARG cc_start: 0.7189 (OUTLIER) cc_final: 0.6901 (ptt-90) REVERT: C 473 GLU cc_start: 0.9157 (tt0) cc_final: 0.8871 (tt0) REVERT: C 509 GLU cc_start: 0.8646 (OUTLIER) cc_final: 0.8320 (pm20) REVERT: C 519 ASP cc_start: 0.8649 (t0) cc_final: 0.8007 (t0) REVERT: C 565 HIS cc_start: 0.8457 (t70) cc_final: 0.8003 (t70) REVERT: C 568 GLU cc_start: 0.8625 (mp0) cc_final: 0.8361 (mp0) REVERT: C 766 TYR cc_start: 0.6185 (OUTLIER) cc_final: 0.5341 (m-10) REVERT: C 796 GLU cc_start: 0.9155 (mm-30) cc_final: 0.8778 (mm-30) REVERT: C 839 ASP cc_start: 0.7448 (t0) cc_final: 0.7031 (t70) REVERT: F 463 ARG cc_start: 0.8248 (OUTLIER) cc_final: 0.7921 (mmp-170) REVERT: F 509 GLU cc_start: 0.8886 (mp0) cc_final: 0.8269 (pm20) REVERT: F 519 ASP cc_start: 0.8219 (t0) cc_final: 0.7316 (t0) REVERT: F 555 MET cc_start: 0.8780 (OUTLIER) cc_final: 0.8216 (ptm) REVERT: F 565 HIS cc_start: 0.6498 (OUTLIER) cc_final: 0.5581 (p90) REVERT: F 567 GLU cc_start: 0.8985 (mp0) cc_final: 0.8219 (pt0) REVERT: F 744 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8416 (pp) REVERT: F 780 ASP cc_start: 0.8618 (OUTLIER) cc_final: 0.8365 (p0) outliers start: 118 outliers final: 54 residues processed: 288 average time/residue: 0.5139 time to fit residues: 170.3669 Evaluate side-chains 254 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 187 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 132 ASN Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 332 PHE Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 351 ASP Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 493 ASN Chi-restraints excluded: chain A residue 592 MET Chi-restraints excluded: chain A residue 598 THR Chi-restraints excluded: chain A residue 723 HIS Chi-restraints excluded: chain A residue 733 PHE Chi-restraints excluded: chain A residue 746 CYS Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 857 ILE Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 236 MET Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 332 PHE Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain B residue 508 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 665 VAL Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 814 SER Chi-restraints excluded: chain B residue 815 ILE Chi-restraints excluded: chain B residue 835 ASP Chi-restraints excluded: chain B residue 865 ARG Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 499 ILE Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain C residue 509 GLU Chi-restraints excluded: chain C residue 516 VAL Chi-restraints excluded: chain C residue 525 VAL Chi-restraints excluded: chain C residue 727 HIS Chi-restraints excluded: chain C residue 766 TYR Chi-restraints excluded: chain C residue 802 LEU Chi-restraints excluded: chain C residue 834 GLU Chi-restraints excluded: chain C residue 845 ASN Chi-restraints excluded: chain C residue 857 ILE Chi-restraints excluded: chain F residue 463 ARG Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 499 ILE Chi-restraints excluded: chain F residue 508 VAL Chi-restraints excluded: chain F residue 555 MET Chi-restraints excluded: chain F residue 557 VAL Chi-restraints excluded: chain F residue 558 MET Chi-restraints excluded: chain F residue 565 HIS Chi-restraints excluded: chain F residue 647 CYS Chi-restraints excluded: chain F residue 744 LEU Chi-restraints excluded: chain F residue 746 CYS Chi-restraints excluded: chain F residue 758 THR Chi-restraints excluded: chain F residue 780 ASP Chi-restraints excluded: chain F residue 802 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 233 optimal weight: 7.9990 chunk 114 optimal weight: 2.9990 chunk 132 optimal weight: 4.9990 chunk 111 optimal weight: 6.9990 chunk 178 optimal weight: 5.9990 chunk 179 optimal weight: 9.9990 chunk 102 optimal weight: 9.9990 chunk 20 optimal weight: 5.9990 chunk 215 optimal weight: 4.9990 chunk 174 optimal weight: 0.8980 chunk 2 optimal weight: 7.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 289 ASN A 377 ASN A 427 ASN ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 498 GLN ** A 756 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 781 HIS A 828 ASN ** B 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 377 ASN B 498 GLN ** B 756 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 781 HIS B 828 ASN ** C 454 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 828 ASN ** F 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 756 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 770 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 781 HIS ** F 828 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.080311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.060370 restraints weight = 49122.521| |-----------------------------------------------------------------------------| r_work (start): 0.2904 rms_B_bonded: 3.72 r_work: 0.2756 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.3680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 20034 Z= 0.281 Angle : 0.741 14.682 27160 Z= 0.378 Chirality : 0.050 0.270 3106 Planarity : 0.005 0.071 3512 Dihedral : 5.921 57.152 2775 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 6.93 % Allowed : 28.73 % Favored : 64.