Starting phenix.real_space_refine on Thu Dec 26 17:01:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ahc_9623/12_2024/6ahc_9623.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ahc_9623/12_2024/6ahc_9623.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6ahc_9623/12_2024/6ahc_9623.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ahc_9623/12_2024/6ahc_9623.map" model { file = "/net/cci-nas-00/data/ceres_data/6ahc_9623/12_2024/6ahc_9623.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ahc_9623/12_2024/6ahc_9623.cif" } resolution = 3.45 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= -0.020 sd= 1.611 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 212 5.16 5 C 29302 2.51 5 N 7854 2.21 5 O 8738 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 46106 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3247 Classifications: {'peptide': 419} Link IDs: {'CIS': 6, 'PTRANS': 20, 'TRANS': 392} Chain: "C" Number of atoms: 6602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 869, 6602 Classifications: {'peptide': 869} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 7, 'PTRANS': 40, 'TRANS': 821} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Restraints were copied for chains: B, E, D, G, F, H Time building chain proxies: 22.72, per 1000 atoms: 0.49 Number of scatterers: 46106 At special positions: 0 Unit cell: (190.4, 180.32, 183.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 212 16.00 O 8738 8.00 N 7854 7.00 C 29302 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.32 Conformation dependent library (CDL) restraints added in 6.6 seconds 12072 Ramachandran restraints generated. 6036 Oldfield, 0 Emsley, 6036 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11268 Finding SS restraints... Secondary structure from input PDB file: 250 helices and 34 sheets defined 49.5% alpha, 9.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.16 Creating SS restraints... Processing helix chain 'A' and resid 466 through 471 Processing helix chain 'A' and resid 472 through 477 Processing helix chain 'A' and resid 487 through 493 Processing helix chain 'A' and resid 496 through 507 removed outlier: 3.567A pdb=" N THR A 500 " --> pdb=" O ALA A 496 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N VAL A 502 " --> pdb=" O GLN A 498 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA A 505 " --> pdb=" O SER A 501 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ALA A 506 " --> pdb=" O VAL A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 536 Processing helix chain 'A' and resid 546 through 561 removed outlier: 3.685A pdb=" N TYR A 559 " --> pdb=" O MET A 555 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N HIS A 561 " --> pdb=" O VAL A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 573 removed outlier: 3.643A pdb=" N LEU A 569 " --> pdb=" O HIS A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 645 through 661 Processing helix chain 'A' and resid 671 through 681 Processing helix chain 'A' and resid 685 through 692 removed outlier: 3.575A pdb=" N GLU A 692 " --> pdb=" O ALA A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 714 removed outlier: 3.531A pdb=" N ARG A 702 " --> pdb=" O VAL A 698 " (cutoff:3.500A) Processing helix chain 'A' and resid 720 through 734 removed outlier: 4.102A pdb=" N SER A 724 " --> pdb=" O GLY A 720 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE A 733 " --> pdb=" O LEU A 729 " (cutoff:3.500A) Processing helix chain 'A' and resid 739 through 753 removed outlier: 3.617A pdb=" N LEU A 744 " --> pdb=" O ALA A 740 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N CYS A 746 " --> pdb=" O ALA A 742 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N ASN A 747 " --> pdb=" O LEU A 743 " (cutoff:3.500A) Processing helix chain 'A' and resid 770 through 783 removed outlier: 3.733A pdb=" N ARG A 774 " --> pdb=" O GLN A 770 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N TYR A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 790 through 800 Processing helix chain 'A' and resid 800 through 810 removed outlier: 3.740A pdb=" N THR A 804 " --> pdb=" O ALA A 800 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLU A 808 " --> pdb=" O THR A 804 " (cutoff:3.500A) Processing helix chain 'A' and resid 815 through 819 Processing helix chain 'A' and resid 821 through 833 removed outlier: 3.841A pdb=" N PHE A 825 " --> pdb=" O GLN A 821 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N ASP A 830 " --> pdb=" O LEU A 826 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N LYS A 831 " --> pdb=" O ALA A 827 " (cutoff:3.500A) Processing helix chain 'A' and resid 850 through 852 No H-bonds generated for 'chain 'A' and resid 850 through 852' Processing helix chain 'A' and resid 853 through 864 removed outlier: 3.796A pdb=" N ILE A 857 " --> pdb=" O GLU A 853 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N TYR A 862 " --> pdb=" O LEU A 858 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 24 Processing helix chain 'B' and resid 27 through 30 removed outlier: 3.558A pdb=" N GLN B 30 " --> pdb=" O THR B 27 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 27 through 30' Processing helix chain 'B' and resid 31 through 45 removed outlier: 3.977A pdb=" N ALA B 45 " --> pdb=" O ALA B 41 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 58 Processing helix chain 'B' and resid 61 through 80 removed outlier: 3.623A pdb=" N LYS B 65 " --> pdb=" O ILE B 61 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ILE B 76 " --> pdb=" O ALA B 72 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N TYR B 80 " --> pdb=" O ILE B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 130 removed outlier: 4.323A pdb=" N ILE B 121 " --> pdb=" O THR B 117 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE B 122 " --> pdb=" O SER B 118 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N THR B 130 " --> pdb=" O ILE B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 159 removed outlier: 3.916A pdb=" N ALA B 159 " --> pdb=" O GLN B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 183 removed outlier: 4.208A pdb=" N SER B 178 " --> pdb=" O SER B 174 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ASN B 179 " --> pdb=" O VAL B 175 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N HIS B 183 " --> pdb=" O ASN B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 204 removed outlier: 3.961A pdb=" N VAL B 199 " --> pdb=" O GLY B 195 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N LYS B 200 " --> pdb=" O PRO B 196 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ALA B 201 " --> pdb=" O GLY B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 239 removed outlier: 3.736A pdb=" N THR B 239 " --> pdb=" O LEU B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 244 removed outlier: 3.537A pdb=" N VAL B 244 " --> pdb=" O ASP B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 268 removed outlier: 3.933A pdb=" N VAL B 262 " --> pdb=" O VAL B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 284 removed outlier: 3.596A pdb=" N ALA B 281 " --> pdb=" O LYS B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 309 removed outlier: 3.558A pdb=" N ILE B 304 " --> pdb=" O PRO B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 334 removed outlier: 3.666A pdb=" N ALA B 333 " --> pdb=" O GLU B 330 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N HIS B 334 " --> pdb=" O PRO B 331 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 330 through 334' Processing helix chain 'B' and resid 348 through 361 Processing helix chain 'B' and resid 378 through 389 removed outlier: 3.608A pdb=" N VAL B 382 " --> pdb=" O GLN B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 438 Processing helix chain 'B' and resid 472 through 477 Processing helix chain 'B' and resid 487 through 493 Processing helix chain 'B' and resid 496 through 507 removed outlier: 4.266A pdb=" N VAL B 502 " --> pdb=" O GLN B 498 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA B 505 " --> pdb=" O SER B 501 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ALA B 506 " --> pdb=" O VAL B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 536 Processing helix chain 'B' and resid 546 through 561 removed outlier: 3.686A pdb=" N TYR B 559 " --> pdb=" O MET B 555 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N HIS B 561 " --> pdb=" O VAL B 557 " (cutoff:3.500A) Processing helix chain 'B' and resid 565 through 573 removed outlier: 3.720A pdb=" N LEU B 569 " --> pdb=" O HIS B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 645 through 661 removed outlier: 3.606A pdb=" N GLY B 650 " --> pdb=" O LEU B 646 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA B 661 " --> pdb=" O HIS B 657 " (cutoff:3.500A) Processing helix chain 'B' and resid 671 through 692 removed outlier: 3.729A pdb=" N ALA B 675 " --> pdb=" O SER B 671 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU B 682 " --> pdb=" O ALA B 678 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N LYS B 683 " --> pdb=" O LEU B 679 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N GLU B 684 " --> pdb=" O LYS B 680 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N TYR B 685 " --> pdb=" O LEU B 681 " (cutoff:3.500A) Proline residue: B 687 - end of helix Processing helix chain 'B' and resid 698 through 715 removed outlier: 3.685A pdb=" N ALA B 715 " --> pdb=" O GLY B 711 " (cutoff:3.500A) Processing helix chain 'B' and resid 720 through 734 removed outlier: 3.938A pdb=" N SER B 724 " --> pdb=" O GLY B 720 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N PHE B 733 " --> pdb=" O LEU B 729 " (cutoff:3.500A) Processing helix chain 'B' and resid 744 through 753 Processing helix chain 'B' and resid 770 through 782 removed outlier: 4.049A pdb=" N ARG B 774 " --> pdb=" O GLN B 770 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N TYR B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 790 through 810 removed outlier: 3.579A pdb=" N TRP B 801 " --> pdb=" O LYS B 797 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LEU B 802 " --> pdb=" O LEU B 798 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLU B 803 " --> pdb=" O LEU B 799 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N THR B 804 " --> pdb=" O ALA B 800 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU B 808 " --> pdb=" O THR B 804 " (cutoff:3.500A) Processing helix chain 'B' and resid 815 through 819 Processing helix chain 'B' and resid 821 through 828 removed outlier: 3.624A pdb=" N PHE B 825 " --> pdb=" O GLN B 821 " (cutoff:3.500A) Processing helix chain 'B' and resid 828 through 839 removed outlier: 4.143A pdb=" N GLU B 834 " --> pdb=" O ASP B 830 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N PHE B 837 " --> pdb=" O SER B 833 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASP B 838 " --> pdb=" O GLU B 834 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ASP B 839 " --> pdb=" O ASP B 835 " (cutoff:3.500A) Processing helix chain 'B' and resid 850 through 863 removed outlier: 3.530A pdb=" N LEU B 854 " --> pdb=" O LEU B 850 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS B 855 " --> pdb=" O ILE B 851 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLN B 856 " --> pdb=" O SER B 852 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ILE B 857 " --> pdb=" O GLU B 853 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N TYR B 862 " --> pdb=" O LEU B 858 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 24 Processing helix chain 'C' and resid 27 through 30 removed outlier: 3.557A pdb=" N GLN C 30 " --> pdb=" O THR C 27 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 27 through 30' Processing helix chain 'C' and resid 31 through 45 removed outlier: 3.977A pdb=" N ALA C 45 " --> pdb=" O ALA C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 58 Processing helix chain 'C' and resid 61 through 80 removed outlier: 3.623A pdb=" N LYS C 65 " --> pdb=" O ILE C 61 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ILE C 76 " --> pdb=" O ALA C 72 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N TYR C 80 " --> pdb=" O ILE C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 130 removed outlier: 4.323A pdb=" N ILE C 121 " --> pdb=" O THR C 117 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE C 122 " --> pdb=" O SER C 118 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N THR C 130 " --> pdb=" O ILE C 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 159 removed outlier: 3.915A pdb=" N ALA C 159 " --> pdb=" O GLN C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 183 removed outlier: 4.207A pdb=" N SER C 178 " --> pdb=" O SER C 174 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ASN C 179 " --> pdb=" O VAL C 175 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N HIS C 183 " --> pdb=" O ASN C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 204 removed outlier: 3.962A pdb=" N VAL C 199 " --> pdb=" O GLY C 195 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N LYS C 200 " --> pdb=" O PRO C 196 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ALA C 201 " --> pdb=" O GLY C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 239 removed outlier: 3.736A pdb=" N THR C 239 " --> pdb=" O LEU C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 244 removed outlier: 3.536A pdb=" N VAL C 244 " --> pdb=" O ASP C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 268 removed outlier: 3.933A pdb=" N VAL C 262 " --> pdb=" O VAL C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 284 removed outlier: 3.595A pdb=" N ALA C 281 " --> pdb=" O LYS C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 309 removed outlier: 3.558A pdb=" N ILE C 304 " --> pdb=" O PRO C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 334 removed outlier: 3.666A pdb=" N ALA C 333 " --> pdb=" O GLU C 330 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N HIS C 334 " --> pdb=" O PRO C 331 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 330 through 334' Processing helix chain 'C' and resid 348 through 361 Processing helix chain 'C' and resid 378 through 389 removed outlier: 3.608A pdb=" N VAL C 382 " --> pdb=" O GLN C 378 " (cutoff:3.500A) Processing helix chain 'C' and resid 434 through 438 Processing helix chain 'C' and resid 472 through 477 Processing helix chain 'C' and resid 487 through 493 Processing helix chain 'C' and resid 496 through 507 removed outlier: 4.266A pdb=" N VAL C 502 " --> pdb=" O GLN C 498 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA C 505 " --> pdb=" O SER C 501 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ALA C 506 " --> pdb=" O VAL C 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 523 through 536 Processing helix chain 'C' and resid 546 through 561 removed outlier: 3.687A pdb=" N TYR C 559 " --> pdb=" O MET C 555 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N HIS C 561 " --> pdb=" O VAL C 557 " (cutoff:3.500A) Processing helix chain 'C' and resid 565 through 573 removed outlier: 3.719A pdb=" N LEU C 569 " --> pdb=" O HIS C 565 " (cutoff:3.500A) Processing helix chain 'C' and resid 645 through 661 removed outlier: 3.606A pdb=" N GLY C 650 " --> pdb=" O LEU C 646 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA C 661 " --> pdb=" O HIS C 657 " (cutoff:3.500A) Processing helix chain 'C' and resid 671 through 692 removed outlier: 3.729A pdb=" N ALA C 675 " --> pdb=" O SER C 671 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU C 682 " --> pdb=" O ALA C 678 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N LYS C 683 " --> pdb=" O LEU C 679 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N GLU C 684 " --> pdb=" O LYS C 680 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N TYR C 685 " --> pdb=" O LEU C 681 " (cutoff:3.500A) Proline residue: C 687 - end of helix Processing helix chain 'C' and resid 698 through 715 removed outlier: 3.684A pdb=" N ALA C 715 " --> pdb=" O GLY C 711 " (cutoff:3.500A) Processing helix chain 'C' and resid 720 through 734 removed outlier: 3.938A pdb=" N SER C 724 " --> pdb=" O GLY C 720 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N PHE C 733 " --> pdb=" O LEU C 729 " (cutoff:3.500A) Processing helix chain 'C' and resid 744 through 753 Processing helix chain 'C' and resid 770 through 782 removed outlier: 4.049A pdb=" N ARG C 774 " --> pdb=" O GLN C 770 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N TYR C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 790 through 810 removed outlier: 3.580A pdb=" N TRP C 801 " --> pdb=" O LYS C 797 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LEU C 802 " --> pdb=" O LEU C 798 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLU C 803 " --> pdb=" O LEU C 799 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N THR C 804 " --> pdb=" O ALA C 800 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU C 808 " --> pdb=" O THR C 804 " (cutoff:3.500A) Processing helix chain 'C' and resid 815 through 819 Processing helix chain 'C' and resid 821 through 828 removed outlier: 3.625A pdb=" N PHE C 825 " --> pdb=" O GLN C 821 " (cutoff:3.500A) Processing helix chain 'C' and resid 828 through 839 removed outlier: 4.142A pdb=" N GLU C 834 " --> pdb=" O ASP C 830 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N PHE C 837 " --> pdb=" O SER C 833 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ASP C 838 " --> pdb=" O GLU C 834 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ASP C 839 " --> pdb=" O ASP C 835 " (cutoff:3.500A) Processing helix chain 'C' and resid 850 through 863 removed outlier: 3.529A pdb=" N LEU C 854 " --> pdb=" O LEU C 850 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS C 855 " --> pdb=" O ILE C 851 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLN C 856 " --> pdb=" O SER C 852 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ILE C 857 " --> pdb=" O GLU C 853 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N TYR C 862 " --> pdb=" O LEU C 858 " (cutoff:3.500A) Processing helix chain 'D' and resid 5 through 24 Processing helix chain 'D' and resid 27 through 30 removed outlier: 3.557A pdb=" N GLN D 30 " --> pdb=" O THR D 27 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 27 through 30' Processing helix chain 'D' and resid 31 through 45 removed outlier: 3.977A pdb=" N ALA D 45 " --> pdb=" O ALA D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 58 Processing helix chain 'D' and resid 61 through 80 removed outlier: 3.622A pdb=" N LYS D 65 " --> pdb=" O ILE D 61 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ILE D 76 " --> pdb=" O ALA D 72 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N TYR D 80 " --> pdb=" O ILE D 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 130 removed outlier: 4.324A pdb=" N ILE D 121 " --> pdb=" O THR D 117 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE D 122 " --> pdb=" O SER D 118 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N THR D 130 " --> pdb=" O ILE D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 159 removed outlier: 3.915A pdb=" N ALA D 159 " --> pdb=" O GLN D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 183 removed outlier: 4.207A pdb=" N SER D 178 " --> pdb=" O SER D 174 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ASN D 179 " --> pdb=" O VAL D 175 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N HIS D 183 " --> pdb=" O ASN D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 204 removed outlier: 3.962A pdb=" N VAL D 199 " --> pdb=" O GLY D 195 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N LYS D 200 " --> pdb=" O PRO D 196 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ALA D 201 " --> pdb=" O GLY D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 239 removed outlier: 3.736A pdb=" N THR D 239 " --> pdb=" O LEU D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 240 through 244 removed outlier: 3.537A pdb=" N VAL D 244 " --> pdb=" O ASP D 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 268 removed outlier: 3.933A pdb=" N VAL D 262 " --> pdb=" O VAL D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 277 through 284 removed outlier: 3.595A pdb=" N ALA D 281 " --> pdb=" O LYS D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 309 removed outlier: 3.559A pdb=" N ILE D 304 " --> pdb=" O PRO D 300 " (cutoff:3.500A) Processing helix chain 'D' and resid 330 through 334 removed outlier: 3.667A pdb=" N ALA D 333 " --> pdb=" O GLU D 330 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N HIS D 334 " --> pdb=" O PRO D 331 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 330 through 334' Processing helix chain 'D' and resid 348 through 361 Processing helix chain 'D' and resid 378 through 389 removed outlier: 3.608A pdb=" N VAL D 382 " --> pdb=" O GLN D 378 " (cutoff:3.500A) Processing helix chain 'D' and resid 434 through 438 Processing helix chain 'D' and resid 472 through 477 Processing helix chain 'D' and resid 487 through 493 Processing helix chain 'D' and resid 496 through 507 removed outlier: 4.267A pdb=" N VAL D 502 " --> pdb=" O GLN D 498 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA D 505 " --> pdb=" O SER D 501 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ALA D 506 " --> pdb=" O VAL D 502 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 536 Processing helix chain 'D' and resid 546 through 561 removed outlier: 3.687A pdb=" N TYR D 559 " --> pdb=" O MET D 555 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N HIS D 561 " --> pdb=" O VAL D 557 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 573 removed outlier: 3.720A pdb=" N LEU D 569 " --> pdb=" O HIS D 565 " (cutoff:3.500A) Processing helix chain 'D' and resid 645 through 661 removed outlier: 3.606A pdb=" N GLY D 650 " --> pdb=" O LEU D 646 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA D 661 " --> pdb=" O HIS D 657 " (cutoff:3.500A) Processing helix chain 'D' and resid 671 through 692 removed outlier: 3.728A pdb=" N ALA D 675 " --> pdb=" O SER D 671 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU D 682 " --> pdb=" O ALA D 678 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N LYS D 683 " --> pdb=" O LEU D 679 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N GLU D 684 " --> pdb=" O LYS D 680 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N TYR D 685 " --> pdb=" O LEU D 681 " (cutoff:3.500A) Proline residue: D 687 - end of helix Processing helix chain 'D' and resid 698 through 715 removed outlier: 3.685A pdb=" N ALA D 715 " --> pdb=" O GLY D 711 " (cutoff:3.500A) Processing helix chain 'D' and resid 720 through 734 removed outlier: 3.939A pdb=" N SER D 724 " --> pdb=" O GLY D 720 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N PHE D 733 " --> pdb=" O LEU D 729 " (cutoff:3.500A) Processing helix chain 'D' and resid 744 through 753 Processing helix chain 'D' and resid 770 through 782 removed outlier: 4.048A pdb=" N ARG D 774 " --> pdb=" O GLN D 770 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N TYR D 775 " --> pdb=" O ALA D 771 " (cutoff:3.500A) Processing helix chain 'D' and resid 790 through 810 removed outlier: 3.580A pdb=" N TRP D 801 " --> pdb=" O LYS D 797 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LEU D 802 " --> pdb=" O LEU D 798 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLU D 803 " --> pdb=" O LEU D 799 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N THR D 804 " --> pdb=" O ALA D 800 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU D 808 " --> pdb=" O THR D 804 " (cutoff:3.500A) Processing helix chain 'D' and resid 815 through 819 Processing helix chain 'D' and resid 821 through 828 removed outlier: 3.625A pdb=" N PHE D 825 " --> pdb=" O GLN D 821 " (cutoff:3.500A) Processing helix chain 'D' and resid 828 through 839 removed outlier: 4.142A pdb=" N GLU D 834 " --> pdb=" O ASP D 830 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N PHE D 837 " --> pdb=" O SER D 833 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ASP D 838 " --> pdb=" O GLU D 834 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ASP D 839 " --> pdb=" O ASP D 835 " (cutoff:3.500A) Processing helix chain 'D' and resid 850 through 863 removed outlier: 3.529A pdb=" N LEU D 854 " --> pdb=" O LEU D 850 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS D 855 " --> pdb=" O ILE D 851 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLN D 856 " --> pdb=" O SER D 852 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ILE D 857 " --> pdb=" O GLU D 853 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N TYR D 862 " --> pdb=" O LEU D 858 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 24 Processing helix chain 'E' and resid 27 through 30 removed outlier: 3.558A pdb=" N GLN E 30 " --> pdb=" O THR E 27 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 27 through 30' Processing helix chain 'E' and resid 31 through 45 removed outlier: 3.977A pdb=" N ALA E 45 " --> pdb=" O ALA E 41 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 58 Processing helix chain 'E' and resid 61 through 80 removed outlier: 3.622A pdb=" N LYS E 65 " --> pdb=" O ILE E 61 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ILE E 76 " --> pdb=" O ALA E 72 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N TYR E 80 " --> pdb=" O ILE E 76 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 130 removed outlier: 4.322A pdb=" N ILE E 121 " --> pdb=" O THR E 117 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE E 122 " --> pdb=" O SER E 118 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N THR E 130 " --> pdb=" O ILE E 126 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 159 removed outlier: 3.915A pdb=" N ALA E 159 " --> pdb=" O GLN E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 174 through 183 removed outlier: 4.207A pdb=" N SER E 178 " --> pdb=" O SER E 174 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ASN E 179 " --> pdb=" O VAL E 175 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N HIS E 183 " --> pdb=" O ASN E 179 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 204 removed outlier: 3.961A