Starting phenix.real_space_refine on Sun Dec 29 08:44:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x1c_37990/12_2024/8x1c_37990_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x1c_37990/12_2024/8x1c_37990.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8x1c_37990/12_2024/8x1c_37990.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x1c_37990/12_2024/8x1c_37990.map" model { file = "/net/cci-nas-00/data/ceres_data/8x1c_37990/12_2024/8x1c_37990_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x1c_37990/12_2024/8x1c_37990_neut.cif" } resolution = 3.2 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= -0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 316 5.49 5 S 254 5.16 5 C 34669 2.51 5 N 10022 2.21 5 O 11258 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 113 residue(s): 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 56519 Number of models: 1 Model: "" Number of chains: 35 Chain: "A" Number of atoms: 898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 898 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 5, 'TRANS': 110} Chain: "B" Number of atoms: 755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 755 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 93} Chain: "C" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 779 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "D" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 646 Classifications: {'peptide': 81} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "E" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 808 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "F" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 736 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "G" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "H" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 638 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "I" Number of atoms: 7031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 852, 7031 Classifications: {'peptide': 852} Link IDs: {'PTRANS': 52, 'TRANS': 799} Chain breaks: 3 Chain: "J" Number of atoms: 1114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1114 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 12, 'TRANS': 122} Chain breaks: 2 Chain: "K" Number of atoms: 3209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3209 Classifications: {'peptide': 394} Link IDs: {'PTRANS': 17, 'TRANS': 376} Chain: "L" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 823 Classifications: {'peptide': 105} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 95} Chain breaks: 1 Chain: "M" Number of atoms: 3293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3293 Classifications: {'peptide': 428} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 16, 'TRANS': 411} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "N" Number of atoms: 3223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 3223 Classifications: {'peptide': 415} Link IDs: {'PTRANS': 10, 'TRANS': 404} Chain breaks: 2 Chain: "O" Number of atoms: 3339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3339 Classifications: {'peptide': 435} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 16, 'TRANS': 418} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "P" Number of atoms: 3287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3287 Classifications: {'peptide': 427} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 11, 'TRANS': 415} Chain breaks: 1 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "Q" Number of atoms: 3368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3368 Classifications: {'peptide': 440} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 17, 'TRANS': 422} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "R" Number of atoms: 3293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 424, 3293 Classifications: {'peptide': 424} Link IDs: {'PTRANS': 10, 'TRANS': 413} Chain breaks: 1 Chain: "S" Number of atoms: 2925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2925 Classifications: {'peptide': 375} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 355} Chain: "T" Number of atoms: 3146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 403, 3146 Classifications: {'peptide': 403} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 380} Chain breaks: 1 Chain: "U" Number of atoms: 2802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 2802 Classifications: {'peptide': 359} Link IDs: {'PTRANS': 19, 'TRANS': 339} Chain breaks: 1 Chain: "V" Number of atoms: 1757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1757 Classifications: {'peptide': 204} Link IDs: {'PTRANS': 9, 'TRANS': 194} Chain breaks: 1 Chain: "W" Number of atoms: 1542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1542 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 8, 'TRANS': 178} Chain: "X" Number of atoms: 3034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3034 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "Y" Number of atoms: 2990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 2990 Classifications: {'DNA': 147} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 146} Chain: "I" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 23.15, per 1000 atoms: 0.41 Number of scatterers: 56519 At special positions: 0 Unit cell: (186.76, 189.428, 224.112, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 254 16.00 P 316 15.00 O 11258 8.00 N 10022 7.00 C 34669 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 Atom "ATOM 51879 O4' DC X 80 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 11.29 Conformation dependent library (CDL) restraints added in 5.1 seconds 12542 Ramachandran restraints generated. 