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.85 % 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: -1.54 (0.16), residues: 2548 helix: -0.74 (0.14), residues: 1202 sheet: -0.60 (0.27), residues: 372 loop : -1.35 (0.20), residues: 974 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG B 773 TYR 0.023 0.002 TYR B 862 PHE 0.028 0.002 PHE A 714 TRP 0.010 0.001 TRP B 424 HIS 0.058 0.002 HIS F 565 Details of bonding type rmsd covalent geometry : bond 0.00645 (20034) covalent geometry : angle 0.74098 (27160) hydrogen bonds : bond 0.04459 ( 661) hydrogen bonds : angle 4.25457 ( 1911) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 192 time to evaluate : 0.806 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 LYS cc_start: 0.9621 (OUTLIER) cc_final: 0.9297 (tppp) REVERT: A 186 ASP cc_start: 0.9116 (OUTLIER) cc_final: 0.8667 (m-30) REVERT: A 473 GLU cc_start: 0.8857 (tt0) cc_final: 0.8494 (tm-30) REVERT: A 576 ILE cc_start: 0.8945 (OUTLIER) cc_final: 0.8704 (pp) REVERT: A 592 MET cc_start: 0.9329 (OUTLIER) cc_final: 0.8602 (tmm) REVERT: A 839 ASP cc_start: 0.7780 (t70) cc_final: 0.7250 (t0) REVERT: B 59 MET cc_start: 0.9525 (OUTLIER) cc_final: 0.9180 (ptt) REVERT: B 74 GLU cc_start: 0.9018 (OUTLIER) cc_final: 0.8456 (pp20) REVERT: B 343 MET cc_start: 0.9373 (OUTLIER) cc_final: 0.8931 (tpp) REVERT: B 582 LYS cc_start: 0.8981 (ptmm) cc_final: 0.8670 (ptpt) REVERT: B 828 ASN cc_start: 0.9316 (OUTLIER) cc_final: 0.8999 (t0) REVERT: B 865 ARG cc_start: 0.8419 (OUTLIER) cc_final: 0.8147 (ptt-90) REVERT: C 473 GLU cc_start: 0.9177 (tt0) cc_final: 0.8893 (tt0) REVERT: C 519 ASP cc_start: 0.8837 (t0) cc_final: 0.8110 (t0) REVERT: C 565 HIS cc_start: 0.8461 (t70) cc_final: 0.8059 (t70) REVERT: C 567 GLU cc_start: 0.6957 (OUTLIER) cc_final: 0.6601 (pt0) REVERT: C 568 GLU cc_start: 0.8573 (mp0) cc_final: 0.8342 (mp0) REVERT: C 591 LYS cc_start: 0.8916 (ptpp) cc_final: 0.8387 (ptmt) REVERT: C 766 TYR cc_start: 0.5917 (OUTLIER) cc_final: 0.5072 (m-10) REVERT: C 853 GLU cc_start: 0.8532 (OUTLIER) cc_final: 0.8289 (pm20) REVERT: F 473 GLU cc_start: 0.9195 (tt0) cc_final: 0.8917 (tt0) REVERT: F 509 GLU cc_start: 0.8897 (mp0) cc_final: 0.8266 (pm20) REVERT: F 519 ASP cc_start: 0.8568 (t0) cc_final: 0.7887 (t0) REVERT: F 555 MET cc_start: 0.9012 (OUTLIER) cc_final: 0.8555 (ptm) REVERT: F 565 HIS cc_start: 0.7030 (p-80) cc_final: 0.6272 (p90) REVERT: F 744 LEU cc_start: 0.9153 (OUTLIER) cc_final: 0.8756 (pp) REVERT: F 780 ASP cc_start: 0.8895 (OUTLIER) cc_final: 0.8652 (p0) outliers start: 143 outliers final: 53 residues processed: 310 average time/residue: 0.5100 time to fit residues: 181.2379 Evaluate side-chains 239 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 171 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 132 ASN Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 332 PHE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 486 THR Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 576 ILE Chi-restraints excluded: chain A residue 592 MET Chi-restraints excluded: chain A residue 723 HIS Chi-restraints excluded: chain A residue 746 CYS Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 815 ILE Chi-restraints excluded: chain A residue 857 ILE Chi-restraints excluded: chain B residue 59 MET Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 332 PHE Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 343 MET Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain B residue 508 VAL Chi-restraints excluded: chain B residue 719 LEU Chi-restraints excluded: chain B residue 746 CYS Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 814 SER Chi-restraints excluded: chain B residue 815 ILE Chi-restraints excluded: chain B residue 828 ASN Chi-restraints excluded: chain B residue 835 ASP Chi-restraints excluded: chain B residue 865 ARG Chi-restraints excluded: chain C residue 463 ARG Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 499 ILE Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain C residue 516 VAL Chi-restraints excluded: chain C residue 525 VAL Chi-restraints excluded: chain C residue 558 MET Chi-restraints excluded: chain C residue 567 GLU Chi-restraints excluded: chain C residue 714 PHE Chi-restraints excluded: chain C residue 727 HIS Chi-restraints excluded: chain C residue 766 TYR Chi-restraints excluded: chain C residue 830 ASP Chi-restraints excluded: chain C residue 834 GLU Chi-restraints excluded: chain C residue 845 ASN Chi-restraints excluded: chain C residue 853 GLU Chi-restraints excluded: chain C residue 857 ILE Chi-restraints