Starting phenix.real_space_refine on Sun Aug 9 20:50:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/32fe_58849/08_2026/32fe_58849.cif Found real_map, /net/cci-nas-00/data/ceres_data/32fe_58849/08_2026/32fe_58849.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/32fe_58849/08_2026/32fe_58849.map" default_real_map = "/net/cci-nas-00/data/ceres_data/32fe_58849/08_2026/32fe_58849.map" model { file = "/net/cci-nas-00/data/ceres_data/32fe_58849/08_2026/32fe_58849.cif" } default_model = "/net/cci-nas-00/data/ceres_data/32fe_58849/08_2026/32fe_58849.cif" } resolution = 3.81 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.009 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 12 5.49 5 S 162 5.16 5 C 23442 2.51 5 N 6426 2.21 5 O 6972 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 37014 Number of models: 1 Model: "" Number of chains: 12 Chain: "C" Number of atoms: 6142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 776, 6142 Classifications: {'peptide': 776} Link IDs: {'PTRANS': 32, 'TRANS': 743} Chain breaks: 1 Chain: "D" Number of atoms: 6142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 776, 6142 Classifications: {'peptide': 776} Link IDs: {'PTRANS': 32, 'TRANS': 743} Chain breaks: 1 Chain: "E" Number of atoms: 6142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 776, 6142 Classifications: {'peptide': 776} Link IDs: {'PTRANS': 32, 'TRANS': 743} Chain breaks: 1 Chain: "F" Number of atoms: 6142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 776, 6142 Classifications: {'peptide': 776} Link IDs: {'PTRANS': 32, 'TRANS': 743} Chain breaks: 1 Chain: "A" Number of atoms: 6142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 776, 6142 Classifications: {'peptide': 776} Link IDs: {'PTRANS': 32, 'TRANS': 743} Chain breaks: 1 Chain: "B" Number of atoms: 6142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 776, 6142 Classifications: {'peptide': 776} Link IDs: {'PTRANS': 32, 'TRANS': 743} Chain breaks: 1 Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.80, per 1000 atoms: 0.24 Number of scatterers: 37014 At special positions: 0 Unit cell: (146.626, 141.358, 218.622, 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 162 16.00 P 12 15.00 O 6972 8.00 N 6426 7.00 C 23442 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 520 " - pdb=" SG CYS A 637 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.83 Conformation dependent library (CDL) restraints added in 1.9 seconds 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8736 Finding SS restraints... Secondary structure from input PDB file: 197 helices and 37 sheets defined 51.9% alpha, 7.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.12 Creating SS restraints... Processing helix chain 'C' and resid 147 through 156 removed outlier: 3.596A pdb=" N GLU C 151 " --> pdb=" O LYS C 147 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LYS C 156 " --> pdb=" O LEU C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 159 No H-bonds generated for 'chain 'C' and resid 157 through 159' Processing helix chain 'C' and resid 174 through 181 Processing helix chain 'C' and resid 288 through 307 removed outlier: 4.255A pdb=" N LEU C 292 " --> pdb=" O GLU C 288 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N THR C 293 " --> pdb=" O VAL C 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 312 through 318 removed outlier: 3.552A pdb=" N GLN C 316 " --> pdb=" O GLU C 312 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N MET C 318 " --> pdb=" O VAL C 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 323 removed outlier: 3.552A pdb=" N ARG C 323 " --> pdb=" O ALA C 320 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 338 removed outlier: 3.652A pdb=" N LEU C 331 " --> pdb=" O ASN C 327 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU C 338 " --> pdb=" O MET C 334 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 352 removed outlier: 3.838A pdb=" N LEU C 346 " --> pdb=" O GLU C 342 " (cutoff:3.500A) Processing helix chain 'C' and resid 354 through 408 removed outlier: 3.537A pdb=" N LEU C 372 " --> pdb=" O LYS C 368 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLU C 406 " --> pdb=" O ILE C 402 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU C 407 " --> pdb=" O ILE C 403 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY C 408 " --> pdb=" O LYS C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 428 removed outlier: 4.153A pdb=" N ILE C 417 " --> pdb=" O ASP C 413 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLU C 427 " --> pdb=" O GLU C 423 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU C 428 " --> pdb=" O ARG C 424 " (cutoff:3.500A) Processing helix chain 'C' and resid 431 through 448 Processing helix chain 'C' and resid 452 through 466 Processing helix chain 'C' and resid 479 through 491 Processing helix chain 'C' and resid 494 through 511 Processing helix chain 'C' and resid 528 through 541 Processing helix chain 'C' and resid 554 through 560 removed outlier: 3.870A pdb=" N ILE C 558 " --> pdb=" O ASP C 554 " (cutoff:3.500A) Processing helix chain 'C' and resid 571 through 581 Processing helix chain 'C' and resid 592 through 595 Processing helix chain 'C' and resid 602 through 612 removed outlier: 3.850A pdb=" N GLU C 609 " --> pdb=" O SER C 605 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N LEU C 610 " --> pdb=" O ALA C 606 " (cutoff:3.500A) Processing helix chain 'C' and resid 614 through 619 Processing helix chain 'C' and resid 646 through 653 removed outlier: 3.657A pdb=" N ARG C 652 " --> pdb=" O PRO C 648 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N MET C 653 " --> pdb=" O LEU C 649 " (cutoff:3.500A) Processing helix chain 'C' and resid 662 through 673 removed outlier: 3.533A pdb=" N ARG C 672 " --> pdb=" O ALA C 668 " (cutoff:3.500A) Processing helix chain 'C' and resid 673 through 682 Processing helix chain 'C' and resid 692 through 703 Processing helix chain 'C' and resid 709 through 729 Processing helix chain 'C' and resid 738 through 746 removed outlier: 4.152A pdb=" N GLN C 743 " --> pdb=" O PRO C 739 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ASP C 744 " --> pdb=" O GLU C 740 " (cutoff:3.500A) Processing helix chain 'C' and resid 807 through 829 Processing helix chain 'C' and resid 834 through 838 Processing helix chain 'C' and resid 849 through 855 Proline residue: C 854 - end of helix Processing helix chain 'C' and resid 856 through 870 removed outlier: 3.505A pdb=" N VAL C 861 " --> pdb=" O GLY C 857 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N THR C 862 " --> pdb=" O CYS C 858 " (cutoff:3.500A) Processing helix chain 'C' and resid 894 through 905 removed outlier: 3.713A pdb=" N ALA C 905 " --> pdb=" O ALA C 901 " (cutoff:3.500A) Processing helix chain 'C' and resid 916 through 921 removed outlier: 3.573A pdb=" N TYR C 921 " --> pdb=" O LYS C 917 " (cutoff:3.500A) Processing helix chain 'C' and resid 922 through 923 No H-bonds generated for 'chain 'C' and resid 922 through 923' Processing helix chain 'C' and resid 924 through 929 removed outlier: 3.592A pdb=" N GLU C 929 " --> pdb=" O PHE C 926 " (cutoff:3.500A) Processing helix chain 'C' and resid 938 through 946 removed outlier: 4.063A pdb=" N ILE C 942 " --> pdb=" O HIS C 938 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 156 removed outlier: 3.587A pdb=" N GLU D 151 " --> pdb=" O LYS D 147 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU D 152 " --> pdb=" O LYS D 148 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS D 156 " --> pdb=" O LEU D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 159 No H-bonds generated for 'chain 'D' and resid 157 through 159' Processing helix chain 'D' and resid 174 through 181 Processing helix chain 'D' and resid 288 through 307 removed outlier: 4.307A pdb=" N LEU D 292 " --> pdb=" O GLU D 288 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N THR D 293 " --> pdb=" O VAL D 289 " (cutoff:3.500A) Processing helix chain 'D' and resid 312 through 318 removed outlier: 3.950A pdb=" N MET D 318 " --> pdb=" O VAL D 314 " (cutoff:3.500A) Processing helix chain 'D' and resid 327 through 337 Processing helix chain 'D' and resid 342 through 352 Processing helix chain 'D' and resid 354 through 390 removed outlier: 4.147A pdb=" N THR D 390 " --> pdb=" O LYS D 386 " (cutoff:3.500A) Processing helix chain 'D' and resid 391 through 405 removed outlier: 4.194A pdb=" N LEU D 395 " --> pdb=" O HIS D 391 " (cutoff:3.500A) Processing helix chain 'D' and resid 413 through 428 removed outlier: 3.828A pdb=" N ILE D 417 " --> pdb=" O ASP D 413 " (cutoff:3.500A) Processing helix chain 'D' and resid 433 through 448 Processing helix chain 'D' and resid 452 through 467 Processing helix chain 'D' and resid 479 through 491 Processing helix chain 'D' and resid 494 through 511 Processing helix chain 'D' and resid 528 through 541 Processing helix chain 'D' and resid 555 through 560 Processing helix chain 'D' and resid 571 through 581 Processing helix chain 'D' and resid 603 through 612 Processing helix chain 'D' and resid 615 through 619 Processing helix chain 'D' and resid 646 through 653 removed outlier: 3.870A pdb=" N ARG D 652 " --> pdb=" O PRO D 648 " (cutoff:3.500A) Processing helix chain 'D' and resid 662 through 673 removed outlier: 3.618A pdb=" N ALA D 668 " --> pdb=" O GLN D 664 " (cutoff:3.500A) Processing helix chain 'D' and resid 673 through 683 Processing helix chain 'D' and resid 692 through 704 removed outlier: 3.892A pdb=" N LEU D 696 " --> pdb=" O SER D 692 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N CYS D 704 " --> pdb=" O ILE D 700 " (cutoff:3.500A) Processing helix chain 'D' and resid 710 through 729 Processing helix chain 'D' and resid 741 through 746 Processing helix chain 'D' and resid 807 through 829 Processing helix chain 'D' and resid 849 through 855 Proline residue: D 854 - end of helix Processing helix chain 'D' and resid 856 through 869 removed outlier: 3.760A pdb=" N THR D 862 " --> pdb=" O CYS D 858 " (cutoff:3.500A) Processing helix chain 'D' and resid 894 through 905 Processing helix chain 'D' and resid 916 through 923 removed outlier: 3.714A pdb=" N PHE D 920 " --> pdb=" O ASN D 916 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N TYR D 921 " --> pdb=" O LYS D 917 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASP D 922 " --> pdb=" O LYS D 918 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU D 923 " --> pdb=" O ASP D 919 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 916 through 923' Processing helix chain 'D' and resid 924 through 929 Processing helix chain 'D' and resid 938 through 947 removed outlier: 3.996A pdb=" N ILE D 942 " --> pdb=" O HIS D 938 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N PHE D 947 " --> pdb=" O PHE D 943 " (cutoff:3.500A) Processing helix chain 'E' and resid 147 through 156 Processing helix chain 'E' and resid 174 through 181 Processing helix chain 'E' and resid 290 through 307 Processing helix chain 'E' and resid 312 through 318 removed outlier: 3.521A pdb=" N MET E 318 " --> pdb=" O VAL E 314 " (cutoff:3.500A) Processing helix chain 'E' and resid 327 through 338 removed outlier: 3.682A pdb=" N LEU E 338 " --> pdb=" O MET E 334 " (cutoff:3.500A) Processing helix chain 'E' and resid 342 through 352 Processing helix chain 'E' and resid 354 through 404 Processing helix chain 'E' and resid 414 through 428 removed outlier: 4.433A pdb=" N GLU E 418 " --> pdb=" O LYS E 414 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU E 428 " --> pdb=" O ARG E 424 " (cutoff:3.500A) Processing helix chain 'E' and resid 431 through 448 Processing helix chain 'E' and resid 452 through 467 Processing helix chain 'E' and resid 479 through 490 removed outlier: 3.735A pdb=" N ALA E 483 " --> pdb=" O ASP E 479 " (cutoff:3.500A) Processing helix chain 'E' and resid 494 through 511 Processing helix chain 'E' and resid 528 through 541 Processing helix chain 'E' and resid 555 through 560 Processing helix chain 'E' and resid 571 through 581 Processing helix chain 'E' and resid 602 through 612 removed outlier: 3.909A pdb=" N ALA E 606 " --> pdb=" O ASP E 602 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLU E 609 " --> pdb=" O SER E 605 " (cutoff:3.500A) Processing helix chain 'E' and resid 615 through 619 Processing helix chain 'E' and resid 641 through 645 Processing helix chain 'E' and resid 646 through 651 Processing helix chain 'E' and resid 662 through 673 removed outlier: 3.679A pdb=" N LEU E 667 " --> pdb=" O ALA E 663 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ALA E 668 " --> pdb=" O GLN E 664 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ARG E 672 " --> pdb=" O ALA E 668 " (cutoff:3.500A) Processing helix chain 'E' and resid 674 through 682 Processing helix chain 'E' and resid 692 through 703 Processing helix chain 'E' and resid 709 through 728 removed outlier: 4.347A pdb=" N VAL E 728 " --> pdb=" O ALA E 724 " (cutoff:3.500A) Processing helix chain 'E' and resid 738 through 747 removed outlier: 4.090A pdb=" N GLN E 743 " --> pdb=" O PRO E 739 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N ASP E 744 " --> pdb=" O GLU E 740 " (cutoff:3.500A) Processing helix chain 'E' and resid 807 through 829 Processing helix chain 'E' and resid 834 through 838 removed outlier: 3.756A pdb=" N THR E 837 " --> pdb=" O TYR E 834 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N SER E 838 " --> pdb=" O LEU E 835 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 834 through 838' Processing helix chain 'E' and resid 849 through 855 Proline residue: E 854 - end of helix Processing helix chain 'E' and resid 856 through 869 removed outlier: 3.625A pdb=" N VAL E 861 " --> pdb=" O GLY E 857 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N THR E 862 " --> pdb=" O CYS E 858 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N MET E 869 " --> pdb=" O LEU E 865 " (cutoff:3.500A) Processing helix chain 'E' and resid 894 through 905 removed outlier: 3.565A pdb=" N ALA E 905 " --> pdb=" O ALA E 901 " (cutoff:3.500A) Processing helix chain 'E' and resid 913 through 915 No H-bonds generated for 'chain 'E' and resid 913 through 915' Processing helix chain 'E' and resid 916 through 921 Processing helix chain 'E' and resid 924 through 929 removed outlier: 3.522A pdb=" N GLU E 929 " --> pdb=" O ALA E 925 " (cutoff:3.500A) Processing helix chain 'E' and resid 939 through 946 Processing helix chain 'F' and resid 147 through 156 removed outlier: 3.903A pdb=" N GLU F 151 " --> pdb=" O LYS F 147 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LEU F 152 " --> pdb=" O LYS F 148 " (cutoff:3.500A) Processing helix chain 'F' and resid 174 through 181 removed outlier: 3.507A pdb=" N VAL F 179 " --> pdb=" O GLU F 175 " (cutoff:3.500A) Processing helix chain 'F' and resid 290 through 307 removed outlier: 3.731A pdb=" N ALA F 294 " --> pdb=" O LYS F 290 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU F 295 " --> pdb=" O ALA F 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 312 through 318 removed outlier: 3.788A pdb=" N MET F 318 " --> pdb=" O VAL F 314 " (cutoff:3.500A) Processing helix chain 'F' and resid 327 through 338 removed outlier: 3.799A pdb=" N LEU F 331 " --> pdb=" O ASN F 327 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU F 338 " --> pdb=" O MET F 334 " (cutoff:3.500A) Processing helix chain 'F' and resid 342 through 352 Processing helix chain 'F' and resid 354 through 389 Processing helix chain 'F' and resid 391 through 407 removed outlier: 3.806A pdb=" N LEU F 395 " --> pdb=" O HIS F 391 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU F 407 " --> pdb=" O ILE F 403 " (cutoff:3.500A) Processing helix chain 'F' and resid 415 through 428 Processing helix chain 'F' and resid 431 through 448 Processing