Starting phenix.real_space_refine on Tue Aug 26 19:11:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6tqm_10555/08_2025/6tqm_10555_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/6tqm_10555/08_2025/6tqm_10555.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6tqm_10555/08_2025/6tqm_10555.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6tqm_10555/08_2025/6tqm_10555.map" model { file = "/net/cci-nas-00/data/ceres_data/6tqm_10555/08_2025/6tqm_10555_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6tqm_10555/08_2025/6tqm_10555_trim.cif" } resolution = 3.8 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= 0.002 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: 7 Type Number sf(0) Gaussians Fe 2 7.16 5 P 4 5.49 5 S 92 5.16 5 C 12586 2.51 5 N 3374 2.21 5 O 3754 1.98 5 H 19804 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 110 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 39616 Number of models: 1 Model: "" Number of chains: 6 Chain: "F" Number of atoms: 6500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 6500 Classifications: {'peptide': 420} Link IDs: {'PTRANS': 20, 'TRANS': 399} Chain: "C" Number of atoms: 6500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 6500 Classifications: {'peptide': 420} Link IDs: {'PTRANS': 20, 'TRANS': 399} Chain: "B" Number of atoms: 13263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 869, 13263 Classifications: {'peptide': 869} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 40, 'TRANS': 828} Chain: "A" Number of atoms: 13263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 869, 13263 Classifications: {'peptide': 869} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 40, 'TRANS': 828} Chain: "B" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 45 Unusual residues: {' FE': 1, 'TXE': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 45 Unusual residues: {' FE': 1, 'TXE': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.94, per 1000 atoms: 0.15 Number of scatterers: 39616 At special positions: 0 Unit cell: (129.95, 157.07, 122.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 2 26.01 S 92 16.00 P 4 15.00 O 3754 8.00 N 3374 7.00 C 12586 6.00 H 19804 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.54 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 715.3 nanoseconds 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4808 Finding SS restraints... Secondary structure from input PDB file: 109 helices and 15 sheets defined 34.9% alpha, 4.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'F' and resid 466 through 471 Processing helix chain 'F' and resid 472 through 477 removed outlier: 3.635A pdb=" N THR F 476 " --> pdb=" O ASP F 472 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ASP F 477 " --> pdb=" O GLU F 473 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 472 through 477' Processing helix chain 'F' and resid 488 through 493 removed outlier: 3.730A pdb=" N ASN F 492 " --> pdb=" O ARG F 488 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ASN F 493 " --> pdb=" O PHE F 489 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 488 through 493' Processing helix chain 'F' and resid 497 through 507 removed outlier: 4.235A pdb=" N VAL F 502 " --> pdb=" O GLN F 498 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU F 503 " --> pdb=" O ILE F 499 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ALA F 506 " --> pdb=" O VAL F 502 " (cutoff:3.500A) Processing helix chain 'F' and resid 523 through 533 removed outlier: 3.550A pdb=" N LYS F 527 " --> pdb=" O SER F 523 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLY F 528 " --> pdb=" O ILE F 524 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA F 529 " --> pdb=" O VAL F 525 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLU F 530 " --> pdb=" O ARG F 526 " (cutoff:3.500A) Processing helix chain 'F' and resid 546 through 558 removed outlier: 3.912A pdb=" N ASP F 550 " --> pdb=" O GLY F 546 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA F 551 " --> pdb=" O SER F 547 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA F 552 " --> pdb=" O PRO F 548 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N MET F 555 " --> pdb=" O ALA F 551 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N TRP F 556 " --> pdb=" O ALA F 552 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N VAL F 557 " --> pdb=" O LYS F 553 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N MET F 558 " --> pdb=" O ILE F 554 " (cutoff:3.500A) Processing helix chain 'F' and resid 649 through 659 removed outlier: 4.937A pdb=" N VAL F 655 " --> pdb=" O GLY F 651 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N THR F 656 " --> pdb=" O LEU F 652 " (cutoff:3.500A) Processing helix chain 'F' and resid 671 through 677 removed outlier: 3.694A pdb=" N ALA F 675 " --> pdb=" O SER F 671 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU F 676 " --> pdb=" O ASP F 672 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLN F 677 " --> pdb=" O GLY F 673 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 671 through 677' Processing helix chain 'F' and resid 677 through 682 removed outlier: 3.612A pdb=" N LEU F 681 " --> pdb=" O GLN F 677 " (cutoff:3.500A) Processing helix chain 'F' and resid 686 through 690 removed outlier: 3.725A pdb=" N TYR F 690 " --> pdb=" O PRO F 687 " (cutoff:3.500A) Processing helix chain 'F' and resid 692 through 696 Processing helix chain 'F' and resid 698 through 715 removed outlier: 3.578A pdb=" N ARG F 702 " --> pdb=" O VAL F 698 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL F 703 " --> pdb=" O ALA F 699 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N HIS F 704 " --> pdb=" O ARG F 700 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N THR F 708 " --> pdb=" O HIS F 704 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N ILE F 709 " --> pdb=" O SER F 705 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE F 712 " --> pdb=" O THR F 708 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA F 713 " --> pdb=" O ILE F 709 " (cutoff:3.500A) Processing helix chain 'F' and resid 721 through 729 removed outlier: 3.650A pdb=" N MET F 725 " --> pdb=" O VAL F 721 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ALA F 726 " --> pdb=" O CYS F 722 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N HIS F 727 " --> pdb=" O HIS F 723 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LYS F 728 " --> pdb=" O SER F 724 " (cutoff:3.500A) Processing helix chain 'F' and resid 738 through 743 Processing helix chain 'F' and resid 744 through 749 removed outlier: 3.939A pdb=" N ILE F 749 " --> pdb=" O ILE F 745 " (cutoff:3.500A) Processing helix chain 'F' and resid 772 through 777 removed outlier: 3.612A pdb=" N ALA F 776 " --> pdb=" O ARG F 772 " (cutoff:3.500A) Processing helix chain 'F' and resid 777 through 782 removed outlier: 3.595A pdb=" N HIS F 781 " --> pdb=" O GLU F 777 " (cutoff:3.500A) Processing helix chain 'F' and resid 790 through 810 removed outlier: 3.624A pdb=" N LYS F 794 " --> pdb=" O ARG F 790 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE F 795 " --> pdb=" O THR F 791 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU F 796 " --> pdb=" O ALA F 792 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS F 797 " --> pdb=" O ALA F 793 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N TRP F 801 " --> pdb=" O LYS F 797 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU F 805 " --> pdb=" O TRP F 801 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LYS F 806 " --> pdb=" O LEU F 802 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N GLU F 808 " --> pdb=" O THR F 804 " (cutoff:3.500A) Processing helix chain 'F' and resid 814 through 819 removed outlier: 3.579A pdb=" N GLU F 817 " --> pdb=" O SER F 814 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLY F 819 " --> pdb=" O ARG F 816 " (cutoff:3.500A) Processing helix chain 'F' and resid 829 through 834 removed outlier: 3.573A pdb=" N GLU F 834 " --> pdb=" O ASP F 830 " (cutoff:3.500A) Processing helix chain 'F' and resid 850 through 861 removed outlier: 3.954A pdb=" N LYS F 855 " --> pdb=" O ILE F 851 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N GLN F 856 " --> pdb=" O SER F 852 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ILE F 857 " --> pdb=" O GLU F 853 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LEU F 858 " --> pdb=" O LEU F 854 " (cutoff:3.500A) Processing helix chain 'C' and resid 466 through 471 Processing helix chain 'C' and resid 472 through 477 removed outlier: 3.795A pdb=" N ASP C 477 " --> pdb=" O GLU C 473 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 493 removed outlier: 3.785A pdb=" N ASN C 492 " --> pdb=" O ARG C 488 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ASN C 493 " --> pdb=" O PHE C 489 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 488 through 493' Processing helix chain 'C' and resid 497 through 505 removed outlier: 4.143A pdb=" N VAL C 502 " --> pdb=" O GLN C 498 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N LEU C 503 " --> pdb=" O ILE C 499 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ALA C 505 " --> pdb=" O SER C 501 " (cutoff:3.500A) Processing helix chain 'C' and resid 523 through 533 Processing helix chain 'C' and resid 546 through 561 removed outlier: 3.951A pdb=" N ASP C 550 " --> pdb=" O GLY C 546 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA C 551 " --> pdb=" O SER C 547 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ALA C 552 " --> pdb=" O PRO C 548 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N TRP C 556 " --> pdb=" O ALA C 552 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N MET C 558 " --> pdb=" O ILE C 554 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N TYR C 559 " --> pdb=" O MET C 555 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLU C 560 " --> pdb=" O TRP C 556 " (cutoff:3.500A) Processing helix chain 'C' and resid 567 through 571 removed outlier: 3.915A pdb=" N ALA C 570 " --> pdb=" O GLU C 567 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LEU C 571 " --> pdb=" O GLU C 568 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 567 through 571' Processing helix chain 'C' and resid 649 through 659 removed outlier: 4.307A pdb=" N VAL C 655 " --> pdb=" O GLY C 651 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N THR C 656 " --> pdb=" O LEU C 652 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N MET C 659 " --> pdb=" O VAL C 655 " (cutoff:3.500A) Processing helix chain 'C' and resid 686 through 690 Processing helix chain 'C' and resid 698 through 706 removed outlier: 3.542A pdb=" N ARG C 702 " --> pdb=" O VAL C 698 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL C 703 " --> pdb=" O ALA C 699 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N HIS C 704 " --> pdb=" O ARG C 700 " (cutoff:3.500A) Processing helix chain 'C' and resid 709 through 714 