excluded: chain F residue 463 ARG Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 499 ILE Chi-restraints excluded: chain F residue 508 VAL Chi-restraints excluded: chain F residue 525 VAL Chi-restraints excluded: chain F residue 543 LEU Chi-restraints excluded: chain F residue 555 MET Chi-restraints excluded: chain F residue 647 CYS Chi-restraints excluded: chain F residue 723 HIS Chi-restraints excluded: chain F residue 744 LEU Chi-restraints excluded: chain F residue 758 THR Chi-restraints excluded: chain F residue 780 ASP Chi-restraints excluded: chain F residue 859 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 212 optimal weight: 0.6980 chunk 173 optimal weight: 0.9990 chunk 228 optimal weight: 4.9990 chunk 125 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 203 optimal weight: 4.9990 chunk 108 optimal weight: 6.9990 chunk 214 optimal weight: 1.9990 chunk 113 optimal weight: 5.9990 chunk 252 optimal weight: 5.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 GLN A 289 ASN ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 756 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 377 ASN B 498 GLN C 450 ASN ** C 454 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 565 HIS F 828 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.083121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.063271 restraints weight = 48970.987| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 3.76 r_work: 0.2821 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.3829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20034 Z= 0.133 Angle : 0.649 9.348 27160 Z= 0.326 Chirality : 0.045 0.162 3106 Planarity : 0.004 0.072 3512 Dihedral : 5.506 56.303 2772 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 4.46 % Allowed : 31.98 % Favored : 63.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.85 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.27 (0.16), residues: 2548 helix: -0.48 (0.15), residues: 1184 sheet: -0.43 (0.29), residues: 340 loop : -1.27 (0.20), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 488 TYR 0.015 0.001 TYR A 662 PHE 0.035 0.002 PHE B 714 TRP 0.010 0.001 TRP F 453 HIS 0.005 0.001 HIS A 704 Details of bonding type rmsd covalent geometry : bond 0.00319 (20034) covalent geometry : angle 0.64872 (27160) hydrogen bonds : bond 0.03299 ( 661) hydrogen bonds : angle 3.98579 ( 1911) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 201 time to evaluate : 0.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 351 ASP cc_start: 0.8220 (OUTLIER) cc_final: 0.7902 (p0) REVERT: A 354 GLU cc_start: 0.8875 (mm-30) cc_final: 0.8520 (mm-30) REVERT: A 473 GLU cc_start: 0.8811 (tt0) cc_final: 0.8543 (tm-30) REVERT: A 576 ILE cc_start: 0.8670 (OUTLIER) cc_final: 0.8421 (pp) REVERT: A 582 LYS cc_start: 0.9115 (ptmm) cc_final: 0.8809 (ptmt) REVERT: A 592 MET cc_start: 0.9232 (OUTLIER) cc_final: 0.8539 (tmm) REVERT: A 839 ASP cc_start: 0.7942 (t70) cc_final: 0.7468 (t70) REVERT: B 59 MET cc_start: 0.9447 (ptm) cc_final: 0.9058 (ptp) REVERT: B 74 GLU cc_start: 0.8975 (OUTLIER) cc_final: 0.8452 (pp20) REVERT: B 164 LYS cc_start: 0.9212 (ttpp) cc_final: 0.8897 (ttpp) REVERT: B 343 MET cc_start: 0.9334 (OUTLIER) cc_final: 0.9087 (tpp) REVERT: B 351 ASP cc_start: 0.8214 (OUTLIER) cc_final: 0.7876 (p0) REVERT: B 473 GLU cc_start: 0.8994 (tt0) cc_final: 0.8638 (tm-30) REVERT: B 487 ASP cc_start: 0.8065 (p0) cc_final: 0.7817 (p0) REVERT: B 498 GLN cc_start: 0.8753 (OUTLIER) cc_final: 0.8335 (pm20) REVERT: B 514 PHE cc_start: 0.8534 (p90) cc_final: 0.7987 (p90) REVERT: B 582 LYS cc_start: 0.8921 (ptmm) cc_final: 0.8610 (ptmt) REVERT: B 865 ARG cc_start: 0.8164 (OUTLIER) cc_final: 0.7720 (ptt-90) REVERT: C 473 GLU cc_start: 0.9168 (tt0) cc_final: 0.8847 (tt0) REVERT: C 509 GLU cc_start: 0.8660 (mp0) cc_final: 0.8054 (pm20) REVERT: C 565 HIS cc_start: 0.8474 (t70) cc_final: 0.8091 (t70) REVERT: C 591 LYS cc_start: 0.8927 (ptpp) cc_final: 0.8387 (ptmt) REVERT: C 766 TYR cc_start: 0.6001 (OUTLIER) cc_final: 0.5159 (m-10) REVERT: F 463 ARG cc_start: 0.8022 (OUTLIER) cc_final: 0.7669 (mmp-170) REVERT: F 473 GLU cc_start: 0.9152 (tt0) cc_final: 0.8836 (tt0) REVERT: F 509 GLU cc_start: 0.8882 (mp0) cc_final: 0.8211 (pm20) REVERT: F 519 ASP cc_start: 0.8426 (t0) cc_final: 0.7752 (t0) REVERT: F 565 HIS cc_start: 0.6550 (p90) cc_final: 0.6070 (p90) REVERT: F 567 GLU cc_start: 0.8817 (mp0) cc_final: 0.8166 (pt0) REVERT: F 744 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8669 (pp) REVERT: F 780 ASP cc_start: 0.8882 (OUTLIER) cc_final: 0.8643 (p0) REVERT: F 828 ASN cc_start: 0.7601 (OUTLIER) cc_final: 0.7294 (t160) outliers start: 92 outliers final: 40 residues processed: 278 average time/residue: 0.5387 time to fit residues: 171.4428 Evaluate side-chains 223 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 170 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 