helix chain 'F' and resid 452 through 468 Processing helix chain 'F' and resid 480 through 491 Processing helix chain 'F' and resid 494 through 511 Processing helix chain 'F' and resid 528 through 540 Processing helix chain 'F' and resid 571 through 581 removed outlier: 3.593A pdb=" N GLN F 575 " --> pdb=" O GLY F 571 " (cutoff:3.500A) Processing helix chain 'F' and resid 602 through 612 removed outlier: 3.807A pdb=" N LEU F 608 " --> pdb=" O SER F 604 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N GLU F 609 " --> pdb=" O SER F 605 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N LEU F 610 " --> pdb=" O ALA F 606 " (cutoff:3.500A) Processing helix chain 'F' and resid 614 through 619 Processing helix chain 'F' and resid 646 through 651 Processing helix chain 'F' and resid 662 through 674 Processing helix chain 'F' and resid 674 through 682 Processing helix chain 'F' and resid 692 through 703 Processing helix chain 'F' and resid 709 through 729 Processing helix chain 'F' and resid 740 through 746 removed outlier: 3.920A pdb=" N ASP F 744 " --> pdb=" O GLU F 740 " (cutoff:3.500A) Processing helix chain 'F' and resid 807 through 829 Processing helix chain 'F' and resid 834 through 838 removed outlier: 3.736A pdb=" N THR F 837 " --> pdb=" O TYR F 834 " (cutoff:3.500A) Processing helix chain 'F' and resid 849 through 855 Proline residue: F 854 - end of helix Processing helix chain 'F' and resid 856 through 870 removed outlier: 3.635A pdb=" N VAL F 861 " --> pdb=" O GLY F 857 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N THR F 862 " --> pdb=" O CYS F 858 " (cutoff:3.500A) Processing helix chain 'F' and resid 894 through 906 Processing helix chain 'F' and resid 916 through 922 Processing helix chain 'F' and resid 924 through 929 Processing helix chain 'F' and resid 939 through 947 removed outlier: 3.650A pdb=" N ALA F 946 " --> pdb=" O ILE F 942 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N PHE F 947 " --> pdb=" O PHE F 943 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 156 removed outlier: 3.534A pdb=" N GLU A 151 " --> pdb=" O LYS A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 181 Processing helix chain 'A' and resid 290 through 307 removed outlier: 3.553A pdb=" N GLU A 295 " --> pdb=" O ALA A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 318 Processing helix chain 'A' and resid 327 through 338 Processing helix chain 'A' and resid 342 through 352 Processing helix chain 'A' and resid 354 through 408 removed outlier: 3.673A pdb=" N LEU A 372 " --> pdb=" O LYS A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 428 removed outlier: 4.485A pdb=" N ILE A 417 " --> pdb=" O ASP A 413 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N GLU A 418 " --> pdb=" O LYS A 414 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ARG A 424 " --> pdb=" O LYS A 420 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLU A 427 " --> pdb=" O GLU A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 448 removed outlier: 3.614A pdb=" N GLY A 446 " --> pdb=" O LEU A 442 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N LEU A 447 " --> pdb=" O SER A 443 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU A 448 " --> pdb=" O LYS A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 467 removed outlier: 3.583A pdb=" N ASN A 456 " --> pdb=" O SER A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 489 removed outlier: 3.521A pdb=" N ALA A 483 " --> pdb=" O ASP A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 512 Processing helix chain 'A' and resid 528 through 540 Processing helix chain 'A' and resid 555 through 559 Processing helix chain 'A' and resid 571 through 581 Processing helix chain 'A' and resid 602 through 612 removed outlier: 4.813A pdb=" N GLU A 609 " --> pdb=" O SER A 605 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N LEU A 610 " --> pdb=" O ALA A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 615 through 619 removed outlier: 3.625A pdb=" N PHE A 619 " --> pdb=" O ASN A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 645 removed outlier: 3.688A pdb=" N THR A 644 " --> pdb=" O VAL A 641 " (cutoff:3.500A) Processing helix chain 'A' and resid 646 through 653 Processing helix chain 'A' and resid 662 through 674 removed outlier: 3.854A pdb=" N LEU A 674 " --> pdb=" O ALA A 670 " (cutoff:3.500A) Processing helix chain 'A' and resid 674 through 682 Processing helix chain 'A' and resid 692 through 703 removed outlier: 3.900A pdb=" N LEU A 696 " --> pdb=" O SER A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 729 Processing helix chain 'A' and resid 741 through 747 removed outlier: 3.501A pdb=" N PHE A 745 " --> pdb=" O ASN A 741 " (cutoff:3.500A) Processing helix chain 'A' and resid 807 through 829 Processing helix chain 'A' and resid 834 through 838 removed outlier: 3.577A pdb=" N SER A 838 " --> pdb=" O LEU A 835 " (cutoff:3.500A) Processing helix chain 'A' and resid 852 through 855 Processing helix chain 'A' and resid 856 through 870 Processing helix chain 'A' and resid 894 through 905 removed outlier: 3.738A pdb=" N LYS A 898 " --> pdb=" O GLY A 894 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 922 Processing helix chain 'A' and resid 924 through 929 Processing helix chain 'A' and resid 938 through 947 removed outlier: 4.253A pdb=" N ILE A 942 " --> pdb=" O HIS A 938 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 156 removed outlier: 3.755A pdb=" N GLU B 151 " --> pdb=" O LYS B 147 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU B 152 " --> pdb=" O LYS B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 181 removed outlier: 3.791A pdb=" N VAL B 179 " --> pdb=" O GLU B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 185 Processing helix chain 'B' and resid 290 through 307 removed outlier: 3.535A pdb=" N GLU B 295 " --> pdb=" O ALA B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 318 Processing helix chain 'B' and resid 327 through 337 Processing helix chain 'B' and resid 342 through 352 Processing helix chain 'B' and resid 354 through 389 Processing helix chain 'B' and resid 392 through 408 Processing helix chain 'B' and resid 414 through 426 removed outlier: 4.641A pdb=" N ARG B 424 " --> pdb=" O LYS B 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 447 removed outlier: 3.526A pdb=" N MET B 435 " --> pdb=" O PRO B 431 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY B 446 " --> pdb=" O LEU B 442 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N LEU B 447 " --> pdb=" O SER B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 468 removed outlier: 3.511A pdb=" N ILE B 468 " --> pdb=" O TRP B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 491 removed outlier: 3.808A pdb=" N ALA B 483 " --> pdb=" O ASP B 479 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N HIS B 491 " --> pdb=" O LEU B 487 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 511 Processing helix chain 'B' and resid 528 through 541 Processing helix chain 'B' and resid 555 through 560 Processing helix chain 'B' and resid 571 through 581 Processing helix chain 'B' and resid 591 through 595 removed outlier: 3.612A pdb=" N ILE B 595 " --> pdb=" O VAL B 592 " (cutoff:3.500A) Processing helix chain 'B' and resid 602 through 612 removed outlier: 3.751A pdb=" N ALA B 606 " --> pdb=" O ASP B 602 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU B 610 " --> pdb=" O ALA B 606 " (cutoff:3.500A) Processing helix chain 'B' and resid 614 through 619 Processing helix chain 'B' and resid 646 through 651 removed outlier: 3.726A pdb=" N ASP B 651 " --> pdb=" O GLU B 647 " (cutoff:3.500A) Processing helix chain 'B' and resid 662 through 674 removed outlier: 3.825A pdb=" N LEU B 667 " --> pdb=" O ALA B 663 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ARG B 672 " --> pdb=" O ALA B 668 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU B 674 " --> pdb=" O ALA B 670 " (cutoff:3.500A) Processing helix chain 'B' and resid 674 through 683 removed outlier: 3.529A pdb=" N ALA B 678 " --> pdb=" O LEU B 674 " (cutoff:3.500A) Processing helix chain 'B' and resid 692 through 703 removed outlier: 4.011A pdb=" N LEU B 696 " --> pdb=" O SER B 692 " (cutoff:3.500A) Processing helix chain 'B' and resid 709 through 729 removed outlier: 3.821A pdb=" N SER B 729 " --> pdb=" O TYR B 725 " (cutoff:3.500A) Processing helix chain 'B' and resid 740 through 746 removed outlier: 3.528A pdb=" N ASP B 744 " --> pdb=" O GLU B 740 " (cutoff:3.500A) Processing helix chain 'B' and resid 808 through 829 Processing helix chain 'B' and resid 833 through 837 Processing helix chain 'B' and resid 849 through 855 Proline residue: B 854 - end of helix Processing helix chain 'B' and resid 856 through 870 removed outlier: 3.541A pdb=" N ILE B 860 " --> pdb=" O ALA B 856 " (cutoff:3.500A) Processing helix chain 'B' and resid 894 through 905 Processing helix chain 'B' and resid 916 through 923 removed outlier: 3.823A pdb=" N LEU B 923 " --> pdb=" O ASP B 919 " (cutoff:3.500A) Processing helix chain 'B' and resid 924 through 929 removed outlier: 4.061A pdb=" N GLU B 929 " --> pdb=" O PHE B 926 " (cutoff:3.500A) Processing helix chain 'B' and resid 938 through 944 removed outlier: 4.217A pdb=" N ILE B 942 " --> pdb=" O HIS B 938 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 139 through 142 Processing sheet with id=AA2, first strand: chain 'C' and resid 163 through 169 removed outlier: 4.396A pdb=" N LEU C 168 " --> pdb=" O THR C 188 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N THR C 188 " --> pdb=" O LEU C 168 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 544 through 548 removed outlier: 7.010A pdb=" N PHE C 545 " --> pdb=" O LEU C 588 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N ASP C 590 " --> pdb=" O PHE C 545 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N PHE C 547 " --> pdb=" O ASP C 590 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE C 636 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N LEU C 519 " --> pdb=" O CYS C 637 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N TYR C 522 " --> pdb=" O ILE C 656 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 764 through 766 Processing sheet with id=AA5, first strand: chain 'C' and resid 877 through 879 removed outlier: 3.614A pdb=" N ILE C 910 " --> pdb=" O GLU C 932 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL C 936 " --> pdb=" O LEU C 912 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 140 through 142 Processing sheet with id=AA7, first strand: chain 'D' and resid 163 through 169 removed outlier: 4.107A pdb=" N LEU D 168 " --> pdb=" O THR D 188 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N THR D 188 " --> pdb=" O LEU D 168 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 546 through 548 removed outlier: 6.983A pdb=" N ILE D 518 " --> pdb=" O GLU D 654 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N ILE D 656 " --> pdb=" O ILE D 518 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N CYS D 520 " --> pdb=" O ILE D 656 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 764 through 766 removed outlier: 6.270A pdb=" N GLU D 801 " --> pdb=" O LEU D 842 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 909 through 913 Processing sheet with id=AB2, first strand: chain 'E' and resid 140 through 143 Processing sheet with id=AB3, first strand: chain 'E' and resid 164 through 169 removed outlier: 4.474A pdb=" N LEU E 168 " --> pdb=" O THR E 188 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N THR E 188 " --> pdb=" O LEU E 168 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 543 through 548 removed outlier: 5.906A pdb=" N GLU E 543 " --> pdb=" O LEU E 586 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N LEU E 588 " --> pdb=" O GLU E 543 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N PHE E 545 " --> pdb=" O LEU E 588 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N ASP E 590 " --> pdb=" O PHE E 545 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N PHE E 547 " --> pdb=" O ASP E 590 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N LEU E 519 " --> pdb=" O CYS E 637 " (cutoff:3.500A) removed outlier: 8.356A pdb=" N ALA E 639 " --> pdb=" O LEU E 519 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N PHE E 521 " --> pdb=" O ALA E 639 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N ILE E 656 " --> pdb=" O ILE E 518 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N CYS E 520 " --> pdb=" O ILE E 656 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 764 through 766 Processing sheet with id=AB6, first strand: chain 'E' and resid 877 through 879 removed outlier: 3.628A pdb=" N ALA E 878 " --> pdb=" O CYS E 909 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N VAL E 911 " --> pdb=" O ALA E 878 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 140 through 143 Processing sheet with id=AB8, first strand: chain 'F' and resid 166 through 169 removed outlier: 7.121A pdb=" N VAL F 166 " --> pdb=" O THR F 188 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N THR F 188 " --> pdb=" O VAL F 166 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N LEU F 168 " --> pdb=" O TYR F 186 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 521 through 522 Processing sheet with id=AC1, first strand: chain 'F' and resid 544 through 548 removed outlier: 6.060A pdb=" N PHE F 545 " --> pdb=" O LEU F 588 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ASP F 590 " --> pdb=" O PHE F 545 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N PHE F 547 " --> pdb=" O ASP F 590 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE F 587 " --> pdb=" O LEU F 634 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ILE F 636 " --> pdb=" O ILE F 587 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 764 through 769 removed outlier: 6.286A pdb=" N GLU F 801 " --> pdb=" O LEU F 842 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 878 through 879 removed outlier: 7.491A pdb=" N ALA F 878 " --> pdb=" O VAL F 911 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N ILE F 910 " --> pdb=" O HIS F 934 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N VAL F 936 " --> pdb=" O ILE F 910 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N LEU F 912 " --> pdb=" O VAL F 936 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'F' and resid 882 through 883 removed outlier: 3.948A pdb=" N GLU F 882 " --> pdb=" O LEU F 890 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 140 through 142 Processing sheet with id=AC6, first strand: chain 'A' and resid 163 through 169 removed outlier: 4.476A pdb=" N LEU A 168 " --> pdb=" O THR A 188 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N THR A 188 " --> pdb=" O LEU A 168 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 637 through 639 removed outlier: 6.766A pdb=" N CYS A 520 " --> pdb=" O ILE A 656 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 544 through 545 Processing sheet with id=AC9, first strand: chain 'A' and resid 689 through 691 removed outlier: 7.108A pdb=" N LYS A 690 " --> pdb=" O VAL A 737 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'A' and resid 764 through 766 Processing sheet with id=AD2, first strand: chain 'A' and resid 769 through 770 Processing sheet with id=AD3, first strand: chain 'A' and resid 877 through 879 removed outlier: 3.653A pdb=" N ILE A 910 " --> pdb=" O GLU A 932 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'A' and resid 882 through 883 removed outlier: 4.196A pdb=" N GLU A 882 " --> pdb=" O LEU A 890 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU A 890 " --> pdb=" O GLU A 882 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'B' and resid 140 through 142 Processing sheet with id=AD6, first strand: chain 'B' and resid 163 through 166 Processing sheet with id=AD7, first strand: chain 'B' and resid 544 through 548 removed outlier: 6.663A pdb=" N PHE B 545 " --> pdb=" O LEU B 588 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N ASP B 590 " --> pdb=" O PHE B 545 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N PHE B 547 " --> pdb=" O ASP B 590 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE B 636 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N LYS B 517 " --> pdb=" O PHE B 635 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N CYS B 637 " --> pdb=" O LYS B 517 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N LEU B 519 " --> pdb=" O CYS B 637 " (cutoff:3.500A) removed outlier: 8.676A pdb=" N ALA B 639 " --> pdb=" O LEU B 519 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N PHE B 521 " --> pdb=" O ALA B 639 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N ILE B 518 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 8.913A pdb=" N ILE B 656 " --> pdb=" O ILE B 518 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N CYS B 520 " --> pdb=" O ILE B 656 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 764 through 765 Processing sheet with id=AD9, first strand: chain 'B' and resid 878 through 879 removed outlier: 7.125A pdb=" N ALA B 878 " --> pdb=" O VAL B 911 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 882 through 883 removed outlier: 4.272A pdb=" N GLU B 882 " --> pdb=" O LEU B 890 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU B 890 " --> pdb=" O GLU B 882 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 1680 hydrogen bonds defined for protein. 