6271 Oldfield, 0 Emsley, 6271 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11864 Finding SS restraints... Secondary structure from input PDB file: 279 helices and 62 sheets defined 49.7% alpha, 10.3% beta 130 base pairs and 249 stacking pairs defined. Time for finding SS restraints: 16.40 Creating SS restraints... Processing helix chain 'A' and resid 16 through 22 Processing helix chain 'A' and resid 26 through 36 Processing helix chain 'A' and resid 46 through 73 Processing helix chain 'A' and resid 79 through 90 Processing helix chain 'A' and resid 90 through 97 Processing helix chain 'A' and resid 111 through 116 removed outlier: 4.267A pdb=" N VAL A 114 " --> pdb=" O ILE A 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 46 removed outlier: 3.693A pdb=" N LYS B 40 " --> pdb=" O VAL B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 81 Processing helix chain 'B' and resid 87 through 99 Processing helix chain 'B' and resid 100 through 102 No H-bonds generated for 'chain 'B' and resid 100 through 102' Processing helix chain 'B' and resid 103 through 120 Processing helix chain 'C' and resid 45 through 57 removed outlier: 3.521A pdb=" N ARG C 49 " --> pdb=" O THR C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 77 removed outlier: 3.989A pdb=" N ASP C 77 " --> pdb=" O GLU C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 114 removed outlier: 3.512A pdb=" N ALA C 114 " --> pdb=" O CYS C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 132 removed outlier: 3.595A pdb=" N ILE C 124 " --> pdb=" O MET C 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 24 through 29 removed outlier: 3.523A pdb=" N ILE D 29 " --> pdb=" O ILE D 26 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 41 Processing helix chain 'D' and resid 49 through 76 removed outlier: 3.516A pdb=" N ALA D 76 " --> pdb=" O TYR D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 93 Processing helix chain 'E' and resid 16 through 21 Processing helix chain 'E' and resid 26 through 35 Processing helix chain 'E' and resid 46 through 73 Processing helix chain 'E' and resid 79 through 90 Processing helix chain 'E' and resid 90 through 97 Processing helix chain 'F' and resid 34 through 46 removed outlier: 3.533A pdb=" N TYR F 39 " --> pdb=" O SER F 35 " (cutoff:3.500A) Processing helix chain 'F' and resid 52 through 81 Processing helix chain 'F' and resid 87 through 99 Processing helix chain 'F' and resid 101 through 121 Processing helix chain 'G' and resid 44 through 55 removed outlier: 3.598A pdb=" N LEU G 48 " --> pdb=" O GLY G 44 " (cutoff:3.500A) Processing helix chain 'G' and resid 63 through 77 removed outlier: 3.749A pdb=" N ASP G 77 " --> pdb=" O GLU G 73 " (cutoff:3.500A) Processing helix chain 'G' and resid 85 through 114 removed outlier: 3.577A pdb=" N LEU G 109 " --> pdb=" O GLU G 105 " (cutoff:3.500A) Processing helix chain 'G' and resid 120 through 131 Processing helix chain 'H' and resid 25 through 29 Processing helix chain 'H' and resid 30 through 41 Processing helix chain 'H' and resid 49 through 76 removed outlier: 3.804A pdb=" N GLU H 53 " --> pdb=" O LEU H 49 " (cutoff:3.500A) Processing helix chain 'H' and resid 82 through 93 Processing helix chain 'I' and resid 95 through 116 removed outlier: 4.383A pdb=" N LYS I 101 " --> pdb=" O ALA I 97 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N HIS I 102 " --> pdb=" O GLU I 98 " (cutoff:3.500A) Processing helix chain 'I' and resid 135 through 251 removed outlier: 3.782A pdb=" N GLN I 204 " --> pdb=" O LYS I 200 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N PHE I 205 " --> pdb=" O ASP I 201 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N TRP I 206 " --> pdb=" O VAL I 202 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N PHE I 215 " --> pdb=" O LYS I 211 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS I 216 " --> pdb=" O VAL I 212 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS I 227 " --> pdb=" O GLU I 223 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N TYR I 243 " --> pdb=" O GLN I 239 " (cutoff:3.500A) Processing helix chain 'I' and resid 619 through 635 Processing helix chain 'I' and resid 648 through 663 Processing helix chain 'I' and resid 675 through 677 No H-bonds generated for 'chain 'I' and resid 675 through 677' Processing helix chain 'I' and resid 678 through 690 Processing helix chain 'I' and resid 701 through 709 Processing helix chain 'I' and resid 724 through 729 Processing helix chain 'I' and resid 731 through 737 removed outlier: 3.618A pdb=" N PHE I 735 " --> pdb=" O ASP I 731 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ARG I 737 " --> pdb=" O GLN I 733 " (cutoff:3.500A) Processing helix chain 'I' and resid 748 through 752 Processing helix chain 'I' and resid 758 through 764 removed outlier: 4.233A pdb=" N ASN I 764 " --> pdb=" O GLN I 