332 PHE Chi-restraints excluded: chain A residue 351 ASP Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 576 ILE Chi-restraints excluded: chain A residue 592 MET Chi-restraints excluded: chain A residue 723 HIS Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 814 SER Chi-restraints excluded: chain A residue 857 ILE Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 332 PHE Chi-restraints excluded: chain B residue 343 MET Chi-restraints excluded: chain B residue 351 ASP Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain B residue 498 GLN Chi-restraints excluded: chain B residue 499 ILE Chi-restraints excluded: chain B residue 580 ILE Chi-restraints excluded: chain B residue 665 VAL Chi-restraints excluded: chain B residue 746 CYS Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 814 SER Chi-restraints excluded: chain B residue 835 ASP Chi-restraints excluded: chain B residue 865 ARG Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 499 ILE Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain C residue 516 VAL Chi-restraints excluded: chain C residue 525 VAL Chi-restraints excluded: chain C residue 714 PHE Chi-restraints excluded: chain C residue 727 HIS Chi-restraints excluded: chain C residue 766 TYR Chi-restraints excluded: chain C residue 830 ASP Chi-restraints excluded: chain C residue 834 GLU Chi-restraints excluded: chain C residue 845 ASN Chi-restraints excluded: chain C residue 857 ILE Chi-restraints excluded: chain F residue 463 ARG Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 497 ASP Chi-restraints excluded: chain F residue 499 ILE Chi-restraints excluded: chain F residue 508 VAL Chi-restraints excluded: chain F residue 543 LEU Chi-restraints excluded: chain F residue 723 HIS Chi-restraints excluded: chain F residue 744 LEU Chi-restraints excluded: chain F residue 758 THR Chi-restraints excluded: chain F residue 780 ASP Chi-restraints excluded: chain F residue 828 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 53 optimal weight: 2.9990 chunk 164 optimal weight: 8.9990 chunk 74 optimal weight: 0.7980 chunk 43 optimal weight: 0.3980 chunk 213 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 246 optimal weight: 0.3980 chunk 47 optimal weight: 3.9990 chunk 51 optimal weight: 5.9990 chunk 197 optimal weight: 8.9990 chunk 249 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 ASN A 377 ASN ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 756 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 299 GLN B 377 ASN B 498 GLN C 450 ASN ** C 454 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 691 HIS F 828 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.083276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.063638 restraints weight = 48858.834| |-----------------------------------------------------------------------------| r_work (start): 0.2976 rms_B_bonded: 3.71 r_work: 0.2830 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.3967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 20034 Z= 0.127 Angle : 0.645 11.897 27160 Z= 0.324 Chirality : 0.045 0.196 3106 Planarity : 0.004 0.071 3512 Dihedral : 5.255 53.257 2768 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 3.97 % Allowed : 32.51 % Favored : 63.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.85 % 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: -1.16 (0.17), residues: 2548 helix: -0.32 (0.15), residues: 1186 sheet: -0.60 (0.28), residues: 360 loop : -1.22 (0.20), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 772 TYR 0.015 0.001 TYR B 862 PHE 0.035 0.001 PHE A 714 TRP 0.011 0.001 TRP B 424 HIS 0.005 0.001 HIS A 704 Details of bonding type rmsd covalent geometry : bond 0.00306 (20034) covalent geometry : angle 0.64525 (27160) hydrogen bonds : bond 0.03214 ( 661) hydrogen bonds : angle 3.89218 ( 1911) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 191 time to evaluate : 0.784 Fit side-chains revert: symmetry clash REVERT: A 14 GLU cc_start: 0.8978 (mp0) cc_final: 0.8696 (mp0) REVERT: A 351 ASP cc_start: 0.8215 (OUTLIER) cc_final: 0.7899 (p0) REVERT: A 354 GLU cc_start: 0.8856 (mm-30) cc_final: 0.8497 (mm-30) REVERT: A 473 GLU cc_start: 0.8807 (tt0) cc_final: 0.8516 (tm-30) REVERT: A 576 ILE cc_start: 0.8684 (OUTLIER) cc_final: 0.8442 (pp) REVERT: A 582 LYS cc_start: 0.9102 (ptmm) cc_final: 0.8794 (ttmm) REVERT: A 592 MET cc_start: 0.9212 (OUTLIER) cc_final: 0.8547 (tmm) REVERT: A 808 GLU cc_start: 0.8777 (OUTLIER) cc_final: 0.8103 (pp20) REVERT: A 839 ASP cc_start: 0.7915 (t70) cc_final: 0.7443 (t70) REVERT: B 59 MET cc_start: 0.9398 (ptm) cc_final: 0.8997 (ptp) REVERT: B 74 GLU cc_start: 0.9023 (OUTLIER) cc_final: 0.8490 (pp20) REVERT: B 164 LYS cc_start: 0.9206 (ttpp) cc_final: 0.8881 (ttpp) REVERT: B 343 MET cc_start: 0.9314 (OUTLIER) cc_final: 0.9051 (tpp) REVERT: B 351 ASP cc_start: 0.8205 (OUTLIER) cc_final: 