4836 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: 8.59 Time building geometry restraints manager: 5.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 12335 1.34 - 1.46: 6414 1.46 - 1.58: 18589 1.58 - 1.70: 18 1.70 - 1.82: 282 Bond restraints: 37638 Sorted by residual: bond pdb=" C LYS B 632 " pdb=" N VAL B 633 " ideal model delta sigma weight residual 1.334 1.304 0.030 1.29e-02 6.01e+03 5.28e+00 bond pdb=" CA MET C 773 " pdb=" CB MET C 773 " ideal model delta sigma weight residual 1.528 1.559 -0.031 1.39e-02 5.18e+03 5.06e+00 bond pdb=" C LEU A 885 " pdb=" N THR A 886 " ideal model delta sigma weight residual 1.332 1.310 0.022 1.40e-02 5.10e+03 2.54e+00 bond pdb=" C4 ADP B1001 " pdb=" C5 ADP B1001 " ideal model delta sigma weight residual 1.490 1.458 0.032 2.00e-02 2.50e+03 2.53e+00 bond pdb=" C4 ADP C1001 " pdb=" C5 ADP C1001 " ideal model delta sigma weight residual 1.490 1.460 0.030 2.00e-02 2.50e+03 2.20e+00 ... (remaining 37633 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.33: 50195 2.33 - 4.65: 556 4.65 - 6.98: 74 6.98 - 9.31: 4 9.31 - 11.63: 15 Bond angle restraints: 50844 Sorted by residual: angle pdb=" C LEU B 409 " pdb=" N GLU B 410 " pdb=" CA GLU B 410 " ideal model delta sigma weight residual 122.82 134.25 -11.43 1.42e+00 4.96e-01 6.48e+01 angle pdb=" CG1 VAL A 497 " pdb=" CB VAL A 497 " pdb=" CG2 VAL A 497 " ideal model delta sigma weight residual 110.80 122.43 -11.63 2.20e+00 2.07e-01 2.80e+01 angle pdb=" CG1 VAL F 497 " pdb=" CB VAL F 497 " pdb=" CG2 VAL F 497 " ideal model delta sigma weight residual 110.80 122.28 -11.48 2.20e+00 2.07e-01 2.72e+01 angle pdb=" CG1 VAL C 809 " pdb=" CB VAL C 809 " pdb=" CG2 VAL C 809 " ideal model delta sigma weight residual 110.80 122.03 -11.23 2.20e+00 2.07e-01 2.60e+01 angle pdb=" CG1 VAL D 507 " pdb=" CB VAL D 507 " pdb=" CG2 VAL D 507 " ideal model delta sigma weight residual 110.80 122.00 -11.20 2.20e+00 2.07e-01 2.59e+01 ... (remaining 50839 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.61: 21715 26.61 - 53.22: 1322 53.22 - 79.83: 140 79.83 - 106.44: 18 106.44 - 133.05: 4 Dihedral angle restraints: 23199 sinusoidal: 9681 harmonic: 13518 Sorted by residual: dihedral pdb=" O1B ADP D1001 " pdb=" O3A ADP D1001 " pdb=" PB ADP D1001 " pdb=" PA ADP D1001 " ideal model delta sinusoidal sigma weight residual -60.00 73.04 -133.05 1 2.00e+01 2.50e-03 4.04e+01 dihedral pdb=" O1B ADP A1001 " pdb=" O3A ADP A1001 " pdb=" PB ADP A1001 " pdb=" PA ADP A1001 " ideal model delta sinusoidal sigma weight residual 300.00 168.73 131.27 1 2.00e+01 2.50e-03 3.98e+01 dihedral pdb=" O1B ADP B1001 " pdb=" O3A ADP B1001 " pdb=" PB ADP B1001 " pdb=" PA ADP B1001 " ideal model delta sinusoidal sigma weight residual -60.00 65.42 -125.43 1 2.00e+01 2.50e-03 3.79e+01 ... (remaining 23196 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.351: 5822 0.351 - 0.702: 1 0.702 - 1.053: 0 1.053 - 1.404: 1 1.404 - 1.755: 8 Chirality restraints: 5832 Sorted by residual: chirality pdb=" CG LEU A 681 " pdb=" CB LEU A 681 " pdb=" CD1 LEU A 681 " pdb=" CD2 LEU A 681 " both_signs ideal model delta sigma weight residual False -2.59 -0.83 -1.76 2.00e-01 2.50e+01 7.70e+01 chirality pdb=" CB VAL F 497 " pdb=" CA VAL F 497 " pdb=" CG1 VAL F 497 " pdb=" CG2 VAL F 497 " both_signs ideal model delta sigma weight residual False -2.63 -1.13 -1.50 2.00e-01 2.50e+01 5.61e+01 chirality pdb=" CB VAL D 507 " pdb=" CA VAL D 507 " pdb=" CG1 VAL D 507 " pdb=" CG2 VAL D 507 " both_signs ideal model delta sigma weight residual False -2.63 -1.15 -1.48 2.00e-01 2.50e+01 5.47e+01 ... (remaining 5829 not shown) Planarity restraints: 6522 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS C 748 " -0.034 5.00e-02 4.00e+02 5.20e-02 4.33e+00 pdb=" N PRO C 749 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO C 749 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 749 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP F 412 " -0.010 2.00e-02 2.50e+03 1.96e-02 3.85e+00 pdb=" C ASP F 412 " 0.034 2.00e-02 2.50e+03 pdb=" O ASP F 412 " -0.013 2.00e-02 2.50e+03 pdb=" N ASP F 413 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL B 430 " 0.030 5.00e-02 4.00e+02 4.57e-02 3.34e+00 pdb=" N PRO B 431 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO B 431 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 431 " 0.026 5.00e-02 4.00e+02 ... (remaining 6519 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 8667 2.78 - 3.31: 41904 3.31 - 3.84: 61196 3.84 - 4.37: 71305 4.37 - 4.90: 114207 Nonbonded interactions: 297279 Sorted by model distance: nonbonded pdb=" C GLY C 528 " pdb=" O2A ADP C1001 " model vdw 2.253 3.270 nonbonded pdb=" OE1 GLU A 543 " pdb=" O THR A 580 " model vdw 2.268 3.040 nonbonded pdb=" O ASP F 412 " pdb=" OD1 ASP F 412 " model vdw 2.290 3.040 nonbonded pdb=" O GLU C 808 " pdb=" OE1 GLU C 808 " model vdw 2.367 3.040 nonbonded pdb=" O ASP F 479 " pdb=" OD1 ASP F 479 " model vdw 2.369 3.040 ... (remaining 297274 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 12.990 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: 0.040 Extract box with map and model: 0.740 Check model and map are aligned: 0.120 Set scattering table: 0.100 Process input model: 37.670 Find NCS groups from input model: 1.130 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 37639 Z= 0.190 Angle : 0.650 11.633 50846 Z= 0.344 Chirality : 0.070 1.755 5832 Planarity : 0.004 0.052 6522 Dihedral : 16.346 133.046 14460 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.29 % Favored : 94.62 % Rotamer: Outliers : 1.56 % Allowed : 18.72 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.17 (0.12), residues: 4632 helix: 0.40 (0.11), residues: 2061 sheet: -2.36 (0.21), residues: 565 loop : -1.48 (0.14), residues: 2006 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 721 TYR 0.027 0.001 TYR A 360 PHE 0.014 0.001 PHE B 779 TRP 0.011 0.001 TRP A 464 HIS 0.006 0.001 HIS C 938 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.19 (37638) covalent geometry : angle 0.64953 / 0.34 (50844) SS BOND : bond 0.00376 / 0.20 ( 1) SS BOND : angle 1.45908 / 0.81 ( 2) hydrogen bonds : bond 0.15172 / 10.35 ( 1680) hydrogen bonds : angle 7.12746 / 5.02 ( 4836) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 4050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 218 time to evaluate : 1.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 197 MET cc_start: 0.5160 (mmm) cc_final: 0.4424 (ttt) REVERT: C 608 LEU cc_start: 0.9388 (OUTLIER) cc_final: 0.9007 (mt) REVERT: D 272 MET cc_start: 0.4843 (mtt) cc_final: 0.2276 (ttt) REVERT: D 459 ARG cc_start: 0.9639 (ttt180) cc_final: 0.9354 (ttp-110) REVERT: D 552 MET cc_start: 0.7504 (ppp) cc_final: 0.7012 (ppp) REVERT: D 569 MET cc_start: 0.8765 (pmm) cc_final: 0.8223 (pmm) REVERT: D 586 LEU cc_start: 0.9106 (tp) cc_final: 0.8738 (tt) REVERT: D 594 LYS cc_start: 0.9293 (mmmt) cc_final: 0.8978 (mmtm) REVERT: D 647 GLU cc_start: 0.9451 (tp30) cc_final: 0.9123 (tm-30) REVERT: D 810 MET cc_start: 0.9100 (ttm) cc_final: 0.8738 (tpp) REVERT: D 826 MET cc_start: 0.7247 (ttt) cc_final: 0.6363 (mtp) REVERT: E 272 MET cc_start: 0.3001 (ptp) cc_final: -0.0204 (pmm) REVERT: E 494 MET cc_start: 0.6786 (mtm) cc_final: 0.6518 (mtp) REVERT: E 653 MET cc_start: 0.1326 (mtp) cc_final: 0.0830 (mpp) REVERT: E 879 MET cc_start: 0.6406 (ptp) cc_final: 0.2222 (tpt) REVERT: F 197 MET cc_start: 0.2029 (ttt) cc_final: 0.1191 (pmm) REVERT: F 318 MET cc_start: -0.6637 (ptt) cc_final: -0.6907 (ptp) REVERT: F 435 MET cc_start: 0.8196 (mmm) cc_final: 0.7902 (mmm) REVERT: F 519 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8384 (tp) REVERT: F 600 GLN cc_start: 0.7892 (OUTLIER) cc_final: 0.7554 (pm20) REVERT: F 653 MET cc_start: 0.8329 (ppp) cc_final: 0.7769 (ppp) REVERT: F 674 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8607 (mt) REVERT: F 717 GLU cc_start: 0.9166 (OUTLIER) cc_final: 0.8676 (tm-30) REVERT: F 773 MET cc_start: 0.8151 (pmm) cc_final: 0.7650 (tpt) REVERT: A 773 MET cc_start: 0.8959 (ppp) cc_final: 0.8293 (ppp) REVERT: A 869 MET cc_start: 0.8901 (ttm) cc_final: 0.8388 (ttt) REVERT: A 879 MET cc_start: 0.8864 (ptp) cc_final: 0.8556 (ptp) REVERT: B 334 MET cc_start: 0.2853 (mmt) cc_final: 0.2597 (mmt) REVERT: B 435 MET cc_start: 0.8977 (mmm) cc_final: 0.8768 (mmm) REVERT: B 576 CYS cc_start: 0.9148 (OUTLIER) cc_final: 0.8918 (p) REVERT: B 597 ARG cc_start: 0.6828 (tpt170) cc_final: 0.6429 (tpt90) REVERT: B 766 MET cc_start: 0.8205 (tpp) cc_final: 0.7861 (tpp) REVERT: B 879 MET cc_start: 0.7892 (ptt) cc_final: 0.7594 (ptt) outliers start: 63 outliers final: 41 residues processed: 275 average time/residue: 0.2536 time to fit residues: 113.5692 Evaluate side-chains 238 residues out of total 4050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 191 time to evaluate : 1.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 394 TYR Chi-restraints excluded: chain C residue 460 ASN Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain C residue 607 LEU Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 860 ILE Chi-restraints excluded: chain C residue 892 VAL Chi-restraints excluded: chain D residue 407 LEU Chi-restraints excluded: chain D residue 500 ARG Chi-restraints excluded: chain D residue 530 THR Chi-restraints excluded: chain D residue 632 LYS Chi-restraints excluded: chain D residue 812 GLU Chi-restraints excluded: chain D residue 886 THR Chi-restraints excluded: chain D residue 931 LEU Chi-restraints excluded: chain D residue 944 ASP Chi-restraints excluded: chain E residue 422 ARG Chi-restraints excluded: chain E residue 433 HIS Chi-restraints excluded: chain E residue 624 LEU Chi-restraints excluded: chain F residue 462 LEU Chi-restraints excluded: chain F residue 519 LEU Chi-restraints excluded: chain F residue 582 THR Chi-restraints excluded: chain F residue 600 GLN Chi-restraints excluded: chain F residue 674 LEU Chi-restraints excluded: chain F residue 712 LEU Chi-restraints excluded: chain F residue 717 GLU Chi-restraints excluded: chain F residue 742 LEU Chi-restraints excluded: chain F residue 858 CYS Chi-restraints excluded: chain A residue 394 TYR Chi-restraints excluded: chain A residue 419 GLU Chi-restraints excluded: chain A residue 444 LYS Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 590 ASP Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 713 GLN Chi-restraints excluded: chain A residue 738 THR Chi-restraints excluded: chain A residue 782 THR Chi-restraints excluded: chain A residue 944 ASP Chi-restraints excluded: chain B residue 420 LYS Chi-restraints excluded: chain B residue 451 HIS Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 576 CYS Chi-restraints excluded: chain B residue 607 LEU Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 637 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 432 optimal weight: 0.0030 chunk 197 optimal weight: 7.9990 chunk 388 optimal weight: 0.9990 chunk 455 optimal weight: 2.9990 chunk 215 optimal weight: 30.0000 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 0.2980 chunk 248 optimal weight: 30.0000 chunk 207 optimal weight: 0.0470 chunk 401 optimal weight: 50.0000 overall best weight: 0.8692 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 399 GLN C 451 HIS C 677 GLN D 195 HIS D 215 HIS D 916 ASN D 938 HIS E 702 GLN F 215 HIS F 491 HIS F 515 GLN F 640 ASN F 743 GLN A 477 ASN A 541 ASN ** A 622 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 640 ASN A 664 GLN B 938 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.099408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.070601 restraints weight = 268502.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.071698 restraints weight = 160464.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.072037 restraints weight = 107320.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.072172 restraints weight = 85895.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.072008 restraints weight = 92093.272| |-----------------------------------------------------------------------------| r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.1209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 37639 Z= 0.143 Angle : 0.653 11.068 50846 Z= 0.319 Chirality : 0.042 0.249 5832 Planarity : 0.004 0.058 6522 Dihedral : 7.813 131.824 5221 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.47 % Favored : 95.47 % Rotamer: Outliers : 2.44 % Allowed : 18.37 % Favored : 79.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.12), residues: 4632 helix: 0.83 (0.11), residues: 2127 sheet: -1.98 (0.22), residues: 548 loop : -1.37 (0.14), residues: 1957 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 378 TYR 0.034 0.001 TYR A 360 PHE 0.013 0.001 PHE F 421 TRP 0.016 0.001 TRP A 464 HIS 0.005 0.001 HIS C 938 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.14 (37638) covalent geometry : angle 0.65295 / 0.32 (50844) SS BOND : bond 0.00395 / 0.21 ( 1) SS BOND : angle 1.69577 / 0.99 ( 2) hydrogen bonds : bond 0.04194 / 2.85 ( 1680) hydrogen bonds : angle 5.30054 / 3.70 ( 4836) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 4050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 221 time to evaluate : 1.148 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 197 MET cc_start: 0.5477 (mmm) cc_final: 0.4579 (ttt) REVERT: C 608 LEU cc_start: 0.9364 (OUTLIER) cc_final: 0.9024 (mt) REVERT: D 272 MET cc_start: 0.4526 (mtt) cc_final: 0.1830 (ttt) REVERT: D 451 HIS cc_start: 0.4623 (OUTLIER) cc_final: 0.4101 (m-70) REVERT: D 459 ARG cc_start: 0.9656 (ttt180) cc_final: 0.9326 (ttp-110) REVERT: D 552 MET cc_start: 0.7256 (ppp) cc_final: 0.6353 (ppp) REVERT: D 569 MET cc_start: 0.8791 (pmm) cc_final: 0.8037 (pmm) REVERT: D 576 CYS cc_start: 0.9408 (OUTLIER) cc_final: 0.9103 (t) REVERT: D 647 GLU cc_start: 0.9378 (tp30) cc_final: 0.9034 (tm-30) REVERT: D 810 MET cc_start: 0.9026 (ttm) cc_final: 0.8651 (mmm) REVERT: D 826 MET cc_start: 0.7573 (ttt) cc_final: 0.6612 (mtp) REVERT: D 912 LEU cc_start: 0.9422 (mt) cc_final: 0.8975 (tt) REVERT: E 272 MET cc_start: 0.2246 (ptp) cc_final: -0.1214 (pmm) REVERT: E 381 ARG cc_start: 0.9173 (OUTLIER) cc_final: 0.8973 (ttp80) REVERT: E 494 MET cc_start: 0.6426 (mtm) cc_final: 0.6105 (mtp) REVERT: E 806 LEU cc_start: 0.7205 (OUTLIER) cc_final: 0.6931 (tp) REVERT: E 879 MET cc_start: 0.6665 (ptp) cc_final: 0.3207 (tpp) REVERT: F 197 MET cc_start: 0.1906 (ttt) cc_final: 0.0954 (pmm) REVERT: F 435 MET cc_start: 0.8400 (mmm) cc_final: 0.8022 (mmm) REVERT: F 511 ARG cc_start: 0.5108 (OUTLIER) cc_final: 0.4793 (mtp180) REVERT: F 519 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.7890 (tp) REVERT: F 552 MET cc_start: 0.5294 (ptt) cc_final: 0.4809 (pmm) REVERT: F 618 ASN cc_start: 0.8943 (t0) cc_final: 0.8606 (p0) REVERT: F 653 MET cc_start: 0.8095 (ppp) cc_final: 0.7611 (ppp) REVERT: F 717 GLU cc_start: 0.9051 (OUTLIER) cc_final: 0.8573 (tm-30) REVERT: F 773 MET cc_start: 0.7928 (pmm) cc_final: 0.7650 (tpt) REVERT: A 208 VAL cc_start: 0.2105 (OUTLIER) cc_final: 0.1595 (p) REVERT: A 415 ASP cc_start: 0.8736 (t0) cc_final: 0.8471 (t0) REVERT: A 742 LEU cc_start: 0.9550 (OUTLIER) cc_final: 0.9342 (tp) REVERT: A 773 MET cc_start: 0.8865 (OUTLIER) cc_final: 0.8148 (ppp) REVERT: A 869 MET cc_start: 0.8892 (ttm) cc_final: 0.8539 (ttt) REVERT: B 334 MET cc_start: 0.2625 (mmt) cc_final: 0.2401 (mmt) REVERT: B 430 VAL cc_start: 0.7883 (OUTLIER) cc_final: 0.7634 (t) REVERT: B 490 ASP cc_start: 0.9076 (OUTLIER) cc_final: 0.8662 (m-30) REVERT: B 576 CYS cc_start: 0.9115 (OUTLIER) cc_final: 0.8874 (p) REVERT: B 865 LEU cc_start: 0.9673 (tp) cc_final: 0.9441 (tp) outliers start: 99 outliers final: 37 residues processed: 308 average time/residue: 0.2112 time to fit residues: 107.5624 Evaluate side-chains 250 residues out of total 4050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 199 time to evaluate : 1.