Starting phenix.real_space_refine on Wed Nov 19 13:13:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6baj_7074/11_2025/6baj_7074_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6baj_7074/11_2025/6baj_7074.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6baj_7074/11_2025/6baj_7074_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6baj_7074/11_2025/6baj_7074_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6baj_7074/11_2025/6baj_7074.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6baj_7074/11_2025/6baj_7074.map" } resolution = 3.2 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= 0.003 sd= 0.027 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 29 5.49 5 S 131 5.16 5 C 15802 2.51 5 N 3829 2.21 5 O 4527 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24318 Number of models: 1 Model: "" Number of chains: 7 Chain: "B" Number of atoms: 7786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1024, 7786 Classifications: {'peptide': 1024} Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 978} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Chain: "C" Number of atoms: 7777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1023, 7777 Classifications: {'peptide': 1023} Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 977} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 2 Chain: "A" Number of atoms: 7544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 995, 7544 Classifications: {'peptide': 995} Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 949} Chain breaks: 1 Chain: "B" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 391 Unusual residues: {'D12': 6, 'PTY': 9} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 131 Unresolved non-hydrogen angles: 134 Unresolved non-hydrogen dihedrals: 127 Chain: "C" Number of atoms: 410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 410 Unusual residues: {'D12': 5, 'PTY': 11} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 200 Unresolved non-hydrogen angles: 210 Unresolved non-hydrogen dihedrals: 196 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PTY:plan-2': 2, 'PTY:plan-1': 2} Unresolved non-hydrogen planarities: 14 Chain: "A" Number of atoms: 409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 409 Unusual residues: {'PTY': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 141 Unresolved non-hydrogen angles: 141 Unresolved non-hydrogen dihedrals: 141 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 5.95, per 1000 atoms: 0.24 Number of scatterers: 24318 At special positions: 0 Unit cell: (114.4, 122.1, 146.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 131 16.00 P 29 15.00 O 4527 8.00 N 3829 7.00 C 15802 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: 2.16 Conformation dependent library (CDL) restraints added in 1.2 seconds 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5578 Finding SS restraints... Secondary structure from input PDB file: 127 helices and 25 sheets defined 52.0% alpha, 13.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.06 Creating SS restraints... Processing helix chain 'B' and resid 1 through 7 removed outlier: 3.910A pdb=" N PHE B 5 " --> pdb=" O MET B 1 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ASP B 7 " --> pdb=" O ASN B 3 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 25 removed outlier: 3.785A pdb=" N ALA B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 59 Processing helix chain 'B' and resid 61 through 66 Processing helix chain 'B' and resid 99 through 113 removed outlier: 3.604A pdb=" N LEU B 113 " --> pdb=" O ASN B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 126 Processing helix chain 'B' and resid 150 through 162 removed outlier: 3.885A pdb=" N ILE B 154 " --> pdb=" O THR B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 167 removed outlier: 3.679A pdb=" N SER B 167 " --> pdb=" O LYS B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 196 Processing helix chain 'B' and resid 199 through 207 Processing helix chain 'B' and resid 242 through 248 Processing helix chain 'B' and resid 261 through 265 removed outlier: 3.537A pdb=" N VAL B 265 " --> pdb=" O LEU B 261 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 261 through 265' Processing helix chain 'B' and resid 298 through 312 Processing helix chain 'B' and resid 313 through 317 removed outlier: 3.724A pdb=" N PHE B 317 " --> pdb=" O GLU B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 360 removed outlier: 3.784A pdb=" N VAL B 333 " --> pdb=" O THR B 329 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N VAL B 340 " --> pdb=" O SER B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 372 Processing helix chain 'B' and resid 372 through 387 removed outlier: 3.528A pdb=" N LEU B 376 " --> pdb=" O VAL B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 399 Processing helix chain 'B' and resid 401 through 423 removed outlier: 4.334A pdb=" N ASP B 408 " --> pdb=" O LEU B 404 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N ALA B 409 " --> pdb=" O LEU B 405 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N VAL B 412 " --> pdb=" O ASP B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 438 Processing helix chain 'B' and resid 438 through 450 removed outlier: 3.655A pdb=" N LEU B 442 " --> pdb=" O ILE B 438 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N VAL B 443 " --> pdb=" O GLN B 439 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER B 450 " --> pdb=" O ALA B 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 459 removed outlier: 4.257A pdb=" N PHE B 459 " --> pdb=" O MET B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 486 removed outlier: 4.055A pdb=" N GLN B 469 " --> pdb=" O ALA B 465 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N PHE B 470 " --> pdb=" O ILE B 466 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N VAL B 475 " --> pdb=" O SER B 471 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU B 483 " --> pdb=" O ALA B 479 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU B 486 " --> pdb=" O VAL B 482 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 496 removed outlier: 3.825A pdb=" N ALA B 491 " --> pdb=" O ILE B 487 " (cutoff:3.500A) Processing helix chain 'B' and resid 514 through 535 Processing helix chain 'B' and resid 538 through 558 Processing helix chain 'B' and resid 583 through 602 removed outlier: 3.845A pdb=" N THR B 587 " --> pdb=" O THR B 583 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N THR B 600 " --> pdb=" O HIS B 596 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLU B 602 " --> pdb=" O TYR B 598 " (cutoff:3.500A) Processing helix chain 'B' and resid 633 through 637 removed outlier: 3.535A pdb=" N ARG B 637 " --> pdb=" O TRP B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 643 through 655 removed outlier: 3.928A pdb=" N MET B 649 " --> pdb=" O GLU B 645 " (cutoff:3.500A) Processing helix chain 'B' and resid 674 through 678 removed outlier: 3.741A pdb=" N ALA B 677 " --> pdb=" O LEU B 674 " (cutoff:3.500A) Processing helix chain 'B' and resid 692 through 703 Processing helix chain 'B' and resid 732 through 739 removed outlier: 3.512A pdb=" N LEU B 739 " --> pdb=" O LYS B 735 " (cutoff:3.500A) Processing helix chain 'B' and resid 742 through 754 removed outlier: 4.061A pdb=" N ALA B 752 " --> pdb=" O THR B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 782 through 788 removed outlier: 3.927A pdb=" N ILE B 786 " --> pdb=" O PRO B 783 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N GLY B 787 " --> pdb=" O ASP B 784 " (cutoff:3.500A) Processing helix chain 'B' and resid 840 through 848 Processing helix chain 'B' and resid 863 through 868 Processing helix chain 'B' and resid 873 through 892 removed outlier: 3.695A pdb=" N TYR B 877 " --> pdb=" O ALA B 873 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ILE B 879 " --> pdb=" O SER B 875 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ILE B 882 " --> pdb=" O ALA B 878 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL B 883 " --> pdb=" O ILE B 879 " (cutoff:3.500A) Processing helix chain 'B' and resid 896 through 902 Processing helix chain 'B' and resid 906 through 920 removed outlier: 3.950A pdb=" N ILE B 910 " --> pdb=" O PRO B 906 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N GLY B 911 " --> pdb=" O LEU B 907 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ALA B 912 " --> pdb=" O GLY B 908 " (cutoff:3.500A) Processing helix chain 'B' and resid 924 through 951 removed outlier: 3.712A pdb=" N GLY B 936 " --> pdb=" O LEU B 932 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL B 946 " --> pdb=" O ALA B 942 " (cutoff:3.500A) Processing helix chain 'B' and resid 960 through 970 Processing helix chain 'B' and resid 972 through 981 removed outlier: 3.641A pdb=" N LEU B 976 " --> pdb=" O LEU B 972 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N MET B 977 " --> pdb=" O ARG B 973 " (cutoff:3.500A) Processing helix chain 'B' and resid 986 through 992 Processing helix chain 'B' and resid 998 through 1017 removed outlier: 4.445A pdb=" N GLY B1006 " --> pdb=" O ALA B1002 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL B1007 " --> pdb=" O VAL B1003 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N MET B1011 " --> pdb=" O VAL B1007 " (cutoff:3.500A) Processing helix chain 'B' and resid 1018 through 1020 No H-bonds generated for 'chain 'B' and resid 1018 through 1020' Processing helix chain 'B' and resid 1021 through 1032 Processing helix chain 'C' and resid 8 through 25 removed outlier: 4.198A pdb=" N ALA C 12 " --> pdb=" O ARG C 8 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE C 19 " --> pdb=" O ILE C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 61 Processing helix chain 'C' and resid 62 through 68 Processing helix chain 'C' and resid 99 through 112 removed outlier: 4.182A pdb=" N LYS C 110 " --> pdb=" O GLN C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 118 Proline residue: C 116 - end of helix No H-bonds generated for 'chain 'C' and resid 113 through 118' Processing helix chain 'C' and resid 150 through 161 Processing helix chain 'C' and resid 162 through 167 removed outlier: 3.570A pdb=" N ILE C 166 " --> pdb=" O MET C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 210 Processing helix chain 'C' and resid 242 through 248 Processing helix chain 'C' and resid 298 through 311 removed outlier: 3.737A pdb=" N ALA C 311 " --> pdb=" O ARG C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 360 removed outlier: 3.597A pdb=" N LYS C 334 " --> pdb=" O THR C 330 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE C 348 " --> pdb=" O LEU C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 369 Processing helix chain 'C' and resid 370 through 386 removed outlier: 3.673A pdb=" N VAL C 374 " --> pdb=" O ILE C 370 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N LEU C 376 " --> pdb=" O VAL C 372 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ALA C 381 " --> pdb=" O LEU C 377 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE C 386 " --> pdb=" O VAL C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 405 removed outlier: 4.775A pdb=" N GLY C 403 " --> pdb=" O VAL C 399 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LEU C 404 " --> pdb=" O LEU C 400 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 424 removed outlier: 4.327A pdb=" N VAL C 412 " --> pdb=" O ASP C 408 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLY C 424 " --> pdb=" O MET C 420 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 436 removed outlier: 3.620A pdb=" N MET C 435 " --> pdb=" O THR C 431 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLY C 436 " --> pdb=" O ARG C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 449 removed outlier: 3.641A pdb=" N VAL C 443 " --> pdb=" O GLN C 439 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N ALA C 446 " --> pdb=" O LEU C 442 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 486 removed outlier: 4.104A pdb=" N GLN C 469 " --> pdb=" O ALA C 465 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE C 470 " --> pdb=" O ILE C 466 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N THR C 473 " --> pdb=" O GLN C 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 487 through 496 removed outlier: 3.826A pdb=" N ALA C 491 " --> pdb=" O ILE C 487 " (cutoff:3.500A) Processing helix chain 'C' and resid 513 through 533 removed outlier: 3.880A pdb=" N ASN C 517 " --> pdb=" O PHE C 513 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N ARG C 518 " --> pdb=" O GLY C 514 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N MET C 519 " --> pdb=" O TRP C 515 " (cutoff:3.500A) Processing helix chain 'C' and resid 539 through 558 removed outlier: 3.592A pdb=" N VAL C 543 " --> pdb=" O GLY C 539 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N LEU C 544 " --> pdb=" O ARG C 540 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N TYR C 545 " --> pdb=" O TYR C 541 " (cutoff:3.500A) Processing helix chain 'C' and resid 583 through 601 removed outlier: 3.701A pdb=" N THR C 587 " --> pdb=" O THR C 583 " (cutoff:3.500A) Processing helix chain 'C' and resid 633 through 637 Processing helix chain 'C' and resid 643 through 655 removed outlier: 3.719A pdb=" N MET C 649 " --> pdb=" O GLU C 645 " (cutoff:3.500A) Processing helix chain 'C' and resid 692 through 698 removed outlier: 4.377A pdb=" N THR C 696 " --> pdb=" O HIS C 692 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLN C 697 " --> pdb=" O GLU C 693 " (cutoff:3.500A) Processing helix chain 'C' and resid 698 through 706 Processing helix chain 'C' and resid 732 through 739 removed outlier: 3.650A pdb=" N ALA C 736 " --> pdb=" O ASP C 732 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 755 Processing helix chain 'C' and resid 782 through 789 removed outlier: 3.706A pdb=" N ASP C 788 " --> pdb=" O ASP C 785 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TRP C 789 " --> pdb=" O ILE C 786 " (cutoff:3.500A) Processing helix chain 'C' and resid 840 through 848 Processing helix chain 'C' and resid 861 through 872 removed outlier: 3.524A pdb=" N GLU C 866 " --> pdb=" O MET C 862 " (cutoff:3.500A) Processing helix chain 'C' and resid 872 through 893 removed outlier: 3.776A pdb=" N LEU C 891 " --> pdb=" O CYS C 887 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU C 893 " --> pdb=" O ALA C 889 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 901 Processing helix chain 'C' and resid 904 through 919 removed outlier: 3.761A pdb=" N GLY C 908 " --> pdb=" O VAL C 904 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N GLY C 911 " --> pdb=" O LEU C 907 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ARG C 919 " --> pdb=" O ALA C 915 " (cutoff:3.500A) Processing helix chain 'C' and resid 924 through 957 removed outlier: 4.331A pdb=" N ALA C 939 " --> pdb=" O ILE C 935 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS C 940 " --> pdb=" O GLY C 936 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ASN C 941 " --> pdb=" O LEU C 937 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ALA C 942 " --> pdb=" O SER C 938 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ILE C 945 " --> pdb=" O ASN C 941 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N PHE C 948 " --> pdb=" O LEU C 944 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLU C 956 " --> pdb=" O LEU C 952 " (cutoff:3.500A) Processing helix chain 'C' and resid 959 through 971 removed outlier: 3.775A pdb=" N MET C 970 " --> pdb=" O ASP C 966 " (cutoff:3.500A) Processing helix chain 'C' and resid 972 through 984 removed outlier: 3.863A pdb=" N PHE C 982 " --> pdb=" O THR C 978 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU C 984 " --> pdb=" O LEU C 980 " (cutoff:3.500A) Processing helix chain 'C' and resid 986 through 991 removed outlier: 3.511A pdb=" N VAL C 990 " --> pdb=" O VAL C 986 " (cutoff:3.500A) Processing helix chain 'C' and resid 998 through 1017 removed outlier: 4.528A pdb=" N GLY C1006 " --> pdb=" O ALA C1002 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N VAL C1007 " --> pdb=" O VAL C1003 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLY C1009 " --> pdb=" O THR C1005 " (cutoff:3.500A) Processing helix chain 'C' and resid 1017 through 1022 Processing helix chain 'C' and resid 1023 through 1028 Processing helix chain 'C' and resid 1028 through 1033 Processing helix chain 'A' and resid 8 through 28 removed outlier: 3.849A pdb=" N ALA A 12 " --> pdb=" O ARG A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 61 removed outlier: 3.657A pdb=" N VAL A 61 " --> pdb=" O VAL A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 67 Processing helix chain 'A' and resid 99 through 113 removed outlier: 3.714A pdb=" N LEU A 113 " --> pdb=" O ASN A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 126 removed outlier: 3.808A pdb=" N GLN A 125 " --> pdb=" O GLU A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 162 removed outlier: 3.622A pdb=" N ILE A 154 " --> pdb=" O THR A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 196 Processing helix chain 'A' and resid 199 through 211 removed outlier: 3.812A pdb=" N VAL A 203 " --> pdb=" O THR A 199 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ILE A 204 " --> pdb=" O PRO A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 247 removed outlier: 3.748A pdb=" N GLY A 247 " --> pdb=" O THR A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 311 removed outlier: 3.513A pdb=" N ALA A 311 " --> pdb=" O ARG A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 358 removed outlier: 4.439A pdb=" N VAL A 333 " --> pdb=" O THR A 329 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LYS A 334 " --> pdb=" O THR A 330 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ILE A 348 " --> pdb=" O LEU A 344 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE A 349 " --> pdb=" O VAL A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 364 No H-bonds generated for 'chain 'A' and resid 362 through 364' Processing helix chain 'A' and resid 365 through 387 removed outlier: 4.118A pdb=" N THR A 369 " --> pdb=" O THR A 365 " (cutoff:3.500A) Proline residue: A 373 - end of helix removed outlier: 4.413A pdb=" N PHE A 380 " --> pdb=" O LEU A 376 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA A 381 " --> pdb=" O LEU A 377 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA A 385 " --> pdb=" O ALA A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 400 Processing helix chain 'A' and resid 405 through 423 removed outlier: 4.525A pdb=" N ALA A 409 " --> pdb=" O LEU A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 434 removed outlier: 3.587A pdb=" N LYS A 433 " --> pdb=" O GLU A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 438 Processing helix chain 'A' and resid 440 through 451 removed outlier: 3.520A pdb=" N GLY A 444 " --> pdb=" O GLY A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 497 removed outlier: 4.026A pdb=" N GLN A 469 " --> pdb=" O ALA A 465 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N PHE A 470 " --> pdb=" O ILE A 466 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU A 486 " --> pdb=" O VAL A 482 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N THR A 489 " --> pdb=" O ALA A 485 " (cutoff:3.500A) Proline residue: A 490 - end of helix removed outlier: 4.042A pdb=" N THR A 495 " --> pdb=" O ALA A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 557 removed outlier: 3.833A pdb=" N VAL A 550 " --> pdb=" O LEU A 546 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU A 555 " --> pdb=" O GLY A 551 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N VAL A 557 " --> pdb=" O ALA A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 602 removed outlier: 4.025A pdb=" N VAL A 590 " --> pdb=" O ARG A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 637 removed outlier: 3.835A pdb=" N ARG A 637 " --> pdb=" O TRP A 634 " (cutoff:3.500A) Processing helix chain 'A' and resid 643 through 654 removed outlier: 4.300A pdb=" N MET A 649 " --> pdb=" O GLU A 645 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N THR A 652 " --> pdb=" O THR A 648 " (cutoff:3.500A) Processing helix chain 'A' and resid 691 through 706 removed outlier: 3.974A pdb=" N LEU A 695 " --> pdb=" O GLY A 691 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA A 698 " --> pdb=" O LYS A 694 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ASN A 700 " --> pdb=" O THR A 696 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N GLN A 701 " --> pdb=" O GLN A 697 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N LEU A 702 " --> pdb=" O ALA A 698 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N LEU A 703 " --> pdb=" O ARG A 699 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 740 Processing helix chain 'A' and resid 742 through 755 Processing helix chain 'A' and resid 777 through 780 Processing helix chain 'A' and resid 782 through 788 Processing helix chain 'A' and resid 861 through 865 Processing helix chain 'A' and resid 872 through 893 removed outlier: 4.026A pdb=" N ALA A 878 " --> pdb=" O PRO A 874 " (cutoff:3.500A) Processing helix chain 'A' and resid 896 through 901 Processing helix chain 'A' and resid 904 through 920 removed outlier: 4.149A pdb=" N GLY A 911 " --> pdb=" O LEU A 907 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA A 916 " --> pdb=" O ALA A 912 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG A 919 " --> pdb=" O ALA A 915 " (cutoff:3.500A) Processing helix chain 'A' and resid 931 through 936 Processing helix chain 'A' and resid 937 through 947 removed outlier: 3.639A pdb=" N LEU A 944 " --> pdb=" O LYS A 940 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ILE A 945 " --> pdb=" O ASN A 941 " (cutoff:3.500A) Processing helix chain 'A' and resid 947 through 956 removed outlier: 4.804A pdb=" N MET A 953 " --> pdb=" O ALA A 949 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N ASP A 954 " --> pdb=" O LYS A 950 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LYS A 955 " --> pdb=" O ASP A 951 " (cutoff:3.500A) Processing helix chain 'A' and resid 960 through 987 removed outlier: 3.508A pdb=" N THR A 964 " --> pdb=" O LEU A 960 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU A 965 " --> pdb=" O ILE A 961 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N ARG A 973 " --> pdb=" O ARG A 969 " (cutoff:3.500A) Proline residue: A 974 - end of helix removed outlier: 4.177A pdb=" N ALA A 981 " --> pdb=" O MET A 977 " (cutoff:3.500A) Processing helix chain 'A' and resid 988 through 990 No H-bonds generated for 'chain 'A' and resid 988 through 990' Processing helix chain 'A' and resid 996 through 1017 removed outlier: 4.548A pdb=" N ALA A1002 " --> pdb=" O GLY A 998 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N VAL A1003 " --> pdb=" O ALA A 999 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N GLY A1006 " --> pdb=" O ALA A1002 " (cutoff:3.500A) Processing helix chain 'A' and resid 1021 through 1033 removed outlier: 3.943A pdb=" N VAL A1027 " --> pdb=" O PRO A1023 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL A1028 " --> pdb=" O VAL A1024 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 128 through 131 removed outlier: 3.682A pdb=" N THR B 87 " --> pdb=" O ASP B 83 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TYR B 77 " --> pdb=" O THR B 93 " (cutoff:3.500A) removed outlier: 12.948A pdb=" N ARG B 815 " --> pdb=" O GLU B 826 " (cutoff:3.500A) removed outlier: 9.300A pdb=" N GLU B 826 " --> pdb=" O ARG B 815 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N GLU B 817 " --> pdb=" O SER B 824 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 280 through 281 removed outlier: 4.005A pdb=" N ASN B 144 " --> pdb=" O PRO B 285 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N VAL B 139 " --> pdb=" O PRO B 326 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 266 through 267 Processing sheet with id=AA4, first strand: chain 'B' and resid 266 through 267 removed outlier: 7.804A pdb=" N TYR B 182 " --> pdb=" O VAL B 768 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N LYS B 770 " --> pdb=" O TYR B 182 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 218 through 219 removed outlier: 6.452A pdb=" N SER B 233 " --> pdb=" O PHE C 727 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ILE C 729 " --> pdb=" O SER B 233 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N ILE B 235 " --> pdb=" O ILE C 729 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N ILE C 731 " --> pdb=" O ILE B 235 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 606 through 613 Processing sheet with id=AA7, first strand: chain 'B' and resid 713 through 714 Processing sheet with id=AA8, first strand: chain 'B' and resid 808 through 811 removed outlier: 8.860A pdb=" N ILE A 235 " --> pdb=" O PRO B 725 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N PHE B 727 " --> pdb=" O ILE A 235 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 790 through 792 Processing sheet with id=AB1, first strand: chain 'C' and resid 128 through 131 removed outlier: 4.485A pdb=" N THR C 87 " --> pdb=" O ASP C 83 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASP C 83 " --> pdb=" O THR C 87 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TYR C 77 " --> pdb=" O THR C 93 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N GLU C 817 " --> pdb=" O SER C 824 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 176 through 177 removed outlier: 3.764A pdb=" N ALA C 286 " --> pdb=" O ALA C 279 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ALA C 279 " --> pdb=" O ALA C 286 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N SER C 630 " --> pdb=" O GLU C 607 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 321 through 328 removed outlier: 6.969A pdb=" N VAL C 139 " --> pdb=" O PRO C 326 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N ASN C 144 " --> pdb=" O PRO C 285 