0.7864 (p0) REVERT: B 473 GLU cc_start: 0.8996 (OUTLIER) cc_final: 0.8672 (tm-30) REVERT: B 498 GLN cc_start: 0.8840 (OUTLIER) cc_final: 0.8507 (pm20) REVERT: B 582 LYS cc_start: 0.8883 (ptmm) cc_final: 0.8580 (ptmt) REVERT: B 865 ARG cc_start: 0.8178 (OUTLIER) cc_final: 0.7802 (ptt-90) REVERT: C 473 GLU cc_start: 0.9160 (tt0) cc_final: 0.8845 (tt0) REVERT: C 509 GLU cc_start: 0.8671 (mp0) cc_final: 0.8070 (pm20) REVERT: C 565 HIS cc_start: 0.8488 (t70) cc_final: 0.8088 (t70) REVERT: C 568 GLU cc_start: 0.8567 (mp0) cc_final: 0.8315 (mp0) REVERT: C 591 LYS cc_start: 0.8903 (ptpp) cc_final: 0.8389 (ptmm) REVERT: C 766 TYR cc_start: 0.5994 (OUTLIER) cc_final: 0.5169 (m-10) REVERT: C 853 GLU cc_start: 0.8424 (OUTLIER) cc_final: 0.8021 (pm20) REVERT: F 463 ARG cc_start: 0.8037 (OUTLIER) cc_final: 0.7690 (mmp-170) REVERT: F 473 GLU cc_start: 0.9131 (tt0) cc_final: 0.8907 (tt0) REVERT: F 509 GLU cc_start: 0.8892 (mp0) cc_final: 0.8251 (pm20) REVERT: F 519 ASP cc_start: 0.8401 (t0) cc_final: 0.7772 (t0) REVERT: F 565 HIS cc_start: 0.6437 (p90) cc_final: 0.5650 (p90) REVERT: F 567 GLU cc_start: 0.8865 (mp0) cc_final: 0.8074 (pt0) REVERT: F 744 LEU cc_start: 0.9060 (OUTLIER) cc_final: 0.8678 (pp) REVERT: F 780 ASP cc_start: 0.8904 (OUTLIER) cc_final: 0.8632 (p0) REVERT: F 828 ASN cc_start: 0.7585 (OUTLIER) cc_final: 0.7217 (t160) outliers start: 82 outliers final: 43 residues processed: 255 average time/residue: 0.5209 time to fit residues: 152.2891 Evaluate side-chains 235 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 176 time to evaluate : 0.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 332 PHE Chi-restraints excluded: chain A residue 351 ASP Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 576 ILE Chi-restraints excluded: chain A residue 592 MET Chi-restraints excluded: chain A residue 723 HIS Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 808 GLU Chi-restraints excluded: chain A residue 857 ILE Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 332 PHE Chi-restraints excluded: chain B residue 343 MET Chi-restraints excluded: chain B residue 351 ASP Chi-restraints excluded: chain B residue 389 MET Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain B residue 473 GLU Chi-restraints excluded: chain B residue 498 GLN Chi-restraints excluded: chain B residue 580 ILE Chi-restraints excluded: chain B residue 665 VAL Chi-restraints excluded: chain B residue 714 PHE Chi-restraints excluded: chain B residue 746 CYS Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 814 SER Chi-restraints excluded: chain B residue 815 ILE Chi-restraints excluded: chain B residue 835 ASP Chi-restraints excluded: chain B residue 865 ARG Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 499 ILE Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain C residue 516 VAL Chi-restraints excluded: chain C residue 525 VAL Chi-restraints excluded: chain C residue 669 GLU Chi-restraints excluded: chain C residue 714 PHE Chi-restraints excluded: chain C residue 727 HIS Chi-restraints excluded: chain C residue 766 TYR Chi-restraints excluded: chain C residue 802 LEU Chi-restraints excluded: chain C residue 830 ASP Chi-restraints excluded: chain C residue 834 GLU Chi-restraints excluded: chain C residue 845 ASN Chi-restraints excluded: chain C residue 853 GLU Chi-restraints excluded: chain C residue 857 ILE Chi-restraints excluded: chain F residue 463 ARG Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 499 ILE Chi-restraints excluded: chain F residue 508 VAL Chi-restraints excluded: chain F residue 524 ILE Chi-restraints excluded: chain F residue 647 CYS Chi-restraints excluded: chain F residue 723 HIS Chi-restraints excluded: chain F residue 744 LEU Chi-restraints excluded: chain F residue 758 THR Chi-restraints excluded: chain F residue 780 ASP Chi-restraints excluded: chain F residue 828 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 169 optimal weight: 2.9990 chunk 22 optimal weight: 10.0000 chunk 142 optimal weight: 5.9990 chunk 4 optimal weight: 0.5980 chunk 196 optimal weight: 1.9990 chunk 9 optimal weight: 9.9990 chunk 56 optimal weight: 2.9990 chunk 16 optimal weight: 10.0000 chunk 221 optimal weight: 4.9990 chunk 184 optimal weight: 0.0030 chunk 224 optimal weight: 3.9990 overall best weight: 1.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 ASN A 377 ASN ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 756 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 377 ASN B 498 GLN C 450 ASN ** C 454 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 828 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.082829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.063243 restraints weight = 48699.064| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 3.72 r_work: 0.2805 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.4095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 20034 Z= 0.146 Angle : 0.650 11.628 27160 Z= 0.327 Chirality : 0.045 0.177 3106 Planarity : 0.004 0.070 3512 Dihedral : 5.247 53.826 2768 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 3.97 % Allowed : 32.80 % Favored : 63.