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 382 GLU Chi-restraints excluded: chain C residue 394 TYR Chi-restraints excluded: chain C residue 460 ASN Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain C residue 575 GLN Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 931 LEU Chi-restraints excluded: chain D residue 451 HIS Chi-restraints excluded: chain D residue 576 CYS Chi-restraints excluded: chain D residue 610 LEU Chi-restraints excluded: chain D residue 812 GLU Chi-restraints excluded: chain D residue 879 MET Chi-restraints excluded: chain D residue 886 THR Chi-restraints excluded: chain D residue 931 LEU Chi-restraints excluded: chain E residue 381 ARG Chi-restraints excluded: chain E residue 433 HIS Chi-restraints excluded: chain E residue 548 SER Chi-restraints excluded: chain E residue 624 LEU Chi-restraints excluded: chain E residue 665 GLU Chi-restraints excluded: chain E residue 709 VAL Chi-restraints excluded: chain E residue 737 VAL Chi-restraints excluded: chain E residue 806 LEU Chi-restraints excluded: chain F residue 462 LEU Chi-restraints excluded: chain F residue 511 ARG Chi-restraints excluded: chain F residue 519 LEU Chi-restraints excluded: chain F residue 582 THR Chi-restraints excluded: chain F residue 634 LEU Chi-restraints excluded: chain F residue 658 VAL Chi-restraints excluded: chain F residue 717 GLU Chi-restraints excluded: chain F residue 742 LEU Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 394 TYR Chi-restraints excluded: chain A residue 444 LYS Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 590 ASP Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 738 THR Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain A residue 752 THR Chi-restraints excluded: chain A residue 773 MET Chi-restraints excluded: chain A residue 927 ILE Chi-restraints excluded: chain B residue 420 LYS Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 451 HIS Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain B residue 490 ASP Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 576 CYS Chi-restraints excluded: chain B residue 607 LEU Chi-restraints excluded: chain B residue 861 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 402 optimal weight: 10.0000 chunk 204 optimal weight: 20.0000 chunk 301 optimal weight: 6.9990 chunk 248 optimal weight: 30.0000 chunk 359 optimal weight: 5.9990 chunk 114 optimal weight: 4.9990 chunk 268 optimal weight: 10.0000 chunk 251 optimal weight: 20.0000 chunk 396 optimal weight: 0.0000 chunk 63 optimal weight: 0.9990 chunk 348 optimal weight: 3.9990 overall best weight: 3.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 211 HIS C 451 HIS D 219 GLN E 132 ASN F 561 HIS F 839 HIS A 187 HIS A 460 ASN A 622 HIS B 174 ASN B 219 GLN B 397 GLN B 456 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.096973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.067583 restraints weight = 270426.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.068799 restraints weight = 155241.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.069280 restraints weight = 99551.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.068990 restraints weight = 103434.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.068969 restraints weight = 85389.607| |-----------------------------------------------------------------------------| r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.1649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 37639 Z= 0.201 Angle : 0.662 13.515 50846 Z= 0.327 Chirality : 0.042 0.249 5832 Planarity : 0.004 0.067 6522 Dihedral : 7.507 130.027 5175 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.97 % Favored : 94.97 % Rotamer: Outliers : 3.23 % Allowed : 18.94 % Favored : 77.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.12), residues: 4632 helix: 0.79 (0.11), residues: 2134 sheet: -1.93 (0.21), residues: 544 loop : -1.35 (0.14), residues: 1954 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 424 TYR 0.030 0.002 TYR A 360 PHE 0.017 0.002 PHE A 521 TRP 0.008 0.001 TRP A 464 HIS 0.008 0.001 HIS C 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.20 (37638) covalent geometry : angle 0.66202 / 0.33 (50844) SS BOND : bond 0.00573 / 0.30 ( 1) SS BOND : angle 1.63156 / 0.92 ( 2) hydrogen bonds : bond 0.03961 / 2.67 ( 1680) hydrogen bonds : angle 5.14924 / 3.60 ( 4836) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 4050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 202 time to evaluate : 1.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 197 MET cc_start: 0.5035 (mmm) cc_final: 0.4325 (ttt) REVERT: C 430 VAL cc_start: 0.7781 (OUTLIER) cc_final: 0.7400 (t) REVERT: C 608 LEU cc_start: 0.9411 (OUTLIER) cc_final: 0.9057 (mt) REVERT: C 634 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8597 (tt) REVERT: C 655 MET cc_start: 0.8503 (mtt) cc_final: 0.8117 (mtm) REVERT: C 846 GLU cc_start: 0.7763 (pm20) cc_final: 0.7472 (pm20) REVERT: C 879 MET cc_start: 0.8588 (ppp) cc_final: 0.7677 (ppp) REVERT: D 272 MET cc_start: 0.5677 (mtt) cc_final: 0.3043 (ttt) REVERT: D 405 LYS cc_start: 0.8568 (OUTLIER) cc_final: 0.8182 (mmmt) REVERT: D 459 ARG cc_start: 0.9639 (ttt180) cc_final: 0.9264 (ttp-110) REVERT: D 552 MET cc_start: 0.7150 (ppp) cc_final: 0.6384 (ppp) REVERT: D 569 MET cc_start: 0.8795 (pmm) cc_final: 0.8100 (pmm) REVERT: D 576 CYS cc_start: 0.9435 (OUTLIER) cc_final: 0.9165 (t) REVERT: D 594 LYS cc_start: 0.9469 (mmmt) cc_final: 0.9248 (mmmt) REVERT: D 647 GLU cc_start: 0.9372 (tp30) cc_final: 0.9019 (tm-30) REVERT: D 690 LYS cc_start: 0.8508 (OUTLIER) cc_final: 0.7993 (pttm) REVERT: D 810 MET cc_start: 0.9054 (ttm) cc_final: 0.8613 (tpp) REVERT: D 826 MET cc_start: 0.7727 (ttt) cc_final: 0.6803 (mtt) REVERT: E 272 MET cc_start: 0.3704 (ptp) cc_final: 0.0346 (pmm) REVERT: E 381 ARG cc_start: 0.9182 (OUTLIER) cc_final: 0.8949 (ttp80) REVERT: E 879 MET cc_start: 0.6817 (ptp) cc_final: 0.3610 (tpp) REVERT: F 197 MET cc_start: 0.1932 (ttt) cc_final: 0.1157 (pmm) REVERT: F 519 LEU cc_start: 0.8530 (OUTLIER) cc_final: 0.8060 (tp) REVERT: F 552 MET cc_start: 0.5329 (ptt) cc_final: 0.4910 (pmm) REVERT: F 600 GLN cc_start: 0.7702 (OUTLIER) cc_final: 0.7397 (pm20) REVERT: F 618 ASN cc_start: 0.9059 (t0) cc_final: 0.8742 (p0) REVERT: F 653 MET cc_start: 0.8333 (ppp) cc_final: 0.7823 (ppp) REVERT: F 717 GLU cc_start: 0.9095 (OUTLIER) cc_final: 0.8616 (tm-30) REVERT: F 773 MET cc_start: 0.8096 (pmm) cc_final: 0.7874 (tpt) REVERT: A 208 VAL cc_start: 0.2198 (OUTLIER) cc_final: 0.1815 (m) REVERT: A 415 ASP cc_start: 0.8769 (t0) cc_final: 0.8490 (t0) REVERT: A 459 ARG cc_start: 0.9065 (ttp80) cc_final: 0.8815 (ttp80) REVERT: A 494 MET cc_start: 0.8345 (tmm) cc_final: 0.7840 (tmm) REVERT: A 756 MET cc_start: 0.8491 (ppp) cc_final: 0.7757 (ppp) REVERT: A 773 MET cc_start: 0.8754 (OUTLIER) cc_final: 0.8079 (ppp) REVERT: A 869 MET cc_start: 0.8911 (ttm) cc_final: 0.8541 (ttt) REVERT: A 879 MET cc_start: 0.8736 (ptp) cc_final: 0.8385 (ptp) REVERT: B 430 VAL cc_start: 0.8005 (OUTLIER) cc_final: 0.7726 (t) REVERT: B 574 ILE cc_start: 0.8975 (mp) cc_final: 0.8772 (pt) REVERT: B 576 CYS cc_start: 0.9213 (OUTLIER) cc_final: 0.8888 (p) REVERT: B 578 LYS cc_start: 0.9642 (OUTLIER) cc_final: 0.9315 (ttpp) outliers start: 131 outliers final: 59 residues processed: 315 average time/residue: 0.1969 time to fit residues: 104.4752 Evaluate side-chains 268 residues out of total 4050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 194 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 394 TYR Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 460 ASN Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain C residue 607 LEU Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 634 LEU Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 720 LEU Chi-restraints excluded: chain C residue 844 VAL Chi-restraints excluded: chain C residue 892 VAL Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 931 LEU Chi-restraints excluded: chain D residue 405 LYS Chi-restraints excluded: chain D residue 576 CYS Chi-restraints excluded: chain D residue 593 ASP Chi-restraints excluded: chain D residue 690 LYS Chi-restraints excluded: chain D residue 776 SER Chi-restraints excluded: chain D residue 812 GLU Chi-restraints excluded: chain D residue 864 LEU Chi-restraints excluded: chain D residue 879 MET Chi-restraints excluded: chain D residue 880 THR Chi-restraints excluded: chain D residue 886 THR Chi-restraints excluded: chain D residue 931 LEU Chi-restraints excluded: chain D residue 944 ASP Chi-restraints excluded: chain E residue 381 ARG Chi-restraints excluded: chain E residue 433 HIS Chi-restraints excluded: chain E residue 548 SER Chi-restraints excluded: chain E residue 624 LEU Chi-restraints excluded: chain E residue 705 ARG Chi-restraints excluded: chain E residue 709 VAL Chi-restraints excluded: chain E residue 737 VAL Chi-restraints excluded: chain E residue 789 ASP Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain F residue 462 LEU Chi-restraints excluded: chain F residue 511 ARG Chi-restraints excluded: chain F residue 519 LEU Chi-restraints excluded: chain F residue 600 GLN Chi-restraints excluded: chain F residue 636 ILE Chi-restraints excluded: chain F residue 717 GLU Chi-restraints excluded: chain F residue 742 LEU Chi-restraints excluded: chain F residue 782 THR Chi-restraints excluded: chain F residue 879 MET Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 394 TYR Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 444 LYS Chi-restraints excluded: chain A residue 503 GLU Chi-restraints excluded: chain A residue 590 ASP Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 738 THR Chi-restraints excluded: chain A residue 752 THR Chi-restraints excluded: chain A residue 773 MET Chi-restraints excluded: chain A residue 782 THR Chi-restraints excluded: chain A residue 909 CYS Chi-restraints excluded: chain A residue 927 ILE Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 420 LYS Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 451 HIS Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 576 CYS Chi-restraints excluded: chain B residue 578 LYS Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain B residue 607 LEU Chi-restraints excluded: chain B residue 628 VAL Chi-restraints excluded: chain B residue 637 CYS Chi-restraints excluded: chain B residue 658 VAL Chi-restraints excluded: chain B residue 681 LEU Chi-restraints excluded: chain B residue 861 VAL Chi-restraints excluded: chain B residue 886 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 395 optimal weight: 1.9990 chunk 243 optimal weight: 7.9990 chunk 274 optimal weight: 6.9990 chunk 100 optimal weight: 5.9990 chunk 97 optimal weight: 20.0000 chunk 127 optimal weight: 1.9990 chunk 354 optimal weight: 3.9990 chunk 306 optimal weight: 6.9990 chunk 305 optimal weight: 0.1980 chunk 152 optimal weight: 10.0000 chunk 208 optimal weight: 20.0000 overall best weight: 2.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 433 HIS ** D 640 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 280 HIS B 622 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.096565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.068700 restraints weight = 268921.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.068252 restraints weight = 191199.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.068283 restraints weight = 126696.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.068351 restraints weight = 107188.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.068469 restraints weight = 98219.247| |-----------------------------------------------------------------------------| r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.2178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 37639 Z= 0.179 Angle : 0.641 9.995 50846 Z= 0.315 Chirality : 0.041 0.246 5832 Planarity : 0.004 0.060 6522 Dihedral : 7.463 124.291 5173 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.90 % Favored : 95.03 % Rotamer: Outliers : 3.36 % Allowed : 19.41 % Favored : 77.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.12), residues: 4632 helix: 0.90 (0.11), residues: 2140 sheet: -1.94 (0.22), residues: 532 loop : -1.32 (0.14), residues: 1960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 542 TYR 0.029 0.002 TYR A 360 PHE 0.015 0.001 PHE F 421 TRP 0.011 0.001 TRP A 464 HIS 0.004 0.001 HIS E 841 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.18 (37638) covalent geometry : angle 0.64048 / 0.31 (50844) SS BOND : bond 0.00489 / 0.26 ( 1) SS BOND : angle 1.69828 / 0.97 ( 2) hydrogen bonds : bond 0.03660 / 2.48 ( 1680) hydrogen bonds : angle 4.92602 / 3.45 ( 4836) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 4050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 203 time to evaluate : 1.