removed outlier: 3.619A pdb=" N ALA C 713 " --> pdb=" O ILE C 709 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N PHE C 714 " --> pdb=" O ALA C 710 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 709 through 714' Processing helix chain 'C' and resid 721 through 730 removed outlier: 3.913A pdb=" N ALA C 726 " --> pdb=" O CYS C 722 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N HIS C 727 " --> pdb=" O HIS C 723 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LYS C 728 " --> pdb=" O SER C 724 " (cutoff:3.500A) Processing helix chain 'C' and resid 748 through 752 Processing helix chain 'C' and resid 771 through 782 removed outlier: 3.545A pdb=" N GLU C 777 " --> pdb=" O ARG C 773 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ILE C 778 " --> pdb=" O ARG C 774 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ALA C 779 " --> pdb=" O TYR C 775 " (cutoff:3.500A) Processing helix chain 'C' and resid 790 through 809 removed outlier: 3.742A pdb=" N LYS C 794 " --> pdb=" O ARG C 790 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE C 795 " --> pdb=" O THR C 791 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS C 797 " --> pdb=" O ALA C 793 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TRP C 801 " --> pdb=" O LYS C 797 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N THR C 804 " --> pdb=" O ALA C 800 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLU C 808 " --> pdb=" O THR C 804 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU C 809 " --> pdb=" O LEU C 805 " (cutoff:3.500A) Processing helix chain 'C' and resid 814 through 819 removed outlier: 3.727A pdb=" N GLU C 817 " --> pdb=" O SER C 814 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N GLY C 819 " --> pdb=" O ARG C 816 " (cutoff:3.500A) Processing helix chain 'C' and resid 829 through 837 removed outlier: 4.634A pdb=" N ASP C 835 " --> pdb=" O LYS C 831 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA C 836 " --> pdb=" O LEU C 832 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N PHE C 837 " --> pdb=" O SER C 833 " (cutoff:3.500A) Processing helix chain 'C' and resid 850 through 861 removed outlier: 3.661A pdb=" N LYS C 855 " --> pdb=" O ILE C 851 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N GLN C 856 " --> pdb=" O SER C 852 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ILE C 857 " --> pdb=" O GLU C 853 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N LEU C 858 " --> pdb=" O LEU C 854 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 24 removed outlier: 3.700A pdb=" N LEU B 9 " --> pdb=" O ASN B 5 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ASN B 10 " --> pdb=" O VAL B 6 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N ALA B 11 " --> pdb=" O ALA B 7 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N GLU B 14 " --> pdb=" O ASN B 10 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG B 15 " --> pdb=" O ALA B 11 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL B 16 " --> pdb=" O LEU B 12 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LYS B 17 " --> pdb=" O VAL B 13 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ARG B 21 " --> pdb=" O LYS B 17 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N GLU B 22 " --> pdb=" O LYS B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 31 removed outlier: 3.517A pdb=" N GLN B 30 " --> pdb=" O THR B 27 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL B 31 " --> pdb=" O GLN B 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 27 through 31' Processing helix chain 'B' and resid 39 through 44 Processing helix chain 'B' and resid 53 through 58 removed outlier: 3.653A pdb=" N SER B 57 " --> pdb=" O ALA B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 122 removed outlier: 3.518A pdb=" N ILE B 121 " --> pdb=" O THR B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 143 removed outlier: 3.611A pdb=" N ALA B 142 " --> pdb=" O HIS B 139 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS B 143 " --> pdb=" O PRO B 140 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 139 through 143' Processing helix chain 'B' and resid 144 through 158 removed outlier: 3.516A pdb=" N LYS B 148 " --> pdb=" O ASP B 144 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ASP B 151 " --> pdb=" O ASN B 147 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL B 153 " --> pdb=" O ALA B 149 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N LEU B 154 " --> pdb=" O ALA B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 161 No H-bonds generated for 'chain 'B' and resid 159 through 161' Processing helix chain 'B' and resid 174 through 179 removed outlier: 3.909A pdb=" N SER B 178 " --> pdb=" O SER B 174 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASN B 179 " --> pdb=" O VAL B 175 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 174 through 179' Processing helix chain 'B' and resid 198 through 203 removed outlier: 3.555A pdb=" N TYR B 203 " --> pdb=" O VAL B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 259 No H-bonds generated for 'chain 'B' and resid 257 through 259' Processing helix chain 'B' and resid 263 through 270 removed outlier: 3.520A pdb=" N ALA B 267 " --> pdb=" O ARG B 263 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N HIS B 269 " --> pdb=" O ARG B 265 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY B 270 " --> pdb=" O PHE B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 283 removed outlier: 3.879A pdb=" N ALA B 281 " --> pdb=" O LYS B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 309 removed outlier: 4.394A pdb=" N ILE B 304 " --> pdb=" O PRO B 300 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ALA B 305 " --> pdb=" O ALA B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 353 Processing helix chain 'B' and resid 356 through 364 removed outlier: 3.501A pdb=" N ALA B 361 " --> pdb=" O GLU B 357 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N MET B 362 " --> pdb=" O LYS B 358 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLY B 363 " --> pdb=" O LEU B 359 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLY B 364 " --> pdb=" O VAL B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 385 removed outlier: 3.565A pdb=" N TYR B 384 " --> pdb=" O ALA B 380 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N PHE B 385 " --> pdb=" O ARG B 381 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 380 through 385' Processing helix chain 'B' and resid 466 through 477 removed outlier: 3.663A pdb=" N ALA B 470 " --> pdb=" O SER B 466 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLU B 473 " --> pdb=" O ILE B 469 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N VAL B 474 " --> pdb=" O ALA B 470 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ILE B 475 " --> pdb=" O LEU B 471 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ASP B 477 " --> pdb=" O GLU B 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 499 removed outlier: 3.652A pdb=" N ILE B 499 " --> pdb=" O ALA B 496 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 496 through 499' Processing helix chain 'B' and resid 500 through 505 Processing helix chain 'B' and resid 523 through 533 removed outlier: 3.727A pdb=" N LYS B 527 " --> pdb=" O SER B 523 " (cutoff:3.500A) Processing helix chain 'B' and resid 553 through 558 removed outlier: 3.983A pdb=" N VAL B 557 " --> pdb=" O LYS B 553 " (cutoff:3.500A) Processing helix chain 'B' and resid 650 through 659 removed outlier: 3.612A pdb=" N ALA B 654 " --> pdb=" O GLY B 650 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL B 655 " --> pdb=" O GLY B 651 " (cutoff:3.500A) Processing helix chain 'B' and resid 672 through 685 removed outlier: 3.586A pdb=" N ALA B 678 " --> pdb=" O GLN B 674 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N LEU B 679 " --> pdb=" O ALA B 675 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LYS B 680 " --> pdb=" O LEU B 676 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU B 681 " --> pdb=" O GLN B 677 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N GLU B 684 " --> pdb=" O LYS B 680 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TYR B 685 " --> pdb=" O LEU B 681 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 692 removed outlier: 3.988A pdb=" N HIS B 691 " --> pdb=" O PRO B 687 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU B 692 " --> pdb=" O ALA B 688 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 687 through 692' Processing helix chain 'B' and resid 698 through 704 removed outlier: 3.719A pdb=" N ARG B 702 " --> pdb=" O VAL B 698 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL B 703 " --> pdb=" O ALA B 699 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 712 Processing helix chain 'B' and resid 721 through 730 removed outlier: 3.597A pdb=" N MET B 725 " --> pdb=" O VAL B 721 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ALA B 726 " --> pdb=" O CYS B 722 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N HIS B 727 " --> pdb=" O HIS B 723 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS B 728 " --> pdb=" O SER B 724 " (cutoff:3.500A) Processing helix chain 'B' and resid 739 through 743 Processing helix chain 'B' and resid 748 through 752 Processing helix chain 'B' and resid 773 through 782 removed outlier: 3.622A pdb=" N GLU B 777 " --> pdb=" O ARG B 773 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ILE B 778 " --> pdb=" O ARG B 774 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ALA B 779 " --> pdb=" O TYR B 775 " (cutoff:3.500A) Processing helix chain 'B' and resid 790 through 809 removed outlier: 3.821A pdb=" N LYS B 794 " --> pdb=" O ARG B 790 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ILE B 795 " --> pdb=" O THR B 791 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLU B 796 " --> pdb=" O ALA B 792 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N TRP B 801 " --> pdb=" O LYS B 797 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLU B 803 " --> pdb=" O LEU B 799 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LYS B 806 " --> pdb=" O LEU B 802 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA B 807 " --> pdb=" O GLU B 803 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N GLU B 808 " --> pdb=" O THR B 804 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU B 809 " --> pdb=" O LEU B 805 " (cutoff:3.500A) Processing helix chain 'B' and resid 814 through 819 removed outlier: 3.605A pdb=" N GLU B 817 " --> pdb=" O SER B 814 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N GLY B 819 " --> pdb=" O ARG B 816 " (cutoff:3.500A) Processing helix chain 'B' and resid 829 through 834 removed outlier: 4.114A pdb=" N GLU B 834 " --> pdb=" O ASP B 830 " (cutoff:3.500A) Processing helix chain 'B' and resid 850 through 854 Processing helix chain 'A' and resid 5 through 24 removed outlier: 3.699A pdb=" N LEU A 9 " --> pdb=" O ASN A 5 