760 " (cutoff:3.500A) Processing helix chain 'I' and resid 782 through 793 removed outlier: 3.703A pdb=" N TRP I 786 " --> pdb=" O LEU I 782 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE I 791 " --> pdb=" O SER I 787 " (cutoff:3.500A) Processing helix chain 'I' and resid 800 through 816 removed outlier: 4.312A pdb=" N LYS I 804 " --> pdb=" O HIS I 800 " (cutoff:3.500A) Proline residue: I 810 - end of helix removed outlier: 3.941A pdb=" N ILE I 815 " --> pdb=" O LEU I 811 " (cutoff:3.500A) Processing helix chain 'I' and resid 824 through 834 Processing helix chain 'I' and resid 841 through 846 Processing helix chain 'I' and resid 862 through 874 removed outlier: 3.726A pdb=" N LEU I 868 " --> pdb=" O ARG I 864 " (cutoff:3.500A) Processing helix chain 'I' and resid 889 through 903 Processing helix chain 'I' and resid 904 through 907 Processing helix chain 'I' and resid 927 through 935 removed outlier: 3.913A pdb=" N ALA I 932 " --> pdb=" O VAL I 929 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N THR I 933 " --> pdb=" O LEU I 930 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ASP I 934 " --> pdb=" O ARG I 931 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL I 935 " --> pdb=" O ALA I 932 " (cutoff:3.500A) Processing helix chain 'I' and resid 936 through 940 removed outlier: 3.609A pdb=" N ARG I 940 " --> pdb=" O PRO I 937 " (cutoff:3.500A) Processing helix chain 'I' and resid 942 through 946 removed outlier: 3.959A pdb=" N ARG I 945 " --> pdb=" O ASP I 942 " (cutoff:3.500A) Processing helix chain 'I' and resid 948 through 952 Processing helix chain 'I' and resid 956 through 962 Processing helix chain 'I' and resid 970 through 978 removed outlier: 3.638A pdb=" N LEU I 974 " --> pdb=" O SER I 970 " (cutoff:3.500A) Processing helix chain 'I' and resid 1886 through 1912 removed outlier: 3.775A pdb=" N GLY I1912 " --> pdb=" O SER I1908 " (cutoff:3.500A) Processing helix chain 'I' and resid 1920 through 1927 Processing helix chain 'I' and resid 1945 through 1951 removed outlier: 3.898A pdb=" N THR I1950 " --> pdb=" O THR I1947 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N TYR I1951 " --> pdb=" O PHE I1948 " (cutoff:3.500A) Processing helix chain 'I' and resid 1952 through 1958 Processing helix chain 'I' and resid 1961 through 1977 removed outlier: 5.725A pdb=" N GLU I1971 " --> pdb=" O ASP I1967 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N ILE I1972 " --> pdb=" O GLN I1968 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE I1977 " --> pdb=" O ILE I1973 " (cutoff:3.500A) Processing helix chain 'I' and resid 1998 through 2019 removed outlier: 3.540A pdb=" N ARG I2002 " --> pdb=" O TRP I1998 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLU I2013 " --> pdb=" O GLN I2009 " (cutoff:3.500A) Proline residue: I2016 - end of helix Processing helix chain 'I' and resid 2021 through 2030 removed outlier: 3.533A pdb=" N ASN I2027 " --> pdb=" O ARG I2023 " (cutoff:3.500A) Processing helix chain 'I' and resid 2036 through 2041 Processing helix chain 'I' and resid 2042 through 2058 removed outlier: 3.547A pdb=" N GLN I2046 " --> pdb=" O CYS I2042 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLN I2054 " --> pdb=" O VAL I2050 " (cutoff:3.500A) Processing helix chain 'I' and resid 2069 through 2083 removed outlier: 3.674A pdb=" N ASP I2073 " --> pdb=" O THR I2069 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N VAL I2074 " --> pdb=" O ARG I2070 " (cutoff:3.500A) Processing helix chain 'I' and resid 2094 through 2106 Processing helix chain 'I' and resid 2143 through 2150 Processing helix chain 'I' and resid 2171 through 2192 removed outlier: 3.576A pdb=" N ASN I2175 " --> pdb=" O THR I2171 " (cutoff:3.500A) Processing helix chain 'J' and resid 171 through 199 removed outlier: 5.169A pdb=" N ILE J 178 " --> pdb=" O ARG J 174 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N THR J 179 " --> pdb=" O GLU J 175 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLU J 180 " --> pdb=" O ALA J 176 " (cutoff:3.500A) Processing helix chain 'J' and resid 273 through 278 removed outlier: 3.517A pdb=" N PHE J 278 " --> pdb=" O PHE J 274 " (cutoff:3.500A) Processing helix chain 'J' and resid 312 through 330 removed outlier: 3.738A pdb=" N PHE J 316 " --> pdb=" O THR J 312 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LYS J 317 " --> pdb=" O ALA J 313 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS J 325 " --> pdb=" O GLU J 321 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYR J 326 " --> pdb=" O ALA J 322 " (cutoff:3.500A) Processing helix chain 'K' and resid 32 through 36 removed outlier: 3.726A pdb=" N ARG K 36 " --> pdb=" O LYS K 33 " (cutoff:3.500A) Processing helix chain 'K' and resid 43 through 48 Processing helix chain 'K' and resid 68 through 79 Processing helix chain 'K' and resid 126 through 139 Processing helix chain 'K' and resid 167 through 170 removed outlier: 3.715A pdb=" N ILE K 170 " --> pdb=" O LYS K 167 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 167 through 170' Processing helix chain 'K' and resid 176 through 190 Processing helix chain 'K' and resid 201 through 209 Processing helix chain 'K' and resid 215 through 224 Processing helix chain 'K' and resid 251 through 255 removed outlier: 3.534A pdb=" N