pdb=" N VAL E 199 " --> pdb=" O GLY E 195 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N LYS E 200 " --> pdb=" O PRO E 196 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ALA E 201 " --> pdb=" O GLY E 197 " (cutoff:3.500A) Processing helix chain 'E' and resid 227 through 239 removed outlier: 3.736A pdb=" N THR E 239 " --> pdb=" O LEU E 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 240 through 244 removed outlier: 3.536A pdb=" N VAL E 244 " --> pdb=" O ASP E 241 " (cutoff:3.500A) Processing helix chain 'E' and resid 258 through 268 removed outlier: 3.934A pdb=" N VAL E 262 " --> pdb=" O VAL E 258 " (cutoff:3.500A) Processing helix chain 'E' and resid 277 through 284 removed outlier: 3.596A pdb=" N ALA E 281 " --> pdb=" O LYS E 277 " (cutoff:3.500A) Processing helix chain 'E' and resid 300 through 309 removed outlier: 3.557A pdb=" N ILE E 304 " --> pdb=" O PRO E 300 " (cutoff:3.500A) Processing helix chain 'E' and resid 330 through 334 removed outlier: 3.667A pdb=" N ALA E 333 " --> pdb=" O GLU E 330 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N HIS E 334 " --> pdb=" O PRO E 331 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 330 through 334' Processing helix chain 'E' and resid 348 through 361 Processing helix chain 'E' and resid 378 through 389 removed outlier: 3.608A pdb=" N VAL E 382 " --> pdb=" O GLN E 378 " (cutoff:3.500A) Processing helix chain 'E' and resid 434 through 438 Processing helix chain 'E' and resid 472 through 477 Processing helix chain 'E' and resid 487 through 493 Processing helix chain 'E' and resid 496 through 507 removed outlier: 4.267A pdb=" N VAL E 502 " --> pdb=" O GLN E 498 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA E 505 " --> pdb=" O SER E 501 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ALA E 506 " --> pdb=" O VAL E 502 " (cutoff:3.500A) Processing helix chain 'E' and resid 523 through 536 Processing helix chain 'E' and resid 546 through 561 removed outlier: 3.686A pdb=" N TYR E 559 " --> pdb=" O MET E 555 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N HIS E 561 " --> pdb=" O VAL E 557 " (cutoff:3.500A) Processing helix chain 'E' and resid 565 through 573 removed outlier: 3.720A pdb=" N LEU E 569 " --> pdb=" O HIS E 565 " (cutoff:3.500A) Processing helix chain 'E' and resid 645 through 661 removed outlier: 3.605A pdb=" N GLY E 650 " --> pdb=" O LEU E 646 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA E 661 " --> pdb=" O HIS E 657 " (cutoff:3.500A) Processing helix chain 'E' and resid 671 through 692 removed outlier: 3.730A pdb=" N ALA E 675 " --> pdb=" O SER E 671 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU E 682 " --> pdb=" O ALA E 678 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N LYS E 683 " --> pdb=" O LEU E 679 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N GLU E 684 " --> pdb=" O LYS E 680 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N TYR E 685 " --> pdb=" O LEU E 681 " (cutoff:3.500A) Proline residue: E 687 - end of helix Processing helix chain 'E' and resid 698 through 715 removed outlier: 3.684A pdb=" N ALA E 715 " --> pdb=" O GLY E 711 " (cutoff:3.500A) Processing helix chain 'E' and resid 720 through 734 removed outlier: 3.938A pdb=" N SER E 724 " --> pdb=" O GLY E 720 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N PHE E 733 " --> pdb=" O LEU E 729 " (cutoff:3.500A) Processing helix chain 'E' and resid 744 through 753 Processing helix chain 'E' and resid 770 through 782 removed outlier: 4.048A pdb=" N ARG E 774 " --> pdb=" O GLN E 770 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N TYR E 775 " --> pdb=" O ALA E 771 " (cutoff:3.500A) Processing helix chain 'E' and resid 790 through 810 removed outlier: 3.579A pdb=" N TRP E 801 " --> pdb=" O LYS E 797 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU E 802 " --> pdb=" O LEU E 798 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLU E 803 " --> pdb=" O LEU E 799 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N THR E 804 " --> pdb=" O ALA E 800 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU E 808 " --> pdb=" O THR E 804 " (cutoff:3.500A) Processing helix chain 'E' and resid 815 through 819 Processing helix chain 'E' and resid 821 through 828 removed outlier: 3.624A pdb=" N PHE E 825 " --> pdb=" O GLN E 821 " (cutoff:3.500A) Processing helix chain 'E' and resid 828 through 839 removed outlier: 4.143A pdb=" N GLU E 834 " --> pdb=" O ASP E 830 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N PHE E 837 " --> pdb=" O SER E 833 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ASP E 838 " --> pdb=" O GLU E 834 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ASP E 839 " --> pdb=" O ASP E 835 " (cutoff:3.500A) Processing helix chain 'E' and resid 850 through 863 removed outlier: 3.530A pdb=" N LEU E 854 " --> pdb=" O LEU E 850 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS E 855 " --> pdb=" O ILE E 851 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLN E 856 " --> pdb=" O SER E 852 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ILE E 857 " --> pdb=" O GLU E 853 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N TYR E 862 " --> pdb=" O LEU E 858 " (cutoff:3.500A) Processing helix chain 'F' and resid 5 through 24 Processing helix chain 'F' and resid 27 through 30 removed outlier: 3.559A pdb=" N GLN F 30 " --> pdb=" O THR F 27 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 27 through 30' Processing helix chain 'F' and resid 31 through 45 removed outlier: 3.976A pdb=" N ALA F 45 " --> pdb=" O ALA F 41 " (cutoff:3.500A) Processing helix chain 'F' and resid 46 through 58 Processing helix chain 'F' and resid 61 through 80 removed outlier: 3.623A pdb=" N LYS F 65 " --> pdb=" O ILE F 61 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ILE F 76 " --> pdb=" O ALA F 72 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N TYR F 80 " --> pdb=" O ILE F 76 " (cutoff:3.500A) Processing helix chain 'F' and resid 117 through 130 removed outlier: 4.323A pdb=" N ILE F 121 " --> pdb=" O THR F 117 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE F 122 " --> pdb=" O SER F 118 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N THR F 130 " --> pdb=" O ILE F 126 " (cutoff:3.500A) Processing helix chain 'F' and resid 143 through 159 removed outlier: 3.915A pdb=" N ALA F 159 " --> pdb=" O GLN F 155 " (cutoff:3.500A) Processing helix chain 'F' and resid 174 through 183 removed outlier: 4.207A pdb=" N SER F 178 " --> pdb=" O SER F 174 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ASN F 179 " --> pdb=" O VAL F 175 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N HIS F 183 " --> pdb=" O ASN F 179 " (cutoff:3.500A) Processing helix chain 'F' and resid 195 through 204 removed outlier: 3.962A pdb=" N VAL F 199 " --> pdb=" O GLY F 195 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N LYS F 200 " --> pdb=" O PRO F 196 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ALA F 201 " --> pdb=" O GLY F 197 " (cutoff:3.500A) Processing helix chain 'F' and resid 227 through 239 removed outlier: 3.736A pdb=" N THR F 239 " --> pdb=" O LEU F 235 " (cutoff:3.500A) Processing helix chain 'F' and resid 240 through 244 removed outlier: 3.537A pdb=" N VAL F 244 " --> pdb=" O ASP F 241 " (cutoff:3.500A) Processing helix chain 'F' and resid 258 through 268 removed outlier: 3.933A pdb=" N VAL F 262 " --> pdb=" O VAL F 258 " (cutoff:3.500A) Processing helix chain 'F' and resid 277 through 284 removed outlier: 3.595A pdb=" N ALA F 281 " --> pdb=" O LYS F 277 " (cutoff:3.500A) Processing helix chain 'F' and resid 300 through 309 removed outlier: 3.557A pdb=" N ILE F 304 " --> pdb=" O PRO F 300 " (cutoff:3.500A) Processing helix chain 'F' and resid 330 through 334 removed outlier: 3.667A pdb=" N ALA F 333 " --> pdb=" O GLU F 330 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N HIS F 334 " --> pdb=" O PRO F 331 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 330 through 334' Processing helix chain 'F' and resid 348 through 361 Processing helix chain 'F' and resid 378 through 389 removed outlier: 3.608A pdb=" N VAL F 382 " --> pdb=" O GLN F 378 " (cutoff:3.500A) Processing helix chain 'F' and resid 434 through 438 Processing helix chain 'F' and resid 472 through 477 Processing helix chain 'F' and resid 487 through 493 Processing helix chain 'F' and resid 496 through 507 removed outlier: 4.267A pdb=" N VAL F 502 " --> pdb=" O GLN F 498 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA F 505 " --> pdb=" O SER F 501 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ALA F 506 " --> pdb=" O VAL F 502 " (cutoff:3.500A) Processing helix chain 'F' and resid 523 through 536 Processing helix chain 'F' and resid 546 through 561 removed outlier: 3.687A pdb=" N TYR F 559 " --> pdb=" O MET F 555 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N HIS F 561 " --> pdb=" O VAL F 557 " (cutoff:3.500A) Processing helix chain 'F' and resid 565 through 573 removed outlier: 3.720A pdb=" N LEU F 569 " --> pdb=" O HIS F 565 " (cutoff:3.500A) Processing helix chain 'F' and resid 645 through 661 removed outlier: 3.606A pdb=" N GLY F 650 " --> pdb=" O LEU F 646 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA F 661 " --> pdb=" O HIS F 657 " (cutoff:3.500A) Processing helix chain 'F' and resid 671 through 692 removed outlier: 3.729A pdb=" N ALA F 675 " --> pdb=" O SER F 671 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU F 682 " --> pdb=" O ALA F 678 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N LYS F 683 " --> pdb=" O LEU F 679 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N GLU F 684 " --> pdb=" O LYS F 680 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N TYR F 685 " --> pdb=" O LEU F 681 " (cutoff:3.500A) Proline residue: F 687 - end of helix Processing helix chain 'F' and resid 698 through 715 removed outlier: 3.684A pdb=" N ALA F 715 " --> pdb=" O GLY F 711 " (cutoff:3.500A) Processing helix chain 'F' and resid 720 through 734 removed outlier: 3.938A pdb=" N SER F 724 " --> pdb=" O GLY F 720 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N PHE F 733 " --> pdb=" O LEU F 729 " (cutoff:3.500A) Processing helix chain 'F' and resid 744 through 753 Processing helix chain 'F' and resid 770 through 782 removed outlier: 4.049A pdb=" N ARG F 774 " --> pdb=" O GLN F 770 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N TYR F 775 " --> pdb=" O ALA F 771 " (cutoff:3.500A) Processing helix chain 'F' and resid 790 through 810 removed outlier: 3.580A pdb=" N TRP F 801 " --> pdb=" O LYS F 797 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LEU F 802 " --> pdb=" O LEU F 798 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N GLU F 803 " --> pdb=" O LEU F 799 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N THR F 804 " --> pdb=" O ALA F 800 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU F 808 " --> pdb=" O THR F 804 " (cutoff:3.500A) Processing helix chain 'F' and resid 815 through 819 Processing helix chain 'F' and resid 821 through 828 removed outlier: 3.624A pdb=" N PHE F 825 " --> pdb=" O GLN F 821 " (cutoff:3.500A) Processing helix chain 'F' and resid 828 through 839 removed outlier: 4.143A pdb=" N GLU F 834 " --> pdb=" O ASP F 830 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N PHE F 837 " --> pdb=" O SER F 833 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ASP F 838 " --> pdb=" O GLU F 834 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ASP F 839 " --> pdb=" O ASP F 835 " (cutoff:3.500A) Processing helix chain 'F' and resid 850 through 863 removed outlier: 3.530A pdb=" N LEU F 854 " --> pdb=" O LEU F 850 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS F 855 " --> pdb=" O ILE F 851 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLN F 856 " --> pdb=" O SER F 852 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ILE F 857 " --> pdb=" O GLU F 853 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N TYR F 862 " --> pdb=" O LEU F 858 " (cutoff:3.500A) Processing helix chain 'G' and resid 5 through 24 Processing helix chain 'G' and resid 27 through 30 removed outlier: 3.558A pdb=" N GLN G 30 " --> pdb=" O THR G 27 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 27 through 30' Processing helix chain 'G' and resid 31 through 45 removed outlier: 3.976A pdb=" N ALA G 45 " --> pdb=" O ALA G 41 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 58 Processing helix chain 'G' and resid 61 through 80 removed outlier: 3.623A pdb=" N LYS G 65 " --> pdb=" O ILE G 61 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ILE G 76 " --> pdb=" O ALA G 72 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TYR G 80 " --> pdb=" O ILE G 76 " (cutoff:3.500A) Processing helix chain 'G' and resid 117 through 130 removed outlier: 4.323A pdb=" N ILE G 121 " --> pdb=" O THR G 117 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE G 122 " --> pdb=" O SER G 118 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N THR G 130 " --> pdb=" O ILE G 126 " (cutoff:3.500A) Processing helix chain 'G' and resid 143 through 159 removed outlier: 3.915A pdb=" N ALA G 159 " --> pdb=" O GLN G 155 " (cutoff:3.500A) Processing helix chain 'G' and resid 174 through 183 removed outlier: 4.206A pdb=" N SER G 178 " --> pdb=" O SER G 174 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ASN G 179 " --> pdb=" O VAL G 175 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N HIS G 183 " --> pdb=" O ASN G 179 " (cutoff:3.500A) Processing helix chain 'G' and resid 195 through 204 removed outlier: 3.962A pdb=" N VAL G 199 " --> pdb=" O GLY G 195 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N LYS G 200 " --> pdb=" O PRO G 196 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ALA G 201 " --> pdb=" O GLY G 197 " (cutoff:3.500A) Processing helix chain 'G' and resid 227 through 239 removed outlier: 3.736A pdb=" N THR G 239 " --> pdb=" O LEU G 235 " (cutoff:3.500A) Processing helix chain 'G' and resid 240 through 244 removed outlier: 3.536A pdb=" N VAL G 244 " --> pdb=" O ASP G 241 " (cutoff:3.500A) Processing helix chain 'G' and resid 258 through 268 removed outlier: 3.933A pdb=" N VAL G 262 " --> pdb=" O VAL G 258 " (cutoff:3.500A) Processing helix chain 'G' and resid 277 through 284 removed outlier: 3.595A pdb=" N ALA G 281 " --> pdb=" O LYS G 277 " (cutoff:3.500A) Processing helix chain 'G' and resid 300 through 309 removed outlier: 3.558A pdb=" N ILE G 304 " --> pdb=" O PRO G 300 " (cutoff:3.500A) Processing helix chain 'G' and resid 330 through 334 removed outlier: 3.665A pdb=" N ALA G 333 " --> pdb=" O GLU G 330 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N HIS G 334 " --> pdb=" O PRO G 331 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 330 through 334' Processing helix chain 'G' and resid 348 through 361 Processing helix chain 'G' and resid 378 through 389 removed outlier: 3.608A pdb=" N VAL G 382 " --> pdb=" O GLN G 378 " (cutoff:3.500A) Processing helix chain 'G' and resid 434 through 438 Processing helix chain 'G' and resid 472 through 477 Processing helix chain 'G' and resid 487 through 493 Processing helix chain 'G' and resid 496 through 507 removed outlier: 4.266A pdb=" N VAL G 502 " --> pdb=" O GLN G 498 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA G 505 " --> pdb=" O SER G 501 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ALA G 506 " --> pdb=" O VAL G 502 " (cutoff:3.500A) Processing helix chain 'G' and resid 523 through 536 Processing helix chain 'G' and resid 546 through 561 removed outlier: 3.687A pdb=" N TYR G 559 " --> pdb=" O MET G 555 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N HIS G 561 " --> pdb=" O VAL G 557 " (cutoff:3.500A) Processing helix chain 'G' and resid 565 through 573 removed outlier: 3.720A pdb=" N LEU G 569 " --> pdb=" O HIS G 565 " (cutoff:3.500A) Processing helix chain 'G' and resid 645 through 661 removed outlier: 3.606A pdb=" N GLY G 650 " --> pdb=" O LEU G 646 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA G 661 " --> pdb=" O HIS G 657 " (cutoff:3.500A) Processing helix chain 'G' and resid 671 through 692 removed outlier: 3.730A pdb=" N ALA G 675 " --> pdb=" O SER G 671 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU G 682 " --> pdb=" O ALA G 678 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N LYS G 683 " --> pdb=" O LEU G 679 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N GLU G 684 " --> pdb=" O LYS G 680 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N TYR G 685 " --> pdb=" O LEU G 681 " (cutoff:3.500A) Proline residue: G 687 - end of helix Processing helix chain 'G' and resid 698 through 715 removed outlier: 3.683A pdb=" N ALA G 715 " --> pdb=" O GLY G 711 " (cutoff:3.500A) Processing helix chain 'G' and resid 720 through 734 removed outlier: 3.938A pdb=" N SER G 724 " --> pdb=" O GLY G 720 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N PHE G 733 " --> pdb=" O LEU G 729 " (cutoff:3.500A) Processing helix chain 'G' and resid 744 through 753 Processing helix chain 'G' and resid 770 through 782 removed outlier: 4.049A pdb=" N ARG G 774 " --> pdb=" O GLN G 770 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N TYR G 775 " --> pdb=" O ALA G 771 " (cutoff:3.500A) Processing helix chain 'G' and resid 790 through 810 removed outlier: 3.579A pdb=" N TRP G 801 " --> pdb=" O LYS G 797 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LEU G 802 " --> pdb=" O LEU G 798 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N GLU G 803 " --> pdb=" O LEU G 799 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N THR G 804 " --> pdb=" O ALA G 800 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU G 808 " --> pdb=" O THR G 804 " (cutoff:3.500A) Processing helix chain 'G' and resid 815 through 819 Processing helix chain 'G' and resid 821 through 828 removed outlier: 3.624A pdb=" N PHE G 825 " --> pdb=" O GLN G 821 " (cutoff:3.500A) Processing helix chain 'G' and resid 828 through 839 removed outlier: 4.143A pdb=" N GLU G 834 " --> pdb=" O ASP G 830 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N PHE G 837 " --> pdb=" O SER G 833 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ASP G 838 " --> pdb=" O GLU G 834 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ASP G 839 " --> pdb=" O ASP G 835 " (cutoff:3.500A) Processing helix chain 'G' and resid 850 through 863 removed outlier: 3.529A pdb=" N LEU G 854 " --> pdb=" O LEU G 850 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS G 855 " --> pdb=" O ILE G 851 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLN G 856 " --> pdb=" O SER G 852 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ILE G 857 " --> pdb=" O GLU G 853 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N TYR G 862 " --> pdb=" O LEU G 858 " (cutoff:3.500A) Processing helix chain 'H' and resid 466 through 471 Processing helix chain 'H' and resid 472 through 477 Processing helix chain 'H' and resid 487 through 493 Processing helix chain 'H' and resid 496 through 507 removed outlier: 3.567A pdb=" N THR H 500 " --> pdb=" O ALA H 496 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N VAL H 502 " --> pdb=" O GLN H 498 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA H 505 " --> pdb=" O SER H 501 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ALA H 506 " --> pdb=" O VAL H 502 " (cutoff:3.500A) Processing helix chain 'H' and resid 523 through 536 Processing helix chain 'H' and resid 546 through 561 removed outlier: 3.684A pdb=" N TYR H 559 " --> pdb=" O MET H 555 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N HIS H 561 " --> pdb=" O VAL H 557 " (cutoff:3.500A) Processing helix chain 'H' and resid 565 through 573 removed outlier: 3.643A pdb=" N LEU H 569 " --> pdb=" O HIS H 565 " (cutoff:3.500A) Processing helix chain 'H' and resid 645 through 661 Processing helix chain 'H' and resid 671 through 681 Processing helix chain 'H' and resid 685 through 692 removed outlier: 3.575A pdb=" N GLU H 692 " --> pdb=" O ALA H 688 " (cutoff:3.500A) Processing helix chain 'H' and resid 698 through 714 removed outlier: 3.532A pdb=" N ARG H 702 " --> pdb=" O VAL H 698 " (cutoff:3.500A) Processing helix chain 'H' and resid 720 through 734 removed outlier: 4.102A pdb=" N SER H 724 " --> pdb=" O GLY H 720 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N PHE H 733 " --> pdb=" O LEU H 729 " (cutoff:3.500A) Processing helix chain 'H' and resid 739 through 753 removed outlier: 3.617A pdb=" N LEU H 744 " --> pdb=" O ALA H 740 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N CYS H 746 " --> pdb=" O ALA H 742 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N ASN H 747 " --> pdb=" O LEU H 743 " (cutoff:3.500A) Processing helix chain 'H' and resid 770 through 783 removed outlier: 3.733A pdb=" N ARG H 774 " --> pdb=" O GLN H 770 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N TYR H 775 " --> pdb=" O ALA H 771 " (cutoff:3.500A) Processing helix chain 'H' and resid 790 through 800 Processing helix chain 'H' and resid 800 through 810 removed outlier: 3.740A pdb=" N THR H 804 " --> pdb=" O ALA H 800 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLU H 808 " --> pdb=" O THR H 804 " (cutoff:3.500A) Processing helix chain 'H' and resid 815 through 819 Processing helix chain 'H' and resid 821 through 833 removed outlier: 3.841A pdb=" N PHE H 825 " --> pdb=" O GLN H 821 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N ASP H 830 " --> pdb=" O LEU H 826 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N LYS H 831 " --> pdb=" O ALA H 827 " (cutoff:3.500A) Processing helix chain 'H' and resid 850 through 852 No H-bonds generated for 'chain 'H' and resid 850 through 852' Processing helix chain 'H' and resid 853 through 864 removed outlier: 3.795A pdb=" N ILE H 857 " --> pdb=" O GLU H 853 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N TYR H 862 " --> pdb=" O LEU H 858 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 459 through 462 removed outlier: 6.904A pdb=" N SER A 459 " --> pdb=" O ALA A 632 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N VAL A 634 " --> pdb=" O SER A 459 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N TYR A 461 " --> pdb=" O VAL A 634 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N MET A 592 " --> pdb=" O MET A 631 " (cutoff:3.500A) removed outlier: 8.424A pdb=" N ILE A 633 " --> pdb=" O MET A 592 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ALA A 594 " --> pdb=" O ILE A 633 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N LEU A 483 " --> pdb=" O ILE A 541 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N LEU A 543 " --> pdb=" O LEU A 483 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N VAL A 485 " --> pdb=" O LEU A 543 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N ILE A 484 " --> pdb=" O PHE A 513 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 608 through 612 Processing sheet with id=AA3, first strand: chain 'B' and resid 88 through 91 removed outlier: 6.676A pdb=" N VAL B 88 " --> pdb=" O ALA B 101 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N ALA B 101 " --> pdb=" O VAL B 88 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER B 90 " --> pdb=" O THR B 99 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE B 98 " --> pdb=" O VAL B 444 " (cutoff:3.500A) removed outlier: 8.688A pdb=" N ILE C 394 " --> pdb=" O LYS B 441 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N THR B 443 " --> pdb=" O ILE C 394 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N ILE C 396 " --> pdb=" O THR B 443 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ALA B 445 " --> pdb=" O ILE C 396 " (cutoff:3.500A) removed outlier: 8.004A pdb=" N TYR C 372 " --> pdb=" O PRO C 218 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N VAL C 220 " --> pdb=" O TYR C 372 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N THR C 217 " --> pdb=" O SER C 251 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N VAL C 253 " --> pdb=" O THR C 217 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N VAL C 219 " --> pdb=" O VAL C 253 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N VAL C 255 " --> pdb=" O VAL C 219 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N ILE C 221 " --> pdb=" O VAL C 255 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N GLN C 250 " --> pdb=" O ALA C 342 " (cutoff:3.500A) removed outlier: 8.448A pdb=" N TYR C 344 " --> pdb=" O GLN C 250 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N VAL C 252 " --> pdb=" O TYR C 344 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N ALA C 346 " --> pdb=" O VAL C 252 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N VAL C 254 " --> pdb=" O ALA C 346 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N LEU C 319 " --> pdb=" O LEU C 341 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N MET C 343 " --> pdb=" O LEU C 319 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N GLY C 321 " --> pdb=" O MET C 343 " (cutoff:3.500A) removed outlier: 8.634A pdb=" N ARG C 345 " --> pdb=" O GLY C 321 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N TYR C 272 " --> pdb=" O ILE C 320 " (cutoff:3.500A) removed outlier: 8.359A pdb=" N GLU C 322 " --> pdb=" O TYR C 272 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 167 through 169 removed outlier: 3.692A pdb=" N LEU B 189 " --> pdb=" O ILE B 106 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N THR B 193 " --> pdb=" O ILE B 110 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ILE B 190 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N VAL B 212 " --> pdb=" O ILE B 190 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N ALA B 192 " --> pdb=" O VAL B 212 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 271 through 273 removed outlier: 6.442A pdb=" N TYR B 272 " --> pdb=" O ILE B 320 " (cutoff:3.500A) removed outlier: 8.358A pdb=" N GLU B 322 " --> pdb=" O TYR B 272 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N LEU B 319 " --> pdb=" O LEU B 341 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N MET B 343 " --> pdb=" O LEU B 319 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N