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ALA C 286 " --> pdb=" O ALA C 279 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ALA C 279 " --> pdb=" O ALA C 286 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 266 through 272 removed outlier: 8.153A pdb=" N TYR C 182 " --> pdb=" O VAL C 768 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N LYS C 770 " --> pdb=" O TYR C 182 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ASN C 760 " --> pdb=" O VAL C 771 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N VAL C 773 " --> pdb=" O TYR C 758 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N TYR C 758 " --> pdb=" O VAL C 773 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 215 through 218 removed outlier: 4.720A pdb=" N GLY C 217 " --> pdb=" O ILE C 234 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE C 234 " --> pdb=" O GLY C 217 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N SER C 233 " --> pdb=" O PHE A 727 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N ILE A 729 " --> pdb=" O SER C 233 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ILE C 235 " --> pdb=" O ILE A 729 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ILE A 731 " --> pdb=" O ILE C 235 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 681 through 682 removed outlier: 3.560A pdb=" N ARG C 717 " --> pdb=" O LEU C 828 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N GLN C 830 " --> pdb=" O SER C 715 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N SER C 715 " --> pdb=" O GLN C 830 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 791 through 792 Processing sheet with id=AB8, first strand: chain 'A' and resid 128 through 130 removed outlier: 4.063A pdb=" N THR A 87 " --> pdb=" O ASP A 83 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASP A 83 " --> pdb=" O THR A 87 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 138 through 139 Processing sheet with id=AC1, first strand: chain 'A' and resid 141 through 143 removed outlier: 3.581A pdb=" N LYS A 322 " --> pdb=" O ILE A 143 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 266 through 272 removed outlier: 8.466A pdb=" N TYR A 182 " --> pdb=" O VAL A 768 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N LYS A 770 " --> pdb=" O TYR A 182 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N TYR A 772 " --> pdb=" O MET A 184 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ASN A 760 " --> pdb=" O VAL A 771 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N VAL A 773 " --> pdb=" O TYR A 758 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N TYR A 758 " --> pdb=" O VAL A 773 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 250 through 253 removed outlier: 6.943A pdb=" N VAL A 260 " --> pdb=" O LEU A 251 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 284 through 285 removed outlier: 3.579A pdb=" N SER A 608 " --> pdb=" O SER A 630 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 284 through 285 removed outlier: 3.745A pdb=" N MET A 573 " --> pdb=" O PHE A 666 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 717 through 718 Processing sheet with id=AC7, first strand: chain 'A' and resid 790 through 792 1184 hydrogen bonds defined for protein. 3360 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: 5.40 Time building geometry restraints manager: 2.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 3900 1.30 - 1.43: 5920 1.43 - 1.56: 14573 1.56 - 1.68: 60 1.68 - 1.81: 256 Bond restraints: 24709 Sorted by residual: bond pdb=" C GLU A 314 " pdb=" N PRO A 315 " ideal model delta sigma weight residual 1.337 1.385 -0.049 9.80e-03 1.04e+04 2.49e+01 bond pdb=" C GLU C 314 " pdb=" N PRO C 315 " ideal model delta sigma weight residual 1.337 1.382 -0.046 9.80e-03 1.04e+04 2.17e+01 bond pdb=" C MET A 987 " pdb=" N PRO A 988 " ideal model delta sigma weight residual 1.334 1.370 -0.036 8.40e-03 1.42e+04 1.84e+01 bond pdb=" C8 PTY A1101 " pdb=" O7 PTY A1101 " ideal model delta sigma weight residual 1.331 1.407 -0.076 2.00e-02 2.50e+03 1.46e+01 bond pdb=" C8 PTY C1108 " pdb=" O7 PTY C1108 " ideal model delta sigma weight residual 1.331 1.405 -0.074 2.00e-02 2.50e+03 1.38e+01 ... (remaining 24704 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.67: 32361 3.67 - 7.34: 734 7.34 - 11.01: 151 11.01 - 14.67: 4 14.67 - 18.34: 29 Bond angle restraints: 33279 Sorted by residual: angle pdb=" O11 PTY B1107 " pdb=" P1 PTY B1107 " pdb=" O14 PTY B1107 " ideal model delta sigma weight residual 92.90 111.24 -18.34 3.00e+00 1.11e-01 3.74e+01 angle pdb=" O11 PTY C1101 " pdb=" P1 PTY C1101 " pdb=" O14 PTY C1101 " ideal model delta sigma weight residual 92.90 110.78 -17.88 3.00e+00 1.11e-01 3.55e+01 angle pdb=" O11 PTY A1108 " pdb=" P1 PTY A1108 " pdb=" O14 PTY A1108 " ideal model delta sigma weight residual 92.90 110.56 -17.66 3.00e+00 1.11e-01 3.46e+01 angle pdb=" O11 PTY A1110 " pdb=" P1 PTY A1110 " pdb=" O14 PTY A1110 " ideal model delta sigma weight residual 92.90 110.32 -17.42 3.00e+00 1.11e-01 3.37e+01 angle pdb=" O11 PTY B1104 " pdb=" P1 PTY B1104 " pdb=" O14 PTY B1104 " ideal model delta sigma weight residual 92.90 110.32 -17.42 3.00e+00 1.11e-01 3.37e+01 ... (remaining 33274 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.98: 14527 34.98 - 69.96: 420 69.96 - 104.94: 53 104.94 - 139.92: 16 139.92 - 174.91: 3 Dihedral angle restraints: 15019 sinusoidal: 6325 harmonic: 8694 Sorted by residual: dihedral pdb=" CA PRO B 579 " pdb=" C PRO B 579 " pdb=" N ALA B 580 " pdb=" CA ALA B 580 " ideal model delta harmonic sigma weight residual 180.00 150.49 29.51 0 5.00e+00 4.00e-02 3.48e+01 dihedral pdb=" CA ALA B 704 " pdb=" C ALA B 704 " pdb=" N GLU B 705 " pdb=" CA GLU B 705 " ideal model delta harmonic sigma weight residual 180.00 153.36 26.64 0 5.00e+00 4.00e-02 2.84e+01 dihedral pdb=" CA ILE B 207 " pdb=" C ILE B 207 " pdb=" N LYS B 208 " pdb=" CA LYS B 208 " ideal model delta harmonic sigma weight residual 180.00 153.37 26.63 0 5.00e+00 4.00e-02 2.84e+01 ... (remaining 15016 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 2937 0.066 - 0.131: 751 0.131 - 0.197: 109 0.197 - 0.263: 11 0.263 - 0.328: 7 Chirality restraints: 3815 Sorted by residual: chirality pdb=" CA LEU C 75 " pdb=" N LEU C 75 " pdb=" C LEU C 75 " pdb=" CB LEU C 75 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.69e+00 chirality pdb=" CA ASN C 74 " pdb=" N ASN C 74 " pdb=" C ASN C 74 " pdb=" CB ASN C 74 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.54e+00 chirality pdb=" CB ILE B 729 " pdb=" CA ILE B 729 " pdb=" CG1 ILE B 729 " pdb=" CG2 ILE B 729 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.30 2.00e-01 2.50e+01 2.25e+00 ... (remaining 3812 not shown) Planarity restraints: 4144 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE B 671 " 0.016 2.00e-02 2.50e+03 3.20e-02 1.02e+01 pdb=" C ILE B 671 " -0.055 2.00e-02 2.50e+03 pdb=" O ILE B 671 " 0.021 2.00e-02 2.50e+03 pdb=" N VAL B 672 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE B 982 " -0.014 2.00e-02 2.50e+03 2.82e-02 7.94e+00 pdb=" C PHE B 982 " 0.049 2.00e-02 2.50e+03 pdb=" O PHE B 982 " -0.018 2.00e-02 2.50e+03 pdb=" N ILE B 983 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU C 822 " 0.043 5.00e-02 4.00e+02 6.48e-02 6.72e+00 pdb=" N PRO C 823 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO C 823 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO C 823 " 0.035 5.00e-02 4.00e+02 ... (remaining 4141 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 551 2.68 - 3.24: 21582 3.24 - 3.79: 36525 3.79 - 4.35: 48564 4.35 - 4.90: 82611 Nonbonded interactions: 189833 Sorted by model distance: nonbonded pdb=" O ILE B 268 " pdb=" O GLU B 269 " model vdw 2.131 3.040 nonbonded pdb=" O ASN C 820 " pdb=" ND2 ASN C 820 " model vdw 2.151 3.120 nonbonded pdb=" NZ LYS B 958 " pdb=" OD2 ASP B 966 " model vdw 2.199 3.120 nonbonded pdb=" O THR B 676 " pdb=" CB ALA B 677 " model vdw 2.205 3.460 nonbonded pdb=" NH2 ARG B 307 " pdb=" OD2 ASP B 328 " model vdw 2.219 3.120 ... (remaining 189828 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 341 or (resid 342 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name CE )) or resid 343 through \ 452 or (resid 453 and (name N or name CA or name C or name CB or name CG or nam \ e CD1 or name CD2 or name CE1 or name CE2 or name CZ )) or resid 454 or (resid 4 \ 55 and (name N or name CA or name C or name O or name CB or name CG )) or resid \ 456 through 1033 or (resid 1101 and (name C1 or name C11 or name C12 or name C13 \ or name C14 or name C15 or name C16 or name C17 or name C2 or name C3 or name C \ 30 or name C31 or name C32 or name C33 or name C34 or name C35 or name C5 or nam \ e C6 or name C8 or name N1 or name O10 or name O11 or name O12 or name O13 or na \ me O14 or name O30 or name O4 or name O7 or name P1 )) or (resid 1102 and (name \ C11 or name C12 or name C13 or name C14 or name C15 or name C16 or name C17 or n \ ame C18 or name C19 or name C2 or name C3 or name C5 or name C6 or name C8 or na \ me N1 or name O10 or name O11 or name O12 or name O13 or name O14 or name O7 or \ name P1 )) or (resid 1103 and (name C1 or name C11 or name C12 or name C13 or na \ me C14 or name C15 or name C16 or name C17 or name C18 or name C2 or name C3 or \ name C30 or name C31 or name C32 or name C33 or name C5 or name C6 or name C8 or \ name N1 or name O10 or name O11 or name O12 or name O13 or name O14 or name O30 \ or name O4 or name O7 or name P1 )) or (resid 1104 and (name C11 or name C12 or \ name C13 or name C14 or name C15 or name C16 or name C8 )) or resid 1105 or (re \ sid 1106 and (name C1 or name C11 or name C12 or name C13 or name C14 or name C1 \ 5 or name C16 or name C5 or name C6 or name C8 or name N1 or name O10 or name O1 \ 1 or name O12 or name O13 or name O14 or name O30 or name O4 or name O7 or name \ P1 )) or (resid 1107 and (name C1 or name C11 or name C2 or name C3 or name C30 \ or name C31 or name C32 or name C33 or name C34 or name C35 or name C36 or name \ C37 or name C38 or name C5 or name C6 or name C8 or name N1 or name O10 or name \ O11 or name O12 or name O13 or name O14 or name O30 or name O4 or name O7 or nam \ e P1 )) or (resid 1108 and (name C1 or name C11 or name C12 or name C13 or name \ C14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C2 or na \ me C3 or name C30 or name C31 or name C32 or name C33 or name C34 or name C35 or \ name C36 or name C5 or name C6 or name C8 or name N1 or name O10 or name O11 or \ name O12 or name O13 or name O14 or name O30 or name O4 or name O7 or name P1 ) \ ))) selection = (chain 'B' and (resid 1 through 454 or (resid 455 and (name N or name CA or name \ C or name O or name CB or name CG )) or resid 456 through 499 or resid 539 thro \ ugh 1033 or resid 1102 or (resid 1103 and (name C11 or name C12 or name C13 or n \ ame C14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C2 o \ r name C3 or name C5 or name C6 or name C8 or name N1 or name O10 or name O11 or \ name O12 or name O13 or name O14 or name O7 or name P1 )) or (resid 1104 and (n \ ame C1 or name C11 or name C12 or name C13 or name C14 or name C15 or name C16 o \ r name C17 or name C18 or name C2 or name C3 or name C30 or name C31 or name C32 \ or name C33 or name C5 or name C6 or name C8 or name N1 or name O10 or name O11 \ or name O12 or name O13 or name O14 or name O30 or name O4 or name O7 or name P \ 1 )) or (resid 1105 and (name C11 or name C12 or name C13 or name C14 or name C1 \ 5 or name C16 or name C8 )) or (resid 1106 and (name C1 or name C11 or name C12 \ or name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name \ C19 or name C2 or name C20 or name C3 or name C30 or name C31 or name C32 or nam \ e C33 or name C34 or name C5 or name C6 or name C8 or name N1 or name O10 or nam \ e O11 or name O12 or name O13 or name O14 or name O30 or name O4 or name O7 or n \ ame P1 )) or (resid 1107 and (name C1 or name C11 or name C12 or name C13 or nam \ e C14 or name C15 or name C16 or name C5 or name C6 or name C8 or name N1 or nam \ e O10 or name O11 or name O12 or name O13 or name O14 or name O30 or name O4 or \ name O7 or name P1 )) or (resid 1108 and (name C1 or name C11 or name C2 or name \ C3 or name C30 or name C31 or name C32 or name C33 or name C34 or name C35 or n \ ame C36 or name C37 or name C38 or name C5 or name C6 or name C8 or name N1 or n \ ame O10 or name O11 or name O12 or name O13 or name O14 or name O30 or name O4 o \ r name O7 or name P1 )) or (resid 1109 and (name C1 or name C11 or name C12 or n \ ame C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name C19 \ or name C2 or name C3 or name C30 or name C31 or name C32 or name C33 or name C3 \ 4 or name C35 or name C36 or name C5 or name C6 or name C8 or name N1 or name O1 \ 0 or name O11 or name O12 or name O13 or name O14 or name O30 or name O4 or name \ O7 or name P1 )))) selection = (chain 'C' and (resid 1 through 341 or (resid 342 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name CE )) or resid 343 