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 197 MET cc_start: 0.5333 (mmm) cc_final: 0.4402 (ttt) REVERT: C 430 VAL cc_start: 0.7913 (OUTLIER) cc_final: 0.7527 (t) REVERT: C 608 LEU cc_start: 0.9428 (OUTLIER) cc_final: 0.9029 (mt) REVERT: C 846 GLU cc_start: 0.7758 (pm20) cc_final: 0.7488 (pm20) REVERT: C 879 MET cc_start: 0.8602 (ppp) cc_final: 0.7835 (ppp) REVERT: C 888 LYS cc_start: 0.8703 (OUTLIER) cc_final: 0.8496 (mmmm) REVERT: C 915 GLU cc_start: 0.8544 (OUTLIER) cc_final: 0.8273 (pm20) REVERT: D 272 MET cc_start: 0.5216 (mtt) cc_final: 0.2417 (ttt) REVERT: D 451 HIS cc_start: 0.5113 (OUTLIER) cc_final: 0.4648 (m-70) REVERT: D 459 ARG cc_start: 0.9606 (ttt180) cc_final: 0.9282 (ttp-110) REVERT: D 552 MET cc_start: 0.7506 (ppp) cc_final: 0.6193 (ppp) REVERT: D 569 MET cc_start: 0.8785 (pmm) cc_final: 0.8183 (pmm) REVERT: D 576 CYS cc_start: 0.9357 (OUTLIER) cc_final: 0.9142 (t) REVERT: D 594 LYS cc_start: 0.9495 (mmmt) cc_final: 0.9268 (mmmt) REVERT: D 647 GLU cc_start: 0.9435 (tp30) cc_final: 0.9087 (tm-30) REVERT: D 690 LYS cc_start: 0.8550 (OUTLIER) cc_final: 0.7996 (pttm) REVERT: D 810 MET cc_start: 0.9093 (ttm) cc_final: 0.8760 (mmm) REVERT: D 826 MET cc_start: 0.7959 (ttt) cc_final: 0.7034 (mtm) REVERT: E 272 MET cc_start: 0.3598 (ptp) cc_final: -0.0107 (pmm) REVERT: E 381 ARG cc_start: 0.9205 (OUTLIER) cc_final: 0.8974 (ttp80) REVERT: E 552 MET cc_start: 0.3526 (OUTLIER) cc_final: 0.3039 (ptm) REVERT: E 879 MET cc_start: 0.6679 (ptp) cc_final: 0.3303 (tpp) REVERT: F 197 MET cc_start: 0.2234 (ttt) cc_final: 0.1312 (pmm) REVERT: F 519 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.8086 (tp) REVERT: F 552 MET cc_start: 0.5291 (ptt) cc_final: 0.4917 (pmm) REVERT: F 618 ASN cc_start: 0.9043 (t0) cc_final: 0.8732 (p0) REVERT: F 653 MET cc_start: 0.8581 (ppp) cc_final: 0.8167 (ppp) REVERT: F 717 GLU cc_start: 0.9101 (OUTLIER) cc_final: 0.8598 (tm-30) REVERT: F 773 MET cc_start: 0.8192 (pmm) cc_final: 0.7978 (tpt) REVERT: F 909 CYS cc_start: 0.8647 (OUTLIER) cc_final: 0.8029 (m) REVERT: A 208 VAL cc_start: 0.1600 (OUTLIER) cc_final: 0.1060 (p) REVERT: A 415 ASP cc_start: 0.8874 (t0) cc_final: 0.8582 (t0) REVERT: A 494 MET cc_start: 0.8382 (tmm) cc_final: 0.7991 (tmm) REVERT: A 756 MET cc_start: 0.8577 (ppp) cc_final: 0.8078 (ppp) REVERT: A 773 MET cc_start: 0.8780 (OUTLIER) cc_final: 0.8119 (ppp) REVERT: A 826 MET cc_start: 0.9113 (mmm) cc_final: 0.8893 (mmm) REVERT: A 869 MET cc_start: 0.8946 (ttm) cc_final: 0.8583 (ttt) REVERT: A 879 MET cc_start: 0.8976 (ptp) cc_final: 0.8658 (ptp) REVERT: B 490 ASP cc_start: 0.9089 (OUTLIER) cc_final: 0.8729 (m-30) REVERT: B 576 CYS cc_start: 0.9252 (OUTLIER) cc_final: 0.8995 (p) REVERT: B 630 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8815 (mt) REVERT: B 766 MET cc_start: 0.8427 (tpp) cc_final: 0.8158 (tpp) REVERT: B 810 MET cc_start: 0.9419 (tpp) cc_final: 0.9112 (tpp) outliers start: 136 outliers final: 67 residues processed: 320 average time/residue: 0.1971 time to fit residues: 105.8073 Evaluate side-chains 279 residues out of total 4050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 195 time to evaluate : 1.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 141 ILE Chi-restraints excluded: chain C residue 394 TYR Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 460 ASN Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain C residue 607 LEU Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 811 LYS Chi-restraints excluded: chain C residue 844 VAL Chi-restraints excluded: chain C residue 849 THR Chi-restraints excluded: chain C residue 888 LYS Chi-restraints excluded: chain C residue 892 VAL Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 915 GLU Chi-restraints excluded: chain C residue 931 LEU Chi-restraints excluded: chain D residue 451 HIS Chi-restraints excluded: chain D residue 576 CYS Chi-restraints excluded: chain D residue 636 ILE Chi-restraints excluded: chain D residue 667 LEU Chi-restraints excluded: chain D residue 681 LEU Chi-restraints excluded: chain D residue 690 LYS Chi-restraints excluded: chain D residue 725 TYR Chi-restraints excluded: chain D residue 812 GLU Chi-restraints excluded: chain D residue 864 LEU Chi-restraints excluded: chain D residue 879 MET Chi-restraints excluded: chain D residue 880 THR Chi-restraints excluded: chain D residue 886 THR Chi-restraints excluded: chain D residue 931 LEU Chi-restraints excluded: chain E residue 381 ARG Chi-restraints excluded: chain E residue 422 ARG Chi-restraints excluded: chain E residue 433 HIS Chi-restraints excluded: chain E residue 548 SER Chi-restraints excluded: chain E residue 552 MET Chi-restraints excluded: chain E residue 624 LEU Chi-restraints excluded: chain E residue 665 GLU Chi-restraints excluded: chain E residue 705 ARG Chi-restraints excluded: chain E residue 709 VAL Chi-restraints excluded: chain E residue 737 VAL Chi-restraints excluded: chain E residue 789 ASP Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain F residue 407 LEU Chi-restraints excluded: chain F residue 462 LEU Chi-restraints excluded: chain F residue 511 ARG Chi-restraints excluded: chain F residue 519 LEU Chi-restraints excluded: chain F residue 695 VAL Chi-restraints excluded: chain F residue 717 GLU Chi-restraints excluded: chain F residue 742 LEU Chi-restraints excluded: chain F residue 782 THR Chi-restraints excluded: chain F residue 819 THR Chi-restraints excluded: chain F residue 859 THR Chi-restraints excluded: chain F residue 879 MET Chi-restraints excluded: chain F residue 909 CYS Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 394 TYR Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 444 LYS Chi-restraints excluded: chain A residue 503 GLU Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 541 ASN Chi-restraints excluded: chain A residue 590 ASP Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 738 THR Chi-restraints excluded: chain A residue 752 THR Chi-restraints excluded: chain A residue 773 MET Chi-restraints excluded: chain A residue 909 CYS Chi-restraints excluded: chain A residue 927 ILE Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 420 LYS Chi-restraints excluded: chain B residue 451 HIS Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain B residue 490 ASP Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 576 CYS Chi-restraints excluded: chain B residue 607 LEU Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 637 CYS Chi-restraints excluded: chain B residue 681 LEU Chi-restraints excluded: chain B residue 771 THR Chi-restraints excluded: chain B residue 773 MET Chi-restraints excluded: chain B residue 861 VAL Chi-restraints excluded: chain B residue 886 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 91 optimal weight: 1.9990 chunk 188 optimal weight: 20.0000 chunk 209 optimal weight: 0.0470 chunk 191 optimal weight: 0.9990 chunk 333 optimal weight: 0.6980 chunk 350 optimal weight: 7.9990 chunk 205 optimal weight: 4.9990 chunk 315 optimal weight: 10.0000 chunk 60 optimal weight: 7.9990 chunk 165 optimal weight: 10.0000 chunk 301 optimal weight: 10.0000 overall best weight: 1.7484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 711 ASN A 460 ASN A 828 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.097019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.067797 restraints weight = 268160.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.068932 restraints weight = 157634.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.069096 restraints weight = 103143.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.069180 restraints weight = 110502.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.069109 restraints weight = 97296.984| |-----------------------------------------------------------------------------| r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 37639 Z= 0.135 Angle : 0.624 13.093 50846 Z= 0.300 Chirality : 0.041 0.345 5832 Planarity : 0.004 0.087 6522 Dihedral : 7.368 123.641 5173 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.34 % Favored : 95.60 % Rotamer: Outliers : 3.41 % Allowed : 20.02 % Favored : 76.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.12), residues: 4632 helix: 1.00 (0.11), residues: 2142 sheet: -1.73 (0.22), residues: 532 loop : -1.28 (0.14), residues: 1958 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 815 TYR 0.028 0.001 TYR A 360 PHE 0.015 0.001 PHE E 504 TRP 0.010 0.001 TRP A 464 HIS 0.012 0.001 HIS E 841 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.14 (37638) covalent geometry : angle 0.62410 / 0.30 (50844) SS BOND : bond 0.02863 / 1.51 ( 1) SS BOND : angle 1.78021 / 1.05 ( 2) hydrogen bonds : bond 0.03482 / 2.36 ( 1680) hydrogen bonds : angle 4.76620 / 3.32 ( 4836) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 4050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 200 time to evaluate : 1.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 197 MET cc_start: 0.5312 (mmm) cc_final: 0.4442 (ttt) REVERT: C 518 ILE cc_start: 0.8875 (OUTLIER) cc_final: 0.8522 (pt) REVERT: C 608 LEU cc_start: 0.9411 (OUTLIER) cc_final: 0.9009 (mt) REVERT: C 634 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8643 (tt) REVERT: C 692 SER cc_start: 0.7899 (OUTLIER) cc_final: 0.7221 (p) REVERT: C 846 GLU cc_start: 0.7777 (pm20) cc_final: 0.7510 (pm20) REVERT: C 858 CYS cc_start: 0.9354 (OUTLIER) cc_final: 0.8704 (t) REVERT: C 879 MET cc_start: 0.8556 (ppp) cc_final: 0.7307 (ppp) REVERT: C 888 LYS cc_start: 0.8708 (OUTLIER) cc_final: 0.8459 (mmmm) REVERT: C 915 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.8278 (pm20) REVERT: D 272 MET cc_start: 0.5093 (mtt) cc_final: 0.2265 (ttt) REVERT: D 405 LYS cc_start: 0.8826 (OUTLIER) cc_final: 0.8482 (mmmt) REVERT: D 451 HIS cc_start: 0.4964 (OUTLIER) cc_final: 0.4490 (m-70) REVERT: D 552 MET cc_start: 0.7377 (ppp) cc_final: 0.5937 (ppp) REVERT: D 569 MET cc_start: 0.8805 (pmm) cc_final: 0.8169 (pmm) REVERT: D 594 LYS cc_start: 0.9543 (mmmt) cc_final: 0.9298 (mmmt) REVERT: D 647 GLU cc_start: 0.9406 (tp30) cc_final: 0.9058 (tm-30) REVERT: D 690 LYS cc_start: 0.8560 (OUTLIER) cc_final: 0.8103 (pttm) REVERT: D 810 MET cc_start: 0.9071 (ttm) cc_final: 0.8703 (mmm) REVERT: D 826 MET cc_start: 0.8013 (ttt) cc_final: 0.7134 (mtt) REVERT: E 272 MET cc_start: 0.3670 (ptp) cc_final: -0.0101 (pmm) REVERT: E 381 ARG cc_start: 0.9225 (OUTLIER) cc_final: 0.9020 (ttp80) REVERT: E 552 MET cc_start: 0.3749 (OUTLIER) cc_final: 0.3301 (ptm) REVERT: E 879 MET cc_start: 0.6797 (ptp) cc_final: 0.3554 (tpp) REVERT: F 197 MET cc_start: 0.2156 (ttt) cc_final: 0.1330 (pmm) REVERT: F 428 LEU cc_start: 0.5364 (OUTLIER) cc_final: 0.4874 (pt) REVERT: F 519 LEU cc_start: 0.8392 (OUTLIER) cc_final: 0.7988 (tp) REVERT: F 552 MET cc_start: 0.5397 (ptt) cc_final: 0.4970 (pmm) REVERT: F 569 MET cc_start: 0.7181 (mpp) cc_final: 0.6552 (mpp) REVERT: F 618 ASN cc_start: 0.9051 (t0) cc_final: 0.8750 (p0) REVERT: F 653 MET cc_start: 0.8706 (ppp) cc_final: 0.8243 (ppp) REVERT: F 654 GLU cc_start: 0.7234 (OUTLIER) cc_final: 0.6942 (mt-10) REVERT: F 717 GLU cc_start: 0.9040 (OUTLIER) cc_final: 0.8516 (tm-30) REVERT: F 742 LEU cc_start: 0.8130 (OUTLIER) cc_final: 0.7929 (tt) REVERT: F 796 LYS cc_start: 0.8906 (OUTLIER) cc_final: 0.8609 (mmtm) REVERT: F 909 CYS cc_start: 0.8645 (OUTLIER) cc_final: 0.8004 (m) REVERT: A 208 VAL cc_start: 0.1909 (OUTLIER) cc_final: 0.1421 (m) REVERT: A 415 ASP cc_start: 0.8841 (t0) cc_final: 0.8542 (t0) REVERT: A 655 MET cc_start: 0.8446 (mmm) cc_final: 0.8193 (mmm) REVERT: A 756 MET cc_start: 0.8533 (ppp) cc_final: 0.8169 (ppp) REVERT: A 773 MET cc_start: 0.8707 (OUTLIER) cc_final: 0.8085 (ppp) REVERT: A 869 MET cc_start: 0.8917 (ttm) cc_final: 0.8533 (ttt) REVERT: A 879 MET cc_start: 0.8982 (ptp) cc_final: 0.8668 (ptp) REVERT: B 490 ASP cc_start: 0.9098 (OUTLIER) cc_final: 0.8776 (m-30) REVERT: B 578 LYS cc_start: 0.9627 (OUTLIER) cc_final: 0.9347 (ttpp) REVERT: B 630 LEU cc_start: 0.8996 (OUTLIER) cc_final: 0.8793 (mt) REVERT: B 879 MET cc_start: 0.8716 (ppp) cc_final: 0.7999 (ppp) outliers start: 138 outliers final: 64 residues processed: 322 average time/residue: 0.2122 time to fit residues: 113.8437 Evaluate side-chains 284 residues out of total 4050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 196 time to evaluate : 1.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 141 ILE Chi-restraints excluded: chain C residue 370 PHE Chi-restraints excluded: chain C residue 394 TYR Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 460 ASN Chi-restraints excluded: chain C residue 464 TRP Chi-restraints excluded: chain C residue 518 ILE Chi-restraints excluded: chain C residue 607 LEU Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 634 LEU Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 692 SER Chi-restraints excluded: chain C residue 844 VAL Chi-restraints excluded: chain C residue 858 CYS Chi-restraints excluded: chain C residue 888 LYS Chi-restraints excluded: chain C residue 892 VAL Chi-restraints excluded: chain C residue 909 CYS Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 915 GLU Chi-restraints excluded: chain C residue 931 LEU Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 405 LYS Chi-restraints excluded: chain D residue 451 HIS Chi-restraints excluded: chain D residue 667 LEU Chi-restraints excluded: chain D residue 690 LYS Chi-restraints excluded: chain D residue 725 TYR Chi-restraints excluded: chain D residue 776 SER Chi-restraints excluded: chain D residue 812 GLU Chi-restraints excluded: chain D residue 864 LEU Chi-restraints excluded: chain D residue 879 MET Chi-restraints excluded: chain D residue 880 THR Chi-restraints excluded: chain D residue 886 THR Chi-restraints excluded: chain D residue 931 LEU Chi-restraints excluded: chain D residue 944 ASP Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 381 ARG Chi-restraints excluded: chain E residue 433 HIS Chi-restraints excluded: chain E residue 548 SER Chi-restraints excluded: chain E residue 552 MET Chi-restraints excluded: chain E residue 624 LEU Chi-restraints excluded: chain E residue 665 GLU Chi-restraints excluded: chain E residue 705 ARG Chi-restraints excluded: chain E residue 709 VAL Chi-restraints excluded: chain E residue 737 VAL Chi-restraints excluded: chain E residue 789 ASP Chi-restraints excluded: chain E residue 844 VAL Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain F residue 407 LEU Chi-restraints excluded: chain F residue 428 LEU Chi-restraints excluded: chain F residue 462 LEU Chi-restraints excluded: chain F residue 511 ARG Chi-restraints excluded: chain F residue 519 LEU Chi-restraints excluded: chain F residue 654 GLU Chi-restraints excluded: chain F residue 717 GLU Chi-restraints excluded: chain F residue 742 LEU Chi-restraints excluded: chain F residue 782 THR Chi-restraints excluded: chain F residue 796 LYS Chi-restraints excluded: chain F residue 815 ARG Chi-restraints excluded: chain F residue 819 THR Chi-restraints excluded: chain F residue 909 CYS Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 394 TYR Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 444 LYS Chi-restraints excluded: chain A residue 503 GLU Chi-restraints excluded: chain A residue 590 ASP Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 738 THR Chi-restraints excluded: chain A residue 752 THR Chi-restraints excluded: chain A residue 773 MET Chi-restraints excluded: chain A residue 782 THR Chi-restraints excluded: chain B residue 209 MET Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 451 HIS Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain B residue 490 ASP Chi-restraints excluded: chain B residue 576 CYS Chi-restraints excluded: chain B residue 578 LYS Chi-restraints excluded: chain B residue 607 LEU Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 637 CYS Chi-restraints excluded: chain B residue 771 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 861 VAL Chi-restraints excluded: chain B residue 886 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 231 optimal weight: 30.0000 chunk 21 optimal weight: 10.0000 chunk 453 optimal weight: 0.7980 chunk 177 optimal weight: 8.9990 chunk 452 optimal weight: 0.7980 chunk 138 optimal weight: 10.0000 chunk 213 optimal weight: 30.0000 chunk 332 optimal weight: 6.9990 chunk 92 optimal weight: 20.0000 chunk 262 optimal weight: 6.9990 chunk 183 optimal weight: 9.9990 overall best weight: 4.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 219 GLN C 916 ASN D 123 HIS ** D 640 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 713 GLN D 876 ASN ** E 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 219 GLN F 713 GLN B 451 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.094005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.065946 restraints weight = 272584.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.065827 restraints weight = 183077.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.065720 restraints weight = 121942.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.065910 restraints weight = 102102.