MET K 255 " --> pdb=" O ARG K 252 " (cutoff:3.500A) Processing helix chain 'K' and resid 272 through 277 Processing helix chain 'K' and resid 278 through 281 Processing helix chain 'K' and resid 293 through 301 Processing helix chain 'K' and resid 302 through 304 No H-bonds generated for 'chain 'K' and resid 302 through 304' Processing helix chain 'K' and resid 306 through 308 No H-bonds generated for 'chain 'K' and resid 306 through 308' Processing helix chain 'K' and resid 309 through 314 Processing helix chain 'K' and resid 321 through 326 removed outlier: 3.633A pdb=" N LEU K 325 " --> pdb=" O GLY K 322 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N PHE K 326 " --> pdb=" O ASN K 323 " (cutoff:3.500A) Processing helix chain 'K' and resid 328 through 341 removed outlier: 3.555A pdb=" N CYS K 339 " --> pdb=" O SER K 335 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU K 340 " --> pdb=" O GLU K 336 " (cutoff:3.500A) Processing helix chain 'K' and resid 357 through 370 Processing helix chain 'K' and resid 378 through 386 Processing helix chain 'K' and resid 386 through 394 removed outlier: 4.242A pdb=" N CYS K 390 " --> pdb=" O GLY K 386 " (cutoff:3.500A) Processing helix chain 'L' and resid 20 through 35 removed outlier: 4.059A pdb=" N ARG L 24 " --> pdb=" O ASP L 20 " (cutoff:3.500A) Processing helix chain 'L' and resid 88 through 93 Processing helix chain 'L' and resid 137 through 146 Processing helix chain 'M' and resid 42 through 59 removed outlier: 3.601A pdb=" N GLU M 54 " --> pdb=" O GLY M 50 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU M 55 " --> pdb=" O VAL M 51 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE M 56 " --> pdb=" O ILE M 52 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS M 59 " --> pdb=" O LEU M 55 " (cutoff:3.500A) Processing helix chain 'M' and resid 75 through 88 removed outlier: 3.652A pdb=" N GLY M 88 " --> pdb=" O ALA M 84 " (cutoff:3.500A) Processing helix chain 'M' and resid 99 through 102 Processing helix chain 'M' and resid 107 through 120 removed outlier: 3.967A pdb=" N ALA M 119 " --> pdb=" O ASN M 115 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N ILE M 120 " --> pdb=" O PHE M 116 " (cutoff:3.500A) Processing helix chain 'M' and resid 173 through 175 No H-bonds generated for 'chain 'M' and resid 173 through 175' Processing helix chain 'M' and resid 176 through 183 Processing helix chain 'M' and resid 240 through 247 Processing helix chain 'M' and resid 256 through 262 Processing helix chain 'M' and resid 275 through 289 Processing helix chain 'M' and resid 304 through 307 Processing helix chain 'M' and resid 308 through 319 removed outlier: 4.094A pdb=" N ARG M 317 " --> pdb=" O THR M 313 " (cutoff:3.500A) Processing helix chain 'M' and resid 347 through 350 Processing helix chain 'M' and resid 351 through 356 Processing helix chain 'M' and resid 367 through 383 Processing helix chain 'M' and resid 387 through 401 removed outlier: 3.536A pdb=" N HIS M 393 " --> pdb=" O GLU M 389 " (cutoff:3.500A) Processing helix chain 'M' and resid 402 through 420 removed outlier: 4.126A pdb=" N SER M 406 " --> pdb=" O THR M 402 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N VAL M 407 " --> pdb=" O LEU M 403 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N GLN M 408 " --> pdb=" O ARG M 404 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N THR M 411 " --> pdb=" O VAL M 407 " (cutoff:3.500A) Proline residue: M 412 - end of helix Processing helix chain 'M' and resid 426 through 434 removed outlier: 3.804A pdb=" N VAL M 430 " --> pdb=" O GLU M 426 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU M 431 " --> pdb=" O LYS M 427 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLU M 432 " --> pdb=" O GLU M 428 " (cutoff:3.500A) Processing helix chain 'M' and resid 439 through 447 Processing helix chain 'M' and resid 448 through 450 No H-bonds generated for 'chain 'M' and resid 448 through 450' Processing helix chain 'N' and resid 49 through 66 Processing helix chain 'N' and resid 82 through 95 removed outlier: 3.828A pdb=" N ALA N 87 " --> pdb=" O LYS N 83 " (cutoff:3.500A) Processing helix chain 'N' and resid 114 through 126 Processing helix chain 'N' and resid 175 through 185 Processing helix chain 'N' and resid 244 through 251 Processing helix chain 'N' and resid 258 through 262 Processing helix chain 'N' and resid 273 through 284 removed outlier: 3.787A pdb=" N ASN N 277 " --> pdb=" O ARG N 273 " (cutoff:3.500A) Processing helix chain 'N' and resid 301 through 304 Processing helix chain 'N' and resid 305 through 316 removed outlier: 4.004A pdb=" N ARG N 314 " --> pdb=" O SER N 310 " (cutoff:3.500A) Processing helix chain 'N' and resid 347 through 352 Processing helix chain 'N' and resid 363 through 378 Processing helix chain 'N' and resid 383 through 397 Processing helix chain 'N' and resid 398 through 416 removed outlier: 4.021A pdb=" N ALA N 402 " --> pdb=" O SER N 398 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N THR N 407 " --> pdb=" O ILE N 403 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA N 408 " --> pdb=" O GLN N 404 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG N 416 " --> pdb=" O VAL N 412 " (cutoff:3.500A) Processing helix chain 'N' and resid 422 through 