through \ 452 or (resid 453 and (name N or name CA or name C or name CB or name CG or nam \ e CD1 or name CD2 or name CE1 or name CE2 or name CZ )) or resid 454 through 499 \ or resid 539 through 1033 or (resid 1102 and (name C1 or name C11 or name C12 o \ r name C13 or name C14 or name C15 or name C16 or name C17 or name C2 or name C3 \ or name C30 or name C31 or name C32 or name C33 or name C34 or name C35 or name \ C5 or name C6 or name C8 or name N1 or name O10 or name O11 or name O12 or name \ O13 or name O14 or name O30 or name O4 or name O7 or name P1 )) or resid 1103 o \ r (resid 1104 and (name C1 or name C11 or name C12 or name C13 or name C14 or na \ me C15 or name C16 or name C17 or name C18 or name C2 or name C3 or name C30 or \ name C31 or name C32 or name C33 or name C5 or name C6 or name C8 or name N1 or \ name O10 or name O11 or name O12 or name O13 or name O14 or name O30 or name O4 \ or name O7 or name P1 )) or (resid 1105 and (name C11 or name C12 or name C13 or \ name C14 or name C15 or name C16 or name C8 )) or (resid 1106 and (name C1 or n \ ame C11 or name C12 or name C13 or name C14 or name C15 or name C16 or name C17 \ or name C18 or name C19 or name C2 or name C20 or name C3 or name C30 or name C3 \ 1 or name C32 or name C33 or name C34 or name C5 or name C6 or name C8 or name N \ 1 or name O10 or name O11 or name O12 or name O13 or name O14 or name O30 or nam \ e O4 or name O7 or name P1 )) or (resid 1107 and (name C1 or name C11 or name C1 \ 2 or name C13 or name C14 or name C15 or name C16 or name C5 or name C6 or name \ C8 or name N1 or name O10 or name O11 or name O12 or name O13 or name O14 or nam \ e O30 or name O4 or name O7 or name P1 )) or (resid 1108 and (name C1 or name C1 \ 1 or name C2 or name C3 or name C30 or name C31 or name C32 or name C33 or name \ C34 or name C35 or name C36 or name C37 or name C38 or name C5 or name C6 or nam \ e C8 or name N1 or name O10 or name O11 or name O12 or name O13 or name O14 or n \ ame O30 or name O4 or name O7 or name P1 )) or (resid 1109 and (name C1 or name \ C11 or name C12 or name C13 or name C14 or name C15 or name C16 or name C17 or n \ ame C18 or name C19 or name C2 or name C3 or name C30 or name C31 or name C32 or \ name C33 or name C34 or name C35 or name C36 or name C5 or name C6 or name C8 o \ r name N1 or name O10 or name O11 or name O12 or name O13 or name O14 or name O3 \ 0 or name O4 or name O7 or name P1 )))) } 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: 0.470 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: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 24.550 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 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 : 0.008 0.087 24709 Z= 0.363 Angle : 1.401 18.343 33279 Z= 0.637 Chirality : 0.059 0.328 3815 Planarity : 0.008 0.065 4144 Dihedral : 16.650 174.905 9441 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.43 % Allowed : 6.57 % Favored : 93.00 % Rotamer: Outliers : 1.74 % Allowed : 6.91 % Favored : 91.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: -4.66 (0.12), residues: 3030 helix: -3.10 (0.09), residues: 1492 sheet: -2.44 (0.23), residues: 407 loop : -3.03 (0.15), residues: 1131 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 717 TYR 0.039 0.003 TYR A 49 PHE 0.037 0.003 PHE A 572 TRP 0.021 0.003 TRP B 754 HIS 0.004 0.001 HIS C 338 Details of bonding type rmsd covalent geometry : bond 0.00816 (24709) covalent geometry : angle 1.40078 (33279) hydrogen bonds : bond 0.17046 ( 1162) hydrogen bonds : angle 7.59139 ( 3360) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 648 residues out of total 2476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 604 time to evaluate : 0.839 Fit side-chains revert: symmetry clash revert: symmetry clash Corrupt residue: chain: C residue: PRO 455 >>> skipping revert: symmetry clash REVERT: B 76 MET cc_start: 0.8693 (mtm) cc_final: 0.8391 (mtm) REVERT: B 184 MET cc_start: 0.8771 (tpp) cc_final: 0.8411 (tpp) REVERT: B 269 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.7562 (tp30) REVERT: B 298 ASN cc_start: 0.7515 (OUTLIER) cc_final: 0.7286 (p0) REVERT: B 391 ASN cc_start: 0.8603 (m-40) cc_final: 0.8342 (m-40) REVERT: B 456 MET cc_start: 0.9072 (ttp) cc_final: 0.8793 (ttm) REVERT: B 472 ILE cc_start: 0.7908 (pp) cc_final: 0.7610 (mt) REVERT: B 547 ILE cc_start: 0.8607 (OUTLIER) cc_final: 0.8366 (mp) REVERT: B 573 MET cc_start: 0.7706 (mpt) cc_final: 0.7322 (mpt) REVERT: B 653 ARG cc_start: 0.8090 (ttt90) cc_final: 0.7783 (mtp85) REVERT: B 662 MET cc_start: 0.6837 (mmp) cc_final: 0.6413 (mtp) REVERT: B 857 TYR cc_start: 0.8398 (p90) cc_final: 0.7806 (p90) REVERT: B 867 ARG cc_start: 0.6454 (mmt180) cc_final: 0.5973 (ttp-170) REVERT: B 987 MET cc_start: 0.7111 (mmm) cc_final: 0.6797 (tpt) REVERT: B 1008 MET cc_start: 0.7784 (tpp) cc_final: 0.7473 (tpt) REVERT: C 2 PRO cc_start: 0.8137 (Cg_exo) cc_final: 0.7860 (Cg_endo) REVERT: C 123 GLN cc_start: 0.7310 (tt0) cc_final: 0.7015 (mp10) REVERT: C 195 LYS cc_start: 0.8322 (ttpp) cc_final: 0.7874 (ttmm) REVERT: C 242 SER cc_start: 0.8998 (p) cc_final: 0.8660 (t) REVERT: C 349 ILE cc_start: 0.8331 (OUTLIER) cc_final: 0.8120 (mt) REVERT: C 353 LEU cc_start: 0.8418 (mm) cc_final: 0.8207 (mm) REVERT: C 414 GLU cc_start: 0.8130 (tm-30) cc_final: 0.7922 (tm-30) REVERT: C 435 MET cc_start: 0.7737 (tmm) cc_final: 0.7049 (tmm) REVERT: C 728 LYS cc_start: 0.8384 (tptt) cc_final: 0.7927 (tptt) REVERT: C 792 ARG cc_start: 0.7296 (ttp-170) cc_final: 0.6991 (ttp-170) REVERT: C 797 GLN cc_start: 0.6781 (mt0) cc_final: 0.6403 (mt0) REVERT: C 799 VAL cc_start: 0.8518 (m) cc_final: 0.8315 (p) REVERT: C 842 GLU cc_start: 0.7615 (tm-30) cc_final: 0.7126 (tt0) REVERT: C 948 PHE cc_start: 0.8407 (t80) cc_final: 0.8049 (t80) REVERT: A 1 MET cc_start: 0.8408 (mtm) cc_final: 0.8176 (mtp) REVERT: A 150 THR cc_start: 0.8843 (p) cc_final: 0.8586 (t) REVERT: A 226 LYS cc_start: 0.8395 (mmmm) cc_final: 0.8109 (mtmm) REVERT: A 313 MET cc_start: 0.8651 (ptp) cc_final: 0.8320 (ptp) REVERT: A 426 PRO cc_start: 0.8122 (Cg_exo) cc_final: 0.7876 (Cg_endo) REVERT: A 435 MET cc_start: 0.8359 (tmt) cc_final: 0.7192 (tmt) REVERT: A 737 GLN cc_start: 0.7925 (mm110) cc_final: 0.7707 (mt0) REVERT: A 781 MET cc_start: 0.8858 (mmp) cc_final: 0.8489 (mmt) REVERT: A 810 GLU cc_start: 0.7759 (pt0) cc_final: 0.7550 (mt-10) REVERT: A 858 ASP cc_start: 0.7585 (m-30) cc_final: 0.7212 (m-30) outliers start: 44 outliers final: 11 residues processed: 629 average time/residue: 0.1771 time to fit residues: 171.4114 Evaluate side-chains 388 residues out of total 2476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 373 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 269 GLU Chi-restraints excluded: chain B residue 298 ASN Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain B residue 547 ILE Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 76 MET Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 349 ILE Chi-restraints excluded: chain C residue 455 PRO Chi-restraints excluded: chain C residue 629 VAL Chi-restraints excluded: chain A residue 55 LYS Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 931 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 0.0970 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 5.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 338 HIS B 526 HIS B 871 ASN ** C 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 68 ASN ** C 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 181 GLN C 415 ASN ** A 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 68 ASN A 181 GLN ** A 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 298 ASN A 469 GLN A 667 ASN A 928 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.136040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.102866 restraints weight = 28721.283| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 1.96 r_work: 0.3051 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2922 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 24709 Z= 0.121 Angle : 0.643 11.307 33279 Z= 0.323 Chirality : 0.043 0.177 3815 Planarity : 0.005 0.063 4144 Dihedral : 17.357 176.753 4194 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.36 % Favored : 95.58 % Rotamer: Outliers : 2.95 % Allowed : 11.80 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: -2.84 (0.14), residues: 3030 helix: -1.31 (0.12), residues: 1505 sheet: -2.14 (0.23), residues: 427 loop : -2.38 (0.16), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 259 TYR 0.017 0.002 TYR A 356 PHE 0.024 0.001 PHE B 362 TRP 0.009 0.001 TRP B 515 HIS 0.003 0.000 HIS A 692 Details of bonding type rmsd covalent geometry : bond 0.00255 (24709) covalent geometry : angle 0.64347 (33279) hydrogen bonds : bond 0.04113 ( 1162) hydrogen bonds : angle 5.22810 ( 3360) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 526 residues out of total 2476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 452 time to evaluate : 0.926 Fit side-chains revert: symmetry clash Corrupt residue: chain: C residue: PRO 455 >>> skipping REVERT: B 1 MET cc_start: 0.8161 (OUTLIER) cc_final: 0.7854 (pmm) REVERT: B 268 ILE cc_start: 0.7591 (mm) cc_final: 0.7337 (mm) REVERT: B 407 ASP cc_start: 0.7926 (t0) cc_final: 0.7440 (t0) REVERT: B 558 ARG cc_start: 0.6733 (ttm110) cc_final: 0.6529 (ttm110) REVERT: B 573 MET cc_start: 0.7961 (mpt) cc_final: 0.7379 (mpt) REVERT: B 653 ARG cc_start: 0.8326 (ttt90) cc_final: 0.7922 (mtp85) REVERT: B 662 MET cc_start: 0.7361 (mmp) cc_final: 0.6578 (mtp) REVERT: B 711 ASP cc_start: 0.8549 (p0) cc_final: 0.7972 (m-30) REVERT: B 745 ASP cc_start: 0.7911 (m-30) cc_final: 0.7607 (t0) REVERT: B 841 MET cc_start: 0.7315 (mtp) cc_final: 0.7009 (mtm) REVERT: B 867 ARG cc_start: 0.6803 (mmt180) cc_final: 0.6119 (ttp-170) REVERT: B 947 GLU cc_start: 0.7512 (tp30) cc_final: 0.7205 (tp30) REVERT: B 976 LEU cc_start: 0.7331 (OUTLIER) cc_final: 0.6958 (mt) REVERT: B 993 THR cc_start: 0.9061 (p) cc_final: 0.8736 (m) REVERT: C 123 GLN cc_start: 0.7867 (tt0) cc_final: 0.7094 (mp10) REVERT: C 195 LYS cc_start: 0.8288 (ttpp) cc_final: 0.8047 (ttmm) REVERT: C 353 LEU cc_start: 0.8307 (mm) cc_final: 0.8073 (mm) REVERT: C 408 ASP cc_start: 0.8615 (OUTLIER) cc_final: 0.8309 (m-30) REVERT: C 568 ASP cc_start: 0.8517 (t0) cc_final: 0.8196 (t0) REVERT: C 653 ARG cc_start: 0.8472 (ttp80) cc_final: 0.8258 (ttp80) REVERT: C 728 LYS cc_start: 0.8327 (tptt) cc_final: 0.7814 (tptt) REVERT: C 797 GLN cc_start: 0.6614 (mt0) cc_final: 0.6364 (mt0) REVERT: C 842 GLU cc_start: 0.7962 (tm-30) cc_final: 0.7406 (tt0) REVERT: C 899 PHE cc_start: 0.7845 (t80) cc_final: 0.7195 (m-80) REVERT: C 948 PHE cc_start: 0.8188 (t80) cc_final: 0.7910 (t80) REVERT: C 983 ILE cc_start: 0.7964 (pt) cc_final: 0.7715 (mt) REVERT: C 1008 MET cc_start: 0.7902 (ttp) cc_final: 0.7585 (ttt) REVERT: A 1 MET cc_start: 0.8255 (mtm) cc_final: 0.8051 (mtp) REVERT: A 226 LYS cc_start: 0.8473 (mmmm) cc_final: 0.7992 (mtmm) REVERT: A 426 PRO cc_start: 0.8205 (Cg_exo) cc_final: 0.7968 (Cg_endo) REVERT: A 435 MET cc_start: 0.8089 (tmt) cc_final: 0.7107 (tmt) REVERT: A 722 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.7307 (mt-10) REVERT: A 737 GLN cc_start: 0.7999 (mm110) cc_final: 0.7794 (mt0) REVERT: A 810 GLU cc_start: 0.8051 (pt0) cc_final: 0.7652 (mt-10) REVERT: A 1008 MET cc_start: 0.7821 (tpp) cc_final: 0.7599 (tpp) outliers start: 74 outliers final: 32 residues processed: 502 average time/residue: 0.1586 time to fit residues: 128.2940 Evaluate side-chains 409 residues out of total 2476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 373 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain B residue 716 VAL Chi-restraints excluded: chain B residue 749 THR Chi-restraints excluded: chain B residue 768 VAL Chi-restraints excluded: chain B residue 900 SER Chi-restraints excluded: chain B residue 976 LEU Chi-restraints excluded: chain C residue 7 ASP Chi-restraints excluded: chain C residue 27 ILE Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 408 ASP Chi-restraints excluded: chain C residue 423 GLU Chi-restraints excluded: chain C residue 455 PRO Chi-restraints excluded: chain C residue 561 SER Chi-restraints excluded: chain C residue 937 LEU Chi-restraints excluded: chain A residue 55 LYS Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 370 ILE Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 478 MET Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 571 VAL Chi-restraints excluded: chain A residue 583 THR Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 671 ILE Chi-restraints excluded: chain A residue 722 GLU Chi-restraints excluded: chain A residue 806 SER Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 945 ILE Chi-restraints excluded: chain A residue 986 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 148 optimal weight: 2.9990 chunk 233 optimal weight: 10.0000 chunk 284 optimal weight: 20.0000 chunk 84 optimal weight: 0.7980 chunk 44 optimal weight: 4.9990 chunk 225 optimal weight: 0.7980 chunk 87 optimal weight: 5.9990 chunk 243 optimal weight: 0.9980 chunk 106 optimal weight: 3.9990 chunk 230 optimal weight: 0.4980 chunk 12 optimal weight: 5.