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ASN A 10 " --> pdb=" O VAL A 6 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N GLU A 14 " --> pdb=" O ASN A 10 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARG A 15 " --> pdb=" O ALA A 11 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL A 16 " --> pdb=" O LEU A 12 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYS A 17 " --> pdb=" O VAL A 13 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ARG A 21 " --> pdb=" O LYS A 17 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N GLU A 22 " --> pdb=" O LYS A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 27 through 31 removed outlier: 3.517A pdb=" N GLN A 30 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL A 31 " --> pdb=" O GLN A 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 27 through 31' Processing helix chain 'A' and resid 39 through 44 Processing helix chain 'A' and resid 53 through 58 removed outlier: 3.654A pdb=" N SER A 57 " --> pdb=" O ALA A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 122 removed outlier: 3.518A pdb=" N ILE A 121 " --> pdb=" O THR A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 143 removed outlier: 3.612A pdb=" N ALA A 142 " --> pdb=" O HIS A 139 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LYS A 143 " --> pdb=" O PRO A 140 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 139 through 143' Processing helix chain 'A' and resid 144 through 158 removed outlier: 3.517A pdb=" N LYS A 148 " --> pdb=" O ASP A 144 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASP A 151 " --> pdb=" O ASN A 147 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL A 153 " --> pdb=" O ALA A 149 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N LEU A 154 " --> pdb=" O ALA A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 161 No H-bonds generated for 'chain 'A' and resid 159 through 161' Processing helix chain 'A' and resid 174 through 179 removed outlier: 3.908A pdb=" N SER A 178 " --> pdb=" O SER A 174 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASN A 179 " --> pdb=" O VAL A 175 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 174 through 179' Processing helix chain 'A' and resid 198 through 203 removed outlier: 3.554A pdb=" N TYR A 203 " --> pdb=" O VAL A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 259 No H-bonds generated for 'chain 'A' and resid 257 through 259' Processing helix chain 'A' and resid 263 through 270 removed outlier: 3.519A pdb=" N ALA A 267 " --> pdb=" O ARG A 263 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N HIS A 269 " --> pdb=" O ARG A 265 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY A 270 " --> pdb=" O PHE A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 283 removed outlier: 3.880A pdb=" N ALA A 281 " --> pdb=" O LYS A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 309 removed outlier: 4.394A pdb=" N ILE A 304 " --> pdb=" O PRO A 300 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ALA A 305 " --> pdb=" O ALA A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 353 Processing helix chain 'A' and resid 356 through 364 removed outlier: 3.501A pdb=" N ALA A 361 " --> pdb=" O GLU A 357 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N MET A 362 " --> pdb=" O LYS A 358 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLY A 363 " --> pdb=" O LEU A 359 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY A 364 " --> pdb=" O VAL A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 385 removed outlier: 3.564A pdb=" N TYR A 384 " --> pdb=" O ALA A 380 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N PHE A 385 " --> pdb=" O ARG A 381 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 380 through 385' Processing helix chain 'A' and resid 466 through 477 removed outlier: 3.662A pdb=" N ALA A 470 " --> pdb=" O SER A 466 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLU A 473 " --> pdb=" O ILE A 469 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N VAL A 474 " --> pdb=" O ALA A 470 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N ILE A 475 " --> pdb=" O LEU A 471 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ASP A 477 " --> pdb=" O GLU A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 499 removed outlier: 3.652A pdb=" N ILE A 499 " --> pdb=" O ALA A 496 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 496 through 499' Processing helix chain 'A' and resid 500 through 505 Processing helix chain 'A' and resid 523 through 533 removed outlier: 3.728A pdb=" N LYS A 527 " --> pdb=" O SER A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 558 removed outlier: 3.984A pdb=" N VAL A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 659 removed outlier: 3.613A pdb=" N ALA A 654 " --> pdb=" O GLY A 650 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL A 655 " --> pdb=" O GLY A 651 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 685 removed outlier: 3.586A pdb=" N ALA A 678 " --> pdb=" O GLN A 674 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N LEU A 679 " --> pdb=" O ALA A 675 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LYS A 680 " --> pdb=" O LEU A 676 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU A 681 " --> pdb=" O GLN A 677 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N GLU A 684 " --> pdb=" O LYS A 680 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TYR A 685 " --> pdb=" O LEU A 681 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 692 removed outlier: 3.988A pdb=" N HIS A 691 " --> pdb=" O PRO A 687 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU A 692 " --> pdb=" O ALA A 688 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 687 through 692' Processing helix chain 'A' and resid 698 through 704 removed outlier: 3.718A pdb=" N ARG A 702 " --> pdb=" O VAL A 698 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL A 703 " --> pdb=" O ALA A 699 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 712 Processing helix chain 'A' and resid 721 through 730 removed outlier: 3.599A pdb=" N MET A 725 " --> pdb=" O VAL A 721 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ALA A 726 " --> pdb=" O CYS A 722 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N HIS A 727 " --> pdb=" O HIS A 723 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS A 728 " --> pdb=" O SER A 724 " (cutoff:3.500A) Processing helix chain 'A' and resid 739 through 743 Processing helix chain 'A' and resid 748 through 752 Processing helix chain 'A' and resid 773 through 782 removed outlier: 3.622A pdb=" N GLU A 777 " --> pdb=" O ARG A 773 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ILE A 778 " --> pdb=" O ARG A 774 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ALA A 779 " --> pdb=" O TYR A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 790 through 809 removed outlier: 3.820A pdb=" N LYS A 794 " --> pdb=" O ARG A 790 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ILE A 795 " --> pdb=" O THR A 791 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLU A 796 " --> pdb=" O ALA A 792 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N TRP A 801 " --> pdb=" O LYS A 797 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLU A 803 " --> pdb=" O LEU A 799 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LYS A 806 " --> pdb=" O LEU A 802 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA A 807 " --> pdb=" O GLU A 803 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N GLU A 808 " --> pdb=" O THR A 804 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU A 809 " --> pdb=" O LEU A 805 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 819 removed outlier: 3.606A pdb=" N GLU A 817 " --> pdb=" O SER A 814 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N GLY A 819 " --> pdb=" O ARG A 816 " (cutoff:3.500A) Processing helix chain 'A' and resid 829 through 834 removed outlier: 4.114A pdb=" N GLU A 834 " --> pdb=" O ASP A 830 " (cutoff:3.500A) Processing helix chain 'A' and resid 850 through 854 Processing sheet with id=AA1, first strand: chain 'F' and resid 460 through 462 removed outlier: 6.869A pdb=" N TYR F 461 " --> pdb=" O VAL F 634 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'F' and resid 509 through 511 removed outlier: 3.867A pdb=" N GLU F 511 " --> pdb=" O ALA F 482 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE F 484 " --> pdb=" O GLU F 511 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N ARG F 481 " --> pdb=" O VAL F 539 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N ILE F 541 " --> pdb=" O ARG F 481 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N LEU F 483 " --> pdb=" O ILE F 541 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ILE F 540 " --> pdb=" O ILE F 593 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'F' and resid 609 through 612 removed outlier: 3.675A pdb=" N ALA F 609 " --> pdb=" O LEU F 622 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL F 611 " --> pdb=" O TYR F 620 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 460 through 462 removed outlier: 6.877A pdb=" N TYR C 461 " --> pdb=" O VAL C 634 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 482 through 484 removed outlier: 6.606A pdb=" N LEU C 483 " --> pdb=" O ILE C 541 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N ILE C 540 " --> pdb=" O ILE C 593 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 91 through 92 removed outlier: 3.738A pdb=" N ASP B 92 " --> pdb=" O THR B 97 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ILE B 98 " --> pdb=" O VAL B 444 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N TYR A 372 " --> pdb=" O PRO A 218 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N VAL A 220 " --> pdb=" O TYR A 372 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N THR A 217 " --> pdb=" O SER A 251 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N VAL A 253 " --> pdb=" O THR A 217 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N VAL A 219 " --> pdb=" O VAL A 253 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N VAL A 255 " --> pdb=" O VAL A 219 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N ILE A 221 " --> pdb=" O VAL A 255 " (cutoff:3.500A) removed outlier: 8.466A pdb=" N TYR A 344 " --> pdb=" O GLN A 250 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N VAL A 252 " --> pdb=" O TYR A 344 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N ALA A 346 " --> pdb=" O VAL A 252 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N VAL A 254 " --> pdb=" O ALA A 346 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 101 through 102 removed outlier: 3.635A pdb=" N ASN B 440 " --> pdb=" O GLU B 102 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 167 through 168 removed outlier: 6.780A pdb=" N ILE B 134 " --> pdb=" O GLY B 168 " (cutoff:3.500A) removed outlier: 8.477A pdb=" N LEU B 191 " --> pdb=" O ILE B 106 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N