GLY B 321 " --> pdb=" O MET B 343 " (cutoff:3.500A) removed outlier: 8.634A pdb=" N ARG B 345 " --> pdb=" O GLY B 321 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N GLN B 250 " --> pdb=" O ALA B 342 " (cutoff:3.500A) removed outlier: 8.447A pdb=" N TYR B 344 " --> pdb=" O GLN B 250 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N VAL B 252 " --> pdb=" O TYR B 344 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N ALA B 346 " --> pdb=" O VAL B 252 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N VAL B 254 " --> pdb=" O ALA B 346 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N THR B 217 " --> pdb=" O SER B 251 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N VAL B 253 " --> pdb=" O THR B 217 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N VAL B 219 " --> pdb=" O VAL B 253 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N VAL B 255 " --> pdb=" O VAL B 219 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N ILE B 221 " --> pdb=" O VAL B 255 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N TYR B 372 " --> pdb=" O PRO B 218 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N VAL B 220 " --> pdb=" O TYR B 372 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE C 98 " --> pdb=" O VAL C 444 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER C 90 " --> pdb=" O THR C 99 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N ALA C 101 " --> pdb=" O VAL C 88 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N VAL C 88 " --> pdb=" O ALA C 101 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 419 through 420 Processing sheet with id=AA7, first strand: chain 'B' and resid 460 through 462 removed outlier: 6.719A pdb=" N TYR B 461 " --> pdb=" O VAL B 634 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N MET B 592 " --> pdb=" O MET B 631 " (cutoff:3.500A) removed outlier: 8.442A pdb=" N ILE B 633 " --> pdb=" O MET B 592 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ALA B 594 " --> pdb=" O ILE B 633 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N LEU B 483 " --> pdb=" O ILE B 541 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N LEU B 543 " --> pdb=" O LEU B 483 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N VAL B 485 " --> pdb=" O LEU B 543 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N ILE B 484 " --> pdb=" O PHE B 513 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 608 through 612 Processing sheet with id=AA9, first strand: chain 'C' and resid 167 through 169 removed outlier: 3.692A pdb=" N LEU C 189 " --> pdb=" O ILE C 106 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N THR C 193 " --> pdb=" O ILE C 110 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ILE C 190 " --> pdb=" O ILE C 210 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N VAL C 212 " --> pdb=" O ILE C 190 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N ALA C 192 " --> pdb=" O VAL C 212 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 419 through 420 Processing sheet with id=AB2, first strand: chain 'C' and resid 452 through 455 removed outlier: 3.547A pdb=" N ILE D 460 " --> pdb=" O HIS C 454 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N SER D 459 " --> pdb=" O ALA D 632 " (cutoff:3.500A) removed outlier: 8.165A pdb=" N VAL D 634 " --> pdb=" O SER D 459 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N TYR D 461 " --> pdb=" O VAL D 634 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N MET D 592 " --> pdb=" O MET D 631 " (cutoff:3.500A) removed outlier: 8.443A pdb=" N ILE D 633 " --> pdb=" O MET D 592 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ALA D 594 " --> pdb=" O ILE D 633 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N LEU D 483 " --> pdb=" O ILE D 541 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N LEU D 543 " --> pdb=" O LEU D 483 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N VAL D 485 " --> pdb=" O LEU D 543 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N ILE D 484 " --> pdb=" O PHE D 513 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 512 through 513 removed outlier: 7.176A pdb=" N ILE C 484 " --> pdb=" O PHE C 513 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N LEU C 483 " --> pdb=" O ILE C 541 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N LEU C 543 " --> pdb=" O LEU C 483 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N VAL C 485 " --> pdb=" O LEU C 543 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N MET C 592 " --> pdb=" O MET C 631 " (cutoff:3.500A) removed outlier: 8.443A pdb=" N ILE C 633 " --> pdb=" O MET C 592 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ALA C 594 " --> pdb=" O ILE C 633 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N SER C 459 " --> pdb=" O ALA C 632 " (cutoff:3.500A) removed outlier: 8.166A pdb=" N VAL C 634 " --> pdb=" O SER C 459 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N TYR C 461 " --> pdb=" O VAL C 634 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE C 460 " --> pdb=" O HIS D 454 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 608 through 612 Processing sheet with id=AB5, first strand: chain 'D' and resid 88 through 91 removed outlier: 6.677A pdb=" N VAL D 88 " --> pdb=" O ALA D 101 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N ALA D 101 " --> pdb=" O VAL D 88 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER D 90 " --> pdb=" O THR D 99 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE D 98 " --> pdb=" O VAL D 444 " (cutoff:3.500A) removed outlier: 8.816A pdb=" N ILE E 394 " --> pdb=" O LYS D 441 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N THR D 443 " --> pdb=" O ILE E 394 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N ILE E 396 " --> pdb=" O THR D 443 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ALA D 445 " --> pdb=" O ILE E 396 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N TYR E 372 " --> pdb=" O PRO E 218 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N VAL E 220 " --> pdb=" O TYR E 372 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N THR E 217 " --> pdb=" O SER E 251 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N VAL E 253 " --> pdb=" O THR E 217 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N VAL E 219 " --> pdb=" O VAL E 253 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N VAL E 255 " --> pdb=" O VAL E 219 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N ILE E 221 " --> pdb=" O VAL E 255 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N GLN E 250 " --> pdb=" O ALA E 342 " (cutoff:3.500A) removed outlier: 8.448A pdb=" N TYR E 344 " --> pdb=" O GLN E 250 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N VAL E 252 " --> pdb=" O TYR E 344 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N ALA E 346 " --> pdb=" O VAL E 252 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N VAL E 254 " --> pdb=" O ALA E 346 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N LEU E 319 " --> pdb=" O LEU E 341 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N MET E 343 " --> pdb=" O LEU E 319 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N GLY E 321 " --> pdb=" O MET E 343 " (cutoff:3.500A) removed outlier: 8.634A pdb=" N ARG E 345 " --> pdb=" O GLY E 321 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N TYR E 272 " --> pdb=" O ILE E 320 " (cutoff:3.500A) removed outlier: 8.358A pdb=" N GLU E 322 " --> pdb=" O TYR E 272 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 167 through 169 removed outlier: 3.693A pdb=" N LEU D 189 " --> pdb=" O ILE D 106 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N THR D 193 " --> pdb=" O ILE D 110 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ILE D 190 " --> pdb=" O ILE D 210 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N VAL D 212 " --> pdb=" O ILE D 190 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N ALA D 192 " --> pdb=" O VAL D 212 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 271 through 273 removed outlier: 6.442A pdb=" N TYR D 272 " --> pdb=" O ILE D 320 " (cutoff:3.500A) removed outlier: 8.359A pdb=" N GLU D 322 " --> pdb=" O TYR D 272 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N LEU D 319 " --> pdb=" O LEU D 341 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N MET D 343 " --> pdb=" O LEU D 319 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N GLY D 321 " --> pdb=" O MET D 343 " (cutoff:3.500A) removed outlier: 8.634A pdb=" N ARG D 345 " --> pdb=" O GLY D 321 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N GLN D 250 " --> pdb=" O ALA D 342 " (cutoff:3.500A) removed outlier: 8.447A pdb=" N TYR D 344 " --> pdb=" O GLN D 250 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N VAL D 252 " --> pdb=" O TYR D 344 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N ALA D 346 " --> pdb=" O VAL D 252 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N VAL D 254 " --> pdb=" O ALA D 346 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N THR D 217 " --> pdb=" O SER D 251 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N VAL D 253 " --> pdb=" O THR D 217 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N VAL D 219 " --> pdb=" O VAL D 253 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N VAL D 255 " --> pdb=" O VAL D 219 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N ILE D 221 " --> pdb=" O VAL D 255 " (cutoff:3.500A) removed outlier: 8.004A pdb=" N TYR D 372 " --> pdb=" O PRO D 218 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N VAL D 220 " --> pdb=" O TYR D 372 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE E 98 " --> pdb=" O VAL E 444 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER E 90 " --> pdb=" O THR E 99 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N ALA E 101 " --> pdb=" O VAL E 88 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N VAL E 88 " --> pdb=" O ALA E 101 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 419 through 420 Processing sheet with id=AB9, first strand: chain 'D' and resid 608 through 612 Processing sheet with id=AC1, first strand: chain 'E' and resid 167 through 169 removed outlier: 3.692A pdb=" N LEU E 189 " --> pdb=" O ILE E 106 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N THR E 193 " --> pdb=" O ILE E 110 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ILE E 190 " --> pdb=" O ILE E 210 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N VAL E 212 " --> pdb=" O ILE E 190 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N ALA E 192 " --> pdb=" O VAL E 212 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 419 through 420 Processing sheet with id=AC3, first strand: chain 'E' and resid 452 through 455 removed outlier: 3.539A pdb=" N ILE F 460 " --> pdb=" O HIS E 454 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N SER F 459 " --> pdb=" O ALA F 632 " (cutoff:3.500A) removed outlier: 8.166A pdb=" N VAL F 634 " --> pdb=" O SER F 459 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N TYR F 461 " --> pdb=" O VAL F 634 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N MET F 592 " --> pdb=" O MET F 631 " (cutoff:3.500A) removed outlier: 8.441A pdb=" N ILE F 633 " --> pdb=" O MET F 592 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ALA F 594 " --> pdb=" O ILE F 633 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N LEU F 483 " --> pdb=" O ILE F 541 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N LEU F 543 " --> pdb=" O LEU F 483 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N VAL F 485 " --> pdb=" O LEU F 543 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N ILE F 484 " --> pdb=" O PHE F 513 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 512 through 513 removed outlier: 7.176A pdb=" N ILE E 484 " --> pdb=" O PHE E 513 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N LEU E 483 " --> pdb=" O ILE E 541 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N LEU E 543 " --> pdb=" O LEU E 483 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N VAL E 485 " --> pdb=" O LEU E 543 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N MET E 592 " --> pdb=" O MET E 631 " (cutoff:3.500A) removed outlier: 8.442A pdb=" N ILE E 633 " --> pdb=" O MET E 592 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ALA E 594 " --> pdb=" O ILE E 633 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N SER E 459 " --> pdb=" O ALA E 632 " (cutoff:3.500A) removed outlier: 8.165A pdb=" N VAL E 634 " --> pdb=" O SER E 459 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N TYR E 461 " --> pdb=" O VAL E 634 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 608 through 612 Processing sheet with id=AC6, first strand: chain 'F' and resid 88 through 91 removed outlier: 6.677A pdb=" N VAL F 88 " --> pdb=" O ALA F 101 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ALA F 101 " --> pdb=" O VAL F 88 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER F 90 " --> pdb=" O THR F 99 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE F 98 " --> pdb=" O VAL F 444 " (cutoff:3.500A) removed outlier: 8.752A pdb=" N ILE G 394 " --> pdb=" O LYS F 441 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N THR F 443 " --> pdb=" O ILE G 394 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N ILE G 396 " --> pdb=" O THR F 443 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ALA F 445 " --> pdb=" O ILE G 396 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N TYR G 372 " --> pdb=" O PRO G 218 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N VAL G 220 " --> pdb=" O TYR G 372 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N THR G 217 " --> pdb=" O SER G 251 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N VAL G 253 " --> pdb=" O THR G 217 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N VAL G 219 " --> pdb=" O VAL G 253 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N VAL G 255 " --> pdb=" O VAL G 219 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N ILE G 221 " --> pdb=" O VAL G 255 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N GLN G 250 " --> pdb=" O ALA G 342 " (cutoff:3.500A) removed outlier: 8.447A pdb=" N TYR G 344 " --> pdb=" O GLN G 250 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N VAL G 252 " --> pdb=" O TYR G 344 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N ALA G 346 " --> pdb=" O VAL G 252 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N VAL G 254 " --> pdb=" O ALA G 346 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N LEU G 319 " --> pdb=" O LEU G 341 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N MET G 343 " --> pdb=" O LEU G 319 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N GLY G 321 " --> pdb=" O MET G 343 " (cutoff:3.500A) removed outlier: 8.634A pdb=" N ARG G 345 " --> pdb=" O GLY G 321 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N TYR G 272 " --> pdb=" O ILE G 320 " (cutoff:3.500A) removed outlier: 8.358A pdb=" N GLU G 322 " --> pdb=" O TYR G 272 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 167 through 169 removed outlier: 3.692A pdb=" N LEU F 189 " --> pdb=" O ILE F 106 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N THR F 193 " --> pdb=" O ILE F 110 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ILE F 190 " --> pdb=" O ILE F 210 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N VAL F 212 " --> pdb=" O ILE F 190 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N ALA F 192 " --> pdb=" O VAL F 212 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 271 through 273 removed outlier: 6.441A pdb=" N TYR F 272 " --> pdb=" O ILE F 320 " (cutoff:3.500A) removed outlier: 8.359A pdb=" N GLU F 322 " --> pdb=" O TYR F 272 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N LEU F 319 " --> pdb=" O LEU F 341 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N MET F 343 " --> pdb=" O LEU F 319 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N GLY F 321 " --> pdb=" O MET F 343 " (cutoff:3.500A) removed outlier: 8.634A pdb=" N ARG F 345 " --> pdb=" O GLY F 321 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N GLN F 250 " --> pdb=" O ALA F 342 " (cutoff:3.500A) removed outlier: 8.447A pdb=" N TYR F 344 " --> pdb=" O GLN F 250 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N VAL F 252 " --> pdb=" O TYR F 344 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N ALA F 346 " --> pdb=" O VAL F 252 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N VAL F 254 " --> pdb=" O ALA F 346 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N THR F 217 " --> pdb=" O SER F 251 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N VAL F 253 " --> pdb=" O THR F 217 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N VAL F 219 " --> pdb=" O VAL F 253 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N VAL F 255 " --> pdb=" O VAL F 219 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N ILE F 221 " --> pdb=" O VAL F 255 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N TYR F 372 " --> pdb=" O PRO F 218 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N VAL F 220 " --> pdb=" O TYR F 372 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE G 98 " --> pdb=" O VAL G 444 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER G 90 " --> pdb=" O THR G 99 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ALA G 101 " --> pdb=" O VAL G 88 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL G 88 " --> pdb=" O ALA G 101 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 419 through 420 Processing sheet with id=AD1, first strand: chain 'F' and resid 608 through 612 Processing sheet with id=AD2, first strand: chain 'G' and resid 167 through 169 removed outlier: 3.691A pdb=" N LEU G 189 " --> pdb=" O ILE G 106 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N THR G 193 " --> pdb=" O ILE G 110 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ILE G 190 " --> pdb=" O ILE G 210 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N VAL G 212 " --> pdb=" O ILE G 190 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N ALA G 192 " --> pdb=" O VAL G 212 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 419 through 420 Processing sheet with id=AD4, first strand: chain 'G' and resid 452 through 455 removed outlier: 6.903A pdb=" N SER H 459 " --> pdb=" O ALA H 632 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N VAL H 634 " --> pdb=" O SER H 459 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N TYR H 461 " --> pdb=" O VAL H 634 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N MET H 592 " --> pdb=" O MET H 631 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N ILE H 633 " --> pdb=" O MET H 592 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ALA H 594 " --> pdb=" O ILE H 633 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N LEU H 483 " --> pdb=" O ILE H 541 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N LEU H 543 " --> pdb=" O LEU H 483 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N VAL H 485 " --> pdb=" O LEU H 543 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ILE H 484 " --> pdb=" O PHE H 513 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 512 through 513 removed outlier: 7.175A pdb=" N ILE G 484 " --> pdb=" O PHE G 513 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N LEU G 483 " --> pdb=" O ILE G 541 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N LEU G 543 " --> pdb=" O LEU G 483 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N VAL G 485 " --> pdb=" O LEU G 543 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N MET G 592 " --> pdb=" O MET G 631 " (cutoff:3.500A) removed outlier: 8.442A pdb=" N ILE G 633 " --> pdb=" O MET G 592 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ALA G 594 " --> pdb=" O ILE G 633 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N SER G 459 " --> pdb=" O ALA G 632 " (cutoff:3.500A) removed outlier: 8.165A pdb=" N VAL G 634 " --> pdb=" O SER G 459 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N TYR G 461 " --> pdb=" O VAL G 634 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE G 460 " --> pdb=" O HIS H 454 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU H 452 " --> pdb=" O PHE G 462 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 608 through 612 Processing sheet with id=AD7, first strand: chain 'H' and resid 608 through 612 1836 hydrogen bonds defined for protein. 5355 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: 23.59 Time building geometry restraints manager: 12.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 14575 1.34 - 1.45: 6666 1.45 - 1.57: 25409 1.57 - 1.69: 4 1.69 - 1.81: 362 Bond restraints: 47016 Sorted by residual: bond pdb=" N THR G 842 " pdb=" CA THR G 842 " ideal model delta sigma weight residual 1.458 1.502 -0.044 1.90e-02 2.77e+03 5.34e+00 bond pdb=" N THR E 842 " pdb=" CA THR E 842 " ideal model delta sigma weight residual 1.458 1.502 -0.044 1.90e-02 2.77e+03 5.33e+00 bond pdb=" N THR C 842 " pdb=" CA THR C 842 " ideal model delta sigma weight residual 1.458 1.502 -0.044 1.90e-02 2.77e+03 5.30e+00 bond pdb=" N THR D 842 " pdb=" CA THR D 842 " ideal model delta sigma weight residual 1.458 1.502 -0.044 1.90e-02 2.77e+03 5.29e+00 bond pdb=" N THR B 842 " pdb=" CA THR B 842 " ideal model delta sigma weight residual 1.458 1.502 -0.044 1.90e-02 2.77e+03 5.26e+00 ... (remaining 47011 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.92: 63071 3.92 - 7.84: 642 7.84 - 11.77: 57 11.77 - 15.69: 0 15.69 - 19.61: 8 Bond angle restraints: 63778 Sorted by residual: angle pdb=" N THR F 842 " pdb=" CA THR F 842 " pdb=" C THR F 842 " ideal model delta sigma weight residual 111.00 130.61 -19.61 2.80e+00 1.28e-01 4.90e+01 angle pdb=" N THR D 842 " pdb=" CA THR D 842 " pdb=" C THR D 842 " ideal model delta sigma weight residual 111.00 130.60 -19.60 2.80e+00 1.28e-01 4.90e+01 angle pdb=" N THR G 842 " pdb=" CA THR G 842 " pdb=" C THR G 842 " ideal model delta sigma weight residual 111.00 130.59 -19.59 2.80e+00 1.28e-01 4.90e+01 angle pdb=" N THR C 842 " pdb=" CA THR C 842 " pdb=" C THR C 842 " ideal model delta sigma weight residual 111.00 130.56 -19.56 2.80e+00 1.28e-01 4.88e+01 angle pdb=" N THR B 842 " pdb=" CA THR B 842 " pdb=" C THR B 842 " ideal model delta sigma weight residual 111.00 130.56 -19.56 2.80e+00 1.28e-01 4.88e+01 ... (remaining 63773 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.11: 26560 15.11 - 30.23: 1556 30.23 - 45.34: 302 45.34 - 60.46: 16 60.46 - 75.57: 30 Dihedral angle restraints: 28464 sinusoidal: 10952 harmonic: 17512 Sorted by residual: dihedral pdb=" CA PHE B 462 " pdb=" C PHE B 462 " pdb=" N ARG B 463 " pdb=" CA ARG B 463 " ideal model delta harmonic sigma weight residual 180.00 126.63 53.37 0 5.00e+00 4.00e-02 1.14e+02 dihedral pdb=" CA PHE E 462 " pdb=" C PHE E 462 " pdb=" N ARG E 463 " pdb=" CA ARG E 463 " ideal model delta harmonic sigma weight residual 180.00 126.64 53.36 0 5.00e+00 4.00e-02 1.14e+02 dihedral pdb=" CA PHE D 462 " pdb=" C PHE D 462 " pdb=" N ARG D 463 " pdb=" CA ARG D 463 " ideal model delta harmonic sigma weight residual 180.00 126.65 53.35 0 5.00e+00 4.00e-02 1.14e+02 ... (remaining 28461 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 5246 0.065 - 0.129: 1693 0.129 - 0.194: 345 0.194 - 0.258: 26 0.258 - 0.323: 8 Chirality restraints: 7318 Sorted by residual: chirality pdb=" CA THR D 842 " pdb=" N THR D 842 " pdb=" C THR D 842 " pdb=" CB THR D 842 " both_signs ideal model delta sigma weight residual False 2.53 2.20 0.32 2.00e-01 2.50e+01 2.60e+00 chirality pdb=" CA THR F 842 " pdb=" N THR F 842 " pdb=" C THR F 842 " pdb=" CB THR F 842 " both_signs ideal model delta sigma weight residual False 2.53 2.20 0.32 2.00e-01 2.50e+01 2.58e+00 chirality pdb=" CA THR B 842 " pdb=" N THR B 842 " pdb=" C THR B 842 " pdb=" CB THR B 842 " both_signs ideal model delta sigma weight residual False 2.53 2.21 0.32 2.00e-01 2.50e+01 2.57e+00 ... (remaining 7315 not shown) Planarity restraints: 8262 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE F 462 " -0.018 2.00e-02 2.50e+03 3.69e-02 1.36e+01 pdb=" C PHE F 462 " 0.064 2.00e-02 2.50e+03 pdb=" O PHE F 462 " -0.024 2.00e-02 2.50e+03 pdb=" N ARG F 463 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE C 462 " -0.018 2.00e-02 2.50e+03 3.67e-02 1.35e+01 pdb=" C PHE C 462 " 0.063 2.00e-02 2.50e+03 pdb=" O PHE C 462 " -0.024 2.00e-02 2.50e+03 pdb=" N ARG C 463 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE G 462 " -0.018 2.00e-02 2.50e+03 3.67e-02 1.35e+01 pdb=" C PHE G 462 " 0.063 2.00e-02 2.50e+03 pdb=" O PHE G 462 " -0.024 2.00e-02 2.50e+03 pdb=" N ARG G 463 " -0.021 2.00e-02 2.50e+03 ... (remaining 8259 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 11887 2.79 - 3.32: 41012 3.32 - 3.85: 72239 3.85 - 4.37: 79728 4.37 - 4.90: 141070 Nonbonded interactions: 345936 Sorted by model distance: nonbonded pdb=" OG SER H 814 " pdb=" OE1 GLU H 817 " model vdw 2.268 3.040 nonbonded pdb=" OG SER A 814 " pdb=" OE1 GLU A 817 " model vdw 2.269 3.040 nonbonded pdb=" OG1 THR D 217 " pdb=" O SER D 248 " model vdw 2.273 3.040 nonbonded pdb=" OG1 THR B 217 " pdb=" O SER B 248 " model vdw 2.273 3.040 nonbonded pdb=" OG1 THR E 217 " pdb=" O SER E 248 " model vdw 2.273 3.040 ... (remaining 345931 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 'H' } ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 1.830 Check model and map are aligned: 0.330 Set scattering table: 0.500 Process input model: 101.000 Find NCS groups from input model: 2.000 Set up NCS constraints: 0.160 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:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 110.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.078 47016 Z= 0.543 Angle : 1.059 19.610 63778 Z= 0.564 Chirality : 0.064 0.323 7318 Planarity : 0.008 0.066 8262 Dihedral : 10.665 75.574 17196 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.87 % Favored : 92.00 % Rotamer: Outliers : 0.66 % Allowed : 3.76 % Favored : 95.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.80 % Twisted Proline : 0.00 % Twisted General : 0.28 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.33 (0.08), residues: 6036 helix: -2.76 (0.07), residues: 2518 sheet: -1.36 (0.16), residues: 916 loop : -3.51 (0.10), residues: 2602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP D 556 HIS 0.017 0.003 HIS A 727 PHE 0.046 0.004 PHE C 670 TYR 0.028 0.002 TYR A 461 ARG 0.012 0.001 ARG H 488 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12072 Ramachandran restraints generated. 6036 Oldfield, 0 Emsley, 6036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12072 Ramachandran restraints generated. 6036 Oldfield, 0 Emsley, 6036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1358 residues out of total 4850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 1326 time to evaluate : 5.238 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 480 LYS cc_start: 0.6577 (mmmt) cc_final: 0.6330 (tptm) REVERT: A 509 GLU cc_start: 0.7438 (mp0) cc_final: 0.6771 (mp0) REVERT: A 538 ASP cc_start: 0.7402 (p0) cc_final: 0.6695 (t0) REVERT: A 540 ILE cc_start: 0.7959 (mt) cc_final: 0.7696 (mm) REVERT: A 555 MET cc_start: 0.7357 (ptp) cc_final: 0.7062 (ptm) REVERT: A 588 VAL cc_start: 0.7422 (t) cc_final: 0.6360 (m) REVERT: A 613 ASP cc_start: 0.5946 (t70) cc_final: 0.5109 (t0) REVERT: A 642 MET cc_start: 0.6796 (ptt) cc_final: 0.6546 (ppp) REVERT: A 741 ASN cc_start: 0.4656 (p0) cc_final: 0.4198 (p0) REVERT: A 777 GLU cc_start: 0.7043 (mt-10) cc_final: 0.6843 (mm-30) REVERT: A 799 LEU cc_start: 0.5797 (OUTLIER) cc_final: 0.5581 (tp) REVERT: A 847 ARG cc_start: 0.3636 (ttp80) cc_final: 0.2988 (mtp180) REVERT: A 862 TYR cc_start: 0.3523 (t80) cc_final: 0.3261 (t80) REVERT: B 92 ASP cc_start: 0.5459 (t0) cc_final: 0.5231 (t0) REVERT: B 102 GLU cc_start: 0.8188 (pp20) cc_final: 0.7866 (pp20) REVERT: B 165 ASP cc_start: 0.8364 (p0) cc_final: 0.8159 (p0) REVERT: B 176 GLU cc_start: 0.8234 (pt0) cc_final: 0.7296 (mm-30) REVERT: B 222 ASP cc_start: 0.8918 (p0) cc_final: 0.8716 (p0) REVERT: B 318 ILE cc_start: 0.8179 (mm) cc_final: 0.7648 (pt) REVERT: B 347 LYS cc_start: 0.7827 (mtmt) cc_final: 0.7575 (ttmm) REVERT: B 357 GLU cc_start: 0.8411 (mt-10) cc_final: 0.8186 (mt-10) REVERT: B 365 ILE cc_start: 0.8908 (mt) cc_final: 0.8574 (mp) REVERT: B 381 ARG cc_start: 0.6830 (mtt180) cc_final: 0.6376 (mmm-85) REVERT: B 447 ARG cc_start: 0.6899 (ttt-90) cc_final: 0.6052 (ttp80) REVERT: B 479 HIS cc_start: 0.5699 (m-70) cc_final: 0.5395 (m-70) REVERT: B 521 THR cc_start: 0.7334 (p) cc_final: 0.7121 (p) REVERT: B 530 GLU cc_start: 0.7821 (tm-30) cc_final: 0.7563 (tm-30) REVERT: B 555 MET cc_start: 0.8146 (ptp) cc_final: 0.7882 (ptp) REVERT: B 577 ARG cc_start: 0.6532 (mtm110) cc_final: 0.6255 (mtp180) REVERT: B 604 GLU cc_start: 0.8140 (pm20) cc_final: 0.7686 (pm20) REVERT: B 641 ASP cc_start: 0.7598 (m-30) cc_final: 0.6540 (t70) REVERT: B 723 HIS cc_start: 0.7667 (t70) cc_final: 0.7407 (t-170) REVERT: B 727 HIS cc_start: 0.8196 (m-70) cc_final: 0.7522 (m-70) REVERT: B 773 ARG cc_start: 0.7988 (ttm170) cc_final: 0.7511 (ttt180) REVERT: B 828 ASN cc_start: 0.7475 (m-40) cc_final: 0.6600 (t0) REVERT: B 832 LEU cc_start: 0.7903 (mt) cc_final: 0.7671 (mp) REVERT: B 834 GLU cc_start: 0.7912 (pm20) cc_final: 0.7657 (pm20) REVERT: B 848 TYR cc_start: 0.7773 (t80) cc_final: 0.7540 (t80) REVERT: B 853 GLU cc_start: 0.7313 (mt-10) cc_final: 0.7002 (mp0) REVERT: C 12 LEU cc_start: 0.7974 (OUTLIER) cc_final: 0.7649 (tp) REVERT: C 17 LYS cc_start: 0.8159 (tttt) cc_final: 0.7760 (tttp) REVERT: C 59 MET cc_start: 0.7402 (pmt) cc_final: 0.7024 (pmm) REVERT: C 148 LYS cc_start: 0.8787 (tptt) cc_final: 0.8376 (mptt) REVERT: C 251 SER cc_start: 0.6920 (m) cc_final: 0.6648 (t) REVERT: C 336 LYS cc_start: 0.8369 (mtmm) cc_final: 0.8140 (mtmt) REVERT: C 351 ASP cc_start: 0.8386 (t0) cc_final: 0.8061 (t0) REVERT: C 582 LYS cc_start: 0.8551 (ptmt) cc_final: 0.8231 (ttmm) REVERT: C 631 MET cc_start: 0.8814 (ttp) cc_final: 0.8461 (ttp) REVERT: C 642 MET cc_start: 0.8227 (ptt) cc_final: 0.7994 (ptm) REVERT: C 835 ASP cc_start: 0.8266 (t70) cc_final: 0.7935 (t0) REVERT: D 12 LEU cc_start: 0.8148 (OUTLIER) cc_final: 0.7922 (pt) REVERT: D 18 LYS cc_start: 0.8544 (tttm) cc_final: 0.8134 (ttmm) REVERT: D 84 LYS cc_start: 0.8752 (mppt) cc_final: 0.8430 (mtmt) REVERT: D 98 ILE cc_start: 0.8397 (mt) cc_final: 0.8188 (mm) REVERT: D 99 THR cc_start: 0.9010 (m) cc_final: 0.8808 (p) REVERT: D 228 LYS cc_start: 0.8905 (mttm) cc_final: 0.8624 (mtmm) REVERT: D 390 LYS cc_start: 0.8315 (mtmt) cc_final: 0.8052 (mtmt) REVERT: D 421 CYS cc_start: 0.8301 (t) cc_final: 0.7950 (t) REVERT: D 515 GLU cc_start: 0.7303 (mp0) cc_final: 0.6639 (mp0) REVERT: D 727 HIS cc_start: 0.8099 (m-70) cc_final: 0.7623 (m-70) REVERT: E 5 ASN cc_start: 0.7182 (m-40) cc_final: 0.6969 (m-40) REVERT: E 12 LEU cc_start: 0.7682 (OUTLIER) cc_final: 0.7394 (pt) REVERT: E 59 MET cc_start: 0.8097 (pmt) cc_final: 0.7646 (pmt) REVERT: E 64 ASP cc_start: 0.8348 (m-30) cc_final: 0.7851 (m-30) REVERT: E 172 GLN cc_start: 0.8621 (mp10) cc_final: 0.7962 (mp10) REVERT: E 219 VAL cc_start: 0.9221 (t) cc_final: 0.8925 (m) REVERT: E 310 PHE cc_start: 0.7999 (p90) cc_final: 0.7790 (p90) REVERT: E 388 LYS cc_start: 0.8435 (mmmm) cc_final: 0.8215 (tppt) REVERT: E 472 ASP cc_start: 0.8227 (t0) cc_final: 0.7902 (t0) REVERT: E 477 ASP cc_start: 0.7555 (t0) cc_final: 0.7097 (p0) REVERT: E 732 GLN cc_start: 0.8649 (tm-30) cc_final: 0.7889 (tm-30) REVERT: F 18 LYS cc_start: 0.8226 (tttm) cc_final: 0.7985 (tppt) REVERT: F 59 MET cc_start: 0.7964 (pmt) cc_final: 0.7313 (pmm) REVERT: F 90 SER cc_start: 0.8349 (m) cc_final: 0.7782 (p) REVERT: F 114 THR cc_start: 0.8650 (p) cc_final: 0.8421 (t) REVERT: F 200 LYS cc_start: 0.8536 (mttt) cc_final: 0.8279 (mttp) REVERT: F 229 ARG cc_start: 0.8054 (mtt180) cc_final: 0.7576 (mmm160) REVERT: F 241 ASP cc_start: 0.7885 (t0) cc_final: 0.7554 (t0) REVERT: F 263 ARG cc_start: 0.8113 (mtp-110) cc_final: 0.7835 (ttp-110) REVERT: F 272 TYR cc_start: 0.6312 (t80) cc_final: 0.5711 (t80) REVERT: F 317 LYS cc_start: 0.8070 (mttt) cc_final: 0.7840 (mtmm) REVERT: F 378 GLN cc_start: 0.8360 (mp10) cc_final: 0.7695 (mp10) REVERT: F 381 ARG cc_start: 0.7688 (mtt180) cc_final: 0.7392 (mtp85) REVERT: F 424 TRP cc_start: 0.7526 (t-100) cc_final: 0.7320 (t-100) REVERT: F 458 LYS cc_start: 0.8967 (ttpt) cc_final: 0.8672 (tttp) REVERT: F 582 LYS cc_start: 0.8517 (ptmt) cc_final: 0.7850 (mttm) REVERT: F 784 LEU cc_start: 0.8583 (mt) cc_final: 0.8179 (mp) REVERT: F 799 LEU cc_start: 0.8451 (pt) cc_final: 0.8196 (tp) REVERT: G 18 LYS cc_start: 0.8614 (tttm) cc_final: 0.8206 (tppp) REVERT: G 236 MET cc_start: 0.9027 (ttt) cc_final: 0.8691 (tmm) REVERT: G 284 ASP cc_start: 0.8067 (t0) cc_final: 0.7783 (t0) REVERT: G 345 ARG cc_start: 0.9092 (ttm170) cc_final: 0.8814 (tpp80) REVERT: G 388 LYS cc_start: 0.8694 (mmmm) cc_final: 0.8432 (mmmt) REVERT: G 391 THR cc_start: 0.9047 (p) cc_final: 0.8783 (p) REVERT: G 447 ARG cc_start: 0.7751 (ttt-90) cc_final: 0.6896 (ttp-170) REVERT: G 458 LYS cc_start: 0.7786 (ttpt) cc_final: 0.7026 (tptp) REVERT: G 472 ASP cc_start: 0.8666 (t0) cc_final: 0.8373 (m-30) REVERT: G 555 MET cc_start: 0.8555 (ptp) cc_final: 0.8279 (ptm) REVERT: G 566 PHE cc_start: 0.8287 (t80) cc_final: 0.8011 (t80) REVERT: G 574 MET cc_start: 0.7826 (mtm) cc_final: 0.7594 (mmm) REVERT: G 575 ASP cc_start: 0.8096 (p0) cc_final: 0.7835 (p0) REVERT: G 698 VAL cc_start: 0.8027 (t) cc_final: 0.7759 (p) REVERT: G 817 GLU cc_start: 0.8673 (mp0) cc_final: 0.8423 (mp0) REVERT: G 831 LYS cc_start: 0.8177 (tppt) cc_final: 0.7966 (ttmm) REVERT: G 833 SER cc_start: 0.8860 (t) cc_final: 0.8642 (p) REVERT: G 834 GLU cc_start: 0.8085 (pm20) cc_final: 0.7595 (pm20) REVERT: G 850 LEU cc_start: 0.7843 (pt) cc_final: 0.7275 (pt) REVERT: G 852 SER cc_start: 0.9056 (p) cc_final: 0.8312 (m) REVERT: G 855 LYS cc_start: 0.7891 (ptmt) cc_final: 0.7604 (tttt) REVERT: G 866 ASP cc_start: 0.6968 (p0) cc_final: 0.6707 (m-30) REVERT: H 477 ASP cc_start: 0.7858 (t0) cc_final: 0.7107 (p0) REVERT: H 555 MET cc_start: 0.8467 (ptp) cc_final: 0.8174 (ptm) REVERT: H 574 MET cc_start: 0.6948 (mtm) cc_final: 0.6480 (tmm) REVERT: H 631 MET cc_start: 0.7747 (ttp) cc_final: 0.7423 (ttp) REVERT: H 785 SER cc_start: 0.9016 (p) cc_final: 0.8551 (t) REVERT: H 796 GLU cc_start: 0.8485 (tm-30) cc_final: 0.7873 (mm-30) REVERT: H 799 LEU cc_start: 0.7848 (OUTLIER) cc_final: 0.7310 (tp) REVERT: H 859 LEU cc_start: 0.6727 (mt) cc_final: 0.5957 (pp) REVERT: H 862 TYR cc_start: 0.5650 (t80) cc_final: 0.4608 (t80) outliers start: 32 outliers final: 3 residues processed: 1349 average time/residue: 0.6220 time to fit residues: 1344.6078 Evaluate side-chains 711 residues out of total 4850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 703 time to evaluate : 5.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 799 LEU Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain H residue 799 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 598 random chunks: chunk 504 optimal weight: 6.9990 chunk 453 optimal weight: 1.9990 chunk 251 optimal weight: 6.9990 chunk 154 optimal weight: 20.0000 chunk 305 optimal weight: 3.9990 chunk 242 optimal weight: 5.9990 chunk 468 optimal weight: 5.9990 chunk 181 optimal weight: 6.9990 chunk 285 optimal weight: 1.9990 chunk 348 optimal weight: 2.9990 chunk 543 optimal weight: 4.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 533 ASN A 561 HIS A 674 GLN A 754 ASN A 845 ASN B 30 GLN B 188 ASN B 367 HIS B 437 HIS B 479 HIS B 561 HIS B 691 HIS B 737 HIS B 752 ASN B 754 ASN B 781 HIS B 845 ASN C 30 GLN C 188 ASN ** C 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 367 HIS C 402 GLN C 427 ASN C 437 HIS C 561 HIS C 565 HIS C 754 ASN C 781 HIS D 30 GLN D 188 ASN D 367 HIS D 437 HIS D 737 HIS D 754 ASN E 30 GLN E 147 ASN E 188 ASN E 367 HIS E 402 GLN E 427 ASN E 737 HIS E 754 ASN E 845 ASN F 30 GLN F 188 ASN F 367 HIS F 427 ASN F 754 ASN G 30 GLN G 147 ASN G 188 ASN G 367 HIS G 402 GLN G 427 ASN G 437 HIS G 479 HIS G 657 HIS G 727 HIS H 752 ASN H 754 ASN H 840 GLN Total number of N/Q/H flips: 60 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.2723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 47016 Z= 0.253 Angle : 0.699 15.097 63778 Z= 0.358 Chirality : 0.048 0.257 7318 Planarity : 0.006 0.064 8262 Dihedral : 6.180 59.186 6490 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 2.95 % Allowed : 11.56 % Favored : 85.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.80 % Twisted Proline : 0.00 % Twisted General : 0.28 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.73 (0.10), residues: 6036 helix: -1.16 (0.09), residues: 2608 sheet: -0.98 (0.16), residues: 948 loop : -2.82 (0.11), residues: 2480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 556 HIS 0.009 0.001 HIS A 723 PHE 0.028 0.002 PHE H 489 TYR 0.021 0.002 TYR C 77 ARG 0.006 0.001 ARG D 790 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12072 Ramachandran restraints generated. 6036 Oldfield, 0 Emsley, 6036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12072 Ramachandran restraints generated. 6036 Oldfield, 0 Emsley, 6036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 942 residues out of total 4850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 799 time to evaluate : 5.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 509 GLU cc_start: 0.7549 (mp0) cc_final: 0.6877 (mp0) REVERT: A 530 GLU cc_start: 0.8383 (mt-10) cc_final: 0.8181 (mp0) REVERT: A 538 ASP cc_start: 0.7573 (p0) cc_final: 0.6767 (t0) REVERT: A 560 GLU cc_start: 0.5631 (tt0) cc_final: 0.4858 (tt0) REVERT: A 577 ARG cc_start: 0.4440 (mtm110) cc_final: 0.3475 (tmm160) REVERT: A 631 MET cc_start: 0.8029 (ttp) cc_final: 0.7766 (ttp) REVERT: A 642 MET cc_start: 0.6817 (ptt) cc_final: 0.6581 (ppp) REVERT: A 777 GLU cc_start: 0.7034 (mt-10) cc_final: 0.6823 (mm-30) REVERT: A 847 ARG cc_start: 0.3833 (ttp80) cc_final: 0.3101 (mtp180) REVERT: B 92 ASP cc_start: 0.5093 (t0) cc_final: 0.4519 (p0) REVERT: B 102 GLU cc_start: 0.8355 (pp20) cc_final: 0.8121 (pp20) REVERT: B 158 ILE cc_start: 0.8794 (mm) cc_final: 0.8532 (pt) REVERT: B 176 GLU cc_start: 0.8268 (pt0) cc_final: 0.7337 (mm-30) REVERT: B 318 ILE cc_start: 0.8450 (mm) cc_final: 0.7925 (pt) REVERT: B 335 GLU cc_start: 0.8113 (pp20) cc_final: 0.7661 (pp20) REVERT: B 357 GLU cc_start: 0.8369 (mt-10) cc_final: 0.8004 (mt-10) REVERT: B 365 ILE cc_start: 0.8876 (mt) cc_final: 0.8520 (mp) REVERT: B 424 TRP cc_start: 0.7756 (t-100) cc_final: 0.7515 (t-100) REVERT: B 447 ARG cc_start: 0.7376 (ttt-90) cc_final: 0.5806 (ttp80) REVERT: B 563 GLU cc_start: 0.8865 (tp30) cc_final: 0.8122 (mp0) REVERT: B 641 ASP cc_start: 0.7349 (m-30) cc_final: 0.6114 (t70) REVERT: B 712 ILE cc_start: 0.7957 (mt) cc_final: 0.7718 (mt) REVERT: B 773 ARG cc_start: 0.7912 (ttm170) cc_final: 0.7485 (ttt-90) REVERT: B 782 LEU cc_start: 0.8279 (tp) cc_final: 0.7934 (tp) REVERT: B 801 TRP cc_start: 0.6774 (t60) cc_final: 0.6531 (t60) REVERT: B 834 GLU cc_start: 0.7628 (pm20) cc_final: 0.7413 (pm20) REVERT: B 848 TYR cc_start: 0.7848 (t80) cc_final: 0.7413 (t80) REVERT: B 853 GLU cc_start: 0.7310 (mt-10) cc_final: 0.7083 (mp0) REVERT: C 17 LYS cc_start: 0.8200 (tttt) cc_final: 0.7744 (tttp) REVERT: C 59 MET cc_start: 0.7476 (pmt) cc_final: 0.7191 (pmm) REVERT: C 90 SER cc_start: 0.7615 (m) cc_final: 0.6985 (p) REVERT: C 148 LYS cc_start: 0.8934 (tptt) cc_final: 0.8480 (mptt) REVERT: C 200 LYS cc_start: 0.7618 (OUTLIER) cc_final: 0.7385 (mmtp) REVERT: C 251 SER cc_start: 0.7226 (m) cc_final: 0.6878 (t) REVERT: C 377 ASN cc_start: 0.7768 (m110) cc_final: 0.7426 (p0) REVERT: C 578 LYS cc_start: 0.8499 (mmtt) cc_final: 0.8139 (mmtt) REVERT: C 582 LYS cc_start: 0.8453 (ptmt) cc_final: 0.8078 (ttmm) REVERT: C 604 GLU cc_start: 0.8852 (pm20) cc_final: 0.8529 (pm20) REVERT: C 631 MET cc_start: 0.8910 (ttp) cc_final: 0.8604 (ttp) REVERT: C 728 LYS cc_start: 0.8449 (mmmt) cc_final: 0.7803 (mmtp) REVERT: C 799 LEU cc_start: 0.8175 (OUTLIER) cc_final: 0.7923 (tp) REVERT: D 18 LYS cc_start: 0.8632 (tttm) cc_final: 0.8269 (ttmm) REVERT: D 99 THR cc_start: 0.9091 (m) cc_final: 0.8788 (p) REVERT: D 128 LEU cc_start: 0.8425 (OUTLIER) cc_final: 0.8204 (pt) REVERT: D 216 ASN cc_start: 0.9196 (p0) cc_final: 0.8988 (p0) REVERT: D 228 LYS cc_start: 0.8844 (mttm) cc_final: 0.8624 (mtmt) REVERT: D 421 CYS cc_start: 0.8296 (t) cc_final: 0.7916 (t) REVERT: D 477 ASP cc_start: 0.7991 (t0) cc_final: 0.7778 (t0) REVERT: D 515 GLU cc_start: 0.7282 (mp0) cc_final: 0.6852 (mp0) REVERT: D 565 HIS cc_start: 0.7893 (t-90) cc_final: 0.7591 (t-90) REVERT: D 727 HIS cc_start: 0.8316 (m-70) cc_final: 0.7901 (t70) REVERT: D 799 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8222 (pt) REVERT: E 59 MET cc_start: 0.7934 (pmt) cc_final: 0.7644 (pmm) REVERT: E 64 ASP cc_start: 0.8266 (m-30) cc_final: 0.7536 (m-30) REVERT: E 172 GLN cc_start: 0.8698 (mp10) cc_final: 0.8063 (mp10) REVERT: E 335 GLU cc_start: 0.8738 (mt-10) cc_final: 0.8467 (mt-10) REVERT: E 365 ILE cc_start: 0.9339 (mt) cc_final: 0.9032 (mm) REVERT: E 388 LYS cc_start: 0.8306 (mmmm) cc_final: 0.8048 (tppt) REVERT: E 472 ASP cc_start: 0.8233 (t0) cc_final: 0.7886 (t0) REVERT: E 477 ASP cc_start: 0.7585 (t0) cc_final: 0.7326 (p0) REVERT: E 517 GLU cc_start: 0.8498 (mm-30) cc_final: 0.8136 (mm-30) REVERT: E 592 MET cc_start: 0.8928 (ttt) cc_final: 0.8715 (ttt) REVERT: F 18 LYS cc_start: 0.8295 (tttm) cc_final: 0.8075 (tppt) REVERT: F 59 MET cc_start: 0.7712 (pmt) cc_final: 0.6975 (pmm) REVERT: F 90 SER cc_start: 0.8159 (m) cc_final: 0.7813 (p) REVERT: F 229 ARG cc_start: 0.8256 (mtt180) cc_final: 0.7696 (mmp-170) REVERT: F 241 ASP cc_start: 0.7841 (t0) cc_final: 0.7293 (t0) REVERT: F 272 TYR cc_start: 0.6803 (t80) cc_final: 0.5845 (t80) REVERT: F 378 GLN cc_start: 0.8444 (mp10) cc_final: 0.7919 (mp10) REVERT: F 582 LYS cc_start: 0.8431 (ptmt) cc_final: 0.7753 (mttm) REVERT: F 640 MET cc_start: 0.8502 (mmt) cc_final: 0.7964 (mmt) REVERT: F 784 LEU cc_start: 0.8598 (mt) cc_final: 0.8190 (mp) REVERT: G 91 GLU cc_start: 0.7884 (pm20) cc_final: 0.7551 (pm20) REVERT: G 236 MET cc_start: 0.8981 (ttt) cc_final: 0.8590 (tmm) REVERT: G 254 VAL cc_start: 0.9251 (t) cc_final: 0.9019 (p) REVERT: G 284 ASP cc_start: 0.7982 (t0) cc_final: 0.7733 (t0) REVERT: G 354 GLU cc_start: 0.8699 (tp30) cc_final: 0.8324 (tm-30) REVERT: G 389 MET cc_start: 0.9108 (mmm) cc_final: 0.8863 (tpp) REVERT: G 391 THR cc_start: 0.9081 (p) cc_final: 0.8698 (p) REVERT: G 447 ARG cc_start: 0.7639 (ttt-90) cc_final: 0.6823 (ttp-170) REVERT: G 458 LYS cc_start: 0.8072 (ttpt) cc_final: 0.7388 (tptp) REVERT: G 472 ASP cc_start: 0.8806 (t0) cc_final: 0.8499 (m-30) REVERT: G 473 GLU cc_start: 0.7240 (tp30) cc_final: 0.6951 (tp30) REVERT: G 495 TYR cc_start: 0.7874 (m-10) cc_final: 0.7639 (m-80) REVERT: G 555 MET cc_start: 0.8494 (ptp) cc_final: 0.8260 (ptm) REVERT: G 817 GLU cc_start: 0.9008 (mp0) cc_final: 0.8772 (mp0) REVERT: G 834 GLU cc_start: 0.7961 (pm20) cc_final: 0.7542 (pm20) REVERT: G 858 LEU cc_start: 0.9049 (mt) cc_final: 0.8810 (mt) REVERT: H 451 MET cc_start: 0.3021 (ttp) cc_final: 0.2686 (ttp) REVERT: H 477 ASP cc_start: 0.7972 (t0) cc_final: 0.7379 (p0) REVERT: H 481 ARG cc_start: 0.6820 (mtp85) cc_final: 0.6426 (ttm110) REVERT: H 581 TYR cc_start: 0.7377 (m-80) cc_final: 0.7123 (t80) REVERT: H 582 LYS cc_start: 0.7672 (mmmt) cc_final: 0.7215 (mmtt) REVERT: H 592 MET cc_start: 0.8646 (ttt) cc_final: 0.8411 (ttp) REVERT: H 631 MET cc_start: 0.8337 (ttp) cc_final: 0.8020 (ttp) REVERT: H 750 ARG cc_start: 0.6907 (mtt90) cc_final: 0.6198 (ptp-110) REVERT: H 777 GLU cc_start: 0.8120 (mm-30) cc_final: 0.7858 (mm-30) REVERT: H 795 ILE cc_start: 0.6857 (mm) cc_final: 0.6639 (mm) REVERT: H 796 GLU cc_start: 0.8498 (tm-30) cc_final: 0.7849 (mm-30) REVERT: H 811 ILE cc_start: 0.8297 (pt) cc_final: 0.8029 (mp) REVERT: H 848 TYR cc_start: 0.7335 (t80) cc_final: 0.7023 (t80) REVERT: H 859 LEU cc_start: 0.6611 (mt) cc_final: 0.5887 (pp) outliers start: 143 outliers final: 81 residues processed: 896 average time/residue: 0.5509 time to fit residues: 830.3682 Evaluate side-chains 734 residues out of total 4850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 649 time to evaluate : 5.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 108 CYS Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 588 VAL Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 634 VAL Chi-restraints excluded: chain C residue 108 CYS Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 200 LYS Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 362 MET Chi-restraints excluded: chain C residue 391 THR Chi-restraints excluded: chain C residue 547 SER Chi-restraints excluded: chain C residue 549 MET Chi-restraints excluded: chain C residue 598 THR Chi-restraints excluded: chain C residue 701 GLU Chi-restraints excluded: chain C residue 799 LEU Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 237 SER Chi-restraints excluded: chain D residue 323 VAL Chi-restraints excluded: chain D residue 568 GLU Chi-restraints excluded: chain D residue 576 ILE Chi-restraints excluded: chain D residue 580 ILE Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain D residue 652 LEU Chi-restraints excluded: chain D residue 668 SER Chi-restraints excluded: chain D residue 799 LEU Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain E residue 338 SER Chi-restraints excluded: chain E residue 340 THR Chi-restraints excluded: chain E residue 439 ILE Chi-restraints excluded: chain E residue 564 THR Chi-restraints excluded: chain E residue 568 GLU Chi-restraints excluded: chain E residue 580 ILE Chi-restraints excluded: chain E residue 599 SER Chi-restraints excluded: chain E residue 668 SER Chi-restraints excluded: chain E residue 731 SER Chi-restraints excluded: chain E residue 845 ASN Chi-restraints excluded: chain F residue 127 SER Chi-restraints excluded: chain F residue 128 LEU Chi-restraints excluded: chain F residue 210 ILE Chi-restraints excluded: chain F residue 251 SER Chi-restraints excluded: chain F residue 353 VAL Chi-restraints excluded: chain F residue 439 ILE Chi-restraints excluded: chain F residue 547 SER Chi-restraints excluded: chain F residue 576 ILE Chi-restraints excluded: chain F residue 580 ILE Chi-restraints excluded: chain F residue 592 MET Chi-restraints excluded: chain F residue 598 THR Chi-restraints excluded: chain F residue 603 SER Chi-restraints excluded: chain F residue 820 VAL Chi-restraints excluded: chain F residue 829 VAL Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 27 THR Chi-restraints excluded: chain G residue 74 GLU Chi-restraints excluded: chain G residue 88 VAL Chi-restraints excluded: chain G residue 237 SER Chi-restraints excluded: chain G residue 323 VAL Chi-restraints excluded: chain G residue 332 PHE Chi-restraints excluded: chain G residue 358 LYS Chi-restraints excluded: chain G residue 398 THR Chi-restraints excluded: chain G residue 436 LYS Chi-restraints excluded: chain G residue 576 ILE Chi-restraints excluded: chain G residue 712 ILE Chi-restraints excluded: chain H residue 576 ILE Chi-restraints excluded: chain H residue 598 THR Chi-restraints excluded: chain H residue 611 VAL Chi-restraints excluded: chain H residue 614 ASP Chi-restraints excluded: chain H residue 712 ILE Chi-restraints excluded: chain H residue 782 LEU Chi-restraints excluded: chain H residue 799 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 598 random chunks: chunk 301 optimal weight: 8.9990 chunk 168 optimal weight: 8.9990 chunk 451 optimal weight: 6.9990 chunk 369 optimal weight: 1.9990 chunk 149 optimal weight: 0.6980 chunk 544 optimal weight: 5.9990 chunk 587 optimal weight: 6.9990 chunk 484 optimal weight: 6.9990 chunk 539 optimal weight: 9.9990 chunk 185 optimal weight: 6.9990 chunk 436 optimal weight: 9.9990 overall best weight: 4.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 78 ASN B 147 ASN B 737 HIS ** B 845 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 250 GLN C 737 HIS C 845 ASN D 147 ASN D 387 GLN D 402 GLN D 840 GLN E 30 GLN E 565 HIS E 737 HIS ** E 752 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 188 ASN F 269 HIS F 727 HIS G 69 ASN G 727 HIS G 760 GLN G 781 HIS H 737 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.3454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 47016 Z= 0.321 Angle : 0.718 15.745 63778 Z= 0.366 Chirality : 0.049 0.267 7318 Planarity : 0.005 0.059 8262 Dihedral : 5.714 59.032 6484 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.60 % Favored : 92.40 % Rotamer: Outliers : 3.94 % Allowed : 13.60 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.85 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.06 (0.10), residues: 6036 helix: -0.48 (0.10), residues: 2622 sheet: -0.70 (0.16), residues: 930 loop : -2.60 (0.12), residues: 2484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 556 HIS 0.009 0.001 HIS H 704 PHE 0.022 0.002 PHE G 71 TYR 0.020 0.002 TYR E 23 ARG 0.005 0.001 ARG D 790 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12072 Ramachandran restraints generated. 6036 Oldfield, 0 Emsley, 6036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12072 Ramachandran restraints generated. 