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.85 % 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: -1.14 (0.17), residues: 2548 helix: -0.30 (0.15), residues: 1192 sheet: -0.57 (0.28), residues: 362 loop : -1.22 (0.20), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 772 TYR 0.016 0.001 TYR A 23 PHE 0.034 0.002 PHE B 489 TRP 0.015 0.001 TRP B 424 HIS 0.005 0.001 HIS A 704 Details of bonding type rmsd covalent geometry : bond 0.00350 (20034) covalent geometry : angle 0.64999 (27160) hydrogen bonds : bond 0.03285 ( 661) hydrogen bonds : angle 3.88391 ( 1911) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 187 time to evaluate : 0.781 Fit side-chains revert: symmetry clash REVERT: A 351 ASP cc_start: 0.8228 (OUTLIER) cc_final: 0.7963 (p0) REVERT: A 354 GLU cc_start: 0.8866 (mm-30) cc_final: 0.8496 (mm-30) REVERT: A 473 GLU cc_start: 0.8814 (tt0) cc_final: 0.8517 (tm-30) REVERT: A 576 ILE cc_start: 0.8702 (OUTLIER) cc_final: 0.8457 (pp) REVERT: A 582 LYS cc_start: 0.9116 (ptmm) cc_final: 0.8822 (ttmm) REVERT: A 592 MET cc_start: 0.9225 (OUTLIER) cc_final: 0.8556 (tmm) REVERT: A 808 GLU cc_start: 0.8809 (OUTLIER) cc_final: 0.8126 (pp20) REVERT: A 839 ASP cc_start: 0.7770 (t70) cc_final: 0.7300 (t70) REVERT: B 59 MET cc_start: 0.9411 (OUTLIER) cc_final: 0.9031 (ptp) REVERT: B 74 GLU cc_start: 0.9072 (OUTLIER) cc_final: 0.8509 (pp20) REVERT: B 164 LYS cc_start: 0.9211 (ttpp) cc_final: 0.8896 (ttpp) REVERT: B 343 MET cc_start: 0.9318 (OUTLIER) cc_final: 0.9048 (tpp) REVERT: B 351 ASP cc_start: 0.8214 (OUTLIER) cc_final: 0.7952 (p0) REVERT: B 354 GLU cc_start: 0.8924 (mm-30) cc_final: 0.8562 (mm-30) REVERT: B 473 GLU cc_start: 0.9014 (OUTLIER) cc_final: 0.8659 (tm-30) REVERT: B 498 GLN cc_start: 0.8877 (OUTLIER) cc_final: 0.8504 (pm20) REVERT: B 582 LYS cc_start: 0.8911 (ptmm) cc_final: 0.8652 (ptmt) REVERT: B 865 ARG cc_start: 0.8255 (OUTLIER) cc_final: 0.7941 (ptt-90) REVERT: C 473 GLU cc_start: 0.9170 (tt0) cc_final: 0.8902 (tt0) REVERT: C 509 GLU cc_start: 0.8681 (mp0) cc_final: 0.8107 (pm20) REVERT: C 565 HIS cc_start: 0.8473 (t70) cc_final: 0.8070 (t70) REVERT: C 591 LYS cc_start: 0.8931 (ptpp) cc_final: 0.8421 (ptmt) REVERT: C 766 TYR cc_start: 0.6034 (OUTLIER) cc_final: 0.5216 (m-10) REVERT: C 834 GLU cc_start: 0.8467 (OUTLIER) cc_final: 0.7981 (pm20) REVERT: C 853 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.8063 (pm20) REVERT: F 463 ARG cc_start: 0.8114 (OUTLIER) cc_final: 0.7747 (mmp-170) REVERT: F 509 GLU cc_start: 0.8865 (mp0) cc_final: 0.8233 (pm20) REVERT: F 565 HIS cc_start: 0.6442 (p90) cc_final: 0.5645 (p90) REVERT: F 567 GLU cc_start: 0.8867 (mp0) cc_final: 0.8105 (pt0) REVERT: F 744 LEU cc_start: 0.9100 (OUTLIER) cc_final: 0.8725 (pp) REVERT: F 780 ASP cc_start: 0.8967 (OUTLIER) cc_final: 0.8672 (p0) REVERT: F 828 ASN cc_start: 0.7624 (OUTLIER) cc_final: 0.7277 (OUTLIER) outliers start: 82 outliers final: 49 residues processed: 250 average time/residue: 0.5342 time to fit residues: 153.6652 Evaluate side-chains 242 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 176 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 332 PHE Chi-restraints excluded: chain A residue 351 ASP Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 499 ILE Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 576 ILE Chi-restraints excluded: chain A residue 592 MET Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 723 HIS Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 808 GLU Chi-restraints excluded: chain A residue 814 SER Chi-restraints excluded: chain A residue 815 ILE Chi-restraints excluded: chain A residue 857 ILE Chi-restraints excluded: chain B residue 59 MET Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 332 PHE Chi-restraints excluded: chain B residue 343 MET Chi-restraints excluded: chain B residue 351 ASP Chi-restraints excluded: chain B residue 389 MET Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain B residue 473 GLU Chi-restraints excluded: chain B residue 498 GLN Chi-restraints excluded: chain B residue 508 VAL Chi-restraints excluded: chain B residue 665 VAL Chi-restraints excluded: chain B residue 746 CYS Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 814 SER Chi-restraints excluded: chain B residue 815 ILE Chi-restraints excluded: chain B residue 835 ASP Chi-restraints excluded: chain B residue 865 ARG Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 499 ILE Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain C residue 516 VAL Chi-restraints excluded: chain C residue 525 VAL Chi-restraints excluded: chain C residue 669 GLU Chi-restraints excluded: chain C residue 