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 391 ASN ** C 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 74 ASN ** A 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 108 GLN ** A 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.134691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.100918 restraints weight = 28869.164| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 2.07 r_work: 0.2992 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2859 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.2364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 24709 Z= 0.114 Angle : 0.598 11.942 33279 Z= 0.297 Chirality : 0.043 0.196 3815 Planarity : 0.004 0.066 4144 Dihedral : 15.713 171.646 4177 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.65 % Favored : 95.28 % Rotamer: Outliers : 3.60 % Allowed : 12.89 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.99 (0.15), residues: 3030 helix: -0.51 (0.13), residues: 1506 sheet: -1.74 (0.24), residues: 435 loop : -2.15 (0.17), residues: 1089 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 536 TYR 0.019 0.002 TYR A 356 PHE 0.024 0.001 PHE B 362 TRP 0.006 0.001 TRP B 515 HIS 0.002 0.000 HIS A 692 Details of bonding type rmsd covalent geometry : bond 0.00257 (24709) covalent geometry : angle 0.59750 (33279) hydrogen bonds : bond 0.03676 ( 1162) hydrogen bonds : angle 4.77836 ( 3360) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 2476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 391 time to evaluate : 0.933 Fit side-chains revert: symmetry clash Corrupt residue: chain: C residue: PRO 455 >>> skipping REVERT: B 1 MET cc_start: 0.7996 (OUTLIER) cc_final: 0.7768 (pmm) REVERT: B 46 SER cc_start: 0.8793 (t) cc_final: 0.8450 (p) REVERT: B 83 ASP cc_start: 0.7861 (p0) cc_final: 0.7610 (p0) REVERT: B 87 THR cc_start: 0.8371 (OUTLIER) cc_final: 0.7654 (p) REVERT: B 182 TYR cc_start: 0.8553 (OUTLIER) cc_final: 0.7728 (m-80) REVERT: B 346 GLU cc_start: 0.7714 (pt0) cc_final: 0.7118 (tp30) REVERT: B 407 ASP cc_start: 0.7978 (t0) cc_final: 0.7511 (t0) REVERT: B 573 MET cc_start: 0.7844 (mpt) cc_final: 0.7134 (mpt) REVERT: B 653 ARG cc_start: 0.8301 (ttt90) cc_final: 0.7895 (mtp85) REVERT: B 662 MET cc_start: 0.7337 (mmp) cc_final: 0.6533 (mtp) REVERT: B 711 ASP cc_start: 0.8542 (p0) cc_final: 0.7937 (m-30) REVERT: B 745 ASP cc_start: 0.7742 (m-30) cc_final: 0.7437 (t0) REVERT: B 841 MET cc_start: 0.7021 (mtp) cc_final: 0.6818 (mtm) REVERT: B 867 ARG cc_start: 0.6814 (mmt180) cc_final: 0.6068 (ttp-170) REVERT: C 118 LEU cc_start: 0.7199 (OUTLIER) cc_final: 0.6740 (mt) REVERT: C 123 GLN cc_start: 0.7963 (tt0) cc_final: 0.7103 (mp10) REVERT: C 195 LYS cc_start: 0.8237 (ttpp) cc_final: 0.8004 (ttmm) REVERT: C 322 LYS cc_start: 0.8238 (OUTLIER) cc_final: 0.7864 (ttpp) REVERT: C 408 ASP cc_start: 0.8625 (OUTLIER) cc_final: 0.8385 (m-30) REVERT: C 447 MET cc_start: 0.8530 (ttp) cc_final: 0.7808 (ttp) REVERT: C 593 GLU cc_start: 0.8291 (tp30) cc_final: 0.8079 (tp30) REVERT: C 653 ARG cc_start: 0.8450 (ttp80) cc_final: 0.8244 (ttp80) REVERT: C 728 LYS cc_start: 0.8130 (tptt) cc_final: 0.7801 (tptt) REVERT: C 842 GLU cc_start: 0.7846 (tm-30) cc_final: 0.7286 (tt0) REVERT: C 899 PHE cc_start: 0.7644 (t80) cc_final: 0.7111 (m-80) REVERT: C 948 PHE cc_start: 0.8268 (t80) cc_final: 0.8027 (t80) REVERT: C 966 ASP cc_start: 0.7894 (t70) cc_final: 0.7636 (t70) REVERT: C 1008 MET cc_start: 0.7859 (ttp) cc_final: 0.7558 (ttp) REVERT: A 398 MET cc_start: 0.8949 (mtp) cc_final: 0.8579 (mtm) REVERT: A 426 PRO cc_start: 0.8161 (Cg_exo) cc_final: 0.7915 (Cg_endo) REVERT: A 496 MET cc_start: 0.8271 (mmm) cc_final: 0.8002 (mtp) REVERT: A 722 GLU cc_start: 0.7752 (OUTLIER) cc_final: 0.7240 (mt-10) REVERT: A 737 GLN cc_start: 0.7981 (mm110) cc_final: 0.7771 (mt0) REVERT: A 810 GLU cc_start: 0.8043 (pt0) cc_final: 0.7648 (mt-10) REVERT: A 927 PHE cc_start: 0.7374 (OUTLIER) cc_final: 0.6436 (t80) REVERT: A 1008 MET cc_start: 0.7635 (tpp) cc_final: 0.7295 (tpp) outliers start: 90 outliers final: 50 residues processed: 453 average time/residue: 0.1555 time to fit residues: 114.6757 Evaluate side-chains 422 residues out of total 2476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 364 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 182 TYR Chi-restraints excluded: chain B residue 363 ARG Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 478 MET Chi-restraints excluded: chain B residue 608 SER Chi-restraints excluded: chain B residue 671 ILE Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain B residue 716 VAL Chi-restraints excluded: chain B residue 768 VAL Chi-restraints excluded: chain B residue 900 SER Chi-restraints excluded: chain B residue 901 VAL Chi-restraints excluded: chain B residue 937 LEU Chi-restraints excluded: chain C residue 7 ASP Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 322 LYS Chi-restraints excluded: chain C residue 408 ASP Chi-restraints excluded: chain C residue 455 PRO Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 561 SER Chi-restraints excluded: chain C residue 799 VAL Chi-restraints excluded: chain C residue 904 VAL Chi-restraints excluded: chain C residue 937 LEU Chi-restraints excluded: chain C residue 968 VAL Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 78 MET Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 571 VAL Chi-restraints excluded: chain A residue 583 THR Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 671 ILE Chi-restraints excluded: chain A residue 722 GLU Chi-restraints excluded: chain A residue 799 VAL Chi-restraints excluded: chain A residue 806 SER Chi-restraints excluded: chain A residue 825 MET Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 879 ILE Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 900 SER Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 927 PHE Chi-restraints excluded: chain A residue 935 ILE Chi-restraints excluded: chain A residue 984 LEU Chi-restraints excluded: chain A residue 986 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 69 optimal weight: 0.9990 chunk 175 optimal weight: 9.9990 chunk 91 optimal weight: 0.6980 chunk 260 optimal weight: 8.9990 chunk 61 optimal weight: 10.0000 chunk 227 optimal weight: 9.9990 chunk 160 optimal weight: 1.9990 chunk 112 optimal weight: 0.9990 chunk 146 optimal weight: 6.9990 chunk 180 optimal weight: 6.9990 chunk 239 optimal weight: 3.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 109 ASN B 191 ASN B 391 ASN ** C 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 68 ASN C 439 GLN C 687 GLN ** A 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 112 GLN ** A 231 ASN ** 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 = 0.3462 r_free = 0.3462 target = 0.133041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.099695 restraints weight = 28871.224| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 1.99 r_work: 0.3082 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 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 0.036 24709 Z= 0.125 Angle : 0.578 11.942 33279 Z= 0.288 Chirality : 0.042 0.201 3815 Planarity : 0.004 0.059 4144 Dihedral : 14.771 168.737 4173 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.65 % Favored : 95.28 % Rotamer: Outliers : 3.68 % Allowed : 13.58 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.49 (0.15), residues: 3030 helix: -0.09 (0.14), residues: 1513 sheet: -1.51 (0.25), residues: 435 loop : -1.92 (0.17), residues: 1082 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 536 TYR 0.019 0.002 TYR A 356 PHE 0.023 0.001 PHE A1025 TRP 0.007 0.001 TRP A 859 HIS 0.002 0.000 HIS A 692 Details of bonding type rmsd covalent geometry : bond 0.00297 (24709) covalent geometry : angle 0.57850 (33279) hydrogen bonds : bond 0.03529 ( 1162) hydrogen bonds : angle 4.59196 ( 3360) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 2476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 384 time to evaluate : 0.962 Fit side-chains revert: symmetry clash Corrupt residue: chain: C residue: PRO 455 >>> skipping REVERT: B 1 MET cc_start: 0.8336 (OUTLIER) cc_final: 0.8102 (pmm) REVERT: B 46 SER cc_start: 0.8847 (t) cc_final: 0.8609 (p) REVERT: B 87 THR cc_start: 0.8510 (OUTLIER) cc_final: 0.7808 (p) REVERT: B 177 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8266 (mt) REVERT: B 182 TYR cc_start: 0.8795 (OUTLIER) cc_final: 0.7851 (m-80) REVERT: B 346 GLU cc_start: 0.7948 (pt0) cc_final: 0.7500 (tp30) REVERT: B 407 ASP cc_start: 0.8158 (t0) cc_final: 0.7736 (t0) REVERT: B 518 ARG cc_start: 0.7914 (mtm180) cc_final: 0.7677 (mtm180) REVERT: B 573 MET cc_start: 0.7940 (mpt) cc_final: 0.7202 (mpt) REVERT: B 653 ARG cc_start: 0.8402 (ttt90) cc_final: 0.8048 (mtp85) REVERT: B 662 MET cc_start: 0.7502 (mmp) cc_final: 0.6802 (mtp) REVERT: B 711 ASP cc_start: 0.8541 (p0) cc_final: 0.7963 (m-30) REVERT: B 867 ARG cc_start: 0.7269 (mmt180) cc_final: 0.6420 (ttp-170) REVERT: B 937 LEU cc_start: 0.7858 (OUTLIER) cc_final: 0.7565 (tp) REVERT: B 947 GLU cc_start: 0.7707 (tp30) cc_final: 0.7331 (tp30) REVERT: C 118 LEU cc_start: 0.7811 (OUTLIER) cc_final: 0.7107 (mt) REVERT: C 123 GLN cc_start: 0.7950 (tt0) cc_final: 0.7266 (mp10) REVERT: C 195 LYS cc_start: 0.8325 (ttpp) cc_final: 0.8069 (ttmm) REVERT: C 309 GLU cc_start: 0.8552 (tm-30) cc_final: 0.8117 (tm-30) REVERT: C 322 LYS cc_start: 0.8489 (OUTLIER) cc_final: 0.8123 (ttpp) REVERT: C 408 ASP cc_start: 0.8664 (OUTLIER) cc_final: 0.8410 (m-30) REVERT: C 447 MET cc_start: 0.8602 (ttp) cc_final: 0.7890 (ttp) REVERT: C 593 GLU cc_start: 0.8349 (tp30) cc_final: 0.8126 (tp30) REVERT: C 684 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8543 (tm) REVERT: C 728 LYS cc_start: 0.8279 (tptt) cc_final: 0.7952 (tptt) REVERT: C 842 GLU cc_start: 0.8075 (tm-30) cc_final: 0.7568 (tt0) REVERT: C 899 PHE cc_start: 0.7893 (t80) cc_final: 0.7324 (m-80) REVERT: A 152 GLU cc_start: 0.7778 (mp0) cc_final: 0.7565 (mp0) REVERT: A 398 MET cc_start: 0.9110 (mtp) cc_final: 0.8737 (mtm) REVERT: A 496 MET cc_start: 0.8374 (mmm) cc_final: 0.8172 (mtp) REVERT: A 722 GLU cc_start: 0.7780 (OUTLIER) cc_final: 0.7283 (mt-10) REVERT: A 737 GLN cc_start: 0.8104 (mm110) cc_final: 0.7884 (mt0) REVERT: A 810 GLU cc_start: 0.8113 (pt0) cc_final: 0.7877 (mt-10) REVERT: A 902 MET cc_start: 0.8539 (mmm) cc_final: 0.8265 (mmm) REVERT: A 927 PHE cc_start: 0.7357 (OUTLIER) cc_final: 0.6331 (t80) outliers start: 92 outliers final: 52 residues processed: 448 average time/residue: 0.1589 time to fit residues: 115.9454 Evaluate side-chains 417 residues out of total 2476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 354 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 20 MET Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 182 TYR Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 562 SER Chi-restraints excluded: chain B residue 608 SER Chi-restraints excluded: chain B residue 671 ILE Chi-restraints excluded: chain B residue 672 VAL Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain B residue 716 VAL Chi-restraints excluded: chain B residue 749 THR Chi-restraints excluded: chain B residue 768 VAL Chi-restraints excluded: chain B residue 900 SER Chi-restraints excluded: chain B residue 901 VAL Chi-restraints excluded: chain B residue 917 THR Chi-restraints excluded: chain B residue 937 LEU Chi-restraints excluded: chain C residue 7 ASP Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 68 ASN Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 322 LYS Chi-restraints excluded: chain C residue 408 ASP Chi-restraints excluded: chain C residue 455 PRO Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 561 SER Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 684 LEU Chi-restraints excluded: chain C residue 743 ILE Chi-restraints excluded: chain C residue 799 VAL Chi-restraints excluded: chain C residue 904 VAL Chi-restraints excluded: chain C residue 937 LEU Chi-restraints excluded: chain C residue 938 SER Chi-restraints excluded: chain C residue 968 VAL Chi-restraints excluded: chain C residue 1025 PHE Chi-restraints excluded: chain A residue 76 MET Chi-restraints excluded: chain A residue 78 MET Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 571 VAL Chi-restraints excluded: chain A residue 583 THR Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 671 ILE Chi-restraints excluded: chain A residue 713 LEU Chi-restraints excluded: chain A residue 722 GLU Chi-restraints excluded: chain A residue 799 VAL Chi-restraints excluded: chain A residue 825 MET Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 900 SER Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 927 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 265 optimal weight: 9.9990 chunk 271 optimal weight: 4.9990 chunk 175 optimal weight: 7.9990 chunk 73 optimal weight: 3.9990 chunk 166 optimal weight: 9.9990 chunk 129 optimal weight: 8.9990 chunk 182 optimal weight: 10.0000 chunk 80 optimal weight: 9.9990 chunk 116 optimal weight: 4.9990 chunk 126 optimal weight: 0.9990 chunk 169 optimal weight: 1.