CYS B 108 " --> pdb=" O LEU B 191 " (cutoff:3.500A) removed outlier: 9.117A pdb=" N THR B 193 " --> pdb=" O CYS B 108 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N ILE B 190 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N VAL B 212 " --> pdb=" O ILE B 190 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N ALA B 192 " --> pdb=" O VAL B 212 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 343 through 346 removed outlier: 8.466A pdb=" N TYR B 344 " --> pdb=" O GLN B 250 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N VAL B 252 " --> pdb=" O TYR B 344 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N ALA B 346 " --> pdb=" O VAL B 252 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N VAL B 254 " --> pdb=" O ALA B 346 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N THR B 217 " --> pdb=" O SER B 251 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N VAL B 253 " --> pdb=" O THR B 217 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N VAL B 219 " --> pdb=" O VAL B 253 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N VAL B 255 " --> pdb=" O VAL B 219 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N ILE B 221 " --> pdb=" O VAL B 255 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N TYR B 372 " --> pdb=" O PRO B 218 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N VAL B 220 " --> pdb=" O TYR B 372 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ILE B 394 " --> pdb=" O ALA A 445 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ILE A 98 " --> pdb=" O VAL A 444 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASP A 92 " --> pdb=" O THR A 97 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 460 through 462 removed outlier: 6.778A pdb=" N TYR B 461 " --> pdb=" O VAL B 634 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 509 through 511 removed outlier: 3.888A pdb=" N GLU B 511 " --> pdb=" O ALA B 482 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 101 through 102 removed outlier: 3.635A pdb=" N ASN A 440 " --> pdb=" O GLU A 102 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 167 through 168 removed outlier: 6.781A pdb=" N ILE A 134 " --> pdb=" O GLY A 168 " (cutoff:3.500A) removed outlier: 8.478A pdb=" N LEU A 191 " --> pdb=" O ILE A 106 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N CYS A 108 " --> pdb=" O LEU A 191 " (cutoff:3.500A) removed outlier: 9.115A pdb=" N THR A 193 " --> pdb=" O CYS A 108 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N ILE A 190 " --> pdb=" O ILE A 210 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N VAL A 212 " --> pdb=" O ILE A 190 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N ALA A 192 " --> pdb=" O VAL A 212 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 460 through 462 removed outlier: 6.779A pdb=" N TYR A 461 " --> pdb=" O VAL A 634 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 509 through 511 removed outlier: 3.888A pdb=" N GLU A 511 " --> pdb=" O ALA A 482 " (cutoff:3.500A) 275 hydrogen bonds defined for protein. 744 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: 8.91 Time building geometry restraints manager: 3.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 19778 1.03 - 1.23: 63 1.23 - 1.42: 8236 1.42 - 1.62: 11773 1.62 - 1.81: 170 Bond restraints: 40020 Sorted by residual: bond pdb=" C1' TXE A 902 " pdb=" C2' TXE A 902 " ideal model delta sigma weight residual 1.530 1.296 0.234 2.00e-02 2.50e+03 1.37e+02 bond pdb=" C1' TXE B 902 " pdb=" C2' TXE B 902 " ideal model delta sigma weight residual 1.530 1.297 0.233 2.00e-02 2.50e+03 1.36e+02 bond pdb=" C1' TXE A 902 " pdb=" O4' TXE A 902 " ideal model delta sigma weight residual 1.396 1.628 -0.232 2.00e-02 2.50e+03 1.34e+02 bond pdb=" C1' TXE B 902 " pdb=" O4' TXE B 902 " ideal model delta sigma weight residual 1.396 1.628 -0.232 2.00e-02 2.50e+03 1.34e+02 bond pdb=" C1B TXE B 902 " pdb=" C2B TXE B 902 " ideal model delta sigma weight residual 1.534 1.311 0.223 2.00e-02 2.50e+03 1.24e+02 ... (remaining 40015 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.84: 72038 2.84 - 5.69: 437 5.69 - 8.53: 53 8.53 - 11.38: 10 11.38 - 14.22: 12 Bond angle restraints: 72550 Sorted by residual: angle pdb=" O1N TXE A 902 " pdb=" PN TXE A 902 " pdb=" O2N TXE A 902 " ideal model delta sigma weight residual 121.99 107.77 14.22 3.00e+00 1.11e-01 2.25e+01 angle pdb=" O1N TXE B 902 " pdb=" PN TXE B 902 " pdb=" O2N TXE B 902 " ideal model delta sigma weight residual 121.99 107.90 14.09 3.00e+00 1.11e-01 2.21e+01 angle pdb=" N1A TXE B 902 " pdb=" C6A TXE B 902 " pdb=" N6A TXE B 902 " ideal model delta sigma weight residual 119.31 106.01 13.30 3.00e+00 1.11e-01 1.96e+01 angle pdb=" N1A TXE A 902 " pdb=" C6A TXE A 902 " pdb=" N6A TXE A 902 " ideal model delta sigma weight residual 119.31 106.03 13.28 3.00e+00 1.11e-01 1.96e+01 angle pdb=" C PRO B 138 " pdb=" N HIS B 139 " pdb=" CA HIS B 139 " ideal model delta sigma weight residual 120.97 133.35 -12.38 2.84e+00 1.24e-01 1.90e+01 ... (remaining 72545 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.39: 16731 17.39 - 34.78: 1632 34.78 - 52.18: 384 52.18 - 69.57: 146 69.57 - 86.96: 43 Dihedral angle restraints: 18936 sinusoidal: 10336 harmonic: 8600 Sorted by residual: dihedral pdb=" CA ILE B 47 " pdb=" C ILE B 47 " pdb=" N PRO B 48 " pdb=" CA PRO B 48 " ideal model delta harmonic sigma weight residual 180.00 135.72 44.28 0 5.00e+00 4.00e-02 7.84e+01 dihedral pdb=" CA ILE A 47 " pdb=" C ILE A 47 " pdb=" N PRO A 48 " pdb=" CA PRO A 48 " ideal model delta harmonic sigma weight residual 180.00 135.73 44.27 0 5.00e+00 4.00e-02 7.84e+01 dihedral pdb=" CA PHE C 462 " pdb=" C PHE C 462 " pdb=" N ARG C 463 " pdb=" CA ARG C 463 " ideal model delta harmonic sigma weight residual 180.00 152.89 27.11 0 5.00e+00 4.00e-02 2.94e+01 ... (remaining 18933 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.808: 3132 0.808 - 1.617: 0 1.617 - 2.425: 0 2.425 - 3.234: 0 3.234 - 4.042: 2 Chirality restraints: 3134 Sorted by residual: chirality pdb=" C3N TXE B 902 " pdb=" C2N TXE B 902 " pdb=" C4N TXE B 902 " pdb=" C7N TXE B 902 " both_signs ideal model delta sigma weight residual False -2.69 1.35 -4.04 2.00e-01 2.50e+01 4.08e+02 chirality pdb=" C3N TXE A 902 " pdb=" C2N TXE A 902 " pdb=" C4N TXE A 902 " pdb=" C7N TXE A 902 " both_signs ideal model delta sigma weight residual False -2.69 1.35 -4.04 2.00e-01 2.50e+01 4.08e+02 chirality pdb=" CB THR B 324 " pdb=" CA THR B 324 " pdb=" OG1 THR B 324 " pdb=" CG2 THR B 324 " both_signs ideal model delta sigma weight residual False 2.55 2.00 0.56 2.00e-01 2.50e+01 7.71e+00 ... (remaining 3131 not shown) Planarity restraints: 5994 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 47 " 0.051 5.00e-02 4.00e+02 7.62e-02 9.30e+00 pdb=" N PRO B 48 " -0.132 5.00e-02 4.00e+02 pdb=" CA PRO B 48 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO B 48 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 47 " -0.051 5.00e-02 4.00e+02 7.62e-02 9.28e+00 pdb=" N PRO A 48 " 0.132 5.00e-02 4.00e+02 pdb=" CA PRO A 48 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 48 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 714 " -0.025 2.00e-02 2.50e+03 1.44e-02 6.22e+00 pdb=" CG PHE B 714 " 0.042 2.00e-02 2.50e+03 pdb=" CD1 PHE B 714 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE B 714 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE B 714 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 714 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE B 714 " -0.003 2.00e-02 2.50e+03 pdb=" HD1 PHE B 714 " 0.002 2.00e-02 2.50e+03 pdb=" HD2 PHE B 714 " 0.002 2.00e-02 2.50e+03 pdb=" HE1 PHE B 714 " -0.003 2.00e-02 2.50e+03 pdb=" HE2 PHE B 714 " -0.003 2.00e-02 2.50e+03 pdb=" HZ PHE B 714 " -0.000 2.00e-02 2.50e+03 ... (remaining 5991 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.21: 2761 2.21 - 2.81: 83066 2.81 - 3.40: 87560 3.40 - 4.00: 119838 4.00 - 4.60: 187149 Nonbonded interactions: 480374 Sorted by model distance: nonbonded pdb=" OE1 GLN A 760 " pdb=" HG SER A 764 " model vdw 1.612 2.450 nonbonded pdb=" OE1 GLN B 760 " pdb=" HG SER B 764 " model vdw 1.613 2.450 nonbonded pdb=" OD1 ASP A 497 " pdb=" H ASP A 497 " model vdw 1.633 2.450 nonbonded pdb=" OD1 ASP B 497 " pdb=" H ASP B 497 " model vdw 1.634 2.450 nonbonded pdb="HH21 ARG B 46 " pdb=" OD2 ASP A 838 " model vdw 1.637 2.450 ... (remaining 480369 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.090 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: 0.250 Extract box with map and model: 0.360 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 30.910 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0650 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.014 0.234 20216 Z= 0.562 Angle : 0.977 14.219 27434 Z= 0.492 Chirality : 0.119 4.042 3134 Planarity : 0.006 0.076 3540 Dihedral : 16.139 86.962 7498 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.51 % Favored : 85.49 % Rotamer: Outliers : 1.40 % Allowed : 3.67 % Favored : 94.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.67 % 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 aren not related in a simple way. whole: -5.95 (0.13), residues: 2570 helix: -4.75 (0.08), residues: 836 sheet: -3.31 (0.24), residues: 308 loop : -3.68 (0.15), residues: 1426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 750 TYR 0.017 0.002 TYR A 77 PHE 0.043 0.003 PHE B 714 TRP 0.012 0.002 TRP C 453 HIS 0.007 0.002 HIS B 184 Details of bonding type rmsd covalent geometry : bond 0.01372 (20216) covalent geometry : angle 0.97714 (27434) hydrogen bonds : bond 0.37028 ( 275) hydrogen bonds : angle 10.77690 ( 744) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 242 time to evaluate : 0.791 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 604 GLU cc_start: 0.5442 (pm20) cc_final: 0.4733 (mm-30) REVERT: C 826 LEU cc_start: 0.3720 (mp) cc_final: 0.3379 (tt) REVERT: B 408 LEU cc_start: 0.6358 (mp) cc_final: 0.5843 (tt) REVERT: B 530 GLU cc_start: -0.3461 (OUTLIER) cc_final: -0.4135 (mt-10) REVERT: B 574 MET cc_start: 0.1152 (ptt) cc_final: 0.0639 (ttp) REVERT: B 606 THR cc_start: 0.1050 (t) cc_final: -0.0946 (p) REVERT: B 640 MET cc_start: -0.2849 (mmt) cc_final: -0.3117 (mmt) REVERT: B 755 ASP cc_start: -0.5595 (OUTLIER) cc_final: -0.6674 (t70) REVERT: A 112 PRO cc_start: 0.3453 (Cg_endo) cc_final: 0.3250 (Cg_exo) REVERT: A 372 TYR cc_start: -0.2713 (m-80) cc_final: -0.4918 (m-80) REVERT: A 417 LEU cc_start: 0.2691 (pt) cc_final: 0.1969 (mp) outliers start: 29 outliers final: 9 residues processed: 270 average time/residue: 0.2630 time to fit residues: 109.2269 Evaluate side-chains 182 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 171 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 450 ASN Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 69 ASN Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain B residue 407 ASP Chi-restraints excluded: chain B residue 530 GLU Chi-restraints excluded: chain B residue 755 ASP Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 329 SER Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain A residue 760 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 197 optimal weight: 0.0980 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.7980 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 0.6980 chunk 111 optimal weight: 5.9990 chunk 71 optimal weight: 3.