714 PHE Chi-restraints excluded: chain C residue 727 HIS Chi-restraints excluded: chain C residue 766 TYR Chi-restraints excluded: chain C residue 802 LEU Chi-restraints excluded: chain C residue 830 ASP Chi-restraints excluded: chain C residue 834 GLU Chi-restraints excluded: chain C residue 845 ASN Chi-restraints excluded: chain C residue 853 GLU Chi-restraints excluded: chain C residue 857 ILE Chi-restraints excluded: chain F residue 463 ARG Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 499 ILE Chi-restraints excluded: chain F residue 508 VAL Chi-restraints excluded: chain F residue 524 ILE Chi-restraints excluded: chain F residue 647 CYS Chi-restraints excluded: chain F residue 723 HIS Chi-restraints excluded: chain F residue 744 LEU Chi-restraints excluded: chain F residue 758 THR Chi-restraints excluded: chain F residue 780 ASP Chi-restraints excluded: chain F residue 828 ASN Chi-restraints excluded: chain F residue 859 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 30 optimal weight: 0.6980 chunk 159 optimal weight: 5.9990 chunk 219 optimal weight: 5.9990 chunk 59 optimal weight: 9.9990 chunk 41 optimal weight: 1.9990 chunk 76 optimal weight: 9.9990 chunk 21 optimal weight: 4.9990 chunk 243 optimal weight: 5.9990 chunk 236 optimal weight: 1.9990 chunk 75 optimal weight: 6.9990 chunk 255 optimal weight: 8.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 ASN A 377 ASN ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 756 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 377 ASN B 756 ASN C 450 ASN ** C 454 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 756 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 828 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.079485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.059954 restraints weight = 49399.966| |-----------------------------------------------------------------------------| r_work (start): 0.2883 rms_B_bonded: 3.68 r_work: 0.2730 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.4444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 20034 Z= 0.215 Angle : 0.701 11.943 27160 Z= 0.356 Chirality : 0.048 0.173 3106 Planarity : 0.005 0.072 3512 Dihedral : 5.466 55.731 2768 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 3.88 % Allowed : 32.80 % Favored : 63.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.85 % 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: -1.20 (0.16), residues: 2548 helix: -0.38 (0.15), residues: 1208 sheet: -0.29 (0.29), residues: 334 loop : -1.36 (0.20), residues: 1006 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 772 TYR 0.021 0.002 TYR A 23 PHE 0.033 0.002 PHE B 714 TRP 0.013 0.001 TRP B 424 HIS 0.006 0.001 HIS C 704 Details of bonding type rmsd covalent geometry : bond 0.00504 (20034) covalent geometry : angle 0.70142 (27160) hydrogen bonds : bond 0.03717 ( 661) hydrogen bonds : angle 3.99901 ( 1911) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5096 Ramachandran restraints generated. 2548 Oldfield, 0 Emsley, 2548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 178 time to evaluate : 0.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 GLU cc_start: 0.9029 (mp0) cc_final: 0.8742 (mp0) REVERT: A 351 ASP cc_start: 0.8242 (OUTLIER) cc_final: 0.7936 (p0) REVERT: A 354 GLU cc_start: 0.8850 (mm-30) cc_final: 0.8498 (mm-30) REVERT: A 473 GLU cc_start: 0.8811 (tt0) cc_final: 0.8528 (tm-30) REVERT: A 576 ILE cc_start: 0.8824 (OUTLIER) cc_final: 0.8566 (pp) REVERT: A 582 LYS cc_start: 0.9126 (ptmm) cc_final: 0.8865 (ttmm) REVERT: A 592 MET cc_start: 0.9297 (OUTLIER) cc_final: 0.9054 (tpt) REVERT: A 808 GLU cc_start: 0.8918 (OUTLIER) cc_final: 0.8304 (pp20) REVERT: A 839 ASP cc_start: 0.7792 (t70) cc_final: 0.7275 (t70) REVERT: B 59 MET cc_start: 0.9457 (OUTLIER) cc_final: 0.9114 (ptp) REVERT: B 74 GLU cc_start: 0.9081 (OUTLIER) cc_final: 0.8526 (pp20) REVERT: B 164 LYS cc_start: 0.9187 (ttpp) cc_final: 0.8897 (ttmm) REVERT: B 343 MET cc_start: 0.9347 (OUTLIER) cc_final: 0.9082 (tpp) REVERT: B 354 GLU cc_start: 0.8897 (mm-30) cc_final: 0.8543 (mm-30) REVERT: B 473 GLU cc_start: 0.9042 (OUTLIER) cc_final: 0.8667 (tm-30) REVERT: B 865 ARG cc_start: 0.8569 (OUTLIER) cc_final: 0.8271 (ptt-90) REVERT: C 473 GLU cc_start: 0.9145 (tt0) cc_final: 0.8876 (tt0) REVERT: C 509 GLU cc_start: 0.8658 (mp0) cc_final: 0.8115 (pm20) REVERT: C 565 HIS cc_start: 0.8481 (t70) cc_final: 0.8075 (t70) REVERT: C 591 LYS cc_start: 0.8933 (ptpp) cc_final: 0.8428 (ptmt) REVERT: C 766 TYR cc_start: 0.6023 (OUTLIER) cc_final: 0.5193 (m-10) REVERT: C 853 GLU cc_start: 0.8442 (OUTLIER) cc_final: 0.8041 (pm20) REVERT: F 509 GLU cc_start: 0.8862 (mp0) cc_final: 0.8223 (pm20) REVERT: F 565 HIS cc_start: 0.6534 (p90) cc_final: 0.5850 (p90) REVERT: F 567 GLU cc_start: 0.8956 (mp0) cc_final: 0.8149 (pt0) REVERT: F 744 LEU cc_start: 0.9151 (OUTLIER) cc_final: 