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 ASN B 391 ASN ** C 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 692 HIS C 865 GLN ** A 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 231 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 = 0.3413 r_free = 0.3413 target = 0.128792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.095332 restraints weight = 29001.784| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 1.99 r_work: 0.2938 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2811 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.2801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 24709 Z= 0.186 Angle : 0.632 12.904 33279 Z= 0.314 Chirality : 0.045 0.207 3815 Planarity : 0.004 0.053 4144 Dihedral : 14.495 168.360 4173 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.38 % Favored : 94.55 % Rotamer: Outliers : 4.32 % Allowed : 13.78 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.38 (0.15), residues: 3030 helix: 0.02 (0.14), residues: 1521 sheet: -1.46 (0.25), residues: 433 loop : -1.91 (0.17), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 653 TYR 0.022 0.002 TYR B 49 PHE 0.023 0.002 PHE A1025 TRP 0.009 0.001 TRP A 859 HIS 0.003 0.001 HIS A 692 Details of bonding type rmsd covalent geometry : bond 0.00463 (24709) covalent geometry : angle 0.63225 (33279) hydrogen bonds : bond 0.03997 ( 1162) hydrogen bonds : angle 4.60934 ( 3360) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 2476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 347 time to evaluate : 0.935 Fit side-chains revert: symmetry clash Corrupt residue: chain: C residue: PRO 455 >>> skipping REVERT: B 1 MET cc_start: 0.8235 (OUTLIER) cc_final: 0.7922 (pmm) REVERT: B 46 SER cc_start: 0.8838 (t) cc_final: 0.8518 (p) REVERT: B 312 LYS cc_start: 0.7980 (OUTLIER) cc_final: 0.7606 (ptmm) REVERT: B 346 GLU cc_start: 0.7771 (pt0) cc_final: 0.7390 (tp30) REVERT: B 407 ASP cc_start: 0.8323 (t0) cc_final: 0.7776 (t0) REVERT: B 573 MET cc_start: 0.7903 (mpt) cc_final: 0.7159 (mpt) REVERT: B 653 ARG cc_start: 0.8223 (ttt90) cc_final: 0.7787 (mtp85) REVERT: B 662 MET cc_start: 0.7321 (mmp) cc_final: 0.6572 (mtp) REVERT: B 711 ASP cc_start: 0.8516 (p0) cc_final: 0.7943 (m-30) REVERT: B 867 ARG cc_start: 0.7323 (mmt180) cc_final: 0.6361 (ttp-170) REVERT: C 118 LEU cc_start: 0.7638 (OUTLIER) cc_final: 0.6886 (mt) REVERT: C 123 GLN cc_start: 0.8045 (tt0) cc_final: 0.7149 (mp10) REVERT: C 195 LYS cc_start: 0.8309 (ttpp) cc_final: 0.8074 (ttmm) REVERT: C 322 LYS cc_start: 0.8291 (OUTLIER) cc_final: 0.7906 (ttpp) REVERT: C 353 LEU cc_start: 0.8286 (OUTLIER) cc_final: 0.8043 (mm) REVERT: C 447 MET cc_start: 0.8492 (ttp) cc_final: 0.7790 (ttp) REVERT: C 486 LEU cc_start: 0.7931 (OUTLIER) cc_final: 0.7717 (mp) REVERT: C 593 GLU cc_start: 0.8334 (tp30) cc_final: 0.8034 (tp30) REVERT: C 684 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.8364 (tm) REVERT: C 774 MET cc_start: 0.8323 (OUTLIER) cc_final: 0.7857 (ttt) REVERT: C 842 GLU cc_start: 0.7948 (tm-30) cc_final: 0.7485 (tt0) REVERT: C 899 PHE cc_start: 0.7876 (t80) cc_final: 0.7307 (m-80) REVERT: A 152 GLU cc_start: 0.7863 (mp0) cc_final: 0.7609 (mt-10) REVERT: A 398 MET cc_start: 0.9010 (mtp) cc_final: 0.8752 (mtm) REVERT: A 447 MET cc_start: 0.8712 (OUTLIER) cc_final: 0.8233 (mpp) REVERT: A 722 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.7399 (mt-10) REVERT: A 737 GLN cc_start: 0.8127 (mm110) cc_final: 0.7903 (mt0) REVERT: A 810 GLU cc_start: 0.8106 (pt0) cc_final: 0.7771 (mt-10) REVERT: A 902 MET cc_start: 0.8493 (mmm) cc_final: 0.8178 (mmm) REVERT: A 927 PHE cc_start: 0.7511 (OUTLIER) cc_final: 0.6496 (t80) outliers start: 108 outliers final: 64 residues processed: 423 average time/residue: 0.1594 time to fit residues: 110.1222 Evaluate side-chains 406 residues out of total 2476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 331 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 20 MET Chi-restraints excluded: chain B residue 62 THR Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 312 LYS Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 671 ILE Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain B residue 716 VAL Chi-restraints excluded: chain B residue 749 THR Chi-restraints excluded: chain B residue 900 SER Chi-restraints excluded: chain B residue 901 VAL Chi-restraints excluded: chain B residue 917 THR Chi-restraints excluded: chain B residue 937 LEU Chi-restraints excluded: chain B residue 965 LEU Chi-restraints excluded: chain B residue 1029 VAL Chi-restraints excluded: chain C residue 7 ASP Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 322 LYS Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 423 GLU Chi-restraints excluded: chain C residue 455 PRO Chi-restraints excluded: chain C residue 486 LEU Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 552 MET Chi-restraints excluded: chain C residue 561 SER Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 684 LEU Chi-restraints excluded: chain C residue 739 LEU Chi-restraints excluded: chain C residue 743 ILE Chi-restraints excluded: chain C residue 774 MET Chi-restraints excluded: chain C residue 799 VAL Chi-restraints excluded: chain C residue 937 LEU Chi-restraints excluded: chain C residue 938 SER Chi-restraints excluded: chain C residue 943 ILE Chi-restraints excluded: chain C residue 968 VAL Chi-restraints excluded: chain C residue 1025 PHE Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 76 MET Chi-restraints excluded: chain A residue 78 MET Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 447 MET Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 571 VAL Chi-restraints excluded: chain A residue 583 THR Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 671 ILE Chi-restraints excluded: chain A residue 713 LEU Chi-restraints excluded: chain A residue 722 GLU Chi-restraints excluded: chain A residue 799 VAL Chi-restraints excluded: chain A residue 806 SER Chi-restraints excluded: chain A residue 825 MET Chi-restraints excluded: chain A residue 828 LEU Chi-restraints excluded: chain A residue 879 ILE Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 900 SER Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 927 PHE Chi-restraints excluded: chain A residue 986 VAL Chi-restraints excluded: chain A residue 1016 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 4 optimal weight: 1.9990 chunk 287 optimal weight: 0.9990 chunk 250 optimal weight: 0.6980 chunk 228 optimal weight: 0.5980 chunk 140 optimal weight: 0.7980 chunk 261 optimal weight: 9.9990 chunk 91 optimal weight: 0.8980 chunk 147 optimal weight: 7.9990 chunk 192 optimal weight: 3.9990 chunk 39 optimal weight: 0.7980 chunk 149 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.139527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.107811 restraints weight = 28699.438| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 1.93 r_work: 0.3013 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2876 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.3003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 24709 Z= 0.099 Angle : 0.554 10.152 33279 Z= 0.276 Chirality : 0.042 0.237 3815 Planarity : 0.004 0.055 4144 Dihedral : 13.648 165.866 4173 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.06 % Favored : 95.87 % Rotamer: Outliers : 3.03 % Allowed : 15.36 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.15), residues: 3030 helix: 0.36 (0.14), residues: 1507 sheet: -1.41 (0.25), residues: 429 loop : -1.69 (0.18), residues: 1094 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 536 TYR 0.017 0.001 TYR A 327 PHE 0.023 0.001 PHE A1025 TRP 0.007 0.001 TRP B 515 HIS 0.002 0.000 HIS C 596 Details of bonding type rmsd covalent geometry : bond 0.00215 (24709) covalent geometry : angle 0.55355 (33279) hydrogen bonds : bond 0.03212 ( 1162) hydrogen bonds : angle 4.39731 ( 3360) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 2476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 363 time to evaluate : 0.905 Fit side-chains revert: symmetry clash Corrupt residue: chain: C residue: PRO 455 >>> skipping REVERT: B 1 MET cc_start: 0.8357 (OUTLIER) cc_final: 0.8145 (pmm) REVERT: B 87 THR cc_start: 0.8594 (OUTLIER) cc_final: 0.8036 (p) REVERT: B 142 VAL cc_start: 0.8152 (OUTLIER) cc_final: 0.7943 (t) REVERT: B 177 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8187 (mt) REVERT: B 312 LYS cc_start: 0.8046 (OUTLIER) cc_final: 0.7750 (ptmm) REVERT: B 407 ASP cc_start: 0.8343 (t0) cc_final: 0.8027 (t0) REVERT: B 518 ARG cc_start: 0.7954 (mtm180) cc_final: 0.7703 (mtm180) REVERT: B 573 MET cc_start: 0.7820 (mpt) cc_final: 0.7061 (mpt) REVERT: B 653 ARG cc_start: 0.8423 (ttt90) cc_final: 0.8005 (mtp85) REVERT: B 662 MET cc_start: 0.7500 (mmp) cc_final: 0.6884 (mtp) REVERT: B 729 ILE cc_start: 0.7813 (pt) cc_final: 0.7483 (pt) REVERT: B 867 ARG cc_start: 0.7501 (mmt180) cc_final: 0.6670 (ttp-170) REVERT: B 937 LEU cc_start: 0.8064 (OUTLIER) cc_final: 0.7796 (tp) REVERT: C 7 ASP cc_start: 0.8003 (OUTLIER) cc_final: 0.7688 (p0) REVERT: C 123 GLN cc_start: 0.7903 (tt0) cc_final: 0.7268 (mp10) REVERT: C 195 LYS cc_start: 0.8371 (ttpp) cc_final: 0.8109 (ttmm) REVERT: C 309 GLU cc_start: 0.8545 (tm-30) cc_final: 0.8108 (tm-30) REVERT: C 322 LYS cc_start: 0.8444 (OUTLIER) cc_final: 0.8120 (ttpp) REVERT: C 447 MET cc_start: 0.8518 (ttp) cc_final: 0.8105 (tpp) REVERT: C 593 GLU cc_start: 0.8304 (tp30) cc_final: 0.8050 (tp30) REVERT: C 774 MET cc_start: 0.8220 (mmm) cc_final: 0.7735 (ttt) REVERT: C 841 MET cc_start: 0.9041 (ttp) cc_final: 0.8840 (mtp) REVERT: C 842 GLU cc_start: 0.8080 (tm-30) cc_final: 0.7628 (tt0) REVERT: C 899 PHE cc_start: 0.8043 (t80) cc_final: 0.7448 (m-80) REVERT: C 1008 MET cc_start: 0.8144 (ttp) cc_final: 0.7858 (ttt) REVERT: A 398 MET cc_start: 0.9084 (mtp) cc_final: 0.8789 (mtm) REVERT: A 718 PRO cc_start: 0.7517 (Cg_exo) cc_final: 0.7310 (Cg_endo) REVERT: A 722 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.7538 (mt-10) REVERT: A 737 GLN cc_start: 0.8168 (mm110) cc_final: 0.7920 (mt0) REVERT: A 927 PHE cc_start: 0.7507 (OUTLIER) cc_final: 0.7086 (t80) outliers start: 76 outliers final: 50 residues processed: 417 average time/residue: 0.1594 time to fit residues: 109.4110 Evaluate side-chains 399 residues out of total 2476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 339 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 312 LYS Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 363 ARG Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 478 MET Chi-restraints excluded: chain B residue 604 ASN Chi-restraints excluded: chain B residue 671 ILE Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain B residue 716 VAL Chi-restraints excluded: chain B residue 768 VAL Chi-restraints excluded: chain B residue 900 SER Chi-restraints excluded: chain B residue 937 LEU Chi-restraints excluded: chain B residue 965 LEU Chi-restraints excluded: chain B residue 1029 VAL Chi-restraints excluded: chain C residue 7 ASP Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 322 LYS Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 455 PRO Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 552 MET Chi-restraints excluded: chain C residue 561 SER Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 743 ILE Chi-restraints excluded: chain C residue 799 VAL Chi-restraints excluded: chain C residue 937 LEU Chi-restraints excluded: chain C residue 938 SER Chi-restraints excluded: chain C residue 943 ILE Chi-restraints excluded: chain C residue 968 VAL Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 78 MET Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 478 MET Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 571 VAL Chi-restraints excluded: chain A residue 583 THR Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 671 ILE Chi-restraints excluded: chain A residue 713 LEU Chi-restraints excluded: chain A residue 722 GLU Chi-restraints excluded: chain A residue 825 MET Chi-restraints excluded: chain A residue 879 ILE Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 927 PHE Chi-restraints excluded: chain A residue 935 ILE Chi-restraints excluded: chain A residue 1016 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 69 optimal weight: 0.9980 chunk 184 optimal weight: 1.9990 chunk 128 optimal weight: 9.9990 chunk 146 optimal weight: 4.9990 chunk 191 optimal weight: 1.9990 chunk 173 optimal weight: 9.9990 chunk 187 optimal weight: 0.9990 chunk 263 optimal weight: 6.9990 chunk 145 optimal weight: 5.9990 chunk 138 optimal weight: 9.9990 chunk 150 optimal weight: 0.7980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 67 GLN C 439 GLN ** A 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 81 ASN ** A 