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.065956 restraints weight = 94827.895| |-----------------------------------------------------------------------------| r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.3084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 37639 Z= 0.278 Angle : 0.734 12.320 50846 Z= 0.365 Chirality : 0.044 0.360 5832 Planarity : 0.005 0.056 6522 Dihedral : 7.623 124.381 5167 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 16.71 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.68 % Favored : 94.26 % Rotamer: Outliers : 3.60 % Allowed : 20.25 % Favored : 76.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.12), residues: 4632 helix: 0.69 (0.11), residues: 2147 sheet: -1.73 (0.22), residues: 537 loop : -1.38 (0.14), residues: 1948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 679 TYR 0.025 0.002 TYR A 360 PHE 0.023 0.002 PHE B 619 TRP 0.015 0.002 TRP A 464 HIS 0.010 0.001 HIS E 841 Details of bonding type rmsd/Z covalent geometry : bond 0.00575 / 0.28 (37638) covalent geometry : angle 0.73442 / 0.37 (50844) SS BOND : bond 0.00247 / 0.13 ( 1) SS BOND : angle 1.07359 / 0.60 ( 2) hydrogen bonds : bond 0.04011 / 2.71 ( 1680) hydrogen bonds : angle 5.15557 / 3.61 ( 4836) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 4050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 192 time to evaluate : 1.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 197 MET cc_start: 0.5333 (mmm) cc_final: 0.4266 (ttt) REVERT: C 608 LEU cc_start: 0.9461 (OUTLIER) cc_final: 0.9035 (mt) REVERT: C 846 GLU cc_start: 0.7920 (pm20) cc_final: 0.7612 (pm20) REVERT: C 858 CYS cc_start: 0.9328 (OUTLIER) cc_final: 0.8662 (t) REVERT: C 879 MET cc_start: 0.8595 (OUTLIER) cc_final: 0.7374 (ppp) REVERT: C 888 LYS cc_start: 0.8706 (OUTLIER) cc_final: 0.8436 (mmmm) REVERT: D 272 MET cc_start: 0.4655 (mtt) cc_final: 0.1645 (ttt) REVERT: D 405 LYS cc_start: 0.8866 (OUTLIER) cc_final: 0.8505 (mmmt) REVERT: D 451 HIS cc_start: 0.5238 (OUTLIER) cc_final: 0.4758 (m-70) REVERT: D 552 MET cc_start: 0.7944 (ppp) cc_final: 0.6589 (ppp) REVERT: D 569 MET cc_start: 0.8761 (pmm) cc_final: 0.8144 (pmm) REVERT: D 586 LEU cc_start: 0.9375 (OUTLIER) cc_final: 0.9047 (tp) REVERT: D 594 LYS cc_start: 0.9589 (mmmt) cc_final: 0.9374 (mmmt) REVERT: D 690 LYS cc_start: 0.8557 (OUTLIER) cc_final: 0.7965 (pttm) REVERT: D 810 MET cc_start: 0.9116 (ttm) cc_final: 0.8713 (tpp) REVERT: E 272 MET cc_start: 0.3500 (ptp) cc_final: -0.0558 (pmm) REVERT: E 381 ARG cc_start: 0.9241 (OUTLIER) cc_final: 0.8907 (ptm-80) REVERT: E 552 MET cc_start: 0.3131 (OUTLIER) cc_final: 0.2648 (ptm) REVERT: E 665 GLU cc_start: 0.6045 (OUTLIER) cc_final: 0.5645 (tp30) REVERT: E 681 LEU cc_start: 0.4420 (tt) cc_final: 0.3949 (mt) REVERT: E 773 MET cc_start: 0.5972 (tmm) cc_final: 0.5690 (tmm) REVERT: E 879 MET cc_start: 0.6219 (ptp) cc_final: 0.2471 (tpp) REVERT: F 197 MET cc_start: 0.2052 (ttt) cc_final: 0.1280 (pmm) REVERT: F 546 ARG cc_start: 0.8284 (ttm170) cc_final: 0.8078 (ptm160) REVERT: F 569 MET cc_start: 0.7297 (mpp) cc_final: 0.6626 (mpp) REVERT: F 618 ASN cc_start: 0.9121 (t0) cc_final: 0.8827 (p0) REVERT: F 717 GLU cc_start: 0.9144 (OUTLIER) cc_final: 0.8620 (tm-30) REVERT: F 796 LYS cc_start: 0.8826 (OUTLIER) cc_final: 0.8544 (mmtm) REVERT: F 909 CYS cc_start: 0.8784 (OUTLIER) cc_final: 0.8168 (m) REVERT: A 208 VAL cc_start: 0.1423 (OUTLIER) cc_final: 0.0996 (m) REVERT: A 756 MET cc_start: 0.8680 (ppp) cc_final: 0.7866 (ppp) REVERT: A 757 TYR cc_start: 0.8337 (OUTLIER) cc_final: 0.7582 (m-80) REVERT: A 773 MET cc_start: 0.8711 (OUTLIER) cc_final: 0.8082 (ppp) REVERT: A 869 MET cc_start: 0.9008 (ttm) cc_final: 0.8623 (ttt) REVERT: B 578 LYS cc_start: 0.9670 (OUTLIER) cc_final: 0.9419 (ttpp) REVERT: B 766 MET cc_start: 0.8595 (tpp) cc_final: 0.8244 (tpp) outliers start: 146 outliers final: 89 residues processed: 320 average time/residue: 0.2054 time to fit residues: 109.7747 Evaluate side-chains 287 residues out of total 4050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 180 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 141 ILE Chi-restraints excluded: chain C residue 370 PHE Chi-restraints excluded: chain C residue 394 TYR Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 460 ASN Chi-restraints excluded: chain C residue 464 TRP Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain C residue 607 LEU Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 692 SER Chi-restraints excluded: chain C residue 694 ASP Chi-restraints excluded: chain C residue 844 VAL Chi-restraints excluded: chain C residue 849 THR Chi-restraints excluded: chain C residue 858 CYS Chi-restraints excluded: chain C residue 860 ILE Chi-restraints excluded: chain C residue 879 MET Chi-restraints excluded: chain C residue 888 LYS Chi-restraints excluded: chain C residue 892 VAL Chi-restraints excluded: chain C residue 909 CYS Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 931 LEU Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 405 LYS Chi-restraints excluded: chain D residue 451 HIS Chi-restraints excluded: chain D residue 586 LEU Chi-restraints excluded: chain D residue 636 ILE Chi-restraints excluded: chain D residue 667 LEU Chi-restraints excluded: chain D residue 688 LYS Chi-restraints excluded: chain D residue 690 LYS Chi-restraints excluded: chain D residue 725 TYR Chi-restraints excluded: chain D residue 776 SER Chi-restraints excluded: chain D residue 812 GLU Chi-restraints excluded: chain D residue 879 MET Chi-restraints excluded: chain D residue 880 THR Chi-restraints excluded: chain D residue 886 THR Chi-restraints excluded: chain D residue 931 LEU Chi-restraints excluded: chain D residue 944 ASP Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 381 ARG Chi-restraints excluded: chain E residue 433 HIS Chi-restraints excluded: chain E residue 442 LEU Chi-restraints excluded: chain E residue 552 MET Chi-restraints excluded: chain E residue 624 LEU Chi-restraints excluded: chain E residue 665 GLU Chi-restraints excluded: chain E residue 709 VAL Chi-restraints excluded: chain E residue 737 VAL Chi-restraints excluded: chain E residue 789 ASP Chi-restraints excluded: chain E residue 844 VAL Chi-restraints excluded: chain F residue 279 VAL Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain F residue 397 GLN Chi-restraints excluded: chain F residue 407 LEU Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain F residue 462 LEU Chi-restraints excluded: chain F residue 511 ARG Chi-restraints excluded: chain F residue 717 GLU Chi-restraints excluded: chain F residue 742 LEU Chi-restraints excluded: chain F residue 782 THR Chi-restraints excluded: chain F residue 796 LYS Chi-restraints excluded: chain F residue 819 THR Chi-restraints excluded: chain F residue 859 THR Chi-restraints excluded: chain F residue 909 CYS Chi-restraints excluded: chain F residue 916 ASN Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 391 HIS Chi-restraints excluded: chain A residue 394 TYR Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 444 LYS Chi-restraints excluded: chain A residue 503 GLU Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 541 ASN Chi-restraints excluded: chain A residue 590 ASP Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 738 THR Chi-restraints excluded: chain A residue 752 THR Chi-restraints excluded: chain A residue 757 TYR Chi-restraints excluded: chain A residue 773 MET Chi-restraints excluded: chain A residue 780 VAL Chi-restraints excluded: chain A residue 782 THR Chi-restraints excluded: chain A residue 909 CYS Chi-restraints excluded: chain A residue 927 ILE Chi-restraints excluded: chain B residue 209 MET Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 494 MET Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 576 CYS Chi-restraints excluded: chain B residue 578 LYS Chi-restraints excluded: chain B residue 592 VAL Chi-restraints excluded: chain B residue 607 LEU Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 637 CYS Chi-restraints excluded: chain B residue 681 LEU Chi-restraints excluded: chain B residue 742 LEU Chi-restraints excluded: chain B residue 771 THR Chi-restraints excluded: chain B residue 773 MET Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 861 VAL Chi-restraints excluded: chain B residue 886 THR Chi-restraints excluded: chain B residue 919 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 343 optimal weight: 0.6980 chunk 402 optimal weight: 10.0000 chunk 62 optimal weight: 0.6980 chunk 225 optimal weight: 8.9990 chunk 392 optimal weight: 5.9990 chunk 423 optimal weight: 10.0000 chunk 276 optimal weight: 20.0000 chunk 337 optimal weight: 0.9980 chunk 355 optimal weight: 9.9990 chunk 147 optimal weight: 4.9990 chunk 370 optimal weight: 0.8980 overall best weight: 1.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 541 ASN D 657 ASN B 451 HIS B 460 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.095700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.067547 restraints weight = 271178.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.067968 restraints weight = 177973.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.067583 restraints weight = 115563.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.067619 restraints weight = 103211.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.067695 restraints weight = 92134.244| |-----------------------------------------------------------------------------| r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.3334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 37639 Z= 0.136 Angle : 0.665 15.370 50846 Z= 0.315 Chirality : 0.042 0.317 5832 Planarity : 0.004 0.067 6522 Dihedral : 7.246 125.468 5161 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.88 % Favored : 95.06 % Rotamer: Outliers : 2.74 % Allowed : 21.06 % Favored : 76.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.12), residues: 4632 helix: 0.89 (0.11), residues: 2147 sheet: -1.68 (0.22), residues: 552 loop : -1.31 (0.14), residues: 1933 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 422 TYR 0.027 0.001 TYR A 360 PHE 0.026 0.001 PHE C 779 TRP 0.012 0.001 TRP A 464 HIS 0.010 0.001 HIS E 841 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.14 (37638) covalent geometry : angle 0.66534 / 0.32 (50844) SS BOND : bond 0.00317 / 0.17 ( 1) SS BOND : angle 0.60892 / 0.32 ( 2) hydrogen bonds : bond 0.03491 / 2.37 ( 1680) hydrogen bonds : angle 4.78141 / 3.34 ( 4836) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 4050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 192 time to evaluate : 1.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 197 MET cc_start: 0.5274 (mmm) cc_final: 0.4438 (ttt) REVERT: C 317 MET cc_start: 0.1895 (pmm) cc_final: 0.1656 (pmm) REVERT: C 518 ILE cc_start: 0.8973 (OUTLIER) cc_final: 0.8545 (pt) REVERT: C 608 LEU cc_start: 0.9451 (OUTLIER) cc_final: 0.9035 (mt) REVERT: C 846 GLU cc_start: 0.7779 (pm20) cc_final: 0.7487 (pm20) REVERT: C 858 CYS cc_start: 0.9311 (OUTLIER) cc_final: 0.8597 (t) REVERT: C 879 MET cc_start: 0.8573 (OUTLIER) cc_final: 0.7284 (ppp) REVERT: C 888 LYS cc_start: 0.8761 (OUTLIER) cc_final: 0.8395 (mmmm) REVERT: D 272 MET cc_start: 0.5346 (mtt) cc_final: 0.2384 (ttt) REVERT: D 405 LYS cc_start: 0.8917 (OUTLIER) cc_final: 0.8568 (mmmt) REVERT: D 451 HIS cc_start: 0.5215 (OUTLIER) cc_final: 0.4732 (m-70) REVERT: D 552 MET cc_start: 0.7943 (OUTLIER) cc_final: 0.6548 (ppp) REVERT: D 569 MET cc_start: 0.8868 (pmm) cc_final: 0.8311 (pmm) REVERT: D 594 LYS cc_start: 0.9608 (mmmt) cc_final: 0.9372 (mmmt) REVERT: D 647 GLU cc_start: 0.9351 (tp30) cc_final: 0.9121 (tp30) REVERT: D 657 ASN cc_start: 0.9010 (OUTLIER) cc_final: 0.8593 (t0) REVERT: D 690 LYS cc_start: 0.8631 (OUTLIER) cc_final: 0.8209 (pttm) REVERT: D 810 MET cc_start: 0.9109 (ttm) cc_final: 0.8686 (tpp) REVERT: D 826 MET cc_start: 0.8160 (ttt) cc_final: 0.7251 (mtp) REVERT: E 272 MET cc_start: 0.4261 (ptp) cc_final: 0.0586 (pmm) REVERT: E 552 MET cc_start: 0.4098 (OUTLIER) cc_final: 0.3610 (ptm) REVERT: E 773 MET cc_start: 0.5893 (tmm) cc_final: 0.5598 (tmm) REVERT: E 879 MET cc_start: 0.6528 (ptp) cc_final: 0.3232 (tpp) REVERT: F 197 MET cc_start: 0.2035 (ttt) cc_final: 0.1411 (pmm) REVERT: F 552 MET cc_start: 0.4925 (ptt) cc_final: 0.4634 (pmm) REVERT: F 569 MET cc_start: 0.7344 (mpp) cc_final: 0.6687 (mpp) REVERT: F 618 ASN cc_start: 0.9148 (t0) cc_final: 0.8896 (p0) REVERT: F 629 ASP cc_start: 0.7706 (OUTLIER) cc_final: 0.6876 (p0) REVERT: F 637 CYS cc_start: 0.9034 (t) cc_final: 0.8772 (p) REVERT: F 796 LYS cc_start: 0.8900 (OUTLIER) cc_final: 0.8648 (mmtm) REVERT: F 879 MET cc_start: 0.8890 (OUTLIER) cc_final: 0.8247 (tmm) REVERT: F 909 CYS cc_start: 0.8717 (OUTLIER) cc_final: 0.8214 (m) REVERT: A 208 VAL cc_start: 0.1628 (OUTLIER) cc_final: 0.1247 (p) REVERT: A 655 MET cc_start: 0.8527 (mmm) cc_final: 0.8239 (mmm) REVERT: A 773 MET cc_start: 0.8665 (OUTLIER) cc_final: 0.8066 (ppp) REVERT: A 869 MET cc_start: 0.9005 (ttm) cc_final: 0.8596 (ttt) REVERT: B 460 ASN cc_start: 0.8981 (OUTLIER) cc_final: 0.8744 (p0) REVERT: B 490 ASP cc_start: 0.9028 (OUTLIER) cc_final: 0.8783 (m-30) REVERT: B 576 CYS cc_start: 0.9281 (OUTLIER) cc_final: 0.9079 (t) REVERT: B 578 LYS cc_start: 0.9639 (OUTLIER) cc_final: 0.9326 (ttpp) REVERT: B 766 MET cc_start: 0.8605 (tpp) cc_final: 0.8312 (tpp) REVERT: B 879 MET cc_start: 0.8846 (ppp) cc_final: 0.8334 (ppp) outliers start: 111 outliers final: 67 residues processed: 285 average time/residue: 0.1936 time to fit residues: 92.9946 Evaluate side-chains 268 residues out of total 4050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 180 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 141 ILE Chi-restraints excluded: chain C residue 370 PHE Chi-restraints excluded: chain C residue 394 TYR Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 460 ASN Chi-restraints excluded: chain C residue 464 TRP Chi-restraints excluded: chain C residue 518 ILE Chi-restraints excluded: chain C residue 607 LEU Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 692 SER Chi-restraints excluded: chain C residue 694 ASP Chi-restraints excluded: chain C residue 844 VAL Chi-restraints excluded: chain C residue 849 THR Chi-restraints excluded: chain C residue 858 CYS Chi-restraints excluded: chain C residue 879 MET Chi-restraints excluded: chain C residue 888 LYS Chi-restraints excluded: chain C residue 892 VAL Chi-restraints excluded: chain C residue 909 CYS Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 931 LEU Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 405 LYS Chi-restraints excluded: chain D residue 451 HIS Chi-restraints excluded: chain D residue 552 MET Chi-restraints excluded: chain D residue 586 LEU Chi-restraints excluded: chain D residue 657 ASN Chi-restraints excluded: chain D residue 667 LEU Chi-restraints excluded: chain D residue 688 LYS Chi-restraints excluded: chain D residue 690 LYS Chi-restraints excluded: chain D residue 725 TYR Chi-restraints excluded: chain D residue 776 SER Chi-restraints excluded: chain D residue 812 GLU Chi-restraints excluded: chain D residue 879 MET Chi-restraints excluded: chain D residue 880 THR Chi-restraints excluded: chain D residue 886 THR Chi-restraints excluded: chain D residue 931 LEU Chi-restraints excluded: chain D residue 944 ASP Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 433 HIS Chi-restraints excluded: chain E residue 442 LEU Chi-restraints excluded: chain E residue 548 SER Chi-restraints excluded: chain E residue 552 MET Chi-restraints excluded: chain E residue 624 LEU Chi-restraints excluded: chain E residue 709 VAL Chi-restraints excluded: chain E residue 844 VAL Chi-restraints excluded: chain F residue 279 VAL Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain F residue 462 LEU Chi-restraints excluded: chain F residue 511 ARG Chi-restraints excluded: chain F residue 629 ASP Chi-restraints excluded: chain F residue 742 LEU Chi-restraints excluded: chain F residue 782 THR Chi-restraints excluded: chain F residue 796 LYS Chi-restraints excluded: chain F residue 819 THR Chi-restraints excluded: chain F residue 859 THR Chi-restraints excluded: chain F residue 879 MET Chi-restraints excluded: chain F residue 909 CYS Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 391 HIS Chi-restraints excluded: chain A residue 394 TYR Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 444 LYS Chi-restraints excluded: chain A residue 503 GLU Chi-restraints excluded: chain A residue 590 ASP Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 738 THR Chi-restraints excluded: chain A residue 752 THR Chi-restraints excluded: chain A residue 773 MET Chi-restraints excluded: chain A residue 780 VAL Chi-restraints excluded: chain A residue 927 ILE Chi-restraints excluded: chain B residue 209 MET Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 460 ASN Chi-restraints excluded: chain B residue 490 ASP Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 576 CYS Chi-restraints excluded: chain B residue 578 LYS Chi-restraints excluded: chain B residue 607 LEU Chi-restraints excluded: chain B residue 637 CYS Chi-restraints excluded: chain B residue 773 MET Chi-restraints excluded: chain B residue 859 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 268 optimal weight: 8.9990 chunk 28 optimal weight: 6.9990 chunk 331 optimal weight: 10.0000 chunk 192 optimal weight: 4.9990 chunk 203 optimal weight: 0.0570 chunk 332 optimal weight: 5.9990 chunk 51 optimal weight: 4.9990 chunk 368 optimal weight: 5.9990 chunk 231 optimal weight: 0.3980 chunk 6 optimal weight: 30.0000 chunk 91 optimal weight: 20.0000 overall best weight: 3.2904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 433 HIS ** E 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 451 HIS B 460 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.094109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.065690 restraints weight = 272366.