0.8794 (pp) outliers start: 80 outliers final: 51 residues processed: 243 average time/residue: 0.5473 time to fit residues: 152.4910 Evaluate side-chains 236 residues out of total 2064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 173 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 289 ASN Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 332 PHE Chi-restraints excluded: chain A residue 351 ASP Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 499 ILE Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 576 ILE Chi-restraints excluded: chain A residue 592 MET Chi-restraints excluded: chain A residue 616 THR Chi-restraints excluded: chain A residue 723 HIS Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 808 GLU Chi-restraints excluded: chain A residue 814 SER Chi-restraints excluded: chain A residue 815 ILE Chi-restraints excluded: chain A residue 857 ILE Chi-restraints excluded: chain B residue 59 MET Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 332 PHE Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 343 MET Chi-restraints excluded: chain B residue 389 MET Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain B residue 473 GLU Chi-restraints excluded: chain B residue 508 VAL Chi-restraints excluded: chain B residue 665 VAL Chi-restraints excluded: chain B residue 746 CYS Chi-restraints excluded: chain B residue 761 THR Chi-restraints excluded: chain B residue 814 SER Chi-restraints excluded: chain B residue 815 ILE Chi-restraints excluded: chain B residue 835 ASP Chi-restraints excluded: chain B residue 865 ARG Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 499 ILE Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain C residue 516 VAL Chi-restraints excluded: chain C residue 525 VAL Chi-restraints excluded: chain C residue 714 PHE Chi-restraints excluded: chain C residue 727 HIS Chi-restraints excluded: chain C residue 766 TYR Chi-restraints excluded: chain C residue 802 LEU Chi-restraints excluded: chain C residue 830 ASP Chi-restraints excluded: chain C residue 834 GLU Chi-restraints excluded: chain C residue 845 ASN Chi-restraints excluded: chain C residue 853 GLU Chi-restraints excluded: chain C residue 857 ILE Chi-restraints excluded: chain F residue 474 VAL Chi-restraints excluded: chain F residue 497 ASP Chi-restraints excluded: chain F residue 499 ILE Chi-restraints excluded: chain F residue 508 VAL Chi-restraints excluded: chain F residue 524 ILE Chi-restraints excluded: chain F residue 543 LEU Chi-restraints excluded: chain F residue 647 CYS Chi-restraints excluded: chain F residue 723 HIS Chi-restraints excluded: chain F residue 744 LEU Chi-restraints excluded: chain F residue 758 THR Chi-restraints excluded: chain F residue 859 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 176 optimal weight: 4.9990 chunk 99 optimal weight: 0.9980 chunk 93 optimal weight: 4.9990 chunk 74 optimal weight: 0.0970 chunk 39 optimal weight: 4.9990 chunk 60 optimal weight: 0.9980 chunk 149 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 chunk 145 optimal weight: 0.5980 chunk 61 optimal weight: 0.1980 chunk 254 optimal weight: 7.9990 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 289 ASN A 377 ASN ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 756 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 377 ASN ** B 756 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 450 ASN ** C 454 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 756 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.077556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.057729 restraints weight = 49451.785| |-----------------------------------------------------------------------------| r_work (start): 0.2849 rms_B_bonded: 3.71 r_work: 0.2690 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.4457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.226 20034 Z= 0.243 Angle : 0.945 59.052 27160 Z= 0.507 Chirality : 0.050 0.883 3106 Planarity : 0.005 0.130 3512 Dihedral : 5.479 55.716 2768 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.20 % Favored : 93.76 % Rotamer: Outliers : 3.54 % Allowed : 33.04 % Favored : 63.42 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.85 % 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 (0.16), residues: 2548 helix: -0.36 (0.15), residues: 1208 sheet: -0.29 (0.29), residues: 334 loop : -1.36 (0.20), residues: 1006 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 772 TYR 0.019 0.002 TYR B 862 PHE 0.030 0.002 PHE B 714 TRP 0.012 0.001 TRP B 424 HIS 0.005 0.001 HIS C 704 Details of bonding type rmsd covalent geometry : bond 0.00525 (20034) covalent geometry : angle 0.94458 (27160) hydrogen bonds : bond 0.03642 ( 661) hydrogen bonds : angle 4.00229 ( 1911) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5556.95 seconds wall clock time: 95 minutes 55.25 seconds (5755.25 seconds total)