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.132729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.099262 restraints weight = 28720.653| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 1.98 r_work: 0.2989 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2861 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.3123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 24709 Z= 0.111 Angle : 0.566 10.707 33279 Z= 0.280 Chirality : 0.042 0.228 3815 Planarity : 0.004 0.043 4144 Dihedral : 13.198 160.224 4173 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.39 % Favored : 95.54 % Rotamer: Outliers : 3.48 % Allowed : 16.05 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.15), residues: 3030 helix: 0.49 (0.14), residues: 1508 sheet: -1.30 (0.25), residues: 429 loop : -1.60 (0.18), residues: 1093 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 653 TYR 0.021 0.001 TYR A 356 PHE 0.023 0.001 PHE A1025 TRP 0.008 0.001 TRP A 859 HIS 0.001 0.000 HIS C 596 Details of bonding type rmsd covalent geometry : bond 0.00261 (24709) covalent geometry : angle 0.56604 (33279) hydrogen bonds : bond 0.03258 ( 1162) hydrogen bonds : angle 4.34618 ( 3360) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 2476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 350 time to evaluate : 0.939 Fit side-chains revert: symmetry clash Corrupt residue: chain: C residue: PRO 455 >>> skipping REVERT: B 1 MET cc_start: 0.8045 (OUTLIER) cc_final: 0.7813 (pmm) REVERT: B 87 THR cc_start: 0.8429 (OUTLIER) cc_final: 0.7765 (p) REVERT: B 177 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8249 (mt) REVERT: B 312 LYS cc_start: 0.7687 (OUTLIER) cc_final: 0.7424 (ptmm) REVERT: B 407 ASP cc_start: 0.8249 (t0) cc_final: 0.7775 (t0) REVERT: B 573 MET cc_start: 0.7657 (mpt) cc_final: 0.6786 (mpt) REVERT: B 653 ARG cc_start: 0.8228 (ttt90) cc_final: 0.7751 (mtp85) REVERT: B 662 MET cc_start: 0.7251 (mmp) cc_final: 0.6505 (mtp) REVERT: B 711 ASP cc_start: 0.8481 (p0) cc_final: 0.7882 (m-30) REVERT: B 729 ILE cc_start: 0.7369 (pt) cc_final: 0.7061 (pt) REVERT: B 867 ARG cc_start: 0.7268 (mmt180) cc_final: 0.6396 (ttp-170) REVERT: B 937 LEU cc_start: 0.7552 (OUTLIER) cc_final: 0.7292 (tp) REVERT: C 7 ASP cc_start: 0.7870 (OUTLIER) cc_final: 0.7526 (p0) REVERT: C 118 LEU cc_start: 0.7368 (OUTLIER) cc_final: 0.6841 (mt) REVERT: C 123 GLN cc_start: 0.8085 (tt0) cc_final: 0.7231 (mp10) REVERT: C 195 LYS cc_start: 0.8245 (ttpp) cc_final: 0.7995 (ttmm) REVERT: C 309 GLU cc_start: 0.8415 (tm-30) cc_final: 0.7915 (tm-30) REVERT: C 322 LYS cc_start: 0.8118 (OUTLIER) cc_final: 0.7796 (ttpp) REVERT: C 593 GLU cc_start: 0.8242 (tp30) cc_final: 0.7940 (tp30) REVERT: C 774 MET cc_start: 0.8160 (mmm) cc_final: 0.7752 (ttt) REVERT: C 899 PHE cc_start: 0.7843 (t80) cc_final: 0.7225 (m-80) REVERT: A 184 MET cc_start: 0.8843 (tpp) cc_final: 0.8353 (tpp) REVERT: A 246 PHE cc_start: 0.8910 (OUTLIER) cc_final: 0.7809 (t80) REVERT: A 398 MET cc_start: 0.8810 (mtp) cc_final: 0.8532 (mtm) REVERT: A 593 GLU cc_start: 0.7992 (tp30) cc_final: 0.7436 (tp30) REVERT: A 601 LYS cc_start: 0.8087 (mmmt) cc_final: 0.7696 (mptt) REVERT: A 722 GLU cc_start: 0.7825 (OUTLIER) cc_final: 0.7384 (mt-10) REVERT: A 737 GLN cc_start: 0.8074 (mm110) cc_final: 0.7830 (mt0) REVERT: A 810 GLU cc_start: 0.8132 (mt-10) cc_final: 0.7724 (mt-10) outliers start: 87 outliers final: 54 residues processed: 414 average time/residue: 0.1618 time to fit residues: 110.2321 Evaluate side-chains 402 residues out of total 2476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 338 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 20 MET Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 312 LYS Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 363 ARG Chi-restraints excluded: chain B residue 398 MET Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 604 ASN Chi-restraints excluded: chain B residue 671 ILE Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain B residue 716 VAL Chi-restraints excluded: chain B residue 768 VAL Chi-restraints excluded: chain B residue 900 SER Chi-restraints excluded: chain B residue 937 LEU Chi-restraints excluded: chain B residue 965 LEU Chi-restraints excluded: chain B residue 1029 VAL Chi-restraints excluded: chain C residue 7 ASP Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 322 LYS Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 455 PRO Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 552 MET Chi-restraints excluded: chain C residue 561 SER Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 743 ILE Chi-restraints excluded: chain C residue 799 VAL Chi-restraints excluded: chain C residue 937 LEU Chi-restraints excluded: chain C residue 938 SER Chi-restraints excluded: chain C residue 943 ILE Chi-restraints excluded: chain C residue 968 VAL Chi-restraints excluded: chain C residue 1025 PHE Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 78 MET Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 246 PHE Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 478 MET Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 571 VAL Chi-restraints excluded: chain A residue 583 THR Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 671 ILE Chi-restraints excluded: chain A residue 713 LEU Chi-restraints excluded: chain A residue 722 GLU Chi-restraints excluded: chain A residue 806 SER Chi-restraints excluded: chain A residue 825 MET Chi-restraints excluded: chain A residue 900 SER Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 935 ILE Chi-restraints excluded: chain A residue 986 VAL Chi-restraints excluded: chain A residue 1016 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 278 optimal weight: 6.9990 chunk 5 optimal weight: 1.9990 chunk 125 optimal weight: 0.8980 chunk 147 optimal weight: 3.9990 chunk 48 optimal weight: 0.7980 chunk 214 optimal weight: 3.9990 chunk 159 optimal weight: 0.8980 chunk 256 optimal weight: 9.9990 chunk 101 optimal weight: 0.9990 chunk 153 optimal weight: 5.9990 chunk 72 optimal weight: 10.0000 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 67 GLN C 106 GLN C 439 GLN ** A 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.133932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.100395 restraints weight = 28576.382| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 1.98 r_work: 0.3087 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.3255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 24709 Z= 0.104 Angle : 0.559 10.696 33279 Z= 0.275 Chirality : 0.042 0.230 3815 Planarity : 0.003 0.040 4144 Dihedral : 12.707 159.013 4173 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.22 % Favored : 95.71 % Rotamer: Outliers : 2.87 % Allowed : 16.98 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.16), residues: 3030 helix: 0.65 (0.14), residues: 1510 sheet: -1.19 (0.26), residues: 430 loop : -1.53 (0.18), residues: 1090 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 653 TYR 0.019 0.001 TYR A 356 PHE 0.023 0.001 PHE A1025 TRP 0.007 0.001 TRP A 859 HIS 0.001 0.000 HIS C 596 Details of bonding type rmsd covalent geometry : bond 0.00239 (24709) covalent geometry : angle 0.55895 (33279) hydrogen bonds : bond 0.03129 ( 1162) hydrogen bonds : angle 4.29093 ( 3360) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 2476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 360 time to evaluate : 1.064 Fit side-chains revert: symmetry clash Corrupt residue: chain: C residue: PRO 455 >>> skipping REVERT: B 87 THR cc_start: 0.8476 (OUTLIER) cc_final: 0.8036 (p) REVERT: B 177 LEU cc_start: 0.8713 (OUTLIER) cc_final: 0.8126 (mt) REVERT: B 189 ASN cc_start: 0.8088 (t0) cc_final: 0.7662 (t0) REVERT: B 312 LYS cc_start: 0.7908 (OUTLIER) cc_final: 0.7665 (ptmm) REVERT: B 518 ARG cc_start: 0.8048 (mtm180) cc_final: 0.7672 (mtm-85) REVERT: B 573 MET cc_start: 0.7963 (mpt) cc_final: 0.7182 (mpt) REVERT: B 653 ARG cc_start: 0.8456 (ttt90) cc_final: 0.8059 (mtp85) REVERT: B 662 MET cc_start: 0.7495 (mmp) cc_final: 0.6988 (mtp) REVERT: B 711 ASP cc_start: 0.8442 (p0) cc_final: 0.7897 (m-30) REVERT: B 729 ILE cc_start: 0.7916 (pt) cc_final: 0.7584 (pt) REVERT: B 867 ARG cc_start: 0.7629 (mmt180) cc_final: 0.6939 (ttp-170) REVERT: B 937 LEU cc_start: 0.8251 (OUTLIER) cc_final: 0.8012 (tp) REVERT: C 7 ASP cc_start: 0.8019 (OUTLIER) cc_final: 0.7673 (p0) REVERT: C 106 GLN cc_start: 0.8750 (OUTLIER) cc_final: 0.8505 (pt0) REVERT: C 123 GLN cc_start: 0.7771 (tt0) cc_final: 0.7441 (mp10) REVERT: C 195 LYS cc_start: 0.8398 (ttpp) cc_final: 0.8163 (ttmm) REVERT: C 244 GLU cc_start: 0.7469 (OUTLIER) cc_final: 0.6928 (mp0) REVERT: C 309 GLU cc_start: 0.8370 (tm-30) cc_final: 0.8032 (tm-30) REVERT: C 322 LYS cc_start: 0.8547 (OUTLIER) cc_final: 0.8244 (ttpp) REVERT: C 774 MET cc_start: 0.8168 (mmm) cc_final: 0.7736 (ttt) REVERT: A 184 MET cc_start: 0.8623 (tpp) cc_final: 0.8411 (tpp) REVERT: A 246 PHE cc_start: 0.9117 (OUTLIER) cc_final: 0.8148 (t80) REVERT: A 398 MET cc_start: 0.8890 (mtp) cc_final: 0.8611 (mtm) REVERT: A 496 MET cc_start: 0.8527 (mtp) cc_final: 0.8120 (mtt) REVERT: A 593 GLU cc_start: 0.8052 (tp30) cc_final: 0.7615 (tp30) REVERT: A 712 MET cc_start: 0.6232 (ppp) cc_final: 0.5893 (ppp) REVERT: A 722 GLU cc_start: 0.7846 (OUTLIER) cc_final: 0.7581 (mt-10) REVERT: A 737 GLN cc_start: 0.8179 (mm110) cc_final: 0.7963 (mt0) REVERT: A 862 MET cc_start: 0.7436 (ttt) cc_final: 0.7127 (ttt) outliers start: 72 outliers final: 51 residues processed: 409 average time/residue: 0.1597 time to fit residues: 106.9992 Evaluate side-chains 401 residues out of total 2476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 340 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 MET Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 312 LYS Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 398 MET Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 478 MET Chi-restraints excluded: chain B residue 604 ASN Chi-restraints excluded: chain B residue 671 ILE Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain B residue 716 VAL Chi-restraints excluded: chain B residue 768 VAL Chi-restraints excluded: chain B residue 900 SER Chi-restraints excluded: chain B residue 937 LEU Chi-restraints excluded: chain B residue 965 LEU Chi-restraints excluded: chain B residue 1029 VAL Chi-restraints excluded: chain C residue 7 ASP Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 106 GLN Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 244 GLU Chi-restraints excluded: chain C residue 322 LYS Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 455 PRO Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 552 MET Chi-restraints excluded: chain C residue 561 SER Chi-restraints excluded: chain C residue 695 LEU Chi-restraints excluded: chain C residue 743 ILE Chi-restraints excluded: chain C residue 937 LEU Chi-restraints excluded: chain C residue 938 SER Chi-restraints excluded: chain C residue 943 ILE Chi-restraints excluded: chain C residue 968 VAL Chi-restraints excluded: chain C residue 1025 PHE Chi-restraints excluded: chain A residue 78 MET Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 246 PHE Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 478 MET Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 571 VAL Chi-restraints excluded: chain A residue 583 THR Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 671 ILE Chi-restraints excluded: chain A residue 713 LEU Chi-restraints excluded: chain A residue 722 GLU Chi-restraints excluded: chain A residue 806 SER Chi-restraints excluded: chain A residue 825 MET Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 935 ILE Chi-restraints excluded: chain A residue 986 VAL Chi-restraints excluded: chain A residue 1016 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 139 optimal weight: 4.9990 chunk 43 optimal weight: 4.9990 chunk 234 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 205 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 chunk 191 optimal weight: 1.9990 chunk 257 optimal weight: 5.9990 chunk 289 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 194 optimal weight: 6.