6036 Oldfield, 0 Emsley, 6036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 871 residues out of total 4850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 191 poor density : 680 time to evaluate : 5.295 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: A 509 GLU cc_start: 0.7914 (mp0) cc_final: 0.7096 (mp0) REVERT: A 514 PHE cc_start: 0.7306 (p90) cc_final: 0.6684 (p90) REVERT: A 538 ASP cc_start: 0.7464 (p0) cc_final: 0.6913 (t0) REVERT: A 549 MET cc_start: 0.6159 (mtt) cc_final: 0.5944 (mtt) REVERT: A 550 ASP cc_start: 0.8070 (p0) cc_final: 0.7653 (m-30) REVERT: A 577 ARG cc_start: 0.4883 (mtm110) cc_final: 0.3563 (tmm160) REVERT: A 777 GLU cc_start: 0.7218 (mt-10) cc_final: 0.6951 (mm-30) REVERT: A 811 ILE cc_start: 0.7380 (OUTLIER) cc_final: 0.7058 (tp) REVERT: B 29 GLU cc_start: 0.8574 (pm20) cc_final: 0.8286 (pm20) REVERT: B 92 ASP cc_start: 0.5278 (t0) cc_final: 0.4640 (p0) REVERT: B 102 GLU cc_start: 0.8336 (pp20) cc_final: 0.8117 (pp20) REVERT: B 158 ILE cc_start: 0.8631 (mm) cc_final: 0.8363 (pt) REVERT: B 176 GLU cc_start: 0.8418 (pt0) cc_final: 0.7562 (mm-30) REVERT: B 318 ILE cc_start: 0.8469 (mm) cc_final: 0.8010 (pt) REVERT: B 335 GLU cc_start: 0.8031 (pp20) cc_final: 0.7612 (pp20) REVERT: B 357 GLU cc_start: 0.8541 (mt-10) cc_final: 0.7929 (mt-10) REVERT: B 365 ILE cc_start: 0.8895 (mt) cc_final: 0.8520 (mp) REVERT: B 447 ARG cc_start: 0.7371 (ttt-90) cc_final: 0.5926 (ttp80) REVERT: B 451 MET cc_start: 0.8199 (ptm) cc_final: 0.7931 (ptm) REVERT: B 463 ARG cc_start: 0.6044 (ptp-110) cc_final: 0.5773 (mtt90) REVERT: B 549 MET cc_start: 0.5370 (mtm) cc_final: 0.5091 (mtm) REVERT: B 555 MET cc_start: 0.8353 (ptp) cc_final: 0.7999 (ptp) REVERT: B 563 GLU cc_start: 0.8957 (tp30) cc_final: 0.8141 (mp0) REVERT: B 586 MET cc_start: 0.6733 (mtp) cc_final: 0.6459 (mtt) REVERT: B 604 GLU cc_start: 0.7924 (pm20) cc_final: 0.7171 (mp0) REVERT: B 641 ASP cc_start: 0.7461 (m-30) cc_final: 0.5987 (t70) REVERT: B 660 GLU cc_start: 0.8238 (tp30) cc_final: 0.8023 (mm-30) REVERT: B 773 ARG cc_start: 0.8113 (ttm170) cc_final: 0.7733 (ttt180) REVERT: B 848 TYR cc_start: 0.7788 (t80) cc_final: 0.7373 (t80) REVERT: C 17 LYS cc_start: 0.8168 (tttt) cc_final: 0.7717 (tttp) REVERT: C 59 MET cc_start: 0.7609 (pmt) cc_final: 0.7300 (pmm) REVERT: C 90 SER cc_start: 0.7551 (m) cc_final: 0.6886 (p) REVERT: C 148 LYS cc_start: 0.8888 (tptt) cc_final: 0.8429 (mptt) REVERT: C 251 SER cc_start: 0.7299 (m) cc_final: 0.6994 (t) REVERT: C 293 ASN cc_start: 0.6590 (t0) cc_final: 0.5807 (p0) REVERT: C 377 ASN cc_start: 0.7853 (m110) cc_final: 0.7568 (p0) REVERT: C 565 HIS cc_start: 0.7365 (t-90) cc_final: 0.6921 (t-90) REVERT: C 578 LYS cc_start: 0.8490 (mmtt) cc_final: 0.8100 (mmtt) REVERT: C 582 LYS cc_start: 0.8533 (ptmt) cc_final: 0.8141 (ttmm) REVERT: C 604 GLU cc_start: 0.8969 (pm20) cc_final: 0.8609 (pm20) REVERT: C 631 MET cc_start: 0.8930 (ttp) cc_final: 0.8627 (ttp) REVERT: C 728 LYS cc_start: 0.8483 (mmmt) cc_final: 0.7747 (mmtp) REVERT: C 799 LEU cc_start: 0.8184 (OUTLIER) cc_final: 0.7885 (tp) REVERT: D 18 LYS cc_start: 0.8745 (tttm) cc_final: 0.8320 (ttmm) REVERT: D 99 THR cc_start: 0.9050 (m) cc_final: 0.8650 (p) REVERT: D 128 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8375 (pt) REVERT: D 421 CYS cc_start: 0.8438 (t) cc_final: 0.8063 (t) REVERT: D 515 GLU cc_start: 0.7535 (mp0) cc_final: 0.7205 (mp0) REVERT: D 565 HIS cc_start: 0.7844 (OUTLIER) cc_final: 0.7481 (t-90) REVERT: D 784 LEU cc_start: 0.9069 (mt) cc_final: 0.8840 (mt) REVERT: D 799 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.8327 (pt) REVERT: D 808 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7585 (pm20) REVERT: E 59 MET cc_start: 0.8261 (pmt) cc_final: 0.7927 (pmm) REVERT: E 64 ASP cc_start: 0.8350 (m-30) cc_final: 0.7663 (m-30) REVERT: E 172 GLN cc_start: 0.8760 (mp10) cc_final: 0.8088 (mp10) REVERT: E 198 MET cc_start: 0.7774 (pmm) cc_final: 0.7560 (mpp) REVERT: E 335 GLU cc_start: 0.8708 (OUTLIER) cc_final: 0.8421 (mt-10) REVERT: E 388 LYS cc_start: 0.8326 (mmmm) cc_final: 0.7972 (tppt) REVERT: E 472 ASP cc_start: 0.8202 (t0) cc_final: 0.7881 (t0) REVERT: E 477 ASP cc_start: 0.7679 (t0) cc_final: 0.7453 (p0) REVERT: E 517 GLU cc_start: 0.8784 (mm-30) cc_final: 0.8468 (mm-30) REVERT: E 592 MET cc_start: 0.8867 (ttt) cc_final: 0.8657 (ttt) REVERT: E 845 ASN cc_start: 0.8941 (OUTLIER) cc_final: 0.8634 (m-40) REVERT: F 18 LYS cc_start: 0.8267 (tttm) cc_final: 0.8041 (tppt) REVERT: F 59 MET cc_start: 0.7589 (pmt) cc_final: 0.6819 (pmm) REVERT: F 78 ASN cc_start: 0.8218 (m-40) cc_final: 0.7771 (m-40) REVERT: F 82 ASP cc_start: 0.8784 (p0) cc_final: 0.8570 (p0) REVERT: F 90 SER cc_start: 0.8275 (m) cc_final: 0.7984 (p) REVERT: F 229 ARG cc_start: 0.8357 (mtt180) cc_final: 0.7618 (mmp-170) REVERT: F 241 ASP cc_start: 0.7948 (t0) cc_final: 0.7382 (t0) REVERT: F 272 TYR cc_start: 0.6633 (t80) cc_final: 0.5714 (t80) REVERT: F 378 GLN cc_start: 0.8580 (mp10) cc_final: 0.8012 (mp10) REVERT: F 517 GLU cc_start: 0.8144 (tp30) cc_final: 0.7939 (tp30) REVERT: F 558 MET cc_start: 0.8661 (mtp) cc_final: 0.8393 (mtp) REVERT: F 582 LYS cc_start: 0.8550 (ptmt) cc_final: 0.7882 (mttm) REVERT: F 784 LEU cc_start: 0.8642 (mt) cc_final: 0.8422 (mp) REVERT: G 236 MET cc_start: 0.8974 (ttt) cc_final: 0.8550 (tmm) REVERT: G 254 VAL cc_start: 0.9248 (t) cc_final: 0.9042 (p) REVERT: G 284 ASP cc_start: 0.8134 (t0) cc_final: 0.7892 (t0) REVERT: G 447 ARG cc_start: 0.7691 (ttt-90) cc_final: 0.7011 (ttp-170) REVERT: G 458 LYS cc_start: 0.8207 (ttpt) cc_final: 0.7382 (tptt) REVERT: G 471 LEU cc_start: 0.7921 (OUTLIER) cc_final: 0.7627 (pp) REVERT: G 574 MET cc_start: 0.7704 (mmm) cc_final: 0.7370 (mmm) REVERT: G 817 GLU cc_start: 0.9055 (mp0) cc_final: 0.8813 (mp0) REVERT: G 834 GLU cc_start: 0.7849 (pm20) cc_final: 0.7555 (pm20) REVERT: G 858 LEU cc_start: 0.9094 (mt) cc_final: 0.8840 (mt) REVERT: H 477 ASP cc_start: 0.8014 (t0) cc_final: 0.7432 (p0) REVERT: H 519 ASP cc_start: 0.7625 (m-30) cc_final: 0.6884 (t0) REVERT: H 582 LYS cc_start: 0.7578 (mmmt) cc_final: 0.7291 (mmtt) REVERT: H 592 MET cc_start: 0.8676 (ttt) cc_final: 0.8358 (ttp) REVERT: H 631 MET cc_start: 0.8320 (ttp) cc_final: 0.8068 (ttp) REVERT: H 750 ARG cc_start: 0.7011 (mtt90) cc_final: 0.6794 (mtt90) REVERT: H 770 GLN cc_start: 0.6817 (tp-100) cc_final: 0.5985 (mt0) REVERT: H 777 GLU cc_start: 0.8224 (mm-30) cc_final: 0.7941 (mm-30) REVERT: H 796 GLU cc_start: 0.8601 (tm-30) cc_final: 0.7839 (mm-30) REVERT: H 799 LEU cc_start: 0.7906 (OUTLIER) cc_final: 0.7641 (tp) REVERT: H 816 ARG cc_start: 0.7141 (OUTLIER) cc_final: 0.6785 (ptm160) REVERT: H 822 GLU cc_start: 0.5598 (OUTLIER) cc_final: 0.5239 (mp0) REVERT: H 847 ARG cc_start: 0.5208 (ptp-170) cc_final: 0.4635 (ptm160) REVERT: H 859 LEU cc_start: 0.6066 (mt) cc_final: 0.5344 (pp) REVERT: H 866 ASP cc_start: 0.4409 (p0) cc_final: 0.4010 (p0) outliers start: 191 outliers final: 120 residues processed: 818 average time/residue: 0.5239 time to fit residues: 723.3153 Evaluate side-chains 731 residues out of total 4850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 599 time to evaluate : 5.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 604 GLU Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 811 ILE Chi-restraints excluded: chain A residue 857 ILE Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 108 CYS Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 246 CYS Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 370 CYS Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 588 VAL Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 634 VAL Chi-restraints excluded: chain B residue 656 THR Chi-restraints excluded: chain B residue 735 ILE Chi-restraints excluded: chain B residue 857 ILE Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 108 CYS Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 250 GLN Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 391 THR Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 558 MET Chi-restraints excluded: chain C residue 586 MET Chi-restraints excluded: chain C residue 598 THR Chi-restraints excluded: chain C residue 701 GLU Chi-restraints excluded: chain C residue 712 ILE Chi-restraints excluded: chain C residue 799 LEU Chi-restraints excluded: chain C residue 809 LEU Chi-restraints excluded: chain C residue 829 VAL Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 323 VAL Chi-restraints excluded: chain D residue 327 ASP Chi-restraints excluded: chain D residue 486 THR Chi-restraints excluded: chain D residue 522 LEU Chi-restraints excluded: chain D residue 565 HIS Chi-restraints excluded: chain D residue 568 GLU Chi-restraints excluded: chain D residue 576 ILE Chi-restraints excluded: chain D residue 580 ILE Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain D residue 652 LEU Chi-restraints excluded: chain D residue 739 LEU Chi-restraints excluded: chain D residue 799 LEU Chi-restraints excluded: chain D residue 808 GLU Chi-restraints excluded: chain E residue 237 SER Chi-restraints excluded: chain E residue 251 SER Chi-restraints excluded: chain E residue 297 VAL Chi-restraints excluded: chain E residue 304 ILE Chi-restraints excluded: chain E residue 335 GLU Chi-restraints excluded: chain E residue 338 SER Chi-restraints excluded: chain E residue 340 THR Chi-restraints excluded: chain E residue 370 CYS Chi-restraints excluded: chain E residue 416 SER Chi-restraints excluded: chain E residue 439 ILE Chi-restraints excluded: chain E residue 527 LYS Chi-restraints excluded: chain E residue 568 GLU Chi-restraints excluded: chain E residue 580 ILE Chi-restraints excluded: chain E residue 588 VAL Chi-restraints excluded: chain E residue 598 THR Chi-restraints excluded: chain E residue 599 SER Chi-restraints excluded: chain E residue 668 SER Chi-restraints excluded: chain E residue 731 SER Chi-restraints excluded: chain E residue 808 GLU Chi-restraints excluded: chain E residue 834 GLU Chi-restraints excluded: chain E residue 845 ASN Chi-restraints excluded: chain F residue 126 ILE Chi-restraints excluded: chain F residue 127 SER Chi-restraints excluded: chain F residue 128 LEU Chi-restraints excluded: chain F residue 210 ILE Chi-restraints excluded: chain F residue 251 SER Chi-restraints excluded: chain F residue 274 LEU Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 353 VAL Chi-restraints excluded: chain F residue 439 ILE Chi-restraints excluded: chain F residue 510 THR Chi-restraints excluded: chain F residue 547 SER Chi-restraints excluded: chain F residue 576 ILE Chi-restraints excluded: chain F residue 580 ILE Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 646 LEU Chi-restraints excluded: chain F residue 739 LEU Chi-restraints excluded: chain F residue 820 VAL Chi-restraints excluded: chain F residue 829 VAL Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 27 THR Chi-restraints excluded: chain G residue 44 ASP Chi-restraints excluded: chain G residue 74 GLU Chi-restraints excluded: chain G residue 88 VAL Chi-restraints excluded: chain G residue 128 LEU Chi-restraints excluded: chain G residue 323 VAL Chi-restraints excluded: chain G residue 332 PHE Chi-restraints excluded: chain G residue 335 GLU Chi-restraints excluded: chain G residue 358 LYS Chi-restraints excluded: chain G residue 398 THR Chi-restraints excluded: chain G residue 436 LYS Chi-restraints excluded: chain G residue 441 LYS Chi-restraints excluded: chain G residue 471 LEU Chi-restraints excluded: chain G residue 568 GLU Chi-restraints excluded: chain G residue 576 ILE Chi-restraints excluded: chain G residue 695 LYS Chi-restraints excluded: chain G residue 712 ILE Chi-restraints excluded: chain G residue 808 GLU Chi-restraints excluded: chain H residue 510 THR Chi-restraints excluded: chain H residue 598 THR Chi-restraints excluded: chain H residue 611 VAL Chi-restraints excluded: chain H residue 614 ASP Chi-restraints excluded: chain H residue 712 ILE Chi-restraints excluded: chain H residue 722 CYS Chi-restraints excluded: chain H residue 782 LEU Chi-restraints excluded: chain H residue 799 LEU Chi-restraints excluded: chain H residue 816 ARG Chi-restraints excluded: chain H residue 822 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 598 random chunks: chunk 537 optimal weight: 9.9990 chunk 409 optimal weight: 4.9990 chunk 282 optimal weight: 10.0000 chunk 60 optimal weight: 7.9990 chunk 259 optimal weight: 3.9990 chunk 365 optimal weight: 6.9990 chunk 545 optimal weight: 2.9990 chunk 578 optimal weight: 9.9990 chunk 285 optimal weight: 3.9990 chunk 517 optimal weight: 7.9990 chunk 155 optimal weight: 8.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 737 HIS ** B 845 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 250 GLN D 561 HIS E 565 HIS E 737 HIS F 727 HIS F 754 ASN G 78 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.3879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 47016 Z= 0.316 Angle : 0.695 15.441 63778 Z= 0.354 Chirality : 0.049 0.259 7318 Planarity : 0.005 0.056 8262 Dihedral : 5.499 59.392 6480 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 4.27 % Allowed : 14.97 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.87 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (0.11), residues: 6036 helix: -0.21 (0.10), residues: 2658 sheet: -0.67 (0.16), residues: 942 loop : -2.58 (0.12), residues: 2436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP F 424 HIS 0.008 0.001 HIS H 704 PHE 0.020 0.002 PHE G 513 TYR 0.022 0.002 TYR B 690 ARG 0.004 0.001 ARG G 572 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12072 Ramachandran restraints generated. 6036 Oldfield, 0 Emsley, 6036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12072 Ramachandran restraints generated. 6036 Oldfield, 0 Emsley, 6036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 855 residues out of total 4850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 207 poor density : 648 time to evaluate : 4.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 509 GLU cc_start: 0.8232 (mp0) cc_final: 0.7996 (mp0) REVERT: A 514 PHE cc_start: 0.7445 (p90) cc_final: 0.7015 (p90) REVERT: A 538 ASP cc_start: 0.7455 (p0) cc_final: 0.7015 (t0) REVERT: A 549 MET cc_start: 0.6248 (mtt) cc_final: 0.6014 (mtt) REVERT: A 550 ASP cc_start: 0.7836 (p0) cc_final: 0.7514 (m-30) REVERT: A 574 MET cc_start: 0.6936 (mtp) cc_final: 0.6649 (mtm) REVERT: A 777 GLU cc_start: 0.6982 (mt-10) cc_final: 0.6781 (mm-30) REVERT: B 92 ASP cc_start: 0.4896 (t0) cc_final: 0.4347 (p0) REVERT: B 102 GLU cc_start: 0.8319 (pp20) cc_final: 0.8095 (pp20) REVERT: B 176 GLU cc_start: 0.8464 (pt0) cc_final: 0.7606 (mm-30) REVERT: B 318 ILE cc_start: 0.8443 (mm) cc_final: 0.7988 (pt) REVERT: B 335 GLU cc_start: 0.8070 (pp20) cc_final: 0.7606 (pp20) REVERT: B 357 GLU cc_start: 0.8476 (mt-10) cc_final: 0.7927 (mt-10) REVERT: B 365 ILE cc_start: 0.8912 (mt) cc_final: 0.8539 (mp) REVERT: B 447 ARG cc_start: 0.7386 (ttt-90) cc_final: 0.5954 (ttp80) REVERT: B 509 GLU cc_start: 0.6044 (mp0) cc_final: 0.5395 (mp0) REVERT: B 563 GLU cc_start: 0.8976 (tp30) cc_final: 0.8773 (tp30) REVERT: B 574 MET cc_start: 0.7916 (ptm) cc_final: 0.7466 (ptt) REVERT: B 773 ARG cc_start: 0.8166 (ttm170) cc_final: 0.7753 (ttt180) REVERT: B 848 TYR cc_start: 0.7920 (t80) cc_final: 0.7431 (t80) REVERT: B 869 GLU cc_start: 0.4952 (OUTLIER) cc_final: 0.4437 (pt0) REVERT: C 17 LYS cc_start: 0.8146 (tttt) cc_final: 0.7668 (ttmp) REVERT: C 59 MET cc_start: 0.7523 (pmt) cc_final: 0.7134 (pmm) REVERT: C 90 SER cc_start: 0.7549 (m) cc_final: 0.6863 (p) REVERT: C 148 LYS cc_start: 0.8778 (tptt) cc_final: 0.8314 (mptt) REVERT: C 200 LYS cc_start: 0.7711 (OUTLIER) cc_final: 0.7511 (mmtp) REVERT: C 250 GLN cc_start: 0.4774 (OUTLIER) cc_final: 0.4027 (mm-40) REVERT: C 251 SER cc_start: 0.7014 (m) cc_final: 0.6442 (t) REVERT: C 293 ASN cc_start: 0.6278 (t0) cc_final: 0.5572 (p0) REVERT: C 377 ASN cc_start: 0.7984 (m110) cc_final: 0.7734 (p0) REVERT: C 432 ASN cc_start: 0.8012 (p0) cc_final: 0.7477 (t0) REVERT: C 565 HIS cc_start: 0.7522 (t-90) cc_final: 0.7091 (t-90) REVERT: C 578 LYS cc_start: 0.8546 (mmtt) cc_final: 0.8192 (mmtt) REVERT: C 582 LYS cc_start: 0.8571 (ptmt) cc_final: 0.8165 (ttmm) REVERT: C 604 GLU cc_start: 0.9051 (pm20) cc_final: 0.8724 (pm20) REVERT: C 631 MET cc_start: 0.8901 (ttp) cc_final: 0.8621 (ttp) REVERT: C 728 LYS cc_start: 0.8573 (mmmt) cc_final: 0.7875 (mmtp) REVERT: C 799 LEU cc_start: 0.8151 (OUTLIER) cc_final: 0.7862 (tp) REVERT: D 99 THR cc_start: 0.9079 (m) cc_final: 0.8690 (p) REVERT: D 128 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8391 (pt) REVERT: D 155 GLN cc_start: 0.8180 (OUTLIER) cc_final: 0.6797 (mp10) REVERT: D 421 CYS cc_start: 0.8357 (t) cc_final: 0.7963 (t) REVERT: D 515 GLU cc_start: 0.7551 (mp0) cc_final: 0.7230 (mp0) REVERT: D 530 GLU cc_start: 0.8367 (tp30) cc_final: 0.8056 (tp30) REVERT: D 565 HIS cc_start: 0.7794 (OUTLIER) cc_final: 0.7424 (t-90) REVERT: D 576 ILE cc_start: 0.8380 (OUTLIER) cc_final: 0.8142 (mt) REVERT: D 777 GLU cc_start: 0.8235 (mt-10) cc_final: 0.7892 (mt-10) REVERT: D 784 LEU cc_start: 0.9110 (mt) cc_final: 0.8792 (mt) REVERT: D 799 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8317 (pt) REVERT: D 808 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7594 (pm20) REVERT: E 64 ASP cc_start: 0.8359 (m-30) cc_final: 0.7663 (m-30) REVERT: E 172 GLN cc_start: 0.8769 (mp10) cc_final: 0.8118 (mp10) REVERT: E 477 ASP cc_start: 0.7739 (t0) cc_final: 0.7504 (p0) REVERT: E 517 GLU cc_start: 0.8760 (mm-30) cc_final: 0.8476 (mm-30) REVERT: F 18 LYS cc_start: 0.8173 (tttm) cc_final: 0.7959 (tppt) REVERT: F 59 MET cc_start: 0.7448 (pmt) cc_final: 0.6720 (pmm) REVERT: F 82 ASP cc_start: 0.8750 (p0) cc_final: 0.8514 (p0) REVERT: F 86 CYS cc_start: 0.8689 (m) cc_final: 0.8198 (m) REVERT: F 90 SER cc_start: 0.8199 (m) cc_final: 0.7867 (p) REVERT: F 229 ARG cc_start: 0.8406 (mtt180) cc_final: 0.7637 (mmp-170) REVERT: F 241 ASP cc_start: 0.8097 (t0) cc_final: 0.7589 (t0) REVERT: F 272 TYR cc_start: 0.6707 (t80) cc_final: 0.5855 (t80) REVERT: F 378 GLN cc_start: 0.8613 (mp10) cc_final: 0.7954 (mp10) REVERT: F 517 GLU cc_start: 0.8254 (tp30) cc_final: 0.7994 (tp30) REVERT: F 549 MET cc_start: 0.7612 (mtp) cc_final: 0.7399 (mtm) REVERT: F 558 MET cc_start: 0.8656 (mtp) cc_final: 0.8369 (mtp) REVERT: F 582 LYS cc_start: 0.8613 (ptmt) cc_final: 0.7946 (mttm) REVERT: F 770 GLN cc_start: 0.8179 (OUTLIER) cc_final: 0.7842 (mm-40) REVERT: F 784 LEU cc_start: 0.8707 (mt) cc_final: 0.8497 (mp) REVERT: G 102 GLU cc_start: 0.8643 (OUTLIER) cc_final: 0.8389 (pt0) REVERT: G 236 MET cc_start: 0.8911 (ttt) cc_final: 0.8693 (tmm) REVERT: G 254 VAL cc_start: 0.9256 (t) cc_final: 0.9056 (p) REVERT: G 447 ARG cc_start: 0.7689 (ttt-90) cc_final: 0.6958 (ttp-170) REVERT: G 458 LYS cc_start: 0.8197 (ttpt) cc_final: 0.7429 (tptt) REVERT: G 471 LEU cc_start: 0.7903 (OUTLIER) cc_final: 0.7623 (pp) REVERT: G 513 PHE cc_start: 0.8075 (t80) cc_final: 0.7725 (t80) REVERT: G 574 MET cc_start: 0.7860 (mmm) cc_final: 0.7497 (mmm) REVERT: G 640 MET cc_start: 0.7970 (mmt) cc_final: 0.7594 (mmt) REVERT: G 817 GLU cc_start: 0.9071 (mp0) cc_final: 0.8829 (mp0) REVERT: G 834 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.7571 (pm20) REVERT: G 858 LEU cc_start: 0.9077 (mt) cc_final: 0.8788 (mt) REVERT: H 477 ASP cc_start: 0.8016 (t0) cc_final: 0.7432 (p0) REVERT: H 519 ASP cc_start: 0.7842 (m-30) cc_final: 0.7006 (t70) REVERT: H 520 PRO cc_start: 0.7577 (Cg_exo) cc_final: 0.7200 (Cg_endo) REVERT: H 581 TYR cc_start: 0.7760 (t80) cc_final: 0.7527 (t80) REVERT: H 582 LYS cc_start: 0.7572 (mmmt) cc_final: 0.7296 (mmtt) REVERT: H 592 MET cc_start: 0.8703 (ttt) cc_final: 0.8437 (ttp) REVERT: H 750 ARG cc_start: 0.6958 (mtt90) cc_final: 0.6738 (mtt90) REVERT: H 770 GLN cc_start: 0.6870 (tp-100) cc_final: 0.5854 (tt0) REVERT: H 796 GLU cc_start: 0.8540 (tm-30) cc_final: 0.7806 (mm-30) REVERT: H 816 ARG cc_start: 0.7072 (OUTLIER) cc_final: 0.6552 (ptm160) REVERT: H 847 ARG cc_start: 0.5258 (ptp-170) cc_final: 0.4960 (ptm160) REVERT: H 866 ASP cc_start: 0.4629 (p0) cc_final: 0.4185 (p0) outliers start: 207 outliers final: 145 residues processed: 796 average time/residue: 0.5091 time to fit residues: 684.7813 Evaluate side-chains 755 residues out of total 4850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 160 poor density : 595 time to evaluate : 5.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 604 GLU Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 722 CYS Chi-restraints excluded: chain A residue 725 MET Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 857 ILE Chi-restraints excluded: chain A residue 859 LEU Chi-restraints excluded: chain A residue 863 TYR Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 108 CYS Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 182 MET Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 246 CYS Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 370 CYS Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 497 ASP Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 588 VAL Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 634 VAL Chi-restraints excluded: chain B residue 682 LEU Chi-restraints excluded: chain B residue 735 ILE Chi-restraints excluded: chain B residue 834 GLU Chi-restraints excluded: chain B residue 869 GLU Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 46 ARG Chi-restraints excluded: chain C residue 108 CYS Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 200 LYS Chi-restraints excluded: chain C residue 250 GLN Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 316 THR Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 359 LEU Chi-restraints excluded: chain C residue 391 THR Chi-restraints excluded: chain C residue 398 THR Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain C residue 558 MET Chi-restraints excluded: chain C residue 586 MET Chi-restraints excluded: chain C residue 598 THR Chi-restraints excluded: chain C residue 668 SER Chi-restraints excluded: chain C residue 701 GLU Chi-restraints excluded: chain C residue 799 LEU Chi-restraints excluded: chain C residue 829 VAL Chi-restraints excluded: chain C residue 834 GLU Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 155 GLN Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 323 VAL Chi-restraints excluded: chain D residue 486 THR Chi-restraints excluded: chain D residue 565 HIS Chi-restraints excluded: chain D residue 568 GLU Chi-restraints excluded: chain D residue 576 ILE Chi-restraints excluded: chain D residue 580 ILE Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain D residue 652 LEU Chi-restraints excluded: chain D residue 668 SER Chi-restraints excluded: chain D residue 714 PHE Chi-restraints excluded: chain D residue 725 MET Chi-restraints excluded: chain D residue 739 LEU Chi-restraints excluded: chain D residue 799 LEU Chi-restraints excluded: chain D residue 808 GLU Chi-restraints excluded: chain E residue 237 SER Chi-restraints excluded: chain E residue 297 VAL Chi-restraints excluded: chain E residue 304 ILE Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 332 PHE Chi-restraints excluded: chain E residue 338 SER Chi-restraints excluded: chain E residue 340 THR Chi-restraints excluded: chain E residue 370 CYS Chi-restraints excluded: chain E residue 416 SER Chi-restraints excluded: chain E residue 439 ILE Chi-restraints excluded: chain E residue 469 ILE Chi-restraints excluded: chain E residue 580 ILE Chi-restraints excluded: chain E residue 588 VAL Chi-restraints excluded: chain E residue 599 SER Chi-restraints excluded: chain E residue 668 SER Chi-restraints excluded: chain E residue 731 SER Chi-restraints excluded: chain E residue 808 GLU Chi-restraints excluded: chain E residue 811 ILE Chi-restraints excluded: chain E residue 834 GLU Chi-restraints excluded: chain F residue 126 ILE Chi-restraints excluded: chain F residue 127 SER Chi-restraints excluded: chain F residue 128 LEU Chi-restraints excluded: chain F residue 210 ILE Chi-restraints excluded: chain F residue 251 SER Chi-restraints excluded: chain F residue 274 LEU Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 312 VAL Chi-restraints excluded: chain F residue 343 MET Chi-restraints excluded: chain F residue 353 VAL Chi-restraints excluded: chain F residue 368 THR Chi-restraints excluded: chain F residue 439 ILE Chi-restraints excluded: chain F residue 469 ILE Chi-restraints excluded: chain F residue 510 THR Chi-restraints excluded: chain F residue 525 VAL Chi-restraints excluded: chain F residue 547 SER Chi-restraints excluded: chain F residue 576 ILE Chi-restraints excluded: chain F residue 580 ILE Chi-restraints excluded: chain F residue 592 MET Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 646 LEU Chi-restraints excluded: chain F residue 739 LEU Chi-restraints excluded: chain F residue 754 ASN Chi-restraints excluded: chain F residue 770 GLN Chi-restraints excluded: chain F residue 820 VAL Chi-restraints excluded: chain F residue 829 VAL Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 44 ASP Chi-restraints excluded: chain G residue 74 GLU Chi-restraints excluded: chain G residue 86 CYS Chi-restraints excluded: chain G residue 88 VAL Chi-restraints excluded: chain G residue 102 GLU Chi-restraints excluded: chain G residue 128 LEU Chi-restraints excluded: chain G residue 134 ILE Chi-restraints excluded: chain G residue 210 ILE Chi-restraints excluded: chain G residue 226 ASP Chi-restraints excluded: chain G residue 323 VAL Chi-restraints excluded: chain G residue 325 VAL Chi-restraints excluded: chain G residue 332 PHE Chi-restraints excluded: chain G residue 335 GLU Chi-restraints excluded: chain G residue 358 LYS Chi-restraints excluded: chain G residue 398 THR Chi-restraints excluded: chain G residue 436 LYS Chi-restraints excluded: chain G residue 471 LEU Chi-restraints excluded: chain G residue 510 THR Chi-restraints excluded: chain G residue 660 GLU Chi-restraints excluded: chain G residue 668 SER Chi-restraints excluded: chain G residue 695 LYS Chi-restraints excluded: chain G residue 712 ILE Chi-restraints excluded: chain G residue 808 GLU Chi-restraints excluded: chain G residue 834 GLU Chi-restraints excluded: chain H residue 510 THR Chi-restraints excluded: chain H residue 576 ILE Chi-restraints excluded: chain H residue 598 THR Chi-restraints excluded: chain H residue 611 VAL Chi-restraints excluded: chain H residue 712 ILE Chi-restraints excluded: chain H residue 722 CYS Chi-restraints excluded: chain H residue 778 ILE Chi-restraints excluded: chain H residue 782 LEU Chi-restraints excluded: chain H residue 799 LEU Chi-restraints excluded: chain H residue 816 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 598 random chunks: chunk 481 optimal weight: 4.9990 chunk 328 optimal weight: 0.8980 chunk 8 optimal weight: 6.9990 chunk 430 optimal weight: 0.9990 chunk 238 optimal weight: 4.9990 chunk 493 optimal weight: 0.9990 chunk 399 optimal weight: 0.0030 chunk 0 optimal weight: 20.0000 chunk 295 optimal weight: 0.9980 chunk 518 optimal weight: 5.9990 chunk 145 optimal weight: 2.9990 overall best weight: 0.7794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 732 GLN B 737 HIS C 250 GLN D 387 GLN D 828 ASN E 737 HIS F 754 ASN ** G 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 69 ASN G 760 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.4091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 47016 Z= 0.148 Angle : 0.592 14.035 63778 Z= 0.296 Chirality : 0.044 0.247 7318 Planarity : 0.004 0.053 8262 Dihedral : 4.786 50.434 6480 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 2.83 % Allowed : 17.07 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.90 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.11), residues: 6036 helix: 0.28 (0.10), residues: 2640 sheet: -0.51 (0.17), residues: 954 loop : -2.35 (0.12), residues: 2442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 424 HIS 0.005 0.001 HIS B 704 PHE 0.017 0.001 PHE H 489 TYR 0.014 0.001 TYR A 862 ARG 0.004 0.000 ARG C 790 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12072 Ramachandran restraints generated. 6036 Oldfield, 0 Emsley, 6036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12072 Ramachandran restraints generated. 6036 Oldfield, 0 Emsley, 6036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 862 residues out of total 4850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 725 time to evaluate : 5.364 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: A 509 GLU cc_start: 0.8447 (mp0) cc_final: 0.7620 (mp0) REVERT: A 514 PHE cc_start: 0.7426 (p90) cc_final: 0.6763 (p90) REVERT: A 538 ASP cc_start: 0.7329 (p0) cc_final: 0.7048 (t0) REVERT: A 574 MET cc_start: 0.7080 (mtp) cc_final: 0.6737 (mtm) REVERT: A 592 MET cc_start: 0.7732 (tpp) cc_final: 0.7512 (tpp) REVERT: A 777 GLU cc_start: 0.7177 (mt-10) cc_final: 0.6958 (mm-30) REVERT: B 92 ASP cc_start: 0.5139 (t0) cc_final: 0.4563 (p0) REVERT: B 102 GLU cc_start: 0.8274 (pp20) cc_final: 0.7922 (pp20) REVERT: B 176 GLU cc_start: 0.8426 (pt0) cc_final: 0.7520 (mm-30) REVERT: B 318 ILE cc_start: 0.8351 (mm) cc_final: 0.7849 (pt) REVERT: B 335 GLU cc_start: 0.8012 (pp20) cc_final: 0.7574 (pp20) REVERT: B 365 ILE cc_start: 0.8905 (mt) cc_final: 0.8547 (mp) REVERT: B 447 ARG cc_start: 0.7367 (ttt-90) cc_final: 0.5945 (ttp80) REVERT: B 563 GLU cc_start: 0.8995 (tp30) cc_final: 0.8777 (tp30) REVERT: B 574 MET cc_start: 0.7799 (ptm) cc_final: 0.7381 (ptt) REVERT: B 641 ASP cc_start: 0.7159 (m-30) cc_final: 0.6015 (t0) REVERT: B 671 SER cc_start: 0.8754 (p) cc_final: 0.8540 (p) REVERT: B 773 ARG cc_start: 0.8136 (ttm170) cc_final: 0.7740 (ttt180) REVERT: B 775 TYR cc_start: 0.7378 (m-10) cc_final: 0.7131 (m-80) REVERT: B 848 TYR cc_start: 0.7756 (t80) cc_final: 0.7218 (t80) REVERT: C 22 GLU cc_start: 0.7991 (tp30) cc_final: 0.7504 (mt-10) REVERT: C 59 MET cc_start: 0.7501 (pmt) cc_final: 0.7179 (pmm) REVERT: C 148 LYS cc_start: 0.8741 (tptt) cc_final: 0.8298 (mptt) REVERT: C 250 GLN cc_start: 0.4676 (OUTLIER) cc_final: 0.3801 (mm110) REVERT: C 251 SER cc_start: 0.7109 (m) cc_final: 0.6594 (t) REVERT: C 358 LYS cc_start: 0.8103 (tppt) cc_final: 0.7840 (tppt) REVERT: C 389 MET cc_start: 0.8254 (tpp) cc_final: 0.7712 (ttt) REVERT: C 427 ASN cc_start: 0.7753 (m-40) cc_final: 0.7523 (m-40) REVERT: C 432 ASN cc_start: 0.7859 (p0) cc_final: 0.7463 (t0) REVERT: C 565 HIS cc_start: 0.7291 (t-90) cc_final: 0.6762 (t-90) REVERT: C 577 ARG cc_start: 0.8185 (mtm180) cc_final: 0.7581 (mtm180) REVERT: C 578 LYS cc_start: 0.8517 (mmtt) cc_final: 0.8179 (mmtt) REVERT: C 582 LYS cc_start: 0.8521 (ptmt) cc_final: 0.8100 (ttmm) REVERT: C 604 GLU cc_start: 0.9024 (pm20) cc_final: 0.8665 (pm20) REVERT: C 631 MET cc_start: 0.8910 (ttp) cc_final: 0.8651 (ttp) REVERT: C 642 MET cc_start: 0.8338 (ptt) cc_final: 0.8048 (ptm) REVERT: C 660 GLU cc_start: 0.7962 (tp30) cc_final: 0.7564 (tp30) REVERT: C 728 LYS cc_start: 0.8499 (mmmt) cc_final: 0.8117 (mmtp) REVERT: C 755 ASP cc_start: 0.7075 (p0) cc_final: 0.6562 (t70) REVERT: C 799 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.7864 (tp) REVERT: C 845 ASN cc_start: 0.8467 (OUTLIER) cc_final: 0.8225 (m-40) REVERT: D 99 THR cc_start: 0.8953 (m) cc_final: 0.8505 (p) REVERT: D 155 GLN cc_start: 0.8056 (OUTLIER) cc_final: 0.6702 (mp10) REVERT: D 216 ASN cc_start: 0.9106 (p0) cc_final: 0.8680 (p0) REVERT: D 421 CYS cc_start: 0.8312 (t) cc_final: 0.7829 (t) REVERT: D 515 GLU cc_start: 0.7556 (mp0) cc_final: 0.7246 (mp0) REVERT: D 530 GLU cc_start: 0.8346 (tp30) cc_final: 0.8015 (tp30) REVERT: D 565 HIS cc_start: 0.7786 (OUTLIER) cc_final: 0.7544 (t-90) REVERT: D 777 GLU cc_start: 0.8163 (mt-10) cc_final: 0.7912 (mt-10) REVERT: D 784 LEU cc_start: 0.9084 (mt) cc_final: 0.8798 (mt) REVERT: D 799 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8216 (pt) REVERT: D 808 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.7529 (pm20) REVERT: E 59 MET cc_start: 0.8339 (OUTLIER) cc_final: 0.7712 (pmt) REVERT: E 172 GLN cc_start: 0.8748 (mp10) cc_final: 0.8036 (mp10) REVERT: E 335 GLU cc_start: 0.8660 (mt-10) cc_final: 0.8420 (mt-10) REVERT: E 517 GLU cc_start: 0.8528 (mm-30) cc_final: 0.8241 (mm-30) REVERT: E 565 HIS cc_start: 0.7864 (t-90) cc_final: 0.7601 (t-90) REVERT: E 639 VAL cc_start: 0.8806 (t) cc_final: 0.8526 (m) REVERT: F 18 LYS cc_start: 0.8166 (tttm) cc_final: 0.7930 (tppt) REVERT: F 59 MET cc_start: 0.7352 (pmt) cc_final: 0.6649 (pmm) REVERT: F 82 ASP cc_start: 0.8747 (p0) cc_final: 0.8526 (p0) REVERT: F 229 ARG cc_start: 0.8331 (mtt180) cc_final: 0.7620 (mmp-170) REVERT: F 241 ASP cc_start: 0.7879 (t0) cc_final: 0.7353 (t0) REVERT: F 272 TYR cc_start: 0.6737 (t80) cc_final: 0.5732 (t80) REVERT: F 362 MET cc_start: 0.8234 (OUTLIER) cc_final: 0.7948 (mpp) REVERT: F 378 GLN cc_start: 0.8545 (mp10) cc_final: 0.7940 (mp10) REVERT: F 389 MET cc_start: 0.8956 (ttm) cc_final: 0.8713 (mtp) REVERT: F 391 THR cc_start: 0.7590 (p) cc_final: 0.7157 (t) REVERT: F 515 GLU cc_start: 0.8545 (mt-10) cc_final: 0.7558 (mm-30) REVERT: F 517 GLU cc_start: 0.8186 (tp30) cc_final: 0.7915 (tp30) REVERT: F 565 HIS cc_start: 0.8094 (OUTLIER) cc_final: 0.7444 (t-170) REVERT: F 582 LYS cc_start: 0.8488 (ptmt) cc_final: 0.7973 (mttm) REVERT: F 784 LEU cc_start: 0.8582 (mt) cc_final: 0.8204 (mp) REVERT: G 57 SER cc_start: 0.5459 (p) cc_final: 0.5230 (p) REVERT: G 127 SER cc_start: 0.8983 (m) cc_final: 0.8730 (p) REVERT: G 388 LYS cc_start: 0.8302 (mmmm) cc_final: 0.7975 (tppp) REVERT: G 447 ARG cc_start: 0.7588 (ttt-90) cc_final: 0.6884 (ttp-170) REVERT: G 458 LYS cc_start: 0.8128 (ttpt) cc_final: 0.7272 (tptt) REVERT: G 574 MET cc_start: 0.7830 (mmm) cc_final: 0.7503 (mmm) REVERT: G 576 ILE cc_start: 0.8198 (OUTLIER) cc_final: 0.7979 (mm) REVERT: G 604 GLU cc_start: 0.9151 (pm20) cc_final: 0.8711 (pm20) REVERT: G 640 MET cc_start: 0.8166 (mmt) cc_final: 0.7913 (mmt) REVERT: G 642 MET cc_start: 0.8545 (ptm) cc_final: 0.8314 (ptm) REVERT: G 817 GLU cc_start: 0.9068 (mp0) cc_final: 0.8824 (mp0) REVERT: G 834 GLU cc_start: 0.7910 (OUTLIER) cc_final: 0.7605 (pm20) REVERT: H 477 ASP cc_start: 0.7883 (t0) cc_final: 0.7352 (p0) REVERT: H 481 ARG cc_start: 0.7025 (mtp85) cc_final: 0.6482 (ttm110) REVERT: H 519 ASP cc_start: 0.7813 (m-30) cc_final: 0.6978 (t70) REVERT: H 520 PRO cc_start: 0.7429 (Cg_exo) cc_final: 0.6927 (Cg_endo) REVERT: H 581 TYR cc_start: 0.7775 (t80) cc_final: 0.7491 (t80) REVERT: H 750 ARG cc_start: 0.6812 (mtt90) cc_final: 0.6589 (mtt90) REVERT: H 796 GLU cc_start: 0.8528 (tm-30) cc_final: 0.7819 (mm-30) REVERT: H 799 LEU cc_start: 0.7980 (OUTLIER) cc_final: 0.7707 (tt) REVERT: H 847 ARG cc_start: 0.5172 (ptp-170) cc_final: 0.4850 (ptm160) REVERT: H 859 LEU cc_start: 0.5780 (OUTLIER) cc_final: 0.5166 (pp) REVERT: H 866 ASP cc_start: 0.4636 (p0) cc_final: 0.4273 (p0) outliers start: 137 outliers final: 69 residues processed: 824 average time/residue: 0.4792 time to fit residues: 671.2585 Evaluate side-chains 723 residues out of total 4850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 640 time to evaluate : 5.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 725 MET Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 857 ILE Chi-restraints excluded: chain A residue 863 TYR Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 108 CYS Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 588 VAL Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 634 VAL Chi-restraints excluded: chain B residue 682 LEU Chi-restraints excluded: chain B residue 714 PHE Chi-restraints excluded: chain B residue 782 LEU Chi-restraints excluded: chain C residue 108 CYS Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 250 GLN Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 362 MET Chi-restraints excluded: chain C residue 391 THR Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain C residue 668 SER Chi-restraints excluded: chain C residue 701 GLU Chi-restraints excluded: chain C residue 739 LEU Chi-restraints excluded: chain C residue 768 ARG Chi-restraints excluded: chain C residue 799 LEU Chi-restraints excluded: chain C residue 845 ASN Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 155 GLN Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 323 VAL Chi-restraints excluded: chain D residue 387 GLN Chi-restraints excluded: chain D residue 508 VAL Chi-restraints excluded: chain D residue 565 HIS Chi-restraints excluded: chain D residue 652 LEU Chi-restraints excluded: chain D residue 668 SER Chi-restraints excluded: chain D residue 714 PHE Chi-restraints excluded: chain D residue 799 LEU Chi-restraints excluded: chain D residue 808 GLU Chi-restraints excluded: chain E residue 59 MET Chi-restraints excluded: chain E residue 216 ASN Chi-restraints excluded: chain E residue 251 SER Chi-restraints excluded: chain E residue 338 SER Chi-restraints excluded: chain E residue 340 THR Chi-restraints excluded: chain E residue 439 ILE Chi-restraints excluded: chain E residue 580 ILE Chi-restraints excluded: chain E residue 599 SER Chi-restraints excluded: chain E residue 668 SER Chi-restraints excluded: chain F residue 128 LEU Chi-restraints excluded: chain F residue 274 LEU Chi-restraints excluded: chain F residue 312 VAL Chi-restraints excluded: chain F residue 362 MET Chi-restraints excluded: chain F residue 547 SER Chi-restraints excluded: chain F residue 565 HIS Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 646 LEU Chi-restraints excluded: chain F residue 714 PHE Chi-restraints excluded: chain F residue 739 LEU Chi-restraints excluded: chain G residue 74 GLU Chi-restraints excluded: chain G residue 323 VAL Chi-restraints excluded: chain G residue 332 PHE Chi-restraints excluded: chain G residue 335 GLU Chi-restraints excluded: chain G residue 391 THR Chi-restraints excluded: chain G residue 576 ILE Chi-restraints excluded: chain G residue 668 SER Chi-restraints excluded: chain G residue 808 GLU Chi-restraints excluded: chain G residue 834 GLU Chi-restraints excluded: chain H residue 598 THR Chi-restraints excluded: chain H residue 611 VAL Chi-restraints excluded: chain H residue 614 ASP Chi-restraints excluded: chain H residue 712 ILE Chi-restraints excluded: chain H residue 722 CYS Chi-restraints excluded: chain H residue 744 LEU Chi-restraints excluded: chain H residue 799 LEU Chi-restraints excluded: chain H residue 859 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 598 random chunks: chunk 194 optimal weight: 0.4980 chunk 520 optimal weight: 10.0000 chunk 114 optimal weight: 30.0000 chunk 339 optimal weight: 20.0000 chunk 142 optimal weight: 0.5980 chunk 578 optimal weight: 9.9990 chunk 480 optimal weight: 10.0000 chunk 267 optimal weight: 7.9990 chunk 48 optimal weight: 9.9990 chunk 191 optimal weight: 1.9990 chunk 303 optimal weight: 0.7980 overall best weight: 2.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 754 ASN B 737 HIS C 250 GLN E 704 HIS E 737 HIS E 770 GLN F 172 GLN F 479 HIS F 727 HIS G 561 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.4234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 47016 Z= 0.199 Angle : 0.620 14.322 63778 Z= 0.311 Chirality : 0.046 0.237 7318 Planarity : 0.004 0.052 8262 Dihedral : 4.676 46.232 6478 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 3.12 % Allowed : 17.44 % Favored : 79.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.88 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.11), residues: 6036 helix: 0.41 (0.10), residues: 2660 sheet: -0.49 (0.17), residues: 978 loop : -2.34 (0.12), residues: 2398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 424 HIS 0.018 0.001 HIS A 561 PHE 0.020 0.001 PHE E 714 TYR 0.021 0.001 TYR G 302 ARG 0.005 0.000 ARG A 488 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12072 Ramachandran restraints generated. 6036 Oldfield, 0 Emsley, 6036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12072 Ramachandran restraints generated. 6036 Oldfield, 0 Emsley, 6036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 808 residues out of total 4850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 657 time to evaluate : 5.005 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 509 GLU cc_start: 0.8440 (mp0) cc_final: 0.8184 (mp0) REVERT: A 514 PHE cc_start: 0.7362 (p90) cc_final: 0.6852 (p90) REVERT: A 538 ASP cc_start: 0.7337 (p0) cc_final: 0.7028 (t0) REVERT: A 550 ASP cc_start: 0.7778 (p0) cc_final: 0.7490 (m-30) REVERT: A 574 MET cc_start: 0.7161 (mtp) cc_final: 0.6824 (mtm) REVERT: A 592 MET cc_start: 0.7633 (tpp) cc_final: 0.7389 (tpp) REVERT: A 777 GLU cc_start: 0.7191 (mt-10) cc_final: 0.6960 (mm-30) REVERT: B 92 ASP cc_start: 0.4811 (t0) cc_final: 0.4318 (p0) REVERT: B 102 GLU cc_start: 0.8286 (pp20) cc_final: 0.7913 (pp20) REVERT: B 176 GLU cc_start: 0.8465 (pt0) cc_final: 0.7558 (mm-30) REVERT: B 251 SER cc_start: 0.9188 (m) cc_final: 0.8882 (t) REVERT: B 318 ILE cc_start: 0.8468 (mm) cc_final: 0.7949 (pt) REVERT: B 335 GLU cc_start: 0.8041 (pp20) cc_final: 0.7596 (pp20) REVERT: B 365 ILE cc_start: 0.8878 (mt) cc_final: 0.8489 (mp) REVERT: B 387 GLN cc_start: 0.7305 (tm-30) cc_final: 0.6856 (tt0) REVERT: B 447 ARG cc_start: 0.7412 (ttt-90) cc_final: 0.5978 (ttp80) REVERT: B 451 MET cc_start: 0.8322 (ptm) cc_final: 0.7792 (mtm) REVERT: B 563 GLU cc_start: 0.9004 (tp30) cc_final: 0.8785 (tp30) REVERT: B 574 MET cc_start: 0.7793 (ptm) cc_final: 0.7359 (ptt) REVERT: B 671 SER cc_start: 0.8747 (p) cc_final: 0.8534 (p) REVERT: B 773 ARG cc_start: 0.8152 (ttm170) cc_final: 0.7740 (ttt180) REVERT: B 775 TYR cc_start: 0.7339 (m-10) cc_final: 0.7095 (m-80) REVERT: B 848 TYR cc_start: 0.7757 (t80) cc_final: 0.7206 (t80) REVERT: C 22 GLU cc_start: 0.8011 (tp30) cc_final: 0.7543 (mt-10) REVERT: C 59 MET cc_start: 0.7503 (pmt) cc_final: 0.6947 (pmm) REVERT: C 90 SER cc_start: 0.7632 (m) cc_final: 0.6989 (p) REVERT: C 148 LYS cc_start: 0.8838 (tptt) cc_final: 0.8395 (mptt) REVERT: C 250 GLN cc_start: 0.4409 (OUTLIER) cc_final: 0.4059 (mm110) REVERT: C 251 SER cc_start: 0.7188 (m) cc_final: 0.6695 (t) REVERT: C 357 GLU cc_start: 0.8234 (pp20) cc_final: 0.7869 (pt0) REVERT: C 427 ASN cc_start: 0.7745 (m-40) cc_final: 0.7512 (m-40) REVERT: C 432 ASN cc_start: 0.7911 (p0) cc_final: 0.7512 (t0) REVERT: C 565 HIS cc_start: 0.7165 (t-90) cc_final: 0.6907 (t-90) REVERT: C 567 GLU cc_start: 0.8580 (mp0) cc_final: 0.7208 (pt0) REVERT: C 578 LYS cc_start: 0.8537 (mmtt) cc_final: 0.8187 (mmtt) REVERT: C 582 LYS cc_start: 0.8547 (ptmt) cc_final: 0.8118 (ttmm) REVERT: C 604 GLU cc_start: 0.9027 (pm20) cc_final: 0.8669 (pm20) REVERT: C 631 MET cc_start: 0.8891 (ttp) cc_final: 0.8634 (ttp) REVERT: C 728 LYS cc_start: 0.8714 (mmmt) cc_final: 0.7970 (mmtp) REVERT: C 755 ASP cc_start: 0.6958 (p0) cc_final: 0.6454 (m-30) REVERT: C 799 LEU cc_start: 0.8261 (OUTLIER) cc_final: 0.7876 (tp) REVERT: D 59 MET cc_start: 0.8562 (OUTLIER) cc_final: 0.7963 (pmt) REVERT: D 99 THR cc_start: 0.9018 (m) cc_final: 0.8613 (p) REVERT: D 128 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.8240 (pt) REVERT: D 155 GLN cc_start: 0.8097 (OUTLIER) cc_final: 0.6720 (mp10) REVERT: D 421 CYS cc_start: 0.8357 (t) cc_final: 0.7848 (t) REVERT: D 515 GLU cc_start: 0.7625 (mp0) cc_final: 0.7311 (mp0) REVERT: D 530 GLU cc_start: 0.8400 (tp30) cc_final: 0.8065 (tp30) REVERT: D 565 HIS cc_start: 0.7830 (OUTLIER) cc_final: 0.7488 (t-90) REVERT: D 777 GLU cc_start: 0.8170 (mt-10) cc_final: 0.7877 (mt-10) REVERT: D 784 LEU cc_start: 0.9137 (mt) cc_final: 0.8851 (mt) REVERT: D 799 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.8140 (pt) REVERT: D 808 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.7516 (pm20) REVERT: E 59 MET cc_start: 0.8339 (OUTLIER) cc_final: 0.7779 (pmt) REVERT: E 172 GLN cc_start: 0.8748 (mp10) cc_final: 0.8116 (mp10) REVERT: E 275 GLN cc_start: 0.8493 (pp30) cc_final: 0.8262 (pp30) REVERT: E 335 GLU cc_start: 0.8684 (OUTLIER) cc_final: 0.8426 (mt-10) REVERT: E 441 LYS cc_start: 0.8753 (OUTLIER) cc_final: 0.8313 (mtpt) REVERT: E 517 GLU cc_start: 0.8667 (mm-30) cc_final: 0.8378 (mm-30) REVERT: E 565 HIS cc_start: 0.7956 (t-90) cc_final: 0.7691 (t-90) REVERT: E 639 VAL cc_start: 0.8834 (t) cc_final: 0.8488 (m) REVERT: E 770 GLN cc_start: 0.8329 (OUTLIER) cc_final: 0.7698 (mm110) REVERT: F 18 LYS cc_start: 0.8104 (tttm) cc_final: 0.7807 (tppt) REVERT: F 59 MET cc_start: 0.7378 (pmt) cc_final: 0.6676 (pmm) REVERT: F 82 ASP cc_start: 0.8752 (p0) cc_final: 0.8533 (p0) REVERT: F 95 PHE cc_start: 0.7973 (m-80) cc_final: 0.7756 (m-10) REVERT: F 229 ARG cc_start: 0.8390 (mtt180) cc_final: 0.7607 (mmp-170) REVERT: F 241 ASP cc_start: 0.7923 (t0) cc_final: 0.7405 (t0) REVERT: F 272 TYR cc_start: 0.6676 (t80) cc_final: 0.5824 (t80) REVERT: F 362 MET cc_start: 0.8327 (OUTLIER) cc_final: 0.8114 (mpp) REVERT: F 378 GLN cc_start: 0.8533 (mp10) cc_final: 0.7858 (mp10) REVERT: F 381 ARG cc_start: 0.7989 (mtp85) cc_final: 0.7170 (mtp85) REVERT: F 389 MET cc_start: 0.8992 (ttm) cc_final: 0.8692 (mtp) REVERT: F 515 GLU cc_start: 0.8551 (mt-10) cc_final: 0.7639 (mm-30) REVERT: F 517 GLU cc_start: 0.8205 (tp30) cc_final: 0.7897 (tp30) REVERT: F 582 LYS cc_start: 0.8594 (ptmt) cc_final: 0.8003 (mttm) REVERT: F 770 GLN cc_start: 0.8046 (OUTLIER) cc_final: 0.7705 (mm-40) REVERT: F 784 LEU cc_start: 0.8623 (mt) cc_final: 0.8408 (mp) REVERT: G 127 SER cc_start: 0.9042 (m) cc_final: 0.8759 (p) REVERT: G 274 LEU cc_start: 0.8060 (OUTLIER) cc_final: 0.7758 (pp) REVERT: G 388 LYS cc_start: 0.8309 (mmmm) cc_final: 0.8025 (tppp) REVERT: G 447 ARG cc_start: 0.7650 (ttt-90) cc_final: 0.6928 (ttp-170) REVERT: G 458 LYS cc_start: 0.8110 (ttpt) cc_final: 0.7320 (tptt) REVERT: G 574 MET cc_start: 0.7946 (mmm) cc_final: 0.7616 (mmm) REVERT: G 604 GLU cc_start: 0.9146 (pm20) cc_final: 0.8725 (pm20) REVERT: G 640 MET cc_start: 0.8217 (mmt) cc_final: 0.7990 (mmt) REVERT: G 684 GLU cc_start: 0.8565 (mp0) cc_final: 0.8116 (mp0) REVERT: G 817 GLU cc_start: 0.9065 (mp0) cc_final: 0.8821 (mp0) REVERT: G 834 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7579 (pm20) REVERT: H 477 ASP cc_start: 0.7792 (t0) cc_final: 0.7371 (p0) REVERT: H 519 ASP cc_start: 0.7912 (m-30) cc_final: 0.6986 (t70) REVERT: H 520 PRO cc_start: 0.7400 (Cg_exo) cc_final: 0.6944 (Cg_endo) REVERT: H 535 PHE cc_start: 0.7105 (t80) cc_final: 0.6741 (t80) REVERT: H 722 CYS cc_start: 0.7751 (OUTLIER) cc_final: 0.7353 (t) REVERT: H 750 ARG cc_start: 0.6832 (mtt90) cc_final: 0.6629 (mtt90) REVERT: H 796 GLU cc_start: 0.8534 (tm-30) cc_final: 0.7830 (mm-30) REVERT: H 859 LEU cc_start: 0.5810 (OUTLIER) cc_final: 0.5230 (pp) REVERT: H 866 ASP cc_start: 0.4650 (p0) cc_final: 0.4272 (p0) outliers start: 151 outliers final: 107 residues processed: 759 average time/residue: 0.4686 time to fit residues: 604.1393 Evaluate side-chains 753 residues out of total 4850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 628 time to evaluate : 4.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 645 SER Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain A residue 708 THR Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 725 MET Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 808 GLU Chi-restraints excluded: chain A residue 857 ILE Chi-restraints excluded: chain A residue 859 LEU Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 108 CYS Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 436 LYS Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 634 VAL Chi-restraints excluded: chain B residue 682 LEU Chi-restraints excluded: chain B residue 714 PHE Chi-restraints excluded: chain B residue 834 GLU Chi-restraints excluded: chain C residue 46 ARG Chi-restraints excluded: chain C residue 108 CYS Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 250 GLN Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 391 THR Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain C residue 549 MET Chi-restraints excluded: chain C residue 574 MET Chi-restraints excluded: chain C residue 586 MET Chi-restraints excluded: chain C residue 598 THR Chi-restraints excluded: chain C residue 701 GLU Chi-restraints excluded: chain C residue 768 ARG Chi-restraints excluded: chain C residue 799 LEU Chi-restraints excluded: chain C residue 834 GLU Chi-restraints excluded: chain D residue 59 MET Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 155 GLN Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 323 VAL Chi-restraints excluded: chain D residue 343 MET Chi-restraints excluded: chain D residue 387 GLN Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 508 VAL Chi-restraints excluded: chain D residue 565 HIS Chi-restraints excluded: chain D residue 580 ILE Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain D residue 652 LEU Chi-restraints excluded: chain D residue 668 SER Chi-restraints excluded: chain D residue 714 PHE Chi-restraints excluded: chain D residue 799 LEU Chi-restraints excluded: chain D residue 808 GLU Chi-restraints excluded: chain E residue 59 MET Chi-restraints excluded: chain E residue 216 ASN Chi-restraints excluded: chain E residue 297 VAL Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 335 GLU Chi-restraints excluded: chain E residue 338 SER Chi-restraints excluded: chain E residue 340 THR Chi-restraints excluded: chain E residue 439 ILE Chi-restraints excluded: chain E residue 441 LYS Chi-restraints excluded: chain E residue 443 THR Chi-restraints excluded: chain E residue 580 ILE Chi-restraints excluded: chain E residue 599 SER Chi-restraints excluded: chain E residue 668 SER Chi-restraints excluded: chain E residue 770 GLN Chi-restraints excluded: chain E residue 811 ILE Chi-restraints excluded: chain F residue 127 SER Chi-restraints excluded: chain F residue 128 LEU Chi-restraints excluded: chain F residue 172 GLN Chi-restraints excluded: chain F residue 210 ILE Chi-restraints excluded: chain F residue 251 SER Chi-restraints excluded: chain F residue 274 LEU Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 312 VAL Chi-restraints excluded: chain F residue 343 MET Chi-restraints excluded: chain F residue 362 MET Chi-restraints excluded: chain F residue 439 ILE Chi-restraints excluded: chain F residue 469 ILE Chi-restraints excluded: chain F residue 580 ILE Chi-restraints excluded: chain F residue 592 MET Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 646 LEU Chi-restraints excluded: chain F residue 712 ILE Chi-restraints excluded: chain F residue 727 HIS Chi-restraints excluded: chain F residue 739 LEU Chi-restraints excluded: chain F residue 770 GLN Chi-restraints excluded: chain G residue 52 MET Chi-restraints excluded: chain G residue 74 GLU Chi-restraints excluded: chain G residue 86 CYS Chi-restraints excluded: chain G residue 88 VAL Chi-restraints excluded: chain G residue 274 LEU Chi-restraints excluded: chain G residue 323 VAL Chi-restraints excluded: chain G residue 332 PHE Chi-restraints excluded: chain G residue 335 GLU Chi-restraints excluded: chain G residue 358 LYS Chi-restraints excluded: chain G residue 391 THR Chi-restraints excluded: chain G residue 508 VAL Chi-restraints excluded: chain G residue 660 GLU Chi-restraints excluded: chain G residue 668 SER Chi-restraints excluded: chain G residue 712 ILE Chi-restraints excluded: chain G residue 808 GLU Chi-restraints excluded: chain G residue 834 GLU Chi-restraints excluded: chain H residue 510 THR Chi-restraints excluded: chain H residue 576 ILE Chi-restraints excluded: chain H residue 598 THR Chi-restraints excluded: chain H residue 611 VAL Chi-restraints excluded: chain H residue 614 ASP Chi-restraints excluded: chain H residue 712 ILE Chi-restraints excluded: chain H residue 722 CYS Chi-restraints excluded: chain H residue 744 LEU Chi-restraints excluded: chain H residue 778 ILE Chi-restraints excluded: chain H residue 782 LEU Chi-restraints excluded: chain H residue 859 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 598 random chunks: chunk 557 optimal weight: 9.9990 chunk 65 optimal weight: 10.0000 chunk 329 optimal weight: 1.9990 chunk 422 optimal weight: 10.0000 chunk 327 optimal weight: 0.6980 chunk 487 optimal weight: 10.0000 chunk 323 optimal weight: 5.9990 chunk 576 optimal weight: 6.9990 chunk 360 optimal weight: 0.8980 chunk 351 optimal weight: 2.9990 chunk 266 optimal weight: 5.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 737 HIS C 250 GLN D 387 GLN D 479 HIS E 561 HIS E 737 HIS F 172 GLN G 727 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.4345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 47016 Z= 0.204 Angle : 0.622 14.329 63778 Z= 0.312 Chirality : 0.046 0.238 7318 Planarity : 0.004 0.052 8262 Dihedral : 4.616 46.219 6476 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 3.36 % Allowed : 17.86 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.92 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.11), residues: 6036 helix: 0.51 (0.10), residues: 2664 sheet: -0.42 (0.17), residues: 978 loop : -2.30 (0.12), residues: 2394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 424 HIS 0.023 0.001 HIS F 727 PHE 0.030 0.001 PHE E 489 TYR 0.037 0.001 TYR C 867 ARG 0.007 0.000 ARG C 790 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12072 Ramachandran restraints generated. 6036 Oldfield, 0 Emsley, 6036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12072 Ramachandran restraints generated. 6036 Oldfield, 0 Emsley, 6036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 806 residues out of total 4850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 643 time to evaluate : 4.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 509 GLU cc_start: 0.8463 (mp0) cc_final: 0.8198 (mp0) REVERT: A 514 PHE cc_start: 0.7450 (p90) cc_final: 0.6973 (p90) REVERT: A 538 ASP cc_start: 0.7420 (p0) cc_final: 0.7032 (t0) REVERT: A 550 ASP cc_start: 0.7778 (p0) cc_final: 0.7481 (m-30) REVERT: A 574 MET cc_start: 0.7323 (mtp) cc_final: 0.6981 (mtm) REVERT: A 592 MET cc_start: 0.7663 (tpp) cc_final: 0.7425 (tpp) REVERT: A 777 GLU cc_start: 0.7221 (mt-10) cc_final: 0.6973 (mm-30) REVERT: B 92 ASP cc_start: 0.5254 (t0) cc_final: 0.4850 (p0) REVERT: B 176 GLU cc_start: 0.8482 (pt0) cc_final: 0.7598 (mm-30) REVERT: B 251 SER cc_start: 0.9176 (m) cc_final: 0.8856 (t) REVERT: B 318 ILE cc_start: 0.8395 (mm) cc_final: 0.7902 (pt) REVERT: B 335 GLU cc_start: 0.8061 (pp20) cc_final: 0.7613 (pp20) REVERT: B 365 ILE cc_start: 0.8858 (mt) cc_final: 0.8478 (mp) REVERT: B 447 ARG cc_start: 0.7417 (ttt-90) cc_final: 0.5975 (ttp80) REVERT: B 451 MET cc_start: 0.8414 (ptm) cc_final: 0.7864 (mtm) REVERT: B 563 GLU cc_start: 0.9005 (tp30) cc_final: 0.8780 (tp30) REVERT: B 574 MET cc_start: 0.7772 (ptm) cc_final: 0.7338 (ptt) REVERT: B 671 SER cc_start: 0.8736 (p) cc_final: 0.8524 (p) REVERT: B 773 ARG cc_start: 0.8163 (ttm170) cc_final: 0.7738 (ttt180) REVERT: B 775 TYR cc_start: 0.7351 (m-10) cc_final: 0.7114 (m-80) REVERT: B 848 TYR cc_start: 0.7818 (t80) cc_final: 0.7259 (t80) REVERT: B 869 GLU cc_start: 0.4977 (OUTLIER) cc_final: 0.4389 (pt0) REVERT: C 22 GLU cc_start: 0.8000 (tp30) cc_final: 0.7541 (mt-10) REVERT: C 59 MET cc_start: 0.7474 (pmt) cc_final: 0.6855 (pmm) REVERT: C 90 SER cc_start: 0.7631 (m) cc_final: 0.6977 (p) REVERT: C 148 LYS cc_start: 0.8722 (tptt) cc_final: 0.8272 (mptt) REVERT: C 250 GLN cc_start: 0.4366 (OUTLIER) cc_final: 0.4111 (mm110) REVERT: C 251 SER cc_start: 0.7192 (m) cc_final: 0.6743 (t) REVERT: C 343 MET cc_start: 0.6045 (tmm) cc_final: 0.5620 (tmm) REVERT: C 359 LEU cc_start: 0.8221 (OUTLIER) cc_final: 0.7930 (tt) REVERT: C 432 ASN cc_start: 0.7934 (p0) cc_final: 0.7492 (t0) REVERT: C 509 GLU cc_start: 0.8084 (mp0) cc_final: 0.7687 (mp0) REVERT: C 567 GLU cc_start: 0.8560 (mp0) cc_final: 0.7270 (pt0) REVERT: C 578 LYS cc_start: 0.8539 (mmtt) cc_final: 0.8188 (mmtt) REVERT: C 582 LYS cc_start: 0.8618 (ptmt) cc_final: 0.8207 (ttmm) REVERT: C 604 GLU cc_start: 0.9035 (pm20) cc_final: 0.8660 (pm20) REVERT: C 631 MET cc_start: 0.8886 (ttp) cc_final: 0.8624 (ttp) REVERT: C 728 LYS cc_start: 0.8663 (mmmt) cc_final: 0.8025 (mmtp) REVERT: C 755 ASP cc_start: 0.7159 (p0) cc_final: 0.6625 (m-30) REVERT: C 799 LEU cc_start: 0.8241 (OUTLIER) cc_final: 0.7841 (tp) REVERT: D 59 MET cc_start: 0.8578 (OUTLIER) cc_final: 0.7979 (pmt) REVERT: D 99 THR cc_start: 0.9026 (m) cc_final: 0.8628 (p) REVERT: D 128 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8306 (pt) REVERT: D 155 GLN cc_start: 0.8108 (OUTLIER) cc_final: 0.6718 (mp10) REVERT: D 341 LEU cc_start: 0.7899 (OUTLIER) cc_final: 0.7078 (tt) REVERT: D 421 CYS cc_start: 0.8351 (t) cc_final: 0.7960 (t) REVERT: D 515 GLU cc_start: 0.7536 (mp0) cc_final: 0.7230 (mp0) REVERT: D 530 GLU cc_start: 0.8407 (tp30) cc_final: 0.8079 (tp30) REVERT: D 563 GLU cc_start: 0.8665 (mm-30) cc_final: 0.8429 (pm20) REVERT: D 565 HIS cc_start: 0.7768 (OUTLIER) cc_final: 0.7441 (t-90) REVERT: D 777 GLU cc_start: 0.8172 (mt-10) cc_final: 0.7883 (mt-10) REVERT: D 784 LEU cc_start: 0.9158 (mt) cc_final: 0.8870 (mt) REVERT: D 799 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.8159 (pt) REVERT: D 808 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7520 (pm20) REVERT: E 59 MET cc_start: 0.8355 (OUTLIER) cc_final: 0.7795 (pmt) REVERT: E 172 GLN cc_start: 0.8761 (mp10) cc_final: 0.8109 (mp10) REVERT: E 275 GLN cc_start: 0.8534 (pp30) cc_final: 0.8315 (pp30) REVERT: E 335 GLU cc_start: 0.8683 (OUTLIER) cc_final: 0.8429 (mt-10) REVERT: E 477 ASP cc_start: 0.8044 (OUTLIER) cc_final: 0.7582 (p0) REVERT: E 517 GLU cc_start: 0.8636 (mm-30) cc_final: 0.8392 (mm-30) REVERT: E 565 HIS cc_start: 0.7947 (t-90) cc_final: 0.7695 (t-90) REVERT: E 639 VAL cc_start: 0.8888 (t) cc_final: 0.8547 (m) REVERT: E 684 GLU cc_start: 0.8092 (mp0) cc_final: 0.7852 (mp0) REVERT: E 770 GLN cc_start: 0.8049 (tp40) cc_final: 0.7706 (mm110) REVERT: F 18 LYS cc_start: 0.8084 (tttm) cc_final: 0.7779 (tppt) REVERT: F 59 MET cc_start: 0.7377 (pmt) cc_final: 0.6717 (pmm) REVERT: F 82 ASP cc_start: 0.8761 (p0) cc_final: 0.8538 (p0) REVERT: F 95 PHE cc_start: 0.7872 (m-80) cc_final: 0.7659 (m-10) REVERT: F 229 ARG cc_start: 0.8444 (mtt180) cc_final: 0.7606 (mmp-170) REVERT: F 241 ASP cc_start: 0.7964 (t0) cc_final: 0.7465 (t0) REVERT: F 272 TYR cc_start: 0.6682 (t80) cc_final: 0.5814 (t80) REVERT: F 362 MET cc_start: 0.8359 (OUTLIER) cc_final: 0.8149 (mpp) REVERT: F 378 GLN cc_start: 0.8544 (mp10) cc_final: 0.7759 (mp10) REVERT: F 381 ARG cc_start: 0.8057 (mtp85) cc_final: 0.7258 (mtp85) REVERT: F 515 GLU cc_start: 0.8586 (mt-10) cc_final: 0.7660 (mm-30) REVERT: F 565 HIS cc_start: 0.8165 (OUTLIER) cc_final: 0.7473 (t-170) REVERT: F 582 LYS cc_start: 0.8599 (ptmt) cc_final: 0.8066 (mttm) REVERT: F 784 LEU cc_start: 0.8616 (mt) cc_final: 0.8402 (mp) REVERT: G 127 SER cc_start: 0.9055 (m) cc_final: 0.8765 (p) REVERT: G 274 LEU cc_start: 0.8036 (OUTLIER) cc_final: 0.7733 (pp) REVERT: G 388 LYS cc_start: 0.8339 (mmmm) cc_final: 0.8064 (tppp) REVERT: G 447 ARG cc_start: 0.7666 (ttt-90) cc_final: 0.6939 (ttp-170) REVERT: G 458 LYS cc_start: 0.8132 (ttpt) cc_final: 0.7341 (tptt) REVERT: G 472 ASP cc_start: 0.8940 (t0) cc_final: 0.8588 (m-30) REVERT: G 515 GLU cc_start: 0.8563 (mt-10) cc_final: 0.8062 (tt0) REVERT: G 574 MET cc_start: 0.8114 (mmm) cc_final: 0.7819 (mmm) REVERT: G 604 GLU cc_start: 0.9117 (pm20) cc_final: 0.8694 (pm20) REVERT: G 640 MET cc_start: 0.8217 (mmt) cc_final: 0.8014 (mmt) REVERT: G 684 GLU cc_start: 0.8469 (mp0) cc_final: 0.8071 (mp0) REVERT: G 817 GLU cc_start: 0.9064 (mp0) cc_final: 0.8818 (mp0) REVERT: G 834 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7587 (pm20) REVERT: H 477 ASP cc_start: 0.7775 (t0) cc_final: 0.7403 (p0) REVERT: H 519 ASP cc_start: 0.7942 (m-30) cc_final: 0.7095 (t70) REVERT: H 520 PRO cc_start: 0.7416 (Cg_exo) cc_final: 0.6989 (Cg_endo) REVERT: H 722 CYS cc_start: 0.7772 (OUTLIER) cc_final: 0.7388 (t) REVERT: H 796 GLU cc_start: 0.8510 (tm-30) cc_final: 0.7819 (mm-30) REVERT: H 859 LEU cc_start: 0.5825 (OUTLIER) cc_final: 0.5246 (pp) REVERT: H 866 ASP cc_start: 0.4786 (p0) cc_final: 0.4394 (p0) outliers start: 163 outliers final: 121 residues processed: 749 average time/residue: 0.4449 time to fit residues: 567.0444 Evaluate side-chains 760 residues out of total 4850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 619 time to evaluate : 4.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 530 GLU Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 645 SER Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain A residue 708 THR Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 722 CYS Chi-restraints excluded: chain A residue 725 MET Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 808 GLU Chi-restraints excluded: chain A residue 857 ILE Chi-restraints excluded: chain A residue 859 LEU Chi-restraints excluded: chain A residue 863 TYR Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 108 CYS Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 436 LYS Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 634 VAL Chi-restraints excluded: chain B residue 659 MET Chi-restraints excluded: chain B residue 682 LEU Chi-restraints excluded: chain B residue 714 PHE Chi-restraints excluded: chain B residue 782 LEU Chi-restraints excluded: chain B residue 834 GLU Chi-restraints excluded: chain B residue 869 GLU Chi-restraints excluded: chain C residue 46 ARG Chi-restraints excluded: chain C residue 108 CYS Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 250 GLN Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 359 LEU Chi-restraints excluded: chain C residue 391 THR Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain C residue 549 MET Chi-restraints excluded: chain C residue 574 MET Chi-restraints excluded: chain C residue 586 MET Chi-restraints excluded: chain C residue 598 THR Chi-restraints excluded: chain C residue 668 SER Chi-restraints excluded: chain C residue 701 GLU Chi-restraints excluded: chain C residue 735 ILE Chi-restraints excluded: chain C residue 768 ARG Chi-restraints excluded: chain C residue 799 LEU Chi-restraints excluded: chain C residue 834 GLU Chi-restraints excluded: chain D residue 59 MET Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 155 GLN Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 323 VAL Chi-restraints excluded: chain D residue 341 LEU Chi-restraints excluded: chain D residue 343 MET Chi-restraints excluded: chain D residue 387 GLN Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 508 VAL Chi-restraints excluded: chain D residue 565 HIS Chi-restraints excluded: chain D residue 580 ILE Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain D residue 652 LEU Chi-restraints excluded: chain D residue 668 SER Chi-restraints excluded: chain D residue 714 PHE Chi-restraints excluded: chain D residue 799 LEU Chi-restraints excluded: chain D residue 802 LEU Chi-restraints excluded: chain D residue 808 GLU Chi-restraints excluded: chain E residue 59 MET Chi-restraints excluded: chain E residue 216 ASN Chi-restraints excluded: chain E residue 297 VAL Chi-restraints excluded: chain E residue 304 ILE Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 332 PHE Chi-restraints excluded: chain E residue 335 GLU Chi-restraints excluded: chain E residue 338 SER Chi-restraints excluded: chain E residue 340 THR Chi-restraints excluded: chain E residue 370 CYS Chi-restraints excluded: chain E residue 439 ILE Chi-restraints excluded: chain E residue 443 THR Chi-restraints excluded: chain E residue 477 ASP Chi-restraints excluded: chain E residue 580 ILE Chi-restraints excluded: chain E residue 599 SER Chi-restraints excluded: chain E residue 668 SER Chi-restraints excluded: chain E residue 811 ILE Chi-restraints excluded: chain F residue 128 LEU Chi-restraints excluded: chain F residue 172 GLN Chi-restraints excluded: chain F residue 210 ILE Chi-restraints excluded: chain F residue 251 SER Chi-restraints excluded: chain F residue 274 LEU Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 312 VAL Chi-restraints excluded: chain F residue 343 MET Chi-restraints excluded: chain F residue 351 ASP Chi-restraints excluded: chain F residue 362 MET Chi-restraints excluded: chain F residue 439 ILE Chi-restraints excluded: chain F residue 469 ILE Chi-restraints excluded: chain F residue 547 SER Chi-restraints excluded: chain F residue 565 HIS Chi-restraints excluded: chain F residue 580 ILE Chi-restraints excluded: chain F residue 592 MET Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 646 LEU Chi-restraints excluded: chain F residue 739 LEU Chi-restraints excluded: chain G residue 52 MET Chi-restraints excluded: chain G residue 74 GLU Chi-restraints excluded: chain G residue 86 CYS Chi-restraints excluded: chain G residue 88 VAL Chi-restraints excluded: chain G residue 134 ILE Chi-restraints excluded: chain G residue 254 VAL Chi-restraints excluded: chain G residue 274 LEU Chi-restraints excluded: chain G residue 323 VAL Chi-restraints excluded: chain G residue 332 PHE Chi-restraints excluded: chain G residue 358 LYS Chi-restraints excluded: chain G residue 391 THR Chi-restraints excluded: chain G residue 508 VAL Chi-restraints excluded: chain G residue 660 GLU Chi-restraints excluded: chain G residue 668 SER Chi-restraints excluded: chain G residue 712 ILE Chi-restraints excluded: chain G residue 808 GLU Chi-restraints excluded: chain G residue 834 GLU Chi-restraints excluded: chain H residue 576 ILE Chi-restraints excluded: chain H residue 598 THR Chi-restraints excluded: chain H residue 611 VAL Chi-restraints excluded: chain H residue 614 ASP Chi-restraints excluded: chain H residue 712 ILE Chi-restraints excluded: chain H residue 722 CYS Chi-restraints excluded: chain H residue 744 LEU Chi-restraints excluded: chain H residue 778 ILE Chi-restraints excluded: chain H residue 782 LEU Chi-restraints excluded: chain H residue 859 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 598 random chunks: chunk 356 optimal weight: 0.1980 chunk 230 optimal weight: 0.0270 chunk 344 optimal weight: 1.9990 chunk 173 optimal weight: 0.9990 chunk 113 optimal weight: 9.9990 chunk 111 optimal weight: 4.9990 chunk 366 optimal weight: 5.9990 chunk 392 optimal weight: 2.9990 chunk 284 optimal weight: 6.9990 chunk 53 optimal weight: 0.9990 chunk 453 optimal weight: 0.9980 overall best weight: 0.6442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 402 GLN B 737 HIS C 250 GLN E 30 GLN E 737 HIS G 727 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.4497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.073 47016 Z= 0.148 Angle : 0.590 13.470 63778 Z= 0.294 Chirality : 0.044 0.232 7318 Planarity : 0.004 0.052 8262 Dihedral : 4.297 43.802 6476 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 2.70 % Allowed : 18.74 % Favored : 78.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.94 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.11), residues: 6036 helix: 0.73 (0.10), residues: 2664 sheet: -0.26 (0.17), residues: 972 loop : -2.21 (0.13), residues: 2400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 424 HIS 0.007 0.000 HIS A 561 PHE 0.033 0.001 PHE E 489 TYR 0.031 0.001 TYR C 867 ARG 0.007 0.000 ARG C 790 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12072 Ramachandran restraints generated. 6036 Oldfield, 0 Emsley, 6036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12072 Ramachandran restraints generated. 6036 Oldfield, 0 Emsley, 6036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 840 residues out of total 4850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 709 time to evaluate : 4.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 509 GLU cc_start: 0.8533 (mp0) cc_final: 0.8282 (mp0) REVERT: A 514 PHE cc_start: 0.7349 (p90) cc_final: 0.6785 (p90) REVERT: A 550 ASP cc_start: 0.7860 (p0) cc_final: 0.7549 (m-30) REVERT: A 574 MET cc_start: 0.7304 (mtp) cc_final: 0.6962 (mtm) REVERT: A 592 MET cc_start: 0.7727 (tpp) cc_final: 0.7467 (tpp) REVERT: A 629 PRO cc_start: 0.8622 (Cg_exo) cc_final: 0.8345 (Cg_endo) REVERT: A 777 GLU cc_start: 0.7201 (mt-10) cc_final: 0.6914 (mm-30) REVERT: B 81 LYS cc_start: 0.8785 (ttpp) cc_final: 0.8268 (ttmm) REVERT: B 92 ASP cc_start: 0.5227 (t0) cc_final: 0.4828 (p0) REVERT: B 176 GLU cc_start: 0.8464 (pt0) cc_final: 0.7549 (mm-30) REVERT: B 251 SER cc_start: 0.9176 (m) cc_final: 0.8741 (t) REVERT: B 318 ILE cc_start: 0.8453 (mm) cc_final: 0.7974 (pt) REVERT: B 335 GLU cc_start: 0.8023 (pp20) cc_final: 0.7563 (pp20) REVERT: B 365 ILE cc_start: 0.8799 (mt) cc_final: 0.8430 (mp) REVERT: B 387 GLN cc_start: 0.7215 (tm-30) cc_final: 0.6902 (tt0) REVERT: B 447 ARG cc_start: 0.7555 (ttt-90) cc_final: 0.6070 (ttp80) REVERT: B 451 MET cc_start: 0.8327 (ptm) cc_final: 0.8005 (mtm) REVERT: B 574 MET cc_start: 0.7692 (ptm) cc_final: 0.7254 (ptt) REVERT: B 641 ASP cc_start: 0.7553 (m-30) cc_final: 0.6284 (t0) REVERT: B 660 GLU cc_start: 0.8307 (tp30) cc_final: 0.7865 (mm-30) REVERT: B 773 ARG cc_start: 0.8161 (ttm170) cc_final: 0.7706 (ttt-90) REVERT: B 828 ASN cc_start: 0.6973 (m-40) cc_final: 0.6710 (t0) REVERT: B 848 TYR cc_start: 0.7627 (t80) cc_final: 0.7003 (t80) REVERT: B 869 GLU cc_start: 0.4904 (OUTLIER) cc_final: 0.4332 (pt0) REVERT: C 22 GLU cc_start: 0.7918 (tp30) cc_final: 0.7499 (mt-10) REVERT: C 59 MET cc_start: 0.7322 (pmt) cc_final: 0.6963 (pmm) REVERT: C 148 LYS cc_start: 0.8702 (tptt) cc_final: 0.8169 (mptt) REVERT: C 251 SER cc_start: 0.7102 (m) cc_final: 0.6631 (t) REVERT: C 389 MET cc_start: 0.8271 (tpp) cc_final: 0.8037 (ttm) REVERT: C 427 ASN cc_start: 0.7703 (m-40) cc_final: 0.7501 (m-40) REVERT: C 432 ASN cc_start: 0.7899 (p0) cc_final: 0.7512 (t0) REVERT: C 509 GLU cc_start: 0.8023 (mp0) cc_final: 0.7640 (mp0) REVERT: C 567 GLU cc_start: 0.8490 (mp0) cc_final: 0.7209 (pt0) REVERT: C 577 ARG cc_start: 0.8176 (mtm180) cc_final: 0.7641 (mtm180) REVERT: C 578 LYS cc_start: 0.8492 (mmtt) cc_final: 0.8194 (mmtt) REVERT: C 582 LYS cc_start: 0.8541 (ptmt) cc_final: 0.8130 (ttmm) REVERT: C 604 GLU cc_start: 0.9064 (pm20) cc_final: 0.8680 (pm20) REVERT: C 631 MET cc_start: 0.8870 (ttp) cc_final: 0.8620 (ttp) REVERT: C 660 GLU cc_start: 0.8016 (tp30) cc_final: 0.7459 (tp30) REVERT: C 728 LYS cc_start: 0.8620 (mmmt) cc_final: 0.7968 (mmtp) REVERT: C 755 ASP cc_start: 0.7137 (p0) cc_final: 0.6594 (m-30) REVERT: C 799 LEU cc_start: 0.8298 (OUTLIER) cc_final: 0.7931 (tp) REVERT: D 59 MET cc_start: 0.8440 (OUTLIER) cc_final: 0.7847 (pmt) REVERT: D 99 THR cc_start: 0.8952 (m) cc_final: 0.8576 (p) REVERT: D 155 GLN cc_start: 0.8101 (OUTLIER) cc_final: 0.6755 (mp10) REVERT: D 341 LEU cc_start: 0.7811 (OUTLIER) cc_final: 0.7441 (tp) REVERT: D 421 CYS cc_start: 0.8279 (t) cc_final: 0.7754 (t) REVERT: D 515 GLU cc_start: 0.7474 (mp0) cc_final: 0.7172 (mp0) REVERT: D 530 GLU cc_start: 0.8372 (tp30) cc_final: 0.8044 (tp30) REVERT: D 565 HIS cc_start: 0.7767 (OUTLIER) cc_final: 0.7465 (t-90) REVERT: D 777 GLU cc_start: 0.8127 (mt-10) cc_final: 0.7796 (mt-10) REVERT: D 784 LEU cc_start: 0.9136 (mt) cc_final: 0.8865 (mt) REVERT: D 799 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.8158 (pt) REVERT: D 808 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7483 (pm20) REVERT: E 59 MET cc_start: 0.8297 (OUTLIER) cc_final: 0.7784 (pmt) REVERT: E 172 GLN cc_start: 0.8723 (mp10) cc_final: 0.8037 (mp10) REVERT: E 186 ASP cc_start: 0.8308 (p0) cc_final: 0.7983 (p0) REVERT: E 275 GLN cc_start: 0.8579 (pp30) cc_final: 0.8370 (pp30) REVERT: E 391 THR cc_start: 0.8589 (p) cc_final: 0.8273 (p) REVERT: E 477 ASP cc_start: 0.8099 (OUTLIER) cc_final: 0.7707 (p0) REVERT: E 517 GLU cc_start: 0.8594 (mm-30) cc_final: 0.8369 (mm-30) REVERT: E 565 HIS cc_start: 0.7911 (t-90) cc_final: 0.7654 (t-90) REVERT: E 576 ILE cc_start: 0.8706 (mm) cc_final: 0.8442 (mm) REVERT: E 639 VAL cc_start: 0.8735 (t) cc_final: 0.8428 (m) REVERT: E 684 GLU cc_start: 0.8061 (mp0) cc_final: 0.7796 (mp0) REVERT: E 770 GLN cc_start: 0.7996 (tp40) cc_final: 0.7550 (mm110) REVERT: F 18 LYS cc_start: 0.8144 (tttm) cc_final: 0.7926 (tppt) REVERT: F 59 MET cc_start: 0.7298 (pmt) cc_final: 0.6534 (pmm) REVERT: F 82 ASP cc_start: 0.8742 (p0) cc_final: 0.8524 (p0) REVERT: F 229 ARG cc_start: 0.8461 (mtt180) cc_final: 0.7661 (mmp-170) REVERT: F 241 ASP cc_start: 0.8104 (t0) cc_final: 0.7577 (t0) REVERT: F 272 TYR cc_start: 0.6605 (t80) cc_final: 0.5672 (t80) REVERT: F 378 GLN cc_start: 0.8510 (mp10) cc_final: 0.7902 (mp10) REVERT: F 389 MET cc_start: 0.8865 (mtp) cc_final: 0.8594 (mtp) REVERT: F 515 GLU cc_start: 0.8554 (mt-10) cc_final: 0.7712 (mm-30) REVERT: F 565 HIS cc_start: 0.8051 (OUTLIER) cc_final: 0.7603 (t-170) REVERT: F 582 LYS cc_start: 0.8507 (ptmt) cc_final: 0.8097 (mttm) REVERT: F 764 SER cc_start: 0.8172 (m) cc_final: 0.7930 (t) REVERT: F 784 LEU cc_start: 0.8621 (mt) cc_final: 0.8307 (mp) REVERT: G 127 SER cc_start: 0.8984 (m) cc_final: 0.8684 (p) REVERT: G 388 LYS cc_start: 0.8264 (mmmm) cc_final: 0.7939 (tppp) REVERT: G 417 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.8281 (pp) REVERT: G 447 ARG cc_start: 0.7701 (ttt-90) cc_final: 0.6986 (ttp-170) REVERT: G 458 LYS cc_start: 0.8053 (ttpt) cc_final: 0.7264 (tptt) REVERT: G 472 ASP cc_start: 0.8944 (t0) cc_final: 0.8532 (m-30) REVERT: G 515 GLU cc_start: 0.8634 (mt-10) cc_final: 0.8207 (tt0) REVERT: G 574 MET cc_start: 0.8069 (mmm) cc_final: 0.7814 (mmm) REVERT: G 604 GLU cc_start: 0.9128 (pm20) cc_final: 0.8726 (pm20) REVERT: G 684 GLU cc_start: 0.8483 (mp0) cc_final: 0.8081 (mp0) REVERT: G 780 ASP cc_start: 0.8886 (t0) cc_final: 0.8104 (m-30) REVERT: G 817 GLU cc_start: 0.9074 (mp0) cc_final: 0.8803 (mp0) REVERT: G 834 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.7560 (pm20) REVERT: G 858 LEU cc_start: 0.8961 (mt) cc_final: 0.8746 (mt) REVERT: H 477 ASP cc_start: 0.7715 (t0) cc_final: 0.7399 (p0) REVERT: H 519 ASP cc_start: 0.7933 (m-30) cc_final: 0.7053 (t70) REVERT: H 520 PRO cc_start: 0.7272 (Cg_exo) cc_final: 0.6822 (Cg_endo) REVERT: H 796 GLU cc_start: 0.8528 (tm-30) cc_final: 0.7851 (mm-30) REVERT: H 859 LEU cc_start: 0.5781 (OUTLIER) cc_final: 0.5200 (pp) REVERT: H 866 ASP cc_start: 0.4694 (p0) cc_final: 0.4357 (p0) outliers start: 131 outliers final: 86 residues processed: 800 average time/residue: 0.4560 time to fit residues: 624.3953 Evaluate side-chains 760 residues out of total 4850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 660 time to evaluate : 4.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 530 GLU Chi-restraints excluded: chain A residue 547 SER Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 645 SER Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain A residue 708 THR Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 722 CYS Chi-restraints excluded: chain A residue 725 MET Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 808 GLU Chi-restraints excluded: chain A residue 857 ILE Chi-restraints excluded: chain A residue 859 LEU Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 108 CYS Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 634 VAL Chi-restraints excluded: chain B residue 682 LEU Chi-restraints excluded: chain B residue 714 PHE Chi-restraints excluded: chain B residue 782 LEU Chi-restraints excluded: chain B residue 834 GLU Chi-restraints excluded: chain B residue 869 GLU Chi-restraints excluded: chain C residue 46 ARG Chi-restraints excluded: chain C residue 108 CYS Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 391 THR Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain C residue 586 MET Chi-restraints excluded: chain C residue 598 THR Chi-restraints excluded: chain C residue 668 SER Chi-restraints excluded: chain C residue 701 GLU Chi-restraints excluded: chain C residue 768 ARG Chi-restraints excluded: chain C residue 799 LEU Chi-restraints excluded: chain C residue 834 GLU Chi-restraints excluded: chain D residue 59 MET Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 155 GLN Chi-restraints excluded: chain D residue 323 VAL Chi-restraints excluded: chain D residue 341 LEU Chi-restraints excluded: chain D residue 387 GLN Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 508 VAL Chi-restraints excluded: chain D residue 565 HIS Chi-restraints excluded: chain D residue 580 ILE Chi-restraints excluded: chain D residue 652 LEU Chi-restraints excluded: chain D residue 668 SER Chi-restraints excluded: chain D residue 714 PHE Chi-restraints excluded: chain D residue 799 LEU Chi-restraints excluded: chain D residue 808 GLU Chi-restraints excluded: chain E residue 59 MET Chi-restraints excluded: chain E residue 216 ASN Chi-restraints excluded: chain E residue 297 VAL Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 338 SER Chi-restraints excluded: chain E residue 340 THR Chi-restraints excluded: chain E residue 439 ILE Chi-restraints excluded: chain E residue 443 THR Chi-restraints excluded: chain E residue 477 ASP Chi-restraints excluded: chain E residue 580 ILE Chi-restraints excluded: chain E residue 599 SER Chi-restraints excluded: chain E residue 668 SER Chi-restraints excluded: chain E residue 714 PHE Chi-restraints excluded: chain E residue 808 GLU Chi-restraints excluded: chain E residue 811 ILE Chi-restraints excluded: chain F residue 128 LEU Chi-restraints excluded: chain F residue 274 LEU Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 312 VAL Chi-restraints excluded: chain F residue 351 ASP Chi-restraints excluded: chain F residue 547 SER Chi-restraints excluded: chain F residue 565 HIS Chi-restraints excluded: chain F residue 580 ILE Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 646 LEU Chi-restraints excluded: chain F residue 714 PHE Chi-restraints excluded: chain F residue 739 LEU Chi-restraints excluded: chain G residue 74 GLU Chi-restraints excluded: chain G residue 254 VAL Chi-restraints excluded: chain G residue 323 VAL Chi-restraints excluded: chain G residue 332 PHE Chi-restraints excluded: chain G residue 391 THR Chi-restraints excluded: chain G residue 417 LEU Chi-restraints excluded: chain G residue 508 VAL Chi-restraints excluded: chain G residue 668 SER Chi-restraints excluded: chain G residue 808 GLU Chi-restraints excluded: chain G residue 834 GLU Chi-restraints excluded: chain H residue 576 ILE Chi-restraints excluded: chain H residue 598 THR Chi-restraints excluded: chain H residue 614 ASP Chi-restraints excluded: chain H residue 712 ILE Chi-restraints excluded: chain H residue 859 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 598 random chunks: chunk 524 optimal weight: 0.0470 chunk 552 optimal weight: 20.0000 chunk 503 optimal weight: 10.0000 chunk 537 optimal weight: 10.0000 chunk 323 optimal weight: 7.9990 chunk 233 optimal weight: 7.9990 chunk 421 optimal weight: 9.9990 chunk 164 optimal weight: 7.9990 chunk 485 optimal weight: 9.9990 chunk 507 optimal weight: 10.0000 chunk 535 optimal weight: 0.6980 overall best weight: 4.9484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 737 HIS B 737 HIS B 747 ASN ** B 845 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 147 ASN ** C 845 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 387 GLN ** D 752 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 845 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 30 GLN E 737 HIS F 727 HIS F 754 ASN G 69 ASN G 269 HIS G 727 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.4567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 47016 Z= 0.336 Angle : 0.712 14.889 63778 Z= 0.361 Chirality : 0.049 0.234 7318 Planarity : 0.005 0.052 8262 Dihedral : 4.790 37.453 6474 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.79 % Favored : 92.21 % Rotamer: Outliers : 3.03 % Allowed : 18.85 % Favored : 78.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.94 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.11), residues: 6036 helix: 0.57 (0.10), residues: 2670 sheet: -0.50 (0.17), residues: 958 loop : -2.27 (0.13), residues: 2408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP F 424 HIS 0.009 0.001 HIS A 561 PHE 0.032 0.002 PHE E 489 TYR 0.025 0.002 TYR C 867 ARG 0.008 0.001 ARG C 790 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12072 Ramachandran restraints generated. 6036 Oldfield, 0 Emsley, 6036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12072 Ramachandran restraints generated. 6036 Oldfield, 0 Emsley, 6036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 772 residues out of total 4850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 625 time to evaluate : 4.063 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 509 GLU cc_start: 0.8346 (mp0) cc_final: 0.8042 (mp0) REVERT: A 514 PHE cc_start: 0.7411 (p90) cc_final: 0.7067 (p90) REVERT: A 550 ASP cc_start: 0.7783 (p0) cc_final: 0.7422 (m-30) REVERT: A 574 MET cc_start: 0.7255 (mtp) cc_final: 0.6931 (mtm) REVERT: A 592 MET cc_start: 0.7652 (tpp) cc_final: 0.7400 (tpp) REVERT: A 777 GLU cc_start: 0.7121 (mt-10) cc_final: 0.6818 (mm-30) REVERT: B 176 GLU cc_start: 0.8516 (pt0) cc_final: 0.7624 (mm-30) REVERT: B 318 ILE cc_start: 0.8499 (mm) cc_final: 0.8089 (pt) REVERT: B 335 GLU cc_start: 0.8125 (pp20) cc_final: 0.7651 (pp20) REVERT: B 365 ILE cc_start: 0.8784 (mt) cc_final: 0.8426 (mp) REVERT: B 432 ASN cc_start: 0.8181 (m110) cc_final: 0.7941 (m110) REVERT: B 447 ARG cc_start: 0.7659 (ttt-90) cc_final: 0.6254 (ttp80) REVERT: B 574 MET cc_start: 0.7851 (ptm) cc_final: 0.7396 (ptt) REVERT: B 660 GLU cc_start: 0.8398 (tp30) cc_final: 0.8064 (mm-30) REVERT: B 773 ARG cc_start: 0.8083 (ttm170) cc_final: 0.7620 (ttt-90) REVERT: B 828 ASN cc_start: 0.6964 (m-40) cc_final: 0.6615 (t0) REVERT: B 848 TYR cc_start: 0.7787 (t80) cc_final: 0.7205 (t80) REVERT: B 869 GLU cc_start: 0.5449 (OUTLIER) cc_final: 0.4821 (pt0) REVERT: C 59 MET cc_start: 0.7325 (pmt) cc_final: 0.6758 (pmm) REVERT: C 90 SER cc_start: 0.7477 (m) cc_final: 0.6811 (p) REVERT: C 148 LYS cc_start: 0.8856 (tptt) cc_final: 0.8431 (mptt) REVERT: C 250 GLN cc_start: 0.4980 (mm110) cc_final: 0.4297 (mm110) REVERT: C 251 SER cc_start: 0.7121 (m) cc_final: 0.6731 (t) REVERT: C 432 ASN cc_start: 0.7922 (p0) cc_final: 0.7478 (t0) REVERT: C 509 GLU cc_start: 0.8111 (mp0) cc_final: 0.7679 (mp0) REVERT: C 567 GLU cc_start: 0.8542 (mp0) cc_final: 0.7501 (pt0) REVERT: C 578 LYS cc_start: 0.8569 (mmtt) cc_final: 0.8217 (mmtt) REVERT: C 582 LYS cc_start: 0.8604 (ptmt) cc_final: 0.8234 (ttmm) REVERT: C 604 GLU cc_start: 0.9113 (pm20) cc_final: 0.8767 (pm20) REVERT: C 631 MET cc_start: 0.8815 (ttp) cc_final: 0.8546 (ttp) REVERT: C 728 LYS cc_start: 0.8804 (mmmt) cc_final: 0.8199 (mmtp) REVERT: C 755 ASP cc_start: 0.7198 (p0) cc_final: 0.6921 (t70) REVERT: C 799 LEU cc_start: 0.8316 (OUTLIER) cc_final: 0.7843 (tp) REVERT: D 59 MET cc_start: 0.8612 (OUTLIER) cc_final: 0.7972 (pmt) REVERT: D 99 THR cc_start: 0.9122 (m) cc_final: 0.8743 (p) REVERT: D 128 LEU cc_start: 0.8633 (OUTLIER) cc_final: 0.8393 (pt) REVERT: D 155 GLN cc_start: 0.8204 (OUTLIER) cc_final: 0.6884 (mp10) REVERT: D 241 ASP cc_start: 0.9087 (t0) cc_final: 0.8794 (t0) REVERT: D 341 LEU cc_start: 0.8044 (OUTLIER) cc_final: 0.7201 (tt) REVERT: D 374 ASP cc_start: 0.8186 (t0) cc_final: 0.7937 (t0) REVERT: D 421 CYS cc_start: 0.8348 (t) cc_final: 0.7946 (t) REVERT: D 515 GLU cc_start: 0.7617 (mp0) cc_final: 0.7286 (mp0) REVERT: D 530 GLU cc_start: 0.8477 (tp30) cc_final: 0.8084 (tp30) REVERT: D 565 HIS cc_start: 0.7785 (OUTLIER) cc_final: 0.7473 (t-90) REVERT: D 777 GLU cc_start: 0.8214 (mt-10) cc_final: 0.7909 (mt-10) REVERT: D 799 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8213 (pt) REVERT: D 808 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7531 (pm20) REVERT: E 59 MET cc_start: 0.8392 (OUTLIER) cc_final: 0.7829 (pmt) REVERT: E 64 ASP cc_start: 0.8482 (m-30) cc_final: 0.7851 (m-30) REVERT: E 172 GLN cc_start: 0.8766 (mp10) cc_final: 0.8134 (mp10) REVERT: E 277 LYS cc_start: 0.8408 (mtpt) cc_final: 0.7996 (tmtt) REVERT: E 335 GLU cc_start: 0.8697 (mt-10) cc_final: 0.8477 (mt-10) REVERT: E 427 ASN cc_start: 0.8835 (m-40) cc_final: 0.8389 (m-40) REVERT: E 477 ASP cc_start: 0.8145 (OUTLIER) cc_final: 0.7712 (p0) REVERT: E 517 GLU cc_start: 0.8743 (mm-30) cc_final: 0.8531 (mm-30) REVERT: E 565 HIS cc_start: 0.8003 (t-90) cc_final: 0.7766 (t-90) REVERT: E 639 VAL cc_start: 0.8877 (t) cc_final: 0.8449 (m) REVERT: E 684 GLU cc_start: 0.8047 (mp0) cc_final: 0.7678 (mp0) REVERT: E 770 GLN cc_start: 0.8342 (tp40) cc_final: 0.7917 (mm110) REVERT: F 18 LYS cc_start: 0.8004 (tttm) cc_final: 0.7672 (tppt) REVERT: F 59 MET cc_start: 0.7379 (pmt) cc_final: 0.6695 (pmm) REVERT: F 82 ASP cc_start: 0.8805 (p0) cc_final: 0.8575 (p0) REVERT: F 86 CYS cc_start: 0.8590 (m) cc_final: 0.8121 (m) REVERT: F 229 ARG cc_start: 0.8498 (mtt180) cc_final: 0.7812 (mmp-170) REVERT: F 241 ASP cc_start: 0.8143 (t0) cc_final: 0.7654 (t0) REVERT: F 272 TYR cc_start: 0.6741 (t80) cc_final: 0.5894 (t80) REVERT: F 378 GLN cc_start: 0.8432 (mp10) cc_final: 0.7826 (mp10) REVERT: F 389 MET cc_start: 0.9041 (mtp) cc_final: 0.8763 (mtp) REVERT: F 515 GLU cc_start: 0.8654 (mt-10) cc_final: 0.8245 (mt-10) REVERT: F 582 LYS cc_start: 0.8741 (ptmt) cc_final: 0.8382 (mttm) REVERT: F 764 SER cc_start: 0.8026 (m) cc_final: 0.7807 (t) REVERT: F 784 LEU cc_start: 0.8672 (mt) cc_final: 0.8435 (mp) REVERT: G 127 SER cc_start: 0.9097 (m) cc_final: 0.8793 (p) REVERT: G 236 MET cc_start: 0.8688 (tmm) cc_final: 0.8224 (tmm) REVERT: G 388 LYS cc_start: 0.8378 (mmmm) cc_final: 0.8109 (tppp) REVERT: G 417 LEU cc_start: 0.8294 (OUTLIER) cc_final: 0.8086 (pp) REVERT: G 447 ARG cc_start: 0.7758 (ttt-90) cc_final: 0.7006 (ttp-170) REVERT: G 458 LYS cc_start: 0.8220 (ttpt) cc_final: 0.7422 (tptt) REVERT: G 472 ASP cc_start: 0.9036 (t0) cc_final: 0.8588 (m-30) REVERT: G 515 GLU cc_start: 0.8720 (mt-10) cc_final: 0.8156 (tt0) REVERT: G 574 MET cc_start: 0.8216 (mmm) cc_final: 0.7756 (tpp) REVERT: G 684 GLU cc_start: 0.8505 (mp0) cc_final: 0.8070 (mp0) REVERT: G 817 GLU cc_start: 0.9063 (mp0) cc_final: 0.8822 (mp0) REVERT: G 834 GLU cc_start: 0.7727 (OUTLIER) cc_final: 0.7450 (pm20) REVERT: G 858 LEU cc_start: 0.8987 (mt) cc_final: 0.8679 (mt) REVERT: H 477 ASP cc_start: 0.7809 (t0) cc_final: 0.7497 (p0) REVERT: H 519 ASP cc_start: 0.8068 (m-30) cc_final: 0.7379 (t70) REVERT: H 520 PRO cc_start: 0.7649 (Cg_exo) cc_final: 0.7277 (Cg_endo) REVERT: H 750 ARG cc_start: 0.6431 (mtt90) cc_final: 0.5823 (ptp90) REVERT: H 796 GLU cc_start: 0.8534 (tm-30) cc_final: 0.7834 (mm-30) REVERT: H 847 ARG cc_start: 0.5149 (ptm160) cc_final: 0.4929 (ptm160) REVERT: H 859 LEU cc_start: 0.5947 (OUTLIER) cc_final: 0.5347 (pp) REVERT: H 866 ASP cc_start: 0.4534 (p0) cc_final: 0.4301 (p0) outliers start: 147 outliers final: 109 residues processed: 724 average time/residue: 0.4209 time to fit residues: 519.3813 Evaluate side-chains 732 residues out of total 4850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 609 time to evaluate : 3.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 530 GLU Chi-restraints excluded: chain A residue 547 SER Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 645 SER Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 722 CYS Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 857 ILE Chi-restraints excluded: chain A residue 859 LEU Chi-restraints excluded: chain A residue 863 TYR Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 108 CYS Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 436 LYS Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 497 ASP Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 682 LEU Chi-restraints excluded: chain B residue 714 PHE Chi-restraints excluded: chain B residue 744 LEU Chi-restraints excluded: chain B residue 782 LEU Chi-restraints excluded: chain B residue 834 GLU Chi-restraints excluded: chain B residue 869 GLU Chi-restraints excluded: chain C residue 46 ARG Chi-restraints excluded: chain C residue 108 CYS Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 359 LEU Chi-restraints excluded: chain C residue 391 THR Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain C residue 586 MET Chi-restraints excluded: chain C residue 598 THR Chi-restraints excluded: chain C residue 668 SER Chi-restraints excluded: chain C residue 701 GLU Chi-restraints excluded: chain C residue 735 ILE Chi-restraints excluded: chain C residue 768 ARG Chi-restraints excluded: chain C residue 799 LEU Chi-restraints excluded: chain C residue 834 GLU Chi-restraints excluded: chain D residue 59 MET Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 155 GLN Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 323 VAL Chi-restraints excluded: chain D residue 341 LEU Chi-restraints excluded: chain D residue 387 GLN Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 508 VAL Chi-restraints excluded: chain D residue 565 HIS Chi-restraints excluded: chain D residue 580 ILE Chi-restraints excluded: chain D residue 652 LEU Chi-restraints excluded: chain D residue 668 SER Chi-restraints excluded: chain D residue 714 PHE Chi-restraints excluded: chain D residue 799 LEU Chi-restraints excluded: chain D residue 802 LEU Chi-restraints excluded: chain D residue 808 GLU Chi-restraints excluded: chain E residue 59 MET Chi-restraints excluded: chain E residue 216 ASN Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 297 VAL Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 338 SER Chi-restraints excluded: chain E residue 340 THR Chi-restraints excluded: chain E residue 370 CYS Chi-restraints excluded: chain E residue 439 ILE Chi-restraints excluded: chain E residue 443 THR Chi-restraints excluded: chain E residue 477 ASP Chi-restraints excluded: chain E residue 580 ILE Chi-restraints excluded: chain E residue 599 SER Chi-restraints excluded: chain E residue 668 SER Chi-restraints excluded: chain E residue 712 ILE Chi-restraints excluded: chain E residue 811 ILE Chi-restraints excluded: chain F residue 52 MET Chi-restraints excluded: chain F residue 127 SER Chi-restraints excluded: chain F residue 128 LEU Chi-restraints excluded: chain F residue 210 ILE Chi-restraints excluded: chain F residue 251 SER Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 274 LEU Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 312 VAL Chi-restraints excluded: chain F residue 362 MET Chi-restraints excluded: chain F residue 439 ILE Chi-restraints excluded: chain F residue 469 ILE Chi-restraints excluded: chain F residue 580 ILE Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 646 LEU Chi-restraints excluded: chain F residue 735 ILE Chi-restraints excluded: chain F residue 739 LEU Chi-restraints excluded: chain F residue 754 ASN Chi-restraints excluded: chain F residue 802 LEU Chi-restraints excluded: chain G residue 74 GLU Chi-restraints excluded: chain G residue 86 CYS Chi-restraints excluded: chain G residue 88 VAL Chi-restraints excluded: chain G residue 104 ILE Chi-restraints excluded: chain G residue 134 ILE Chi-restraints excluded: chain G residue 254 VAL Chi-restraints excluded: chain G residue 323 VAL Chi-restraints excluded: chain G residue 332 PHE Chi-restraints excluded: chain G residue 358 LYS Chi-restraints excluded: chain G residue 391 THR Chi-restraints excluded: chain G residue 417 LEU Chi-restraints excluded: chain G residue 508 VAL Chi-restraints excluded: chain G residue 712 ILE Chi-restraints excluded: chain G residue 808 GLU Chi-restraints excluded: chain G residue 834 GLU Chi-restraints excluded: chain H residue 510 THR Chi-restraints excluded: chain H residue 576 ILE Chi-restraints excluded: chain H residue 598 THR Chi-restraints excluded: chain H residue 614 ASP Chi-restraints excluded: chain H residue 712 ILE Chi-restraints excluded: chain H residue 859 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 598 random chunks: chunk 352 optimal weight: 6.9990 chunk 567 optimal weight: 6.9990 chunk 346 optimal weight: 10.0000 chunk 269 optimal weight: 0.9990 chunk 394 optimal weight: 9.9990 chunk 595 optimal weight: 5.9990 chunk 548 optimal weight: 9.9990 chunk 474 optimal weight: 8.9990 chunk 49 optimal weight: 5.9990 chunk 366 optimal weight: 1.9990 chunk 290 optimal weight: 2.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 334 HIS B 737 HIS ** C 845 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 752 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 845 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 737 HIS E 845 ASN F 754 ASN G 69 ASN G 727 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.4655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 47016 Z= 0.261 Angle : 0.677 14.633 63778 Z= 0.341 Chirality : 0.047 0.241 7318 Planarity : 0.004 0.051 8262 Dihedral : 4.745 35.569 6474 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer: Outliers : 2.81 % Allowed : 19.59 % Favored : 77.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.92 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.11), residues: 6036 helix: 0.60 (0.10), residues: 2668 sheet: -0.50 (0.17), residues: 958 loop : -2.28 (0.12), residues: 2410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F 424 HIS 0.007 0.001 HIS A 561 PHE 0.050 0.002 PHE H 535 TYR 0.024 0.001 TYR C 867 ARG 0.007 0.000 ARG C 790 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12072 Ramachandran restraints generated. 6036 Oldfield, 0 Emsley, 6036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12072 Ramachandran restraints generated. 6036 Oldfield, 0 Emsley, 6036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 779 residues out of total 4850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 643 time to evaluate : 3.999 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: A 509 GLU cc_start: 0.8361 (mp0) cc_final: 0.8052 (mp0) REVERT: A 514 PHE cc_start: 0.7436 (p90) cc_final: 0.7100 (p90) REVERT: A 550 ASP cc_start: 0.7603 (p0) cc_final: 0.7262 (m-30) REVERT: A 574 MET cc_start: 0.7362 (mtp) cc_final: 0.7019 (mtm) REVERT: A 592 MET cc_start: 0.7688 (tpp) cc_final: 0.7405 (tpp) REVERT: A 629 PRO cc_start: 0.8572 (Cg_exo) cc_final: 0.8289 (Cg_endo) REVERT: A 777 GLU cc_start: 0.7104 (mt-10) cc_final: 0.6764 (mm-30) REVERT: B 176 GLU cc_start: 0.8493 (pt0) cc_final: 0.7618 (mm-30) REVERT: B 318 ILE cc_start: 0.8459 (mm) cc_final: 0.8054 (pt) REVERT: B 335 GLU cc_start: 0.8159 (pp20) cc_final: 0.7623 (pp20) REVERT: B 357 GLU cc_start: 0.8490 (mt-10) cc_final: 0.7883 (tt0) REVERT: B 365 ILE cc_start: 0.8807 (mt) cc_final: 0.8530 (mp) REVERT: B 447 ARG cc_start: 0.7699 (ttt-90) cc_final: 0.6286 (ttp80) REVERT: B 563 GLU cc_start: 0.8826 (tp30) cc_final: 0.8242 (mp0) REVERT: B 574 MET cc_start: 0.7813 (ptm) cc_final: 0.7361 (ptt) REVERT: B 586 MET cc_start: 0.6651 (mtp) cc_final: 0.6290 (mtp) REVERT: B 660 GLU cc_start: 0.8362 (tp30) cc_final: 0.7976 (mm-30) REVERT: B 773 ARG cc_start: 0.8185 (ttm170) cc_final: 0.7736 (ttt180) REVERT: B 828 ASN cc_start: 0.6956 (m-40) cc_final: 0.6601 (t0) REVERT: B 848 TYR cc_start: 0.7707 (t80) cc_final: 0.7060 (t80) REVERT: B 869 GLU cc_start: 0.5738 (OUTLIER) cc_final: 0.5108 (pt0) REVERT: C 59 MET cc_start: 0.7381 (pmt) cc_final: 0.6824 (pmm) REVERT: C 90 SER cc_start: 0.7437 (m) cc_final: 0.6775 (p) REVERT: C 148 LYS cc_start: 0.8735 (tptt) cc_final: 0.8315 (mptt) REVERT: C 250 GLN cc_start: 0.5172 (mm110) cc_final: 0.4331 (mm110) REVERT: C 251 SER cc_start: 0.7151 (m) cc_final: 0.6795 (t) REVERT: C 359 LEU cc_start: 0.8258 (OUTLIER) cc_final: 0.7913 (tt) REVERT: C 432 ASN cc_start: 0.7871 (p0) cc_final: 0.7555 (t0) REVERT: C 509 GLU cc_start: 0.8136 (mp0) cc_final: 0.7689 (mp0) REVERT: C 567 GLU cc_start: 0.8491 (mp0) cc_final: 0.7450 (pt0) REVERT: C 578 LYS cc_start: 0.8567 (mmtt) cc_final: 0.8301 (mmtt) REVERT: C 582 LYS cc_start: 0.8607 (ptmt) cc_final: 0.8200 (ttmm) REVERT: C 604 GLU cc_start: 0.9151 (pm20) cc_final: 0.8811 (pm20) REVERT: C 631 MET cc_start: 0.8820 (ttp) cc_final: 0.8551 (ttp) REVERT: C 728 LYS cc_start: 0.8805 (mmmt) cc_final: 0.8196 (mmtp) REVERT: C 755 ASP cc_start: 0.7136 (p0) cc_final: 0.6925 (t70) REVERT: C 799 LEU cc_start: 0.8199 (OUTLIER) cc_final: 0.7851 (tp) REVERT: D 59 MET cc_start: 0.8600 (OUTLIER) cc_final: 0.7981 (pmt) REVERT: D 99 THR cc_start: 0.9118 (m) cc_final: 0.8717 (p) REVERT: D 155 GLN cc_start: 0.8167 (OUTLIER) cc_final: 0.6828 (mp10) REVERT: D 241 ASP cc_start: 0.9086 (t0) cc_final: 0.8776 (t0) REVERT: D 341 LEU cc_start: 0.8042 (OUTLIER) cc_final: 0.7244 (tt) REVERT: D 374 ASP cc_start: 0.8219 (t0) cc_final: 0.7953 (t0) REVERT: D 421 CYS cc_start: 0.8305 (t) cc_final: 0.7787 (t) REVERT: D 515 GLU cc_start: 0.7549 (mp0) cc_final: 0.7242 (mp0) REVERT: D 530 GLU cc_start: 0.8466 (tp30) cc_final: 0.8167 (tp30) REVERT: D 565 HIS cc_start: 0.7760 (OUTLIER) cc_final: 0.7472 (t-90) REVERT: D 777 GLU cc_start: 0.8213 (mt-10) cc_final: 0.7883 (mt-10) REVERT: D 799 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.8140 (pt) REVERT: D 808 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7502 (pm20) REVERT: E 59 MET cc_start: 0.8434 (OUTLIER) cc_final: 0.7901 (pmt) REVERT: E 64 ASP cc_start: 0.8407 (m-30) cc_final: 0.7743 (m-30) REVERT: E 172 GLN cc_start: 0.8705 (mp10) cc_final: 0.8096 (mp10) REVERT: E 277 LYS cc_start: 0.8420 (mtpt) cc_final: 0.7967 (tmtt) REVERT: E 427 ASN cc_start: 0.8831 (m-40) cc_final: 0.8367 (m-40) REVERT: E 517 GLU cc_start: 0.8705 (mm-30) cc_final: 0.8472 (mm-30) REVERT: E 565 HIS cc_start: 0.7987 (t-90) cc_final: 0.7747 (t-90) REVERT: E 684 GLU cc_start: 0.8070 (mp0) cc_final: 0.7775 (mp0) REVERT: E 770 GLN cc_start: 0.8363 (tp40) cc_final: 0.7856 (mm110) REVERT: E 845 ASN cc_start: 0.9172 (OUTLIER) cc_final: 0.8967 (t0) REVERT: F 18 LYS cc_start: 0.8086 (tttm) cc_final: 0.7795 (tppt) REVERT: F 59 MET cc_start: 0.7408 (pmt) cc_final: 0.6748 (pmm) REVERT: F 82 ASP cc_start: 0.8778 (p0) cc_final: 0.8538 (p0) REVERT: F 86 CYS cc_start: 0.8500 (m) cc_final: 0.8239 (m) REVERT: F 229 ARG cc_start: 0.8488 (mtt180) cc_final: 0.7804 (mmp-170) REVERT: F 241 ASP cc_start: 0.8263 (t0) cc_final: 0.7777 (t0) REVERT: F 272 TYR cc_start: 0.6816 (t80) cc_final: 0.5899 (t80) REVERT: F 378 GLN cc_start: 0.8415 (mp10) cc_final: 0.7816 (mp10) REVERT: F 381 ARG cc_start: 0.7988 (mtt-85) cc_final: 0.7757 (mtp85) REVERT: F 389 MET cc_start: 0.9036 (mtp) cc_final: 0.8764 (mtp) REVERT: F 515 GLU cc_start: 0.8583 (mt-10) cc_final: 0.8219 (mt-10) REVERT: F 565 HIS cc_start: 0.8198 (OUTLIER) cc_final: 0.7542 (t-170) REVERT: F 582 LYS cc_start: 0.8730 (ptmt) cc_final: 0.8380 (mttm) REVERT: F 764 SER cc_start: 0.7772 (m) cc_final: 0.7525 (t) REVERT: F 784 LEU cc_start: 0.8660 (mt) cc_final: 0.8422 (mp) REVERT: G 127 SER cc_start: 0.9078 (m) cc_final: 0.8767 (p) REVERT: G 236 MET cc_start: 0.8673 (tmm) cc_final: 0.8183 (tmm) REVERT: G 388 LYS cc_start: 0.8361 (mmmm) cc_final: 0.8096 (tppp) REVERT: G 417 LEU cc_start: 0.8326 (OUTLIER) cc_final: 0.8114 (pp) REVERT: G 447 ARG cc_start: 0.7743 (ttt-90) cc_final: 0.6985 (ttp-170) REVERT: G 458 LYS cc_start: 0.8189 (ttpt) cc_final: 0.7395 (tptt) REVERT: G 472 ASP cc_start: 0.9042 (t0) cc_final: 0.8564 (m-30) REVERT: G 515 GLU cc_start: 0.8736 (mt-10) cc_final: 0.8195 (tt0) REVERT: G 574 MET cc_start: 0.8222 (mmm) cc_final: 0.7985 (mmm) REVERT: G 604 GLU cc_start: 0.9067 (pm20) cc_final: 0.8641 (pm20) REVERT: G 684 GLU cc_start: 0.8414 (mp0) cc_final: 0.8022 (mp0) REVERT: G 817 GLU cc_start: 0.9045 (mp0) cc_final: 0.8810 (mp0) REVERT: G 834 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7508 (pm20) REVERT: G 853 GLU cc_start: 0.8349 (mp0) cc_final: 0.7564 (mp0) REVERT: H 477 ASP cc_start: 0.7794 (t0) cc_final: 0.7457 (p0) REVERT: H 519 ASP cc_start: 0.8059 (m-30) cc_final: 0.7404 (t70) REVERT: H 520 PRO cc_start: 0.7931 (Cg_exo) cc_final: 0.7542 (Cg_endo) REVERT: H 582 LYS cc_start: 0.7650 (mmpt) cc_final: 0.7364 (mmpt) REVERT: H 750 ARG cc_start: 0.6414 (mtt90) cc_final: 0.5799 (ptp90) REVERT: H 796 GLU cc_start: 0.8585 (tm-30) cc_final: 0.7833 (mm-30) REVERT: H 847 ARG cc_start: 0.5245 (ptm160) cc_final: 0.5003 (ptm160) REVERT: H 859 LEU cc_start: 0.5943 (OUTLIER) cc_final: 0.5356 (pp) REVERT: H 866 ASP cc_start: 0.4548 (p0) cc_final: 0.4316 (p0) outliers start: 136 outliers final: 111 residues processed: 735 average time/residue: 0.4236 time to fit residues: 531.2660 Evaluate side-chains 754 residues out of total 4850 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 628 time to evaluate : 3.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 460 ILE Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 530 GLU Chi-restraints excluded: chain A residue 547 SER Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 645 SER Chi-restraints excluded: chain A residue 679 LEU Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 722 CYS Chi-restraints excluded: chain A residue 725 MET Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 859 LEU Chi-restraints excluded: chain A residue 863 TYR Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 108 CYS Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 436 LYS Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 474 VAL Chi-restraints excluded: chain B residue 598 THR Chi-restraints excluded: chain B residue 682 LEU Chi-restraints excluded: chain B residue 714 PHE Chi-restraints excluded: chain B residue 744 LEU Chi-restraints excluded: chain B residue 782 LEU Chi-restraints excluded: chain B residue 834 GLU Chi-restraints excluded: chain B residue 869 GLU Chi-restraints excluded: chain C residue 108 CYS Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 307 LEU Chi-restraints excluded: chain C residue 359 LEU Chi-restraints excluded: chain C residue 391 THR Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain C residue 586 MET Chi-restraints excluded: chain C residue 598 THR Chi-restraints excluded: chain C residue 668 SER Chi-restraints excluded: chain C residue 701 GLU Chi-restraints excluded: chain C residue 735 ILE Chi-restraints excluded: chain C residue 768 ARG Chi-restraints excluded: chain C residue 799 LEU Chi-restraints excluded: chain C residue 834 GLU Chi-restraints excluded: chain D residue 59 MET Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain D residue 155 GLN Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 273 LEU Chi-restraints excluded: chain D residue 323 VAL Chi-restraints excluded: chain D residue 341 LEU Chi-restraints excluded: chain D residue 383 SER Chi-restraints excluded: chain D residue 387 GLN Chi-restraints excluded: chain D residue 444 VAL Chi-restraints excluded: chain D residue 474 VAL Chi-restraints excluded: chain D residue 508 VAL Chi-restraints excluded: chain D residue 565 HIS Chi-restraints excluded: chain D residue 580 ILE Chi-restraints excluded: chain D residue 606 THR Chi-restraints excluded: chain D residue 652 LEU Chi-restraints excluded: chain D residue 668 SER Chi-restraints excluded: chain D residue 799 LEU Chi-restraints excluded: chain D residue 802 LEU Chi-restraints excluded: chain D residue 808 GLU Chi-restraints excluded: chain E residue 59 MET Chi-restraints excluded: chain E residue 216 ASN Chi-restraints excluded: chain E residue 282 VAL Chi-restraints excluded: chain E residue 297 VAL Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 338 SER Chi-restraints excluded: chain E residue 340 THR Chi-restraints excluded: chain E residue 370 CYS Chi-restraints excluded: chain E residue 439 ILE Chi-restraints excluded: chain E residue 443 THR Chi-restraints excluded: chain E residue 477 ASP Chi-restraints excluded: chain E residue 580 ILE Chi-restraints excluded: chain E residue 599 SER Chi-restraints excluded: chain E residue 668 SER Chi-restraints excluded: chain E residue 714 PHE Chi-restraints excluded: chain E residue 811 ILE Chi-restraints excluded: chain E residue 845 ASN Chi-restraints excluded: chain F residue 52 MET Chi-restraints excluded: chain F residue 126 ILE Chi-restraints excluded: chain F residue 127 SER Chi-restraints excluded: chain F residue 128 LEU Chi-restraints excluded: chain F residue 210 ILE Chi-restraints excluded: chain F residue 251 SER Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 274 LEU Chi-restraints excluded: chain F residue 285 VAL Chi-restraints excluded: chain F residue 312 VAL Chi-restraints excluded: chain F residue 343 MET Chi-restraints excluded: chain F residue 362 MET Chi-restraints excluded: chain F residue 439 ILE Chi-restraints excluded: chain F residue 469 ILE Chi-restraints excluded: chain F residue 565 HIS Chi-restraints excluded: chain F residue 580 ILE Chi-restraints excluded: chain F residue 592 MET Chi-restraints excluded: chain F residue 606 THR Chi-restraints excluded: chain F residue 646 LEU Chi-restraints excluded: chain F residue 739 LEU Chi-restraints excluded: chain F residue 754 ASN Chi-restraints excluded: chain F residue 802 LEU Chi-restraints excluded: chain G residue 74 GLU Chi-restraints excluded: chain G residue 86 CYS Chi-restraints excluded: chain G residue 88 VAL Chi-restraints excluded: chain G residue 134 ILE Chi-restraints excluded: chain G residue 254 VAL Chi-restraints excluded: chain G residue 312 VAL Chi-restraints excluded: chain G residue 323 VAL Chi-restraints excluded: chain G residue 332 PHE Chi-restraints excluded: chain G residue 358 LYS Chi-restraints excluded: chain G residue 391 THR Chi-restraints excluded: chain G residue 417 LEU Chi-restraints excluded: chain G residue 508 VAL Chi-restraints excluded: chain G residue 712 ILE Chi-restraints excluded: chain G residue 727 HIS Chi-restraints excluded: chain G residue 808 GLU Chi-restraints excluded: chain G residue 834 GLU Chi-restraints excluded: chain H residue 576 ILE Chi-restraints excluded: chain H residue 598 THR Chi-restraints excluded: chain H residue 614 ASP Chi-restraints excluded: chain H residue 712 ILE Chi-restraints excluded: chain H residue 722 CYS Chi-restraints excluded: chain H residue 859 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 598 random chunks: chunk 376 optimal weight: 0.9980 chunk 505 optimal weight: 3.9990 chunk 145 optimal weight: 6.9990 chunk 437 optimal weight: 10.0000 chunk 70 optimal weight: 2.9990 chunk 131 optimal weight: 5.9990 chunk 475 optimal weight: 1.9990 chunk 198 optimal weight: 0.9990 chunk 487 optimal weight: 9.9990 chunk 60 optimal weight: 10.0000 chunk 87 optimal weight: 9.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 737 HIS ** C 845 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 752 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 845 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 737 HIS ** E 845 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 69 ASN G 727 HIS H 727 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.151966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.117168 restraints weight = 81795.582| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 2.94 r_work: 0.3276 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.4672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 47016 Z= 0.208 Angle : 0.703 40.637 63778 Z= 0.364 Chirality : 0.047 0.245 7318 Planarity : 0.005 0.110 8262 Dihedral : 4.712 35.510 6474 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 2.68 % Allowed : 19.90 % Favored : 77.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.94 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.11), residues: 6036 helix: 0.64 (0.10), residues: 2666 sheet: -0.50 (0.17), residues: 958 loop : -2.26 (0.12), residues: 2412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 424 HIS 0.023 0.001 HIS G 727 PHE 0.048 0.002 PHE H 535 TYR 0.025 0.001 TYR C 867 ARG 0.007 0.000 ARG C 790 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11393.56 seconds wall clock time: 201 minutes 49.88 seconds (12109.88 seconds total)