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.066149 restraints weight = 172683.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.065562 restraints weight = 115936.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.065842 restraints weight = 115340.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.065729 restraints weight = 100462.812| |-----------------------------------------------------------------------------| r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.3643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 37639 Z= 0.206 Angle : 0.699 14.289 50846 Z= 0.339 Chirality : 0.042 0.276 5832 Planarity : 0.004 0.058 6522 Dihedral : 7.234 124.520 5158 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 15.34 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.46 % Favored : 94.47 % Rotamer: Outliers : 2.94 % Allowed : 21.33 % Favored : 75.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.12), residues: 4632 helix: 0.81 (0.11), residues: 2142 sheet: -1.70 (0.22), residues: 545 loop : -1.32 (0.14), residues: 1945 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 459 TYR 0.025 0.002 TYR A 360 PHE 0.018 0.002 PHE B 619 TRP 0.014 0.001 TRP A 464 HIS 0.008 0.001 HIS E 841 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.21 (37638) covalent geometry : angle 0.69912 / 0.34 (50844) SS BOND : bond 0.00469 / 0.25 ( 1) SS BOND : angle 0.78972 / 0.42 ( 2) hydrogen bonds : bond 0.03689 / 2.49 ( 1680) hydrogen bonds : angle 4.93085 / 3.45 ( 4836) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 4050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 185 time to evaluate : 0.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 197 MET cc_start: 0.5271 (mmm) cc_final: 0.4631 (ttt) REVERT: C 317 MET cc_start: 0.1530 (pmm) cc_final: 0.1242 (pmm) REVERT: C 518 ILE cc_start: 0.8925 (OUTLIER) cc_final: 0.8501 (pt) REVERT: C 608 LEU cc_start: 0.9482 (OUTLIER) cc_final: 0.9074 (mt) REVERT: C 846 GLU cc_start: 0.7964 (pm20) cc_final: 0.7685 (pm20) REVERT: C 858 CYS cc_start: 0.9306 (OUTLIER) cc_final: 0.8618 (t) REVERT: C 879 MET cc_start: 0.8566 (OUTLIER) cc_final: 0.7303 (ppp) REVERT: C 888 LYS cc_start: 0.8757 (OUTLIER) cc_final: 0.8396 (mmmm) REVERT: D 272 MET cc_start: 0.5629 (mtt) cc_final: 0.2770 (ttt) REVERT: D 405 LYS cc_start: 0.8911 (OUTLIER) cc_final: 0.8569 (mmmt) REVERT: D 451 HIS cc_start: 0.5492 (OUTLIER) cc_final: 0.5032 (m-70) REVERT: D 552 MET cc_start: 0.8195 (OUTLIER) cc_final: 0.6947 (ppp) REVERT: D 569 MET cc_start: 0.8862 (pmm) cc_final: 0.8367 (pmm) REVERT: D 594 LYS cc_start: 0.9617 (mmmt) cc_final: 0.9398 (mmmt) REVERT: D 657 ASN cc_start: 0.9326 (OUTLIER) cc_final: 0.9014 (t0) REVERT: D 690 LYS cc_start: 0.8695 (OUTLIER) cc_final: 0.8243 (pttm) REVERT: D 810 MET cc_start: 0.9123 (ttm) cc_final: 0.8726 (tpp) REVERT: E 272 MET cc_start: 0.5060 (ptp) cc_final: 0.1973 (pmm) REVERT: E 552 MET cc_start: 0.4780 (OUTLIER) cc_final: 0.4390 (ptm) REVERT: E 681 LEU cc_start: 0.4960 (tt) cc_final: 0.4490 (mt) REVERT: E 773 MET cc_start: 0.6158 (tmm) cc_final: 0.5876 (tmm) REVERT: E 879 MET cc_start: 0.6635 (ptp) cc_final: 0.3179 (tpp) REVERT: F 197 MET cc_start: 0.2088 (ttt) cc_final: 0.1581 (pmm) REVERT: F 552 MET cc_start: 0.5080 (ptt) cc_final: 0.4819 (pmm) REVERT: F 569 MET cc_start: 0.7408 (mpp) cc_final: 0.6794 (mpp) REVERT: F 618 ASN cc_start: 0.9210 (t0) cc_final: 0.8804 (p0) REVERT: F 637 CYS cc_start: 0.9182 (t) cc_final: 0.8855 (p) REVERT: F 796 LYS cc_start: 0.8908 (OUTLIER) cc_final: 0.8565 (mmtm) REVERT: F 879 MET cc_start: 0.8779 (OUTLIER) cc_final: 0.8304 (tmm) REVERT: F 909 CYS cc_start: 0.8778 (OUTLIER) cc_final: 0.8271 (m) REVERT: A 419 GLU cc_start: 0.9695 (OUTLIER) cc_final: 0.9397 (pt0) REVERT: A 655 MET cc_start: 0.8402 (mmm) cc_final: 0.8137 (mmm) REVERT: A 757 TYR cc_start: 0.8353 (OUTLIER) cc_final: 0.7490 (m-80) REVERT: A 773 MET cc_start: 0.8685 (OUTLIER) cc_final: 0.8136 (ppp) REVERT: A 869 MET cc_start: 0.9034 (ttm) cc_final: 0.8649 (ttt) REVERT: A 879 MET cc_start: 0.9110 (ptp) cc_final: 0.8889 (ptp) REVERT: B 552 MET cc_start: 0.8460 (ptp) cc_final: 0.7192 (ppp) REVERT: B 576 CYS cc_start: 0.9243 (OUTLIER) cc_final: 0.8985 (t) REVERT: B 578 LYS cc_start: 0.9646 (OUTLIER) cc_final: 0.9345 (ttpp) REVERT: B 766 MET cc_start: 0.8607 (tpp) cc_final: 0.8387 (tpp) REVERT: B 879 MET cc_start: 0.8822 (ppp) cc_final: 0.8396 (ppp) outliers start: 119 outliers final: 82 residues processed: 288 average time/residue: 0.1967 time to fit residues: 96.1310 Evaluate side-chains 280 residues out of total 4050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 179 time to evaluate : 1.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 141 ILE Chi-restraints excluded: chain C residue 370 PHE Chi-restraints excluded: chain C residue 394 TYR Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 460 ASN Chi-restraints excluded: chain C residue 464 TRP Chi-restraints excluded: chain C residue 518 ILE Chi-restraints excluded: chain C residue 607 LEU Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 692 SER Chi-restraints excluded: chain C residue 694 ASP Chi-restraints excluded: chain C residue 844 VAL Chi-restraints excluded: chain C residue 849 THR Chi-restraints excluded: chain C residue 858 CYS Chi-restraints excluded: chain C residue 879 MET Chi-restraints excluded: chain C residue 886 THR Chi-restraints excluded: chain C residue 888 LYS Chi-restraints excluded: chain C residue 892 VAL Chi-restraints excluded: chain C residue 909 CYS Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 931 LEU Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 405 LYS Chi-restraints excluded: chain D residue 451 HIS Chi-restraints excluded: chain D residue 552 MET Chi-restraints excluded: chain D residue 586 LEU Chi-restraints excluded: chain D residue 657 ASN Chi-restraints excluded: chain D residue 667 LEU Chi-restraints excluded: chain D residue 688 LYS Chi-restraints excluded: chain D residue 690 LYS Chi-restraints excluded: chain D residue 725 TYR Chi-restraints excluded: chain D residue 776 SER Chi-restraints excluded: chain D residue 812 GLU Chi-restraints excluded: chain D residue 879 MET Chi-restraints excluded: chain D residue 880 THR Chi-restraints excluded: chain D residue 886 THR Chi-restraints excluded: chain D residue 931 LEU Chi-restraints excluded: chain D residue 944 ASP Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 433 HIS Chi-restraints excluded: chain E residue 442 LEU Chi-restraints excluded: chain E residue 552 MET Chi-restraints excluded: chain E residue 624 LEU Chi-restraints excluded: chain E residue 709 VAL Chi-restraints excluded: chain E residue 737 VAL Chi-restraints excluded: chain E residue 844 VAL Chi-restraints excluded: chain F residue 279 VAL Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain F residue 397 GLN Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain F residue 462 LEU Chi-restraints excluded: chain F residue 511 ARG Chi-restraints excluded: chain F residue 742 LEU Chi-restraints excluded: chain F residue 782 THR Chi-restraints excluded: chain F residue 796 LYS Chi-restraints excluded: chain F residue 819 THR Chi-restraints excluded: chain F residue 859 THR Chi-restraints excluded: chain F residue 879 MET Chi-restraints excluded: chain F residue 909 CYS Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 391 HIS Chi-restraints excluded: chain A residue 394 TYR Chi-restraints excluded: chain A residue 419 GLU Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 444 LYS Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 503 GLU Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 541 ASN Chi-restraints excluded: chain A residue 590 ASP Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 738 THR Chi-restraints excluded: chain A residue 752 THR Chi-restraints excluded: chain A residue 757 TYR Chi-restraints excluded: chain A residue 773 MET Chi-restraints excluded: chain A residue 780 VAL Chi-restraints excluded: chain A residue 782 THR Chi-restraints excluded: chain A residue 802 VAL Chi-restraints excluded: chain A residue 842 LEU Chi-restraints excluded: chain A residue 865 LEU Chi-restraints excluded: chain A residue 909 CYS Chi-restraints excluded: chain A residue 927 ILE Chi-restraints excluded: chain B residue 209 MET Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 451 HIS Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 576 CYS Chi-restraints excluded: chain B residue 578 LYS Chi-restraints excluded: chain B residue 607 LEU Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 637 CYS Chi-restraints excluded: chain B residue 681 LEU Chi-restraints excluded: chain B residue 771 THR Chi-restraints excluded: chain B residue 773 MET Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 859 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 125 optimal weight: 4.9990 chunk 372 optimal weight: 1.9990 chunk 261 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 408 optimal weight: 5.9990 chunk 122 optimal weight: 0.9980 chunk 314 optimal weight: 50.0000 chunk 368 optimal weight: 3.9990 chunk 80 optimal weight: 6.9990 chunk 399 optimal weight: 0.0670 chunk 160 optimal weight: 50.0000 overall best weight: 2.2124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 875 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 433 HIS D 657 ASN B 347 GLN ** B 451 HIS ** 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 = 0.4196 r_free = 0.4196 target = 0.094702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.066765 restraints weight = 271783.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.066583 restraints weight = 186119.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.066576 restraints weight = 123415.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.066508 restraints weight = 108052.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.066633 restraints weight = 95199.586| |-----------------------------------------------------------------------------| r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.3879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 37639 Z= 0.151 Angle : 0.678 12.051 50846 Z= 0.323 Chirality : 0.042 0.260 5832 Planarity : 0.004 0.060 6522 Dihedral : 7.148 124.239 5158 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.92 % Favored : 95.01 % Rotamer: Outliers : 2.62 % Allowed : 21.98 % Favored : 75.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.12), residues: 4632 helix: 0.88 (0.11), residues: 2142 sheet: -1.62 (0.22), residues: 545 loop : -1.27 (0.14), residues: 1945 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 378 TYR 0.025 0.001 TYR A 360 PHE 0.017 0.001 PHE E 504 TRP 0.013 0.001 TRP A 464 HIS 0.014 0.001 HIS B 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.15 (37638) covalent geometry : angle 0.67811 / 0.32 (50844) SS BOND : bond 0.00486 / 0.26 ( 1) SS BOND : angle 0.70159 / 0.37 ( 2) hydrogen bonds : bond 0.03457 / 2.34 ( 1680) hydrogen bonds : angle 4.79734 / 3.36 ( 4836) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 4050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 191 time to evaluate : 1.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 197 MET cc_start: 0.5421 (mmm) cc_final: 0.4600 (ttt) REVERT: C 317 MET cc_start: 0.1616 (pmm) cc_final: 0.1310 (pmm) REVERT: C 518 ILE cc_start: 0.8943 (OUTLIER) cc_final: 0.8397 (pt) REVERT: C 608 LEU cc_start: 0.9452 (OUTLIER) cc_final: 0.9032 (mt) REVERT: C 846 GLU cc_start: 0.7809 (pm20) cc_final: 0.7552 (pm20) REVERT: C 858 CYS cc_start: 0.9288 (OUTLIER) cc_final: 0.8550 (t) REVERT: C 879 MET cc_start: 0.8547 (OUTLIER) cc_final: 0.7269 (ppp) REVERT: C 888 LYS cc_start: 0.8794 (OUTLIER) cc_final: 0.8442 (mmmm) REVERT: D 272 MET cc_start: 0.5369 (mtt) cc_final: 0.2297 (ttt) REVERT: D 405 LYS cc_start: 0.8944 (OUTLIER) cc_final: 0.8604 (mmmt) REVERT: D 451 HIS cc_start: 0.5492 (OUTLIER) cc_final: 0.5062 (m-70) REVERT: D 552 MET cc_start: 0.8187 (OUTLIER) cc_final: 0.6902 (ppp) REVERT: D 569 MET cc_start: 0.8859 (pmm) cc_final: 0.8352 (pmm) REVERT: D 594 LYS cc_start: 0.9608 (mmmt) cc_final: 0.9385 (mmmt) REVERT: D 657 ASN cc_start: 0.9138 (OUTLIER) cc_final: 0.8782 (t0) REVERT: D 690 LYS cc_start: 0.8682 (OUTLIER) cc_final: 0.8305 (pttm) REVERT: D 810 MET cc_start: 0.9119 (ttm) cc_final: 0.8759 (mmm) REVERT: D 826 MET cc_start: 0.8400 (ttt) cc_final: 0.7596 (mtt) REVERT: E 272 MET cc_start: 0.4754 (ptp) cc_final: 0.1213 (pmm) REVERT: E 552 MET cc_start: 0.4069 (OUTLIER) cc_final: 0.3635 (ptm) REVERT: E 681 LEU cc_start: 0.4807 (tt) cc_final: 0.4317 (mt) REVERT: E 773 MET cc_start: 0.6215 (tmm) cc_final: 0.5916 (tmm) REVERT: E 879 MET cc_start: 0.6624 (ptp) cc_final: 0.3138 (tpp) REVERT: F 197 MET cc_start: 0.2136 (ttt) cc_final: 0.1576 (pmm) REVERT: F 569 MET cc_start: 0.7349 (mpp) cc_final: 0.6651 (mpp) REVERT: F 618 ASN cc_start: 0.9202 (t0) cc_final: 0.8949 (p0) REVERT: F 629 ASP cc_start: 0.8505 (t0) cc_final: 0.8000 (p0) REVERT: F 637 CYS cc_start: 0.9047 (t) cc_final: 0.8722 (p) REVERT: F 766 MET cc_start: 0.8247 (tpp) cc_final: 0.8036 (tpp) REVERT: F 796 LYS cc_start: 0.8933 (OUTLIER) cc_final: 0.8657 (mmtm) REVERT: F 810 MET cc_start: 0.9188 (mmm) cc_final: 0.8803 (mtp) REVERT: F 842 LEU cc_start: 0.9519 (tp) cc_final: 0.9213 (mm) REVERT: F 879 MET cc_start: 0.8572 (OUTLIER) cc_final: 0.8310 (tmm) REVERT: F 909 CYS cc_start: 0.8733 (OUTLIER) cc_final: 0.8173 (m) REVERT: A 510 LEU cc_start: 0.9384 (tp) cc_final: 0.9132 (tp) REVERT: A 773 MET cc_start: 0.8666 (OUTLIER) cc_final: 0.8105 (ppp) REVERT: A 869 MET cc_start: 0.9019 (ttm) cc_final: 0.8631 (ttt) REVERT: A 879 MET cc_start: 0.9123 (ptp) cc_final: 0.8917 (ptp) REVERT: B 334 MET cc_start: 0.1842 (mmt) cc_final: 0.1571 (mmt) REVERT: B 552 MET cc_start: 0.8450 (ptp) cc_final: 0.7528 (ppp) REVERT: B 576 CYS cc_start: 0.9218 (OUTLIER) cc_final: 0.8962 (t) REVERT: B 578 LYS cc_start: 0.9622 (OUTLIER) cc_final: 0.9301 (ttpp) REVERT: B 766 MET cc_start: 0.8618 (tpp) cc_final: 0.8388 (tpp) REVERT: B 879 MET cc_start: 0.8839 (ppp) cc_final: 0.8520 (ppp) outliers start: 106 outliers final: 75 residues processed: 278 average time/residue: 0.1988 time to fit residues: 93.8711 Evaluate side-chains 275 residues out of total 4050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 183 time to evaluate : 1.