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 ASN C 67 GLN ** A 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.138429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.104170 restraints weight = 28903.705| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 2.34 r_work: 0.3098 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7330 moved from start: 0.3303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 24709 Z= 0.124 Angle : 0.584 10.870 33279 Z= 0.286 Chirality : 0.043 0.234 3815 Planarity : 0.004 0.040 4144 Dihedral : 12.489 164.939 4170 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.55 % Favored : 95.38 % Rotamer: Outliers : 2.79 % Allowed : 16.94 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.16), residues: 3030 helix: 0.69 (0.14), residues: 1513 sheet: -1.18 (0.26), residues: 432 loop : -1.48 (0.18), residues: 1085 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 653 TYR 0.019 0.001 TYR A 356 PHE 0.022 0.001 PHE A1025 TRP 0.012 0.001 TRP A 859 HIS 0.001 0.000 HIS C 692 Details of bonding type rmsd covalent geometry : bond 0.00300 (24709) covalent geometry : angle 0.58379 (33279) hydrogen bonds : bond 0.03322 ( 1162) hydrogen bonds : angle 4.31201 ( 3360) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 2476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 344 time to evaluate : 0.947 Fit side-chains revert: symmetry clash Corrupt residue: chain: C residue: PRO 455 >>> skipping REVERT: B 87 THR cc_start: 0.8100 (OUTLIER) cc_final: 0.7353 (p) REVERT: B 420 MET cc_start: 0.8143 (mtp) cc_final: 0.7745 (mtm) REVERT: B 573 MET cc_start: 0.7373 (mpt) cc_final: 0.6463 (mpt) REVERT: B 653 ARG cc_start: 0.8091 (ttt90) cc_final: 0.7516 (mtp85) REVERT: B 662 MET cc_start: 0.7025 (mmp) cc_final: 0.6188 (mtp) REVERT: B 711 ASP cc_start: 0.8456 (p0) cc_final: 0.7791 (m-30) REVERT: B 729 ILE cc_start: 0.6981 (pt) cc_final: 0.6700 (pt) REVERT: B 847 LEU cc_start: 0.8190 (tp) cc_final: 0.7831 (mt) REVERT: B 867 ARG cc_start: 0.7080 (mmt180) cc_final: 0.6157 (ttp-170) REVERT: B 937 LEU cc_start: 0.7086 (OUTLIER) cc_final: 0.6855 (tp) REVERT: C 118 LEU cc_start: 0.6861 (OUTLIER) cc_final: 0.6478 (mt) REVERT: C 123 GLN cc_start: 0.8208 (tt0) cc_final: 0.7197 (mp10) REVERT: C 309 GLU cc_start: 0.8013 (tm-30) cc_final: 0.7464 (tm-30) REVERT: C 322 LYS cc_start: 0.7772 (OUTLIER) cc_final: 0.7482 (ttpp) REVERT: C 774 MET cc_start: 0.8005 (OUTLIER) cc_final: 0.7606 (ttt) REVERT: A 29 LYS cc_start: 0.7255 (mttm) cc_final: 0.6978 (mttm) REVERT: A 246 PHE cc_start: 0.8710 (OUTLIER) cc_final: 0.7598 (t80) REVERT: A 313 MET cc_start: 0.8259 (ptp) cc_final: 0.7928 (ptp) REVERT: A 398 MET cc_start: 0.8227 (mtp) cc_final: 0.7931 (mtm) REVERT: A 447 MET cc_start: 0.7798 (OUTLIER) cc_final: 0.7519 (mtp) REVERT: A 496 MET cc_start: 0.7774 (mtp) cc_final: 0.7512 (mtt) REVERT: A 593 GLU cc_start: 0.7811 (tp30) cc_final: 0.7289 (tp30) REVERT: A 601 LYS cc_start: 0.8219 (mptt) cc_final: 0.8005 (mptt) REVERT: A 712 MET cc_start: 0.6194 (ppp) cc_final: 0.5708 (ppp) REVERT: A 722 GLU cc_start: 0.7594 (OUTLIER) cc_final: 0.7165 (mt-10) REVERT: A 737 GLN cc_start: 0.7964 (mm110) cc_final: 0.7729 (mt0) REVERT: A 862 MET cc_start: 0.6412 (ttt) cc_final: 0.6178 (ttt) outliers start: 70 outliers final: 54 residues processed: 393 average time/residue: 0.1566 time to fit residues: 101.1751 Evaluate side-chains 395 residues out of total 2476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 333 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 MET Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 398 MET Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 478 MET Chi-restraints excluded: chain B residue 480 LEU Chi-restraints excluded: chain B residue 562 SER Chi-restraints excluded: chain B residue 604 ASN Chi-restraints excluded: chain B residue 671 ILE Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain B residue 716 VAL Chi-restraints excluded: chain B residue 768 VAL Chi-restraints excluded: chain B residue 900 SER Chi-restraints excluded: chain B residue 937 LEU Chi-restraints excluded: chain B residue 965 LEU Chi-restraints excluded: chain B residue 1029 VAL Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 322 LYS Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 455 PRO Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 552 MET Chi-restraints excluded: chain C residue 561 SER Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 695 LEU Chi-restraints excluded: chain C residue 743 ILE Chi-restraints excluded: chain C residue 774 MET Chi-restraints excluded: chain C residue 937 LEU Chi-restraints excluded: chain C residue 938 SER Chi-restraints excluded: chain C residue 943 ILE Chi-restraints excluded: chain C residue 968 VAL Chi-restraints excluded: chain C residue 1025 PHE Chi-restraints excluded: chain A residue 78 MET Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 246 PHE Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 447 MET Chi-restraints excluded: chain A residue 449 LEU Chi-restraints excluded: chain A residue 478 MET Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 571 VAL Chi-restraints excluded: chain A residue 583 THR Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 671 ILE Chi-restraints excluded: chain A residue 713 LEU Chi-restraints excluded: chain A residue 722 GLU Chi-restraints excluded: chain A residue 806 SER Chi-restraints excluded: chain A residue 825 MET Chi-restraints excluded: chain A residue 900 SER Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 935 ILE Chi-restraints excluded: chain A residue 986 VAL Chi-restraints excluded: chain A residue 1016 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 159 optimal weight: 3.9990 chunk 139 optimal weight: 3.9990 chunk 2 optimal weight: 9.9990 chunk 239 optimal weight: 2.9990 chunk 56 optimal weight: 20.0000 chunk 250 optimal weight: 5.9990 chunk 70 optimal weight: 0.3980 chunk 168 optimal weight: 4.9990 chunk 11 optimal weight: 0.0870 chunk 151 optimal weight: 4.9990 chunk 31 optimal weight: 0.1980 overall best weight: 1.5362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 67 GLN ** A 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.138740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.104547 restraints weight = 28907.650| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 2.33 r_work: 0.3105 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 moved from start: 0.3377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 24709 Z= 0.116 Angle : 0.576 10.717 33279 Z= 0.283 Chirality : 0.043 0.231 3815 Planarity : 0.004 0.055 4144 Dihedral : 12.184 170.616 4170 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.42 % Favored : 95.51 % Rotamer: Outliers : 2.67 % Allowed : 17.06 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.16), residues: 3030 helix: 0.74 (0.14), residues: 1518 sheet: -1.11 (0.26), residues: 430 loop : -1.41 (0.18), residues: 1082 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 653 TYR 0.019 0.001 TYR A 356 PHE 0.022 0.001 PHE B 918 TRP 0.012 0.001 TRP A 859 HIS 0.001 0.000 HIS C 596 Details of bonding type rmsd covalent geometry : bond 0.00278 (24709) covalent geometry : angle 0.57588 (33279) hydrogen bonds : bond 0.03240 ( 1162) hydrogen bonds : angle 4.28676 ( 3360) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6060 Ramachandran restraints generated. 3030 Oldfield, 0 Emsley, 3030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 2476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 344 time to evaluate : 0.884 Fit side-chains revert: symmetry clash Corrupt residue: chain: C residue: PRO 455 >>> skipping REVERT: B 87 THR cc_start: 0.8082 (OUTLIER) cc_final: 0.7350 (p) REVERT: B 189 ASN cc_start: 0.6957 (t0) cc_final: 0.6412 (t0) REVERT: B 420 MET cc_start: 0.8161 (mtp) cc_final: 0.7930 (mtm) REVERT: B 573 MET cc_start: 0.7373 (mpt) cc_final: 0.6466 (mpt) REVERT: B 653 ARG cc_start: 0.8079 (ttt90) cc_final: 0.7501 (mtp85) REVERT: B 662 MET cc_start: 0.7000 (mmp) cc_final: 0.6170 (mtp) REVERT: B 729 ILE cc_start: 0.6939 (pt) cc_final: 0.6666 (pt) REVERT: B 798 MET cc_start: 0.7323 (mmt) cc_final: 0.7077 (mmt) REVERT: B 847 LEU cc_start: 0.8178 (tp) cc_final: 0.7833 (mt) REVERT: B 867 ARG cc_start: 0.7082 (mmt180) cc_final: 0.6155 (ttp-170) REVERT: B 899 PHE cc_start: 0.7728 (m-10) cc_final: 0.7441 (m-10) REVERT: B 937 LEU cc_start: 0.7082 (OUTLIER) cc_final: 0.6870 (tp) REVERT: C 123 GLN cc_start: 0.8257 (tt0) cc_final: 0.7269 (mp10) REVERT: C 184 MET cc_start: 0.8486 (tpp) cc_final: 0.8079 (tpt) REVERT: C 244 GLU cc_start: 0.6808 (OUTLIER) cc_final: 0.6550 (mp0) REVERT: C 322 LYS cc_start: 0.7759 (OUTLIER) cc_final: 0.7483 (ttpp) REVERT: C 774 MET cc_start: 0.7990 (OUTLIER) cc_final: 0.7612 (ttt) REVERT: A 29 LYS cc_start: 0.7215 (mttm) cc_final: 0.6966 (mttm) REVERT: A 184 MET cc_start: 0.8713 (tpp) cc_final: 0.8170 (tpp) REVERT: A 246 PHE cc_start: 0.8706 (OUTLIER) cc_final: 0.7666 (t80) REVERT: A 313 MET cc_start: 0.8252 (ptp) cc_final: 0.7927 (ptp) REVERT: A 398 MET cc_start: 0.8156 (mtp) cc_final: 0.7898 (mtm) REVERT: A 447 MET cc_start: 0.7803 (OUTLIER) cc_final: 0.7603 (mtp) REVERT: A 459 PHE cc_start: 0.5433 (m-10) cc_final: 0.4997 (m-10) REVERT: A 496 MET cc_start: 0.7797 (mtp) cc_final: 0.7554 (mtt) REVERT: A 601 LYS cc_start: 0.8183 (mptt) cc_final: 0.7948 (mptt) REVERT: A 718 PRO cc_start: 0.7080 (Cg_exo) cc_final: 0.6874 (Cg_endo) REVERT: A 722 GLU cc_start: 0.7581 (OUTLIER) cc_final: 0.7160 (mt-10) REVERT: A 737 GLN cc_start: 0.7960 (mm110) cc_final: 0.7721 (mt0) REVERT: A 862 MET cc_start: 0.6422 (ttt) cc_final: 0.6203 (ttt) outliers start: 67 outliers final: 54 residues processed: 388 average time/residue: 0.1549 time to fit residues: 98.5203 Evaluate side-chains 395 residues out of total 2476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 333 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 MET Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 398 MET Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 478 MET Chi-restraints excluded: chain B residue 480 LEU Chi-restraints excluded: chain B residue 562 SER Chi-restraints excluded: chain B residue 604 ASN Chi-restraints excluded: chain B residue 671 ILE Chi-restraints excluded: chain B residue 674 LEU Chi-restraints excluded: chain B residue 716 VAL Chi-restraints excluded: chain B residue 768 VAL Chi-restraints excluded: chain B residue 900 SER Chi-restraints excluded: chain B residue 937 LEU Chi-restraints excluded: chain B residue 965 LEU Chi-restraints excluded: chain B residue 1029 VAL Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 182 TYR Chi-restraints excluded: chain C residue 244 GLU Chi-restraints excluded: chain C residue 322 LYS Chi-restraints excluded: chain C residue 452 VAL Chi-restraints excluded: chain C residue 455 PRO Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 552 MET Chi-restraints excluded: chain C residue 561 SER Chi-restraints excluded: chain C residue 600 THR Chi-restraints excluded: chain C residue 695 LEU Chi-restraints excluded: chain C residue 743 ILE Chi-restraints excluded: chain C residue 774 MET Chi-restraints excluded: chain C residue 937 LEU Chi-restraints excluded: chain C residue 938 SER Chi-restraints excluded: chain C residue 943 ILE Chi-restraints excluded: chain C residue 968 VAL Chi-restraints excluded: chain C residue 1025 PHE Chi-restraints excluded: chain A residue 78 MET Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 182 TYR Chi-restraints excluded: chain A residue 246 PHE Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 447 MET Chi-restraints excluded: chain A residue 478 MET Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 571 VAL Chi-restraints excluded: chain A residue 583 THR Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 671 ILE Chi-restraints excluded: chain A residue 713 LEU Chi-restraints excluded: chain A residue 722 GLU Chi-restraints excluded: chain A residue 806 SER Chi-restraints excluded: chain A residue 825 MET Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 986 VAL Chi-restraints excluded: chain A residue 1016 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 263 optimal weight: 0.9980 chunk 211 optimal weight: 2.9990 chunk 289 optimal weight: 0.0070 chunk 81 optimal weight: 0.3980 chunk 300 optimal weight: 8.9990 chunk 74 optimal weight: 7.9990 chunk 246 optimal weight: 6.9990 chunk 120 optimal weight: 3.9990 chunk 282 optimal weight: 2.9990 chunk 251 optimal weight: 0.9980 chunk 202 optimal weight: 3.9990 overall best weight: 1.0800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 67 GLN C 687 GLN ** A 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.140783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.106770 restraints weight = 28748.712| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 2.31 r_work: 0.3112 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 moved from start: 0.3485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 24709 Z= 0.104 Angle : 0.567 10.645 33279 Z= 0.278 Chirality : 0.042 0.229 3815 Planarity : 0.003 0.054 4144 Dihedral : 11.764 176.136 4170 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.09 % Favored : 95.84 % Rotamer: Outliers : 2.51 % Allowed : 17.50 % Favored : 79.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.16), residues: 3030 helix: 0.82 (0.14), residues: 1525 sheet: -1.05 (0.26), residues: 428 loop : -1.36 (0.18), residues: 1077 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 653 TYR 0.017 0.001 TYR A 327 PHE 0.022 0.001 PHE A1025 TRP 0.012 0.001 TRP A 859 HIS 0.001 0.000 HIS C 596 Details of bonding type rmsd covalent geometry : bond 0.00242 (24709) covalent geometry : angle 0.56718 (33279) hydrogen bonds : bond 0.03080 ( 1162) hydrogen bonds : angle 4.23800 ( 3360) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6607.46 seconds wall clock time: 113 minutes 40.41 seconds (6820.41 seconds total)