433 Processing helix chain 'N' and resid 435 through 442 Processing helix chain 'O' and resid 42 through 59 removed outlier: 3.794A pdb=" N VAL O 51 " --> pdb=" O GLU O 47 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LYS O 59 " --> pdb=" O LEU O 55 " (cutoff:3.500A) Processing helix chain 'O' and resid 75 through 88 Processing helix chain 'O' and resid 99 through 102 removed outlier: 3.657A pdb=" N TYR O 102 " --> pdb=" O SER O 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 99 through 102' Processing helix chain 'O' and resid 107 through 119 removed outlier: 3.685A pdb=" N VAL O 111 " --> pdb=" O LYS O 107 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU O 112 " --> pdb=" O LYS O 108 " (cutoff:3.500A) Processing helix chain 'O' and resid 173 through 184 removed outlier: 3.586A pdb=" N PHE O 177 " --> pdb=" O ASP O 173 " (cutoff:3.500A) Processing helix chain 'O' and resid 208 through 212 removed outlier: 4.178A pdb=" N THR O 211 " --> pdb=" O THR O 208 " (cutoff:3.500A) Processing helix chain 'O' and resid 240 through 249 Processing helix chain 'O' and resid 255 through 258 Processing helix chain 'O' and resid 259 through 264 Processing helix chain 'O' and resid 271 through 276 Processing helix chain 'O' and resid 277 through 289 removed outlier: 3.730A pdb=" N GLN O 289 " --> pdb=" O LYS O 285 " (cutoff:3.500A) Processing helix chain 'O' and resid 303 through 307 removed outlier: 3.551A pdb=" N MET O 306 " --> pdb=" O GLU O 303 " (cutoff:3.500A) Processing helix chain 'O' and resid 308 through 321 removed outlier: 3.697A pdb=" N HIS O 316 " --> pdb=" O PHE O 312 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ARG O 317 " --> pdb=" O THR O 313 " (cutoff:3.500A) Processing helix chain 'O' and resid 351 through 356 Processing helix chain 'O' and resid 367 through 382 removed outlier: 3.534A pdb=" N THR O 381 " --> pdb=" O ILE O 377 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLU O 382 " --> pdb=" O ARG O 378 " (cutoff:3.500A) Processing helix chain 'O' and resid 387 through 400 removed outlier: 3.723A pdb=" N LYS O 400 " --> pdb=" O GLU O 396 " (cutoff:3.500A) Processing helix chain 'O' and resid 402 through 407 Processing helix chain 'O' and resid 410 through 420 Processing helix chain 'O' and resid 426 through 437 removed outlier: 3.506A pdb=" N VAL O 430 " --> pdb=" O GLU O 426 " (cutoff:3.500A) Processing helix chain 'O' and resid 439 through 450 removed outlier: 3.581A pdb=" N LYS O 445 " --> pdb=" O LYS O 441 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ILE O 446 " --> pdb=" O SER O 442 " (cutoff:3.500A) Processing helix chain 'O' and resid 451 through 454 removed outlier: 3.728A pdb=" N TYR O 454 " --> pdb=" O GLN O 451 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 451 through 454' Processing helix chain 'P' and resid 49 through 64 Processing helix chain 'P' and resid 82 through 95 Processing helix chain 'P' and resid 106 through 109 removed outlier: 3.665A pdb=" N PHE P 109 " --> pdb=" O SER P 106 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 106 through 109' Processing helix chain 'P' and resid 114 through 125 Processing helix chain 'P' and resid 175 through 186 Processing helix chain 'P' and resid 244 through 251 Processing helix chain 'P' and resid 272 through 287 Processing helix chain 'P' and resid 301 through 304 Processing helix chain 'P' and resid 305 through 316 removed outlier: 4.069A pdb=" N ARG P 314 " --> pdb=" O SER P 310 " (cutoff:3.500A) Processing helix chain 'P' and resid 343 through 346 Processing helix chain 'P' and resid 349 through 353 Processing helix chain 'P' and resid 363 through 378 Processing helix chain 'P' and resid 383 through 397 Processing helix chain 'P' and resid 398 through 416 removed outlier: 3.623A pdb=" N ILE P 406 " --> pdb=" O ALA P 402 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N THR P 407 " --> pdb=" O ILE P 403 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA P 408 " --> pdb=" O GLN P 404 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N VAL P 412 " --> pdb=" O ALA P 408 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N CYS P 413 " --> pdb=" O ALA P 409 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ARG P 414 " --> pdb=" O SER P 410 " (cutoff:3.500A) Processing helix chain 'P' and resid 422 through 433 removed outlier: 3.555A pdb=" N ILE P 426 " --> pdb=" O GLN P 422 " (cutoff:3.500A) Processing helix chain 'P' and resid 436 through 441 removed outlier: 3.876A pdb=" N THR P 440 " --> pdb=" O GLU P 436 " (cutoff:3.500A) Processing helix chain 'Q' and resid 42 through 59 removed outlier: 3.553A pdb=" N GLY Q 50 " --> pdb=" O ARG Q 46 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL Q 51 " --> pdb=" O GLU Q 47 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ILE Q 52 " --> pdb=" O ALA Q 48 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N VAL Q 53 " --> pdb=" O CYS Q 49 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLU Q 54 " --> pdb=" O GLY Q 50 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LYS Q 59 " --> pdb=" O LEU Q 55 " (cutoff:3.500A) Processing helix chain 'Q' and resid 75 through 88 removed outlier: 3.516A pdb=" N ALA Q 82 " --> pdb=" O ALA Q 78 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ILE Q 83 " --> pdb=" O LEU Q 79 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ALA Q 84 " --> pdb=" O ALA Q 80 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLN Q 85 " --> pdb=" O LEU Q 81 " (cutoff:3.500A) Processing helix chain 'Q' and resid 99 through 101 No H-bonds generated for 'chain 'Q' and resid 99 through 101' Processing helix chain 'Q' and resid 107 through 119 removed outlier: 3.747A pdb=" N LEU Q 112 " --> pdb=" O LYS Q 108 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N MET Q 113 " --> pdb=" O THR Q 109 " (cutoff:3.500A) Processing helix chain 'Q' and resid 173 through 184 Processing helix chain 'Q' and resid 240 through 249 Processing helix chain 'Q' and resid 255 through 260 removed outlier: 3.682A pdb=" N MET Q 259 " --> pdb=" O ASP Q 255 " (cutoff:3.500A) Processing helix chain 'Q' and resid 271 through 277 removed outlier: 3.583A pdb=" N LEU Q 275 " --> pdb=" O ILE Q 271 " (cutoff:3.500A) Processing helix chain 'Q' and resid 281 through 288 Processing helix chain 'Q' and resid 304 through 307 Processing helix chain 'Q' and resid 308 through 319 removed outlier: 3.587A pdb=" N HIS Q 316 " --> pdb=" O PHE Q 312 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ARG Q 317 " --> pdb=" O THR Q 313 " (cutoff:3.500A) Processing helix chain 'Q' and resid 346 through 350 Processing helix chain 'Q' and resid 351 through 356 Processing helix chain 'Q' and resid 367 through 383 Processing helix chain 'Q' and resid 387 through 401 removed outlier: 3.645A pdb=" N LYS Q 400 " --> pdb=" O GLU Q 396 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N THR Q 401 " --> pdb=" O ILE Q 397 " (cutoff:3.500A) Processing helix chain 'Q' and resid 402 through 409 removed outlier: 3.501A pdb=" N SER Q 406 " --> pdb=" O THR Q 402 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU Q 409 " --> pdb=" O TYR Q 405 " (cutoff:3.500A) Processing helix chain 'Q' and resid 410 through 420 Processing helix chain 'Q' and resid 426 through 436 removed outlier: 3.713A pdb=" N VAL Q 430 " --> pdb=" O GLU Q 426 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLU Q 431 " --> pdb=" O LYS Q 427 " (cutoff:3.500A) Processing helix chain 'Q' and resid 439 through 450 Processing helix chain 'R' and resid 49 through 66 Processing helix chain 'R' and resid 82 through 94 Processing helix chain 'R' and resid 116 through 126 removed outlier: 3.683A pdb=" N SER R 126 " --> pdb=" O ALA R 122 " (cutoff:3.500A) Processing helix chain 'R' and resid 175 through 185 Processing helix chain 'R' and resid 245 through 250 Processing helix chain 'R' and resid 256 through 261 Processing helix chain 'R' and resid 268 through 287 removed outlier: 4.900A pdb=" N ALA R 278 " --> pdb=" O GLU R 274 " (cutoff:3.500A) Processing helix chain 'R' and resid 301 through 304 Processing helix chain 'R' and resid 305 through 316 removed outlier: 3.735A pdb=" N ARG R 314 " --> pdb=" O SER R 310 " (cutoff:3.500A) Processing helix chain 'R' and resid 347 through 353 removed outlier: 3.870A pdb=" N ARG R 353 " --> pdb=" O ASP R 349 " (cutoff:3.500A) Processing helix chain 'R' and resid 363 through 378 removed outlier: 3.559A pdb=" N LYS R 368 " --> pdb=" O GLU R 364 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLU R 378 " --> pdb=" O ARG R 374 " (cutoff:3.500A) Processing helix chain 'R' and resid 383 through 397 Processing helix chain 'R' and resid 398 through 416 removed outlier: 3.723A pdb=" N ALA R 402 " --> pdb=" O SER R 398 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE R 406 " --> pdb=" O ALA R 402 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N THR R 407 " --> pdb=" O ILE R 403 " (cutoff:3.500A) Processing helix chain 'R' and resid 422 through 433 removed outlier: 3.604A pdb=" N LEU R 432 " --> pdb=" O ARG R 428 " (cutoff:3.500A) Processing helix chain 'R' and resid 435 through 442 Processing helix chain 'S' and resid 55 through 61 removed outlier: 3.669A pdb=" N LYS S 61 " --> pdb=" O GLU S 57 " (cutoff:3.500A) Processing helix chain 'S' and resid 78 through 92 Processing helix chain 'S' and resid 97 through 101 removed outlier: 3.516A pdb=" N HIS S 101 " --> pdb=" O PRO S 98 " (cutoff:3.500A) Processing helix chain 'S' and resid 112 through 126 Processing helix chain 'S' and resid 137 through 146 Processing helix chain 'S' and resid 172 through 175 Processing helix chain 'S' and resid 181 through 197 Processing helix chain 'S' and resid 202 through 217 Processing helix chain 'S' and resid 222 through 233 Processing helix chain 'S' and resid 252 through 257 Processing helix chain 'S' and resid 258 through 262 Processing helix chain 'S' and resid 263 through 268 Processing helix chain 'S' and resid 273 through 284 Processing helix chain 'S' and resid 286 through 296 removed outlier: 4.487A pdb=" N LYS S 291 " --> pdb=" O VAL S 287 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N ASP S 292 " --> pdb=" O ASP S 288 " (cutoff:3.500A) Processing helix chain 'S' and resid 301 through 306 removed outlier: 4.033A pdb=" N TYR S 306 " --> pdb=" O THR S 303 " (cutoff:3.500A) Processing helix chain 'S' and resid 308 through 321 Processing helix chain 'S' and resid 334 through 336 No H-bonds generated for 'chain 'S' and resid 334 through 336' Processing helix chain 'S' and resid 337 through 349 Processing helix