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 141 ILE Chi-restraints excluded: chain C residue 394 TYR Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 460 ASN Chi-restraints excluded: chain C residue 464 TRP Chi-restraints excluded: chain C residue 518 ILE Chi-restraints excluded: chain C residue 607 LEU Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 692 SER Chi-restraints excluded: chain C residue 694 ASP Chi-restraints excluded: chain C residue 844 VAL Chi-restraints excluded: chain C residue 849 THR Chi-restraints excluded: chain C residue 858 CYS Chi-restraints excluded: chain C residue 879 MET Chi-restraints excluded: chain C residue 886 THR Chi-restraints excluded: chain C residue 888 LYS Chi-restraints excluded: chain C residue 892 VAL Chi-restraints excluded: chain C residue 909 CYS Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 931 LEU Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 405 LYS Chi-restraints excluded: chain D residue 451 HIS Chi-restraints excluded: chain D residue 552 MET Chi-restraints excluded: chain D residue 586 LEU Chi-restraints excluded: chain D residue 657 ASN Chi-restraints excluded: chain D residue 667 LEU Chi-restraints excluded: chain D residue 688 LYS Chi-restraints excluded: chain D residue 690 LYS Chi-restraints excluded: chain D residue 725 TYR Chi-restraints excluded: chain D residue 776 SER Chi-restraints excluded: chain D residue 812 GLU Chi-restraints excluded: chain D residue 879 MET Chi-restraints excluded: chain D residue 880 THR Chi-restraints excluded: chain D residue 886 THR Chi-restraints excluded: chain D residue 931 LEU Chi-restraints excluded: chain D residue 944 ASP Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 433 HIS Chi-restraints excluded: chain E residue 442 LEU Chi-restraints excluded: chain E residue 552 MET Chi-restraints excluded: chain E residue 624 LEU Chi-restraints excluded: chain E residue 709 VAL Chi-restraints excluded: chain F residue 279 VAL Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain F residue 331 LEU Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain F residue 462 LEU Chi-restraints excluded: chain F residue 511 ARG Chi-restraints excluded: chain F residue 636 ILE Chi-restraints excluded: chain F residue 685 ASP Chi-restraints excluded: chain F residue 742 LEU Chi-restraints excluded: chain F residue 782 THR Chi-restraints excluded: chain F residue 796 LYS Chi-restraints excluded: chain F residue 819 THR Chi-restraints excluded: chain F residue 859 THR Chi-restraints excluded: chain F residue 879 MET Chi-restraints excluded: chain F residue 909 CYS Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 391 HIS Chi-restraints excluded: chain A residue 394 TYR Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 444 LYS Chi-restraints excluded: chain A residue 503 GLU Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 590 ASP Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 675 VAL Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 738 THR Chi-restraints excluded: chain A residue 752 THR Chi-restraints excluded: chain A residue 773 MET Chi-restraints excluded: chain A residue 780 VAL Chi-restraints excluded: chain A residue 782 THR Chi-restraints excluded: chain A residue 802 VAL Chi-restraints excluded: chain A residue 842 LEU Chi-restraints excluded: chain A residue 865 LEU Chi-restraints excluded: chain A residue 927 ILE Chi-restraints excluded: chain B residue 209 MET Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 576 CYS Chi-restraints excluded: chain B residue 578 LYS Chi-restraints excluded: chain B residue 607 LEU Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 637 CYS Chi-restraints excluded: chain B residue 771 THR Chi-restraints excluded: chain B residue 773 MET Chi-restraints excluded: chain B residue 859 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 233 optimal weight: 0.2980 chunk 357 optimal weight: 5.9990 chunk 148 optimal weight: 2.9990 chunk 394 optimal weight: 30.0000 chunk 73 optimal weight: 0.9980 chunk 353 optimal weight: 0.0770 chunk 142 optimal weight: 8.9990 chunk 121 optimal weight: 0.7980 chunk 352 optimal weight: 0.9980 chunk 433 optimal weight: 0.0570 chunk 16 optimal weight: 40.0000 overall best weight: 0.4456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 433 HIS D 657 ASN F 640 ASN F 713 GLN ** F 839 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 460 ASN B 347 GLN B 451 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.097491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.070262 restraints weight = 289358.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.069998 restraints weight = 182571.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.070018 restraints weight = 123225.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.069886 restraints weight = 113753.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.069752 restraints weight = 91565.302| |-----------------------------------------------------------------------------| r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.3969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 37639 Z= 0.112 Angle : 0.681 15.629 50846 Z= 0.319 Chirality : 0.042 0.326 5832 Planarity : 0.004 0.059 6522 Dihedral : 6.988 123.578 5158 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.32 % Favored : 95.62 % Rotamer: Outliers : 2.32 % Allowed : 22.05 % Favored : 75.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.12), residues: 4632 helix: 1.01 (0.11), residues: 2137 sheet: -1.50 (0.23), residues: 538 loop : -1.24 (0.14), residues: 1957 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 705 TYR 0.025 0.001 TYR A 360 PHE 0.017 0.001 PHE E 504 TRP 0.012 0.001 TRP A 464 HIS 0.009 0.001 HIS E 841 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 (37638) covalent geometry : angle 0.68026 / 0.32 (50844) SS BOND : bond 0.00029 / 0.02 ( 1) SS BOND : angle 5.58430 / 3.27 ( 2) hydrogen bonds : bond 0.03329 / 2.25 ( 1680) hydrogen bonds : angle 4.61313 / 3.23 ( 4836) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9264 Ramachandran restraints generated. 4632 Oldfield, 0 Emsley, 4632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 4050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 200 time to evaluate : 1.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 197 MET cc_start: 0.4911 (mmm) cc_final: 0.4436 (ttt) REVERT: C 317 MET cc_start: 0.1343 (pmm) cc_final: 0.1081 (pmm) REVERT: C 464 TRP cc_start: 0.8864 (OUTLIER) cc_final: 0.8473 (t60) REVERT: C 518 ILE cc_start: 0.8897 (OUTLIER) cc_final: 0.8362 (pt) REVERT: C 608 LEU cc_start: 0.9427 (OUTLIER) cc_final: 0.8945 (mt) REVERT: C 653 MET cc_start: 0.8960 (tmm) cc_final: 0.8742 (tmm) REVERT: C 858 CYS cc_start: 0.9288 (OUTLIER) cc_final: 0.8484 (t) REVERT: C 879 MET cc_start: 0.8415 (OUTLIER) cc_final: 0.7124 (ppp) REVERT: C 888 LYS cc_start: 0.8816 (OUTLIER) cc_final: 0.8429 (mmmm) REVERT: D 272 MET cc_start: 0.6245 (mtt) cc_final: 0.3572 (ttt) REVERT: D 405 LYS cc_start: 0.9009 (OUTLIER) cc_final: 0.8700 (mmmt) REVERT: D 451 HIS cc_start: 0.5454 (OUTLIER) cc_final: 0.5024 (m-70) REVERT: D 552 MET cc_start: 0.8176 (OUTLIER) cc_final: 0.6922 (ppp) REVERT: D 569 MET cc_start: 0.8906 (pmm) cc_final: 0.8469 (pmm) REVERT: D 594 LYS cc_start: 0.9602 (mmmt) cc_final: 0.9380 (mmmt) REVERT: D 647 GLU cc_start: 0.9298 (tp30) cc_final: 0.9096 (tm-30) REVERT: D 810 MET cc_start: 0.9095 (ttm) cc_final: 0.8728 (mmm) REVERT: D 826 MET cc_start: 0.8386 (ttt) cc_final: 0.7583 (mtt) REVERT: E 272 MET cc_start: 0.5683 (ptp) cc_final: 0.3238 (pmm) REVERT: E 773 MET cc_start: 0.6095 (tmm) cc_final: 0.5826 (tmm) REVERT: E 879 MET cc_start: 0.6451 (ptp) cc_final: 0.3203 (tpp) REVERT: F 197 MET cc_start: 0.1940 (ttt) cc_final: 0.1726 (pmm) REVERT: F 569 MET cc_start: 0.7346 (mpp) cc_final: 0.6760 (mpp) REVERT: F 618 ASN cc_start: 0.9272 (t0) cc_final: 0.9046 (p0) REVERT: F 629 ASP cc_start: 0.8621 (t0) cc_final: 0.8056 (p0) REVERT: F 636 ILE cc_start: 0.9282 (OUTLIER) cc_final: 0.8996 (tp) REVERT: F 637 CYS cc_start: 0.9040 (t) cc_final: 0.8687 (p) REVERT: F 742 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.8276 (tt) REVERT: F 766 MET cc_start: 0.8272 (tpp) cc_final: 0.8067 (tpp) REVERT: F 810 MET cc_start: 0.9171 (mmm) cc_final: 0.8746 (mtp) REVERT: F 842 LEU cc_start: 0.9496 (tp) cc_final: 0.9200 (mm) REVERT: F 909 CYS cc_start: 0.8747 (OUTLIER) cc_final: 0.8147 (m) REVERT: A 503 GLU cc_start: 0.8805 (OUTLIER) cc_final: 0.8138 (pt0) REVERT: A 510 LEU cc_start: 0.9357 (tp) cc_final: 0.9117 (tp) REVERT: A 590 ASP cc_start: 0.6818 (OUTLIER) cc_final: 0.6408 (p0) REVERT: A 757 TYR cc_start: 0.8268 (OUTLIER) cc_final: 0.7469 (m-80) REVERT: A 773 MET cc_start: 0.8670 (OUTLIER) cc_final: 0.8115 (ppp) REVERT: A 869 MET cc_start: 0.9028 (ttm) cc_final: 0.8639 (ttt) REVERT: B 334 MET cc_start: 0.1928 (mmt) cc_final: 0.1705 (mmt) REVERT: B 490 ASP cc_start: 0.8966 (OUTLIER) cc_final: 0.8717 (m-30) REVERT: B 552 MET cc_start: 0.8029 (ptp) cc_final: 0.7505 (ppp) REVERT: B 576 CYS cc_start: 0.9153 (OUTLIER) cc_final: 0.8895 (t) REVERT: B 578 LYS cc_start: 0.9581 (OUTLIER) cc_final: 0.9278 (ttpp) REVERT: B 766 MET cc_start: 0.8649 (tpp) cc_final: 0.8439 (tpp) outliers start: 94 outliers final: 58 residues processed: 278 average time/residue: 0.1903 time to fit residues: 90.3018 Evaluate side-chains 265 residues out of total 4050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 188 time to evaluate : 1.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 141 ILE Chi-restraints excluded: chain C residue 370 PHE Chi-restraints excluded: chain C residue 394 TYR Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 460 ASN Chi-restraints excluded: chain C residue 464 TRP Chi-restraints excluded: chain C residue 518 ILE Chi-restraints excluded: chain C residue 607 LEU Chi-restraints excluded: chain C residue 608 LEU Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 692 SER Chi-restraints excluded: chain C residue 694 ASP Chi-restraints excluded: chain C residue 844 VAL Chi-restraints excluded: chain C residue 849 THR Chi-restraints excluded: chain C residue 858 CYS Chi-restraints excluded: chain C residue 879 MET Chi-restraints excluded: chain C residue 888 LYS Chi-restraints excluded: chain C residue 892 VAL Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 931 LEU Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 405 LYS Chi-restraints excluded: chain D residue 451 HIS Chi-restraints excluded: chain D residue 552 MET Chi-restraints excluded: chain D residue 586 LEU Chi-restraints excluded: chain D residue 667 LEU Chi-restraints excluded: chain D residue 688 LYS Chi-restraints excluded: chain D residue 725 TYR Chi-restraints excluded: chain D residue 776 SER Chi-restraints excluded: chain D residue 812 GLU Chi-restraints excluded: chain D residue 879 MET Chi-restraints excluded: chain D residue 886 THR Chi-restraints excluded: chain D residue 931 LEU Chi-restraints excluded: chain D residue 944 ASP Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 433 HIS Chi-restraints excluded: chain E residue 442 LEU Chi-restraints excluded: chain E residue 624 LEU Chi-restraints excluded: chain E residue 709 VAL Chi-restraints excluded: chain F residue 279 VAL Chi-restraints excluded: chain F residue 315 LEU Chi-restraints excluded: chain F residue 429 VAL Chi-restraints excluded: chain F residue 462 LEU Chi-restraints excluded: chain F residue 511 ARG Chi-restraints excluded: chain F residue 636 ILE Chi-restraints excluded: chain F residue 742 LEU Chi-restraints excluded: chain F residue 782 THR Chi-restraints excluded: chain F residue 819 THR Chi-restraints excluded: chain F residue 859 THR Chi-restraints excluded: chain F residue 909 CYS Chi-restraints excluded: chain F residue 916 ASN Chi-restraints excluded: chain A residue 391 HIS Chi-restraints excluded: chain A residue 394 TYR Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 444 LYS Chi-restraints excluded: chain A residue 503 GLU Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 590 ASP Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 692 SER Chi-restraints excluded: chain A residue 738 THR Chi-restraints excluded: chain A residue 757 TYR Chi-restraints excluded: chain A residue 773 MET Chi-restraints excluded: chain A residue 780 VAL Chi-restraints excluded: chain A residue 782 THR Chi-restraints excluded: chain A residue 927 ILE Chi-restraints excluded: chain B residue 209 MET Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 490 ASP Chi-restraints excluded: chain B residue 576 CYS Chi-restraints excluded: chain B residue 578 LYS Chi-restraints excluded: chain B residue 607 LEU Chi-restraints excluded: chain B residue 618 ASN Chi-restraints excluded: chain B residue 637 CYS Chi-restraints excluded: chain B residue 825 LEU Chi-restraints excluded: chain B residue 859 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 462 random chunks: chunk 441 optimal weight: 1.9990 chunk 21 optimal weight: 9.9990 chunk 455 optimal weight: 6.9990 chunk 377 optimal weight: 4.9990 chunk 387 optimal weight: 30.0000 chunk 267 optimal weight: 1.9990 chunk 395 optimal weight: 2.9990 chunk 23 optimal weight: 6.9990 chunk 422 optimal weight: 5.9990 chunk 457 optimal weight: 3.9990 chunk 210 optimal weight: 20.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 377 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 875 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 433 HIS A 460 ASN A 916 ASN B 146 ASN B 451 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.093862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.065600 restraints weight = 274314.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.065778 restraints weight = 178385.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.065829 restraints weight = 127149.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.065589 restraints weight = 104973.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.065663 restraints weight = 100584.992| |-----------------------------------------------------------------------------| r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.4206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 37639 Z= 0.197 Angle : 0.713 18.109 50846 Z= 0.342 Chirality : 0.043 0.423 5832 Planarity : 0.004 0.059 6522 Dihedral : 7.068 122.677 5158 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 14.76 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.07 % Favored : 94.86 % Rotamer: Outliers : 2.35 % Allowed : 22.17 % Favored : 75.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.41 (0.12), residues: 4632 helix: 0.96 (0.11), residues: 2136 sheet: -1.58 (0.22), residues: 533 loop : -1.22 (0.14), residues: 1963 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 378 TYR 0.023 0.002 TYR A 360 PHE 0.017 0.002 PHE E 504 TRP 0.007 0.001 TRP A 464 HIS 0.008 0.001 HIS E 841 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.20 (37638) covalent geometry : angle 0.71166 / 0.34 (50844) SS BOND : bond 0.01506 / 0.79 ( 1) SS BOND : angle 5.89896 / 3.47 ( 2) hydrogen bonds : bond 0.03530 / 2.39 ( 1680) hydrogen bonds : angle 4.83526 / 3.38 ( 4836) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9247.98 seconds wall clock time: 159 minutes 28.02 seconds (9568.02 seconds total)