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 737 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 450 ASN C 657 HIS C 752 ASN C 756 ASN B 283 GLN B 732 GLN A 283 GLN A 410 ASN A 618 GLN A 732 GLN A 760 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5373 r_free = 0.5373 target = 0.273448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.5322 r_free = 0.5322 target = 0.264166 restraints weight = 285228.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.5352 r_free = 0.5352 target = 0.266784 restraints weight = 150605.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.5370 r_free = 0.5370 target = 0.268317 restraints weight = 86470.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.5381 r_free = 0.5381 target = 0.269287 restraints weight = 53578.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.5388 r_free = 0.5388 target = 0.269906 restraints weight = 35125.871| |-----------------------------------------------------------------------------| r_work (final): 0.5242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0669 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 20216 Z= 0.112 Angle : 0.594 7.381 27434 Z= 0.308 Chirality : 0.042 0.172 3134 Planarity : 0.004 0.071 3540 Dihedral : 8.137 84.468 2918 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 1.11 % Allowed : 7.77 % Favored : 91.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.67 % 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 aren not related in a simple way. whole: -5.01 (0.14), residues: 2570 helix: -3.79 (0.12), residues: 818 sheet: -2.87 (0.25), residues: 354 loop : -3.20 (0.15), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 463 TYR 0.012 0.001 TYR F 620 PHE 0.027 0.001 PHE F 714 TRP 0.011 0.001 TRP B 801 HIS 0.013 0.001 HIS F 657 Details of bonding type rmsd covalent geometry : bond 0.00248 (20216) covalent geometry : angle 0.59386 (27434) hydrogen bonds : bond 0.05512 ( 275) hydrogen bonds : angle 6.46852 ( 744) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 181 time to evaluate : 0.937 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: symmetry clash revert: symmetry clash REVERT: C 573 PHE cc_start: 0.2014 (OUTLIER) cc_final: 0.0986 (m-80) REVERT: C 586 MET cc_start: -0.2748 (mtp) cc_final: -0.3113 (mtp) REVERT: C 816 ARG cc_start: -0.1968 (ttp-170) cc_final: -0.4276 (tpt170) REVERT: B 410 ASN cc_start: 0.0316 (t0) cc_final: 0.0071 (t0) REVERT: B 558 MET cc_start: -0.2813 (ptp) cc_final: -0.3957 (mmm) REVERT: B 574 MET cc_start: 0.0933 (ptt) cc_final: 0.0276 (ttp) REVERT: B 606 THR cc_start: 0.1258 (t) cc_final: -0.0637 (p) REVERT: B 755 ASP cc_start: -0.5078 (OUTLIER) cc_final: -0.5540 (m-30) REVERT: A 144 ASP cc_start: -0.0454 (OUTLIER) cc_final: -0.1383 (m-30) outliers start: 23 outliers final: 15 residues processed: 201 average time/residue: 0.2826 time to fit residues: 87.5980 Evaluate side-chains 177 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 159 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 450 ASN Chi-restraints excluded: chain F residue 483 LEU Chi-restraints excluded: chain F residue 573 PHE Chi-restraints excluded: chain C residue 450 ASN Chi-restraints excluded: chain C residue 573 PHE Chi-restraints excluded: chain C residue 631 MET Chi-restraints excluded: chain C residue 821 GLN Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 69 ASN Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 407 ASP Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 755 ASP Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 144 ASP Chi-restraints excluded: chain A residue 302 TYR Chi-restraints excluded: chain A residue 530 GLU Chi-restraints excluded: chain A residue 580 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 151 optimal weight: 8.9990 chunk 118 optimal weight: 9.9990 chunk 28 optimal weight: 9.9990 chunk 182 optimal weight: 4.9990 chunk 67 optimal weight: 3.9990 chunk 158 optimal weight: 2.9990 chunk 203 optimal weight: 0.0970 chunk 69 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 117 optimal weight: 3.9990 chunk 7 optimal weight: 6.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 657 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 840 GLN ** C 674 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 737 HIS C 765 GLN ** B 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 840 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5241 r_free = 0.5241 target = 0.246812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.5094 r_free = 0.5094 target = 0.227576 restraints weight = 203625.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.5135 r_free = 0.5135 target = 0.232659 restraints weight = 123238.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.5159 r_free = 0.5159 target = 0.235751 restraints weight = 82236.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.5173 r_free = 0.5173 target = 0.237761 restraints weight = 59506.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.5183 r_free = 0.5183 target = 0.239209 restraints weight = 46384.891| |-----------------------------------------------------------------------------| r_work (final): 0.5169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1274 moved from start: 0.3709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 20216 Z= 0.174 Angle : 0.656 10.423 27434 Z= 0.344 Chirality : 0.043 0.170 3134 Planarity : 0.005 0.064 3540 Dihedral : 7.278 89.736 2906 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.72 % Favored : 91.28 % Rotamer: Outliers : 1.45 % Allowed : 9.85 % Favored : 88.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.67 % 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 aren not related in a simple way. whole: -4.44 (0.14), residues: 2570 helix: -3.12 (0.14), residues: 832 sheet: -2.68 (0.26), residues: 346 loop : -2.95 (0.15), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 790 TYR 0.018 0.001 TYR A 559 PHE 0.034 0.002 PHE C 714 TRP 0.010 0.002 TRP C 453 HIS 0.011 0.001 HIS F 657 Details of bonding type rmsd covalent geometry : bond 0.00364 (20216) covalent geometry : angle 0.65604 (27434) hydrogen bonds : bond 0.04675 ( 275) hydrogen bonds : angle 5.37055 ( 744) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 164 time to evaluate : 0.685 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: symmetry clash REVERT: F 461 TYR cc_start: -0.0248 (m-80) cc_final: -0.0946 (m-80) REVERT: F 538 ASP cc_start: 0.5377 (t0) cc_final: 0.4091 (p0) REVERT: C 586 MET cc_start: -0.3077 (mtp) cc_final: -0.3325 (mtp) REVERT: C 826 LEU cc_start: 0.6383 (pt) cc_final: 0.5141 (tt) REVERT: B 574 MET cc_start: 0.0786 (ptt) cc_final: -0.1710 (ttp) REVERT: A 74 GLU cc_start: 0.0192 (OUTLIER) cc_final: -0.2795 (mm-30) REVERT: A 80 TYR cc_start: 0.4921 (m-80) cc_final: 0.4667 (m-10) outliers start: 30 outliers final: 21 residues processed: 189 average time/residue: 0.2642 time to fit residues: 78.1144 Evaluate side-chains 165 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 143 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 450 ASN Chi-restraints excluded: chain F residue 483 LEU Chi-restraints excluded: chain F residue 573 PHE Chi-restraints excluded: chain C residue 550 ASP Chi-restraints excluded: chain C residue 573 PHE Chi-restraints excluded: chain C residue 631 MET Chi-restraints excluded: chain C residue 640 MET Chi-restraints excluded: chain C residue 739 LEU Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 69 ASN Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 639 VAL Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain A residue 580 ILE Chi-restraints excluded: chain A residue 659 MET Chi-restraints excluded: chain A residue 732 GLN Chi-restraints excluded: chain A residue 745 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 44 optimal weight: 8.9990 chunk 119 optimal weight: 10.0000 chunk 95 optimal weight: 8.9990 chunk 14 optimal weight: 0.9990 chunk 186 optimal weight: 6.9990 chunk 5 optimal weight: 4.9990 chunk 133 optimal weight: 9.9990 chunk 90 optimal weight: 20.0000 chunk 102 optimal weight: 0.7980 chunk 195 optimal weight: 9.9990 chunk 242 optimal weight: 10.0000 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 657 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 840 GLN C 756 ASN B 30 GLN B 637 ASN ** B 716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 760 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 840 GLN ** A 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 845 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5308 r_free = 0.5308 target = 0.264112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.5263 r_free = 0.5263 target = 0.254992 restraints weight = 288402.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.5294 r_free = 0.5294 target = 0.257534 restraints weight = 148049.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.5312 r_free = 0.5312 target = 0.259014 restraints weight = 83794.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.5321 r_free = 0.5321 target = 0.259912 restraints weight = 51039.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.5328 r_free = 0.5328 target = 0.260476 restraints weight = 33113.479| |-----------------------------------------------------------------------------| r_work (final): 0.5219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1940 moved from start: 0.6223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.126 20216 Z= 0.268 Angle : 0.874 10.245 27434 Z= 0.467 Chirality : 0.049 0.443 3134 Planarity : 0.006 0.089 3540 Dihedral : 8.564 72.538 2902 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 17.95 Ramachandran Plot: Outliers : 0.08 % Allowed : 11.25 % Favored : 88.68 % Rotamer: Outliers : 2.85 % Allowed : 12.69 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.83 % Twisted General : 0.08 % 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 aren not related in a simple way. whole: -4.54 (0.14), residues: 2570 helix: -3.06 (0.14), residues: 846 sheet: -2.89 (0.26), residues: 316 loop : -3.08 (0.15), residues: 1408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 464 TYR 0.036 0.002 TYR A 559 PHE 0.041 0.003 PHE C 714 TRP 0.030 0.003 TRP A 556 HIS 0.016 0.003 HIS F 657 Details of bonding type rmsd covalent geometry : bond 0.00604 (20216) covalent geometry : angle 0.87387 (27434) hydrogen bonds : bond 0.05167 ( 275) hydrogen bonds : angle 6.31501 ( 744) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 152 time to evaluate : 0.912 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 483 LEU cc_start: 0.2274 (OUTLIER) cc_final: 0.1682 (tt) REVERT: F 538 ASP cc_start: 0.6129 (t0) cc_final: 0.4164 (p0) REVERT: F 549 MET cc_start: -0.0121 (mmt) cc_final: -0.0402 (mmm) REVERT: F 640 MET cc_start: 0.2236 (mmt) cc_final: 0.1733 (mmt) REVERT: F 659 MET cc_start: -0.2494 (mmm) cc_final: -0.2741 (mmm) REVERT: C 573 PHE cc_start: 0.3014 (m-80) cc_final: 0.1949 (m-80) REVERT: B 411 PHE cc_start: 0.0803 (m-80) cc_final: -0.0925 (t80) REVERT: B 437 HIS cc_start: 0.0951 (OUTLIER) cc_final: 0.0038 (p90) REVERT: B 574 MET cc_start: 0.2406 (ptt) cc_final: 0.2175 (ptp) REVERT: B 804 THR cc_start: -0.1041 (OUTLIER) cc_final: -0.1312 (m) REVERT: A 74 GLU cc_start: -0.1361 (OUTLIER) cc_final: -0.1946 (pt0) outliers start: 59 outliers final: 31 residues processed: 202 average time/residue: 0.2767 time to fit residues: 89.0197 Evaluate side-chains 172 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 137 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 483 LEU Chi-restraints excluded: chain F residue 573 PHE Chi-restraints excluded: chain F residue 612 THR Chi-restraints excluded: chain C residue 550 ASP Chi-restraints excluded: chain C residue 627 LEU Chi-restraints excluded: chain C residue 714 PHE Chi-restraints excluded: chain C residue 739 LEU Chi-restraints excluded: chain C residue 749 ILE Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 69 ASN Chi-restraints excluded: chain B residue 82 ASP Chi-restraints excluded: chain B residue 86 CYS Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 384 TYR Chi-restraints excluded: chain B residue 437 HIS Chi-restraints excluded: chain B residue 444 VAL Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 549 MET Chi-restraints excluded: chain B residue 637 ASN Chi-restraints excluded: chain B residue 639 VAL Chi-restraints excluded: chain B residue 663 VAL Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 745 ILE Chi-restraints excluded: chain B residue 801 TRP Chi-restraints excluded: chain B residue 804 THR Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 302 TYR Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 430 SER Chi-restraints excluded: chain A residue 580 ILE Chi-restraints excluded: chain A residue 712 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 8 optimal weight: 1.9990 chunk 133 optimal weight: 6.9990 chunk 181 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 chunk 82 optimal weight: 0.6980 chunk 24 optimal weight: 7.9990 chunk 165 optimal weight: 0.3980 chunk 246 optimal weight: 7.9990 chunk 73 optimal weight: 1.9990 chunk 148 optimal weight: 0.5980 chunk 146 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 657 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 637 ASN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5327 r_free = 0.5327 target = 0.265905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.5283 r_free = 0.5283 target = 0.256898 restraints weight = 285939.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.5314 r_free = 0.5314 target = 0.259461 restraints weight = 147086.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.5331 r_free = 0.5331 target = 0.260921 restraints weight = 82764.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.5342 r_free = 0.5342 target = 0.261811 restraints weight = 50014.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.5346 r_free = 0.5346 target = 0.262364 restraints weight = 32221.231| |-----------------------------------------------------------------------------| r_work (final): 0.5233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1724 moved from start: 0.6192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 20216 Z= 0.101 Angle : 0.561 7.352 27434 Z= 0.294 Chirality : 0.041 0.147 3134 Planarity : 0.004 0.059 3540 Dihedral : 6.997 75.900 2900 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.70 % Favored : 92.30 % Rotamer: Outliers : 1.59 % Allowed : 14.14 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.67 % 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 aren not related in a simple way. whole: -4.10 (0.15), residues: 2570 helix: -2.57 (0.15), residues: 880 sheet: -2.52 (0.27), residues: 318 loop : -2.92 (0.15), residues: 1372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 464 TYR 0.017 0.001 TYR A 559 PHE 0.014 0.001 PHE A 608 TRP 0.010 0.001 TRP A 556 HIS 0.005 0.001 HIS B 565 Details of bonding type rmsd covalent geometry : bond 0.00233 (20216) covalent geometry : angle 0.56104 (27434) hydrogen bonds : bond 0.03086 ( 275) hydrogen bonds : angle 5.19288 ( 744) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 143 time to evaluate : 0.757 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 538 ASP cc_start: 0.5337 (t0) cc_final: 0.3825 (p0) REVERT: F 589 LYS cc_start: 0.4010 (tttt) cc_final: 0.3155 (tttm) REVERT: F 640 MET cc_start: 0.2341 (mmt) cc_final: 0.1792 (mmt) REVERT: C 549 MET cc_start: 0.2915 (mtm) cc_final: 0.2614 (mtt) REVERT: C 573 PHE cc_start: 0.1664 (OUTLIER) cc_final: 0.0828 (m-80) REVERT: B 411 PHE cc_start: 0.0563 (m-80) cc_final: -0.1032 (t80) REVERT: B 574 MET cc_start: 0.1339 (ptt) cc_final: 0.0502 (ptp) REVERT: B 659 MET cc_start: 0.6041 (ppp) cc_final: 0.5771 (ppp) REVERT: A 122 PHE cc_start: 0.4467 (OUTLIER) cc_final: 0.3277 (t80) outliers start: 33 outliers final: 24 residues processed: 170 average time/residue: 0.2823 time to fit residues: 75.6432 Evaluate side-chains 166 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 140 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 483 LEU Chi-restraints excluded: chain F residue 573 PHE Chi-restraints excluded: chain C residue 573 PHE Chi-restraints excluded: chain C residue 727 HIS Chi-restraints excluded: chain C residue 739 LEU Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 69 ASN Chi-restraints excluded: chain B residue 86 CYS Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 362 MET Chi-restraints excluded: chain B residue 396 ILE Chi-restraints excluded: chain B residue 407 ASP Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 637 ASN Chi-restraints excluded: chain B residue 639 VAL Chi-restraints excluded: chain B residue 745 ILE Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 122 PHE Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 302 TYR Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain A residue 411 PHE Chi-restraints excluded: chain A residue 530 GLU Chi-restraints excluded: chain A residue 580 ILE Chi-restraints excluded: chain A residue 712 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 208 optimal weight: 5.9990 chunk 3 optimal weight: 0.7980 chunk 131 optimal weight: 6.9990 chunk 100 optimal weight: 9.9990 chunk 93 optimal weight: 0.4980 chunk 167 optimal weight: 5.9990 chunk 217 optimal weight: 1.9990 chunk 193 optimal weight: 6.9990 chunk 8 optimal weight: 2.9990 chunk 199 optimal weight: 20.0000 chunk 243 optimal weight: 3.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 657 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5311 r_free = 0.5311 target = 0.264557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.5266 r_free = 0.5266 target = 0.255503 restraints weight = 288810.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.5297 r_free = 0.5297 target = 0.258023 restraints weight = 148673.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.5315 r_free = 0.5315 target = 0.259464 restraints weight = 83956.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.5325 r_free = 0.5325 target = 0.260316 restraints weight = 50885.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.5331 r_free = 0.5331 target = 0.260858 restraints weight = 32910.981| |-----------------------------------------------------------------------------| r_work (final): 0.5217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1895 moved from start: 0.6745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 20216 Z= 0.144 Angle : 0.595 7.891 27434 Z= 0.312 Chirality : 0.042 0.157 3134 Planarity : 0.004 0.063 3540 Dihedral : 6.950 77.072 2900 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.38 % Favored : 90.62 % Rotamer: Outliers : 1.74 % Allowed : 14.62 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.67 % Twisted General : 0.04 % 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 aren not related in a simple way. whole: -3.97 (0.15), residues: 2570 helix: -2.34 (0.16), residues: 884 sheet: -2.52 (0.28), residues: 308 loop : -2.92 (0.15), residues: 1378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 790 TYR 0.019 0.001 TYR A 559 PHE 0.017 0.001 PHE C 714 TRP 0.013 0.001 TRP B 801 HIS 0.006 0.001 HIS A 561 Details of bonding type rmsd covalent geometry : bond 0.00327 (20216) covalent geometry : angle 0.59536 (27434) hydrogen bonds : bond 0.03174 ( 275) hydrogen bonds : angle 5.18187 ( 744) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 137 time to evaluate : 0.910 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: 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: F 538 ASP cc_start: 0.5565 (t0) cc_final: 0.3819 (p0) REVERT: F 640 MET cc_start: 0.2135 (mmt) cc_final: 0.1923 (mmt) REVERT: F 659 MET cc_start: -0.2229 (mmm) cc_final: -0.2856 (mmm) REVERT: C 662 TYR cc_start: -0.2800 (OUTLIER) cc_final: -0.4313 (t80) REVERT: C 816 ARG cc_start: -0.1687 (ttp-170) cc_final: -0.4503 (tpt170) REVERT: B 411 PHE cc_start: 0.0832 (m-80) cc_final: -0.1022 (t80) REVERT: B 437 HIS cc_start: 0.0878 (OUTLIER) cc_final: 0.0254 (p90) outliers start: 36 outliers final: 27 residues processed: 166 average time/residue: 0.2957 time to fit residues: 77.4724 Evaluate side-chains 166 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 137 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 483 LEU Chi-restraints excluded: chain F residue 573 PHE Chi-restraints excluded: chain C residue 662 TYR Chi-restraints excluded: chain C residue 714 PHE Chi-restraints excluded: chain C residue 739 LEU Chi-restraints excluded: chain C residue 749 ILE Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 69 ASN Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 362 MET Chi-restraints excluded: chain B residue 396 ILE Chi-restraints excluded: chain B residue 407 ASP Chi-restraints excluded: chain B residue 437 HIS Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 639 VAL Chi-restraints excluded: chain B residue 745 ILE Chi-restraints excluded: chain B residue 801 TRP Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 122 PHE Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 302 TYR Chi-restraints excluded: chain A residue 530 GLU Chi-restraints excluded: chain A residue 574 MET Chi-restraints excluded: chain A residue 580 ILE Chi-restraints excluded: chain A residue 625 TYR Chi-restraints excluded: chain A residue 712 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 44 optimal weight: 6.9990 chunk 225 optimal weight: 2.9990 chunk 218 optimal weight: 5.9990 chunk 169 optimal weight: 4.9990 chunk 151 optimal weight: 6.9990 chunk 119 optimal weight: 6.9990 chunk 79 optimal weight: 10.0000 chunk 0 optimal weight: 5.9990 chunk 202 optimal weight: 0.0070 chunk 192 optimal weight: 3.9990 chunk 41 optimal weight: 50.0000 overall best weight: 3.6006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 454 HIS ** F 657 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 723 HIS ** A 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 440 ASN ** A 840 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5278 r_free = 0.5278 target = 0.260367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.5233 r_free = 0.5233 target = 0.251323 restraints weight = 289324.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.5264 r_free = 0.5264 target = 0.253859 restraints weight = 148679.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.5282 r_free = 0.5282 target = 0.255290 restraints weight = 83478.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.5292 r_free = 0.5292 target = 0.256153 restraints weight = 50461.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.5297 r_free = 0.5297 target = 0.256683 restraints weight = 32442.306| |-----------------------------------------------------------------------------| r_work (final): 0.5185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2326 moved from start: 0.8315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 20216 Z= 0.214 Angle : 0.762 8.807 27434 Z= 0.407 Chirality : 0.046 0.214 3134 Planarity : 0.006 0.073 3540 Dihedral : 7.984 79.427 2900 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 18.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.37 % Favored : 87.63 % Rotamer: Outliers : 2.80 % Allowed : 15.40 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.67 % Twisted General : 0.08 % 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 aren not related in a simple way. whole: -4.06 (0.15), residues: 2570 helix: -2.40 (0.16), residues: 876 sheet: -2.74 (0.28), residues: 304 loop : -2.94 (0.15), residues: 1390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 464 TYR 0.028 0.002 TYR A 559 PHE 0.027 0.003 PHE B 608 TRP 0.015 0.002 TRP A 424 HIS 0.015 0.002 HIS A 561 Details of bonding type rmsd covalent geometry : bond 0.00476 (20216) covalent geometry : angle 0.76155 (27434) hydrogen bonds : bond 0.04172 ( 275) hydrogen bonds : angle 5.94074 ( 744) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 140 time to evaluate : 0.772 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 461 TYR cc_start: 0.3085 (m-80) cc_final: 0.2684 (m-80) REVERT: F 463 ARG cc_start: -0.0444 (OUTLIER) cc_final: -0.1137 (tpp-160) REVERT: F 659 MET cc_start: -0.1936 (mmm) cc_final: -0.2707 (mmm) REVERT: B 463 ARG cc_start: 0.1506 (OUTLIER) cc_final: 0.0095 (tpt90) REVERT: B 568 GLU cc_start: 0.4910 (tt0) cc_final: 0.4418 (tt0) REVERT: B 659 MET cc_start: 0.6688 (ppp) cc_final: 0.6275 (ppp) REVERT: A 171 ASP cc_start: -0.2126 (OUTLIER) cc_final: -0.2338 (m-30) REVERT: A 530 GLU cc_start: 0.2887 (OUTLIER) cc_final: 0.2628 (mt-10) outliers start: 58 outliers final: 36 residues processed: 182 average time/residue: 0.2947 time to fit residues: 84.3140 Evaluate side-chains 170 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 130 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 463 ARG Chi-restraints excluded: chain F residue 483 LEU Chi-restraints excluded: chain F residue 573 PHE Chi-restraints excluded: chain C residue 550 ASP Chi-restraints excluded: chain C residue 714 PHE Chi-restraints excluded: chain C residue 727 HIS Chi-restraints excluded: chain C residue 739 LEU Chi-restraints excluded: chain C residue 749 ILE Chi-restraints excluded: chain B residue 26 PHE Chi-restraints excluded: chain B residue 28 GLN Chi-restraints excluded: chain B residue 69 ASN Chi-restraints excluded: chain B residue 86 CYS Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 362 MET Chi-restraints excluded: chain B residue 384 TYR Chi-restraints excluded: chain B residue 396 ILE Chi-restraints excluded: chain B residue 407 ASP Chi-restraints excluded: chain B residue 463 ARG Chi-restraints excluded: chain B residue 549 MET Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 639 VAL Chi-restraints excluded: chain B residue 712 ILE Chi-restraints excluded: chain B residue 745 ILE Chi-restraints excluded: chain B residue 770 GLN Chi-restraints excluded: chain B residue 801 TRP Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 122 PHE Chi-restraints excluded: chain A residue 171 ASP Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 302 TYR Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 411 PHE Chi-restraints excluded: chain A residue 430 SER Chi-restraints excluded: chain A residue 530 GLU Chi-restraints excluded: chain A residue 574 MET Chi-restraints excluded: chain A residue 580 ILE Chi-restraints excluded: chain A residue 712 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 2 optimal weight: 2.9990 chunk 111 optimal weight: 40.0000 chunk 65 optimal weight: 3.9990 chunk 159 optimal weight: 4.9990 chunk 69 optimal weight: 5.9990 chunk 82 optimal weight: 0.7980 chunk 58 optimal weight: 2.9990 chunk 204 optimal weight: 5.9990 chunk 140 optimal weight: 4.9990 chunk 147 optimal weight: 0.9990 chunk 70 optimal weight: 4.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 657 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 727 HIS ** C 716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 440 ASN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 840 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5285 r_free = 0.5285 target = 0.260802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.5239 r_free = 0.5239 target = 0.251885 restraints weight = 287467.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.5270 r_free = 0.5270 target = 0.254365 restraints weight = 148846.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.5288 r_free = 0.5288 target = 0.255785 restraints weight = 83443.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.5298 r_free = 0.5298 target = 0.256645 restraints weight = 50448.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.5304 r_free = 0.5304 target = 0.257179 restraints weight = 32373.270| |-----------------------------------------------------------------------------| r_work (final): 0.5189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2266 moved from start: 0.8584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 20216 Z= 0.142 Angle : 0.618 6.853 27434 Z= 0.326 Chirality : 0.042 0.159 3134 Planarity : 0.005 0.081 3540 Dihedral : 7.309 67.622 2899 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.53 % Favored : 90.47 % Rotamer: Outliers : 2.17 % Allowed : 16.22 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.67 % Twisted General : 0.04 % 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 aren not related in a simple way. whole: -3.89 (0.15), residues: 2570 helix: -2.17 (0.16), residues: 908 sheet: -2.53 (0.29), residues: 294 loop : -2.94 (0.15), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 768 TYR 0.017 0.001 TYR A 559 PHE 0.014 0.002 PHE B 837 TRP 0.013 0.001 TRP B 801 HIS 0.008 0.001 HIS B 565 Details of bonding type rmsd covalent geometry : bond 0.00321 (20216) covalent geometry : angle 0.61803 (27434) hydrogen bonds : bond 0.03162 ( 275) hydrogen bonds : angle 5.50580 ( 744) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 132 time to evaluate : 0.955 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 461 TYR cc_start: 0.2850 (m-80) cc_final: 0.2359 (m-80) REVERT: F 463 ARG cc_start: -0.0944 (OUTLIER) cc_final: -0.1544 (tpp-160) REVERT: F 659 MET cc_start: -0.1860 (mmm) cc_final: -0.2422 (mmm) REVERT: B 463 ARG cc_start: 0.0976 (OUTLIER) cc_final: -0.0226 (tpt-90) REVERT: B 472 ASP cc_start: -0.2668 (OUTLIER) cc_final: -0.2949 (t0) REVERT: B 631 MET cc_start: 0.4968 (mtt) cc_final: 0.4752 (mtm) REVERT: A 530 GLU cc_start: 0.2900 (OUTLIER) cc_final: 0.2640 (mt-10) REVERT: A 558 MET cc_start: -0.1831 (mmm) cc_final: -0.2774 (mtt) outliers start: 45 outliers final: 33 residues processed: 168 average time/residue: 0.2843 time to fit residues: 75.4071 Evaluate side-chains 169 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 132 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 463 ARG Chi-restraints excluded: chain F residue 483 LEU Chi-restraints excluded: chain F residue 573 PHE Chi-restraints excluded: chain F residue 845 ASN Chi-restraints excluded: chain C residue 568 GLU Chi-restraints excluded: chain C residue 572 ARG Chi-restraints excluded: chain C residue 714 PHE Chi-restraints excluded: chain C residue 727 HIS Chi-restraints excluded: chain C residue 739 LEU Chi-restraints excluded: chain C residue 749 ILE Chi-restraints excluded: chain B residue 26 PHE Chi-restraints excluded: chain B residue 69 ASN Chi-restraints excluded: chain B residue 86 CYS Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 396 ILE Chi-restraints excluded: chain B residue 407 ASP Chi-restraints excluded: chain B residue 463 ARG Chi-restraints excluded: chain B residue 472 ASP Chi-restraints excluded: chain B residue 592 MET Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 639 VAL Chi-restraints excluded: chain B residue 745 ILE Chi-restraints excluded: chain B residue 770 GLN Chi-restraints excluded: chain B residue 801 TRP Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 122 PHE Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 302 TYR Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain A residue 530 GLU Chi-restraints excluded: chain A residue 580 ILE Chi-restraints excluded: chain A residue 625 TYR Chi-restraints excluded: chain A residue 712 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 242 optimal weight: 10.0000 chunk 213 optimal weight: 3.9990 chunk 212 optimal weight: 4.9990 chunk 42 optimal weight: 8.9990 chunk 226 optimal weight: 6.9990 chunk 135 optimal weight: 1.9990 chunk 249 optimal weight: 50.0000 chunk 229 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 chunk 114 optimal weight: 50.0000 chunk 153 optimal weight: 0.8980 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 657 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 840 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 840 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5275 r_free = 0.5275 target = 0.259873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.5231 r_free = 0.5231 target = 0.250822 restraints weight = 288931.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.5262 r_free = 0.5262 target = 0.253339 restraints weight = 147827.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.5279 r_free = 0.5279 target = 0.254771 restraints weight = 83201.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.5288 r_free = 0.5288 target = 0.255624 restraints weight = 50360.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.5294 r_free = 0.5294 target = 0.256174 restraints weight = 32738.991| |-----------------------------------------------------------------------------| r_work (final): 0.5181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2361 moved from start: 0.9084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20216 Z= 0.148 Angle : 0.627 6.833 27434 Z= 0.331 Chirality : 0.043 0.164 3134 Planarity : 0.005 0.067 3540 Dihedral : 7.229 62.818 2899 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.17 % Favored : 88.83 % Rotamer: Outliers : 1.98 % Allowed : 16.65 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.83 % Twisted General : 0.04 % 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 aren not related in a simple way. whole: -3.80 (0.15), residues: 2570 helix: -2.04 (0.16), residues: 914 sheet: -2.49 (0.30), residues: 294 loop : -2.93 (0.15), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 265 TYR 0.020 0.001 TYR B 23 PHE 0.019 0.002 PHE B 462 TRP 0.011 0.001 TRP A 424 HIS 0.013 0.001 HIS F 657 Details of bonding type rmsd covalent geometry : bond 0.00332 (20216) covalent geometry : angle 0.62741 (27434) hydrogen bonds : bond 0.03209 ( 275) hydrogen bonds : angle 5.41264 ( 744) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 136 time to evaluate : 1.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 461 TYR cc_start: 0.3078 (m-80) cc_final: 0.2592 (m-80) REVERT: F 463 ARG cc_start: -0.0770 (OUTLIER) cc_final: -0.1429 (tpp-160) REVERT: F 618 GLN cc_start: 0.4229 (OUTLIER) cc_final: 0.4021 (tp40) REVERT: F 659 MET cc_start: -0.1565 (mmm) cc_final: -0.2154 (mmm) REVERT: B 408 LEU cc_start: 0.5193 (mp) cc_final: 0.4525 (tt) REVERT: B 463 ARG cc_start: 0.1552 (OUTLIER) cc_final: -0.0066 (tpt170) REVERT: B 472 ASP cc_start: -0.2558 (OUTLIER) cc_final: -0.2822 (t0) REVERT: B 601 THR cc_start: 0.6276 (OUTLIER) cc_final: 0.5922 (m) REVERT: A 530 GLU cc_start: 0.2988 (OUTLIER) cc_final: 0.2746 (mt-10) REVERT: A 558 MET cc_start: -0.1698 (mmm) cc_final: -0.2686 (mtt) outliers start: 41 outliers final: 31 residues processed: 169 average time/residue: 0.2759 time to fit residues: 73.0163 Evaluate side-chains 169 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 132 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 463 ARG Chi-restraints excluded: chain F residue 483 LEU Chi-restraints excluded: chain F residue 573 PHE Chi-restraints excluded: chain F residue 618 GLN Chi-restraints excluded: chain F residue 845 ASN Chi-restraints excluded: chain C residue 568 GLU Chi-restraints excluded: chain C residue 714 PHE Chi-restraints excluded: chain C residue 727 HIS Chi-restraints excluded: chain C residue 739 LEU Chi-restraints excluded: chain C residue 749 ILE Chi-restraints excluded: chain B residue 26 PHE Chi-restraints excluded: chain B residue 69 ASN Chi-restraints excluded: chain B residue 86 CYS Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 396 ILE Chi-restraints excluded: chain B residue 407 ASP Chi-restraints excluded: chain B residue 463 ARG Chi-restraints excluded: chain B residue 472 ASP Chi-restraints excluded: chain B residue 549 MET Chi-restraints excluded: chain B residue 592 MET Chi-restraints excluded: chain B residue 601 THR Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 639 VAL Chi-restraints excluded: chain B residue 745 ILE Chi-restraints excluded: chain B residue 770 GLN Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 122 PHE Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 302 TYR Chi-restraints excluded: chain A residue 369 SER Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain A residue 530 GLU Chi-restraints excluded: chain A residue 574 MET Chi-restraints excluded: chain A residue 580 ILE Chi-restraints excluded: chain A residue 625 TYR Chi-restraints excluded: chain A residue 712 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 174 optimal weight: 0.8980 chunk 100 optimal weight: 7.9990 chunk 76 optimal weight: 0.7980 chunk 91 optimal weight: 1.9990 chunk 184 optimal weight: 6.9990 chunk 153 optimal weight: 0.7980 chunk 164 optimal weight: 0.9990 chunk 223 optimal weight: 1.9990 chunk 112 optimal weight: 30.0000 chunk 224 optimal weight: 4.9990 chunk 211 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 657 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 754 ASN B 397 ASN A 115 ASN A 155 GLN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 727 HIS ** A 840 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5287 r_free = 0.5287 target = 0.260926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.5245 r_free = 0.5245 target = 0.252009 restraints weight = 287640.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.5274 r_free = 0.5274 target = 0.254526 restraints weight = 147101.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.5292 r_free = 0.5292 target = 0.255938 restraints weight = 82347.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.5302 r_free = 0.5302 target = 0.256803 restraints weight = 49850.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.5308 r_free = 0.5308 target = 0.257343 restraints weight = 32055.805| |-----------------------------------------------------------------------------| r_work (final): 0.5192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2246 moved from start: 0.9089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 20216 Z= 0.101 Angle : 0.559 9.478 27434 Z= 0.290 Chirality : 0.041 0.155 3134 Planarity : 0.004 0.069 3540 Dihedral : 6.714 66.709 2899 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 1.50 % Allowed : 17.13 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.83 % 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 aren not related in a simple way. whole: -3.56 (0.16), residues: 2570 helix: -1.83 (0.17), residues: 910 sheet: -2.47 (0.29), residues: 312 loop : -2.76 (0.16), residues: 1348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 768 TYR 0.012 0.001 TYR A 461 PHE 0.011 0.001 PHE F 714 TRP 0.036 0.001 TRP B 801 HIS 0.014 0.001 HIS F 657 Details of bonding type rmsd covalent geometry : bond 0.00235 (20216) covalent geometry : angle 0.55914 (27434) hydrogen bonds : bond 0.02502 ( 275) hydrogen bonds : angle 5.06606 ( 744) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5140 Ramachandran restraints generated. 2570 Oldfield, 0 Emsley, 2570 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 136 time to evaluate : 0.796 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 451 MET cc_start: -0.1037 (ptm) cc_final: -0.1380 (ptm) REVERT: F 461 TYR cc_start: 0.2716 (m-80) cc_final: 0.2180 (m-80) REVERT: F 463 ARG cc_start: -0.1101 (OUTLIER) cc_final: -0.1636 (tpp-160) REVERT: F 586 MET cc_start: 0.2022 (mmm) cc_final: 0.1641 (mmm) REVERT: B 252 VAL cc_start: 0.6131 (t) cc_final: 0.5737 (p) REVERT: B 408 LEU cc_start: 0.4698 (mp) cc_final: 0.4312 (tt) REVERT: B 640 MET cc_start: -0.0044 (mmm) cc_final: -0.0345 (mmm) REVERT: A 558 MET cc_start: -0.1877 (mmm) cc_final: -0.2930 (mtt) outliers start: 31 outliers final: 26 residues processed: 162 average time/residue: 0.2715 time to fit residues: 69.1254 Evaluate side-chains 159 residues out of total 2072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 132 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 463 ARG Chi-restraints excluded: chain F residue 483 LEU Chi-restraints excluded: chain F residue 573 PHE Chi-restraints excluded: chain F residue 845 ASN Chi-restraints excluded: chain C residue 572 ARG Chi-restraints excluded: chain C residue 714 PHE Chi-restraints excluded: chain C residue 727 HIS Chi-restraints excluded: chain C residue 739 LEU Chi-restraints excluded: chain B residue 69 ASN Chi-restraints excluded: chain B residue 86 CYS Chi-restraints excluded: chain B residue 365 ILE Chi-restraints excluded: chain B residue 407 ASP Chi-restraints excluded: chain B residue 463 ARG Chi-restraints excluded: chain B residue 592 MET Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 639 VAL Chi-restraints excluded: chain B residue 745 ILE Chi-restraints excluded: chain B residue 746 CYS Chi-restraints excluded: chain B residue 770 GLN Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 122 PHE Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 302 TYR Chi-restraints excluded: chain A residue 580 ILE Chi-restraints excluded: chain A residue 625 TYR Chi-restraints excluded: chain A residue 712 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 17 optimal weight: 0.9990 chunk 226 optimal weight: 0.5980 chunk 243 optimal weight: 5.9990 chunk 64 optimal weight: 5.9990 chunk 230 optimal weight: 5.9990 chunk 24 optimal weight: 50.0000 chunk 50 optimal weight: 7.9990 chunk 114 optimal weight: 0.0370 chunk 228 optimal weight: 2.9990 chunk 194 optimal weight: 8.9990 chunk 115 optimal weight: 20.0000 overall best weight: 2.1264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 657 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 840 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 840 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5271 r_free = 0.5271 target = 0.259530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.5226 r_free = 0.5226 target = 0.250368 restraints weight = 288310.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.5257 r_free = 0.5257 target = 0.252860 restraints weight = 149046.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.5274 r_free = 0.5274 target = 0.254281 restraints weight = 83979.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.5284 r_free = 0.5284 target = 0.255165 restraints weight = 51151.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.5291 r_free = 0.5291 target = 0.255720 restraints weight = 33123.078| |-----------------------------------------------------------------------------| r_work (final): 0.5177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2389 moved from start: 0.9542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20216 Z= 0.133 Angle : 0.610 7.659 27434 Z= 0.318 Chirality : 0.043 0.159 3134 Planarity : 0.004 0.066 3540 Dihedral : 6.903 63.883 2899 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.05 % Favored : 88.95 % Rotamer: Outliers : 1.50 % Allowed : 17.08 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.83 % 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 aren not related in a simple way. whole: -3.47 (0.16), residues: 2570 helix: -1.72 (0.17), residues: 873 sheet: -2.55 (0.31), residues: 264 loop : -2.71 (0.15), residues: 1433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 265 TYR 0.017 0.001 TYR B 23 PHE 0.017 0.002 PHE B 462 TRP 0.042 0.002 TRP B 801 HIS 0.016 0.001 HIS F 657 Details of bonding type rmsd covalent geometry : bond 0.00305 (20216) covalent geometry : angle 0.61009 (27434) hydrogen bonds : bond 0.02877 ( 275) hydrogen bonds : angle 5.24153 ( 744) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4867.35 seconds wall clock time: 83 minutes 56.24 seconds (5036.24 seconds total)