chain 'S' and resid 350 through 356 removed outlier: 3.900A pdb=" N GLN S 354 " --> pdb=" O THR S 351 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N TRP S 356 " --> pdb=" O GLN S 353 " (cutoff:3.500A) Processing helix chain 'S' and resid 359 through 366 Processing helix chain 'S' and resid 368 through 374 removed outlier: 3.747A pdb=" N ARG S 372 " --> pdb=" O SER S 368 " (cutoff:3.500A) Processing helix chain 'T' and resid 71 through 76 Processing helix chain 'T' and resid 95 through 109 Processing helix chain 'T' and resid 114 through 118 Processing helix chain 'T' and resid 129 through 143 removed outlier: 3.577A pdb=" N PHE T 141 " --> pdb=" O THR T 137 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N HIS T 143 " --> pdb=" O LEU T 139 " (cutoff:3.500A) Processing helix chain 'T' and resid 154 through 162 Processing helix chain 'T' and resid 189 through 192 Processing helix chain 'T' and resid 198 through 213 Processing helix chain 'T' and resid 219 through 221 No H-bonds generated for 'chain 'T' and resid 219 through 221' Processing helix chain 'T' and resid 247 through 267 Processing helix chain 'T' and resid 275 through 280 Processing helix chain 'T' and resid 299 through 304 removed outlier: 3.692A pdb=" N ILE T 304 " --> pdb=" O GLU T 300 " (cutoff:3.500A) Processing helix chain 'T' and resid 305 through 310 removed outlier: 4.149A pdb=" N PHE T 309 " --> pdb=" O PRO T 305 " (cutoff:3.500A) Processing helix chain 'T' and resid 324 through 335 Processing helix chain 'T' and resid 340 through 347 Processing helix chain 'T' and resid 353 through 357 Processing helix chain 'T' and resid 359 through 372 Processing helix chain 'T' and resid 385 through 391 Processing helix chain 'T' and resid 391 through 401 Processing helix chain 'T' and resid 403 through 410 removed outlier: 3.553A pdb=" N GLN T 408 " --> pdb=" O THR T 405 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N TRP T 410 " --> pdb=" O GLN T 407 " (cutoff:3.500A) Processing helix chain 'T' and resid 413 through 420 Processing helix chain 'T' and resid 423 through 428 Processing helix chain 'U' and resid 3 through 7 Processing helix chain 'U' and resid 55 through 61 Processing helix chain 'U' and resid 80 through 93 removed outlier: 4.046A pdb=" N TYR U 91 " --> pdb=" O HIS U 87 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ASN U 92 " --> pdb=" O HIS U 88 " (cutoff:3.500A) Processing helix chain 'U' and resid 111 through 128 removed outlier: 3.762A pdb=" N LYS U 118 " --> pdb=" O ALA U 114 " (cutoff:3.500A) Processing helix chain 'U' and resid 137 through 143 Processing helix chain 'U' and resid 182 through 193 Processing helix chain 'U' and resid 202 through 204 No H-bonds generated for 'chain 'U' and resid 202 through 204' Processing helix chain 'U' and resid 205 through 214 removed outlier: 3.825A pdb=" N ILE U 212 " --> pdb=" O ILE U 208 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LYS U 213 " --> pdb=" O VAL U 209 " (cutoff:3.500A) Processing helix chain 'U' and resid 227 through 232 Processing helix chain 'U' and resid 251 through 255 Processing helix chain 'U' and resid 263 through 267 Processing helix chain 'U' and resid 273 through 284 Processing helix chain 'U' and resid 289 through 295 removed outlier: 3.880A pdb=" N LEU U 293 " --> pdb=" O ILE U 289 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TYR U 294 " --> pdb=" O ARG U 290 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA U 295 " --> pdb=" O LYS U 291 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 289 through 295' Processing helix chain 'U' and resid 301 through 305 removed outlier: 3.561A pdb=" N MET U 305 " --> pdb=" O GLY U 302 " (cutoff:3.500A) Processing helix chain 'U' and resid 306 through 307 No H-bonds generated for 'chain 'U' and resid 306 through 307' Processing helix chain 'U' and resid 308 through 321 Processing helix chain 'U' and resid 334 through 336 No H-bonds generated for 'chain 'U' and resid 334 through 336' Processing helix chain 'U' and resid 337 through 348 Processing helix chain 'U' and resid 349 through 356 removed outlier: 4.564A pdb=" N GLN U 354 " --> pdb=" O THR U 351 " (cutoff:3.500A) Processing helix chain 'U' and resid 358 through 365 Processing helix chain 'V' and resid 54 through 63 Processing helix chain 'V' and resid 116 through 120 removed outlier: 3.727A pdb=" N GLU V 119 " --> pdb=" O ARG V 116 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLU V 120 " --> pdb=" O ALA V 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 116 through 120' Processing helix chain 'V' and resid 124 through 129 Processing helix chain 'V' and resid 139 through 147 Processing helix chain 'V' and resid 153 through 167 removed outlier: 4.214A pdb=" N HIS V 159 " --> pdb=" O ALA V 155 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N LEU V 160 " --> pdb=" O GLU V 156 " (cutoff:3.500A) Processing helix chain 'V' and resid 170 through 178 removed outlier: 4.673A pdb=" N ASP V 176 " --> pdb=" O VAL V 172 " (cutoff:3.500A) Processing helix chain 'V' and resid 187 through 205 removed outlier: 3.580A pdb=" N LEU V 191 " --> pdb=" O SER V 187 " (cutoff:3.500A) Processing helix chain 'V' and resid 219 through 233 Processing helix chain 'V' and resid 243 through 275 removed outlier: 3.960A pdb=" N LEU V 247 " --> pdb=" O GLU V 243 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ARG V 252 " --> pdb=" O LEU V 248 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLU V 255 " --> pdb=" O LEU V 251 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N LYS V 259 " --> pdb=" O GLU V 255 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ARG V 264 " --> pdb=" O GLU V 260 " (cutoff:3.500A) Processing helix chain 'W' and resid 58 through 61 Processing helix chain 'W' and resid 123 through 129 Processing helix chain 'W' and resid 148 through 157 Processing helix chain 'W' and resid 172 through 204 removed outlier: 3.828A pdb=" N VAL W 177 " --> pdb=" O ALA W 173 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LYS W 182 " --> pdb=" O LYS W 178 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ALA W 185 " --> pdb=" O GLU W 181 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU W 197 " --> pdb=" O GLU W 193 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLU W 199 " --> pdb=" O ALA W 195 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ARG W 200 " --> pdb=" O GLU W 196 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 77 through 78 Processing sheet with id=AA2, first strand: chain 'A' and resid 101 through 102 removed outlier: 6.714A pdb=" N THR A 101 " --> pdb=" O TYR D 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 83 through 84 removed outlier: 7.080A pdb=" N ARG C 83 " --> pdb=" O VAL D 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 118 through 119 Processing sheet with id=AA5, first strand: chain 'E' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'E' and resid 101 through 102 removed outlier: 6.820A pdb=" N THR E 101 " --> pdb=" O TYR H 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'G' and resid 83 through 84 removed outlier: 7.379A pdb=" N ARG G 83 " --> pdb=" O VAL H 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'I' and resid 695 through 697 removed outlier: 6.467A pdb=" N LEU I 696 " --> pdb=" O ILE I 722 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N HIS I 670 " --> pdb=" O CYS I 721 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N THR I 723 " --> pdb=" O HIS I 670 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ILE I 672 " --> pdb=" O THR I 723 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ARG I 741 " --> pdb=" O SER I 767 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLY I 639 " --> pdb=" O ARG I 770 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU I 772 " --> pdb=" O GLY I 639 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ILE I 640 " --> pdb=" O LEU I 838 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 852 through 859 removed outlier: 6.280A pdb=" N VAL I2133 " --> pdb=" O TYR I2164 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N LEU I2166 " --> pdb=" O VAL I2133 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N PHE I2135 " --> pdb=" O LEU I2166 " (cutoff:3.500A) removed outlier: 8.444A pdb=" N SER I2168 " --> pdb=" O PHE I2135 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N LEU I2063 " --> pdb=" O VAL I2134 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N LEU I2116 " --> pdb=" O VAL I2062 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N ILE I2064 " --> pdb=" O LEU I2116 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'I' and resid 924 through 925 removed outlier: 6.403A pdb=" N SER I 924 " --> pdb=" O ALA I1992 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'J' and resid 212 through 217 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 263 through 267 current: chain 'P' and resid 158 through 164 WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 169 through 172 current: chain 'P' and resid 202 through 207 WARNING: can't find start of bonding for strands! previous: chain 'P' and resid 202 through 207 current: chain 'Q' and resid 153 through 162 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 167 through 172 current: chain 'Q' and resid 200 through 205 Processing sheet with id=AB3, first strand: chain 'J' and resid 301 through 302 Processing sheet with id=AB4, first strand: chain 'K' and resid 4 through 6 Processing sheet with id=AB5, first strand: chain 'K' and resid 29 through 31 Processing sheet with id=AB6, first strand: chain 'K' and resid 60 through 61 Processing sheet with id=AB7, first strand: chain 'K' and resid 94 through 95 Processing sheet with id=AB8, first strand: chain 'K' and resid 164 through 165 removed outlier: 3.571A pdb=" N LYS K 164 " --> pdb=" O CYS K 161 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ILE K 146 " --> pdb=" O VAL K 318 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N THR K 320 " --> pdb=" O ILE K 146 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N VAL K 148 " --> pdb=" O THR K 320 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'K' and resid 236 through 237 removed outlier: 3.722A pdb=" N PHE K 248 " --> pdb=" O VAL K 237 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'M' and resid 93 through 97 removed outlier: 6.519A pdb=" N CYS M 94 " --> pdb=" O PHE M 300 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N ASP M 302 " --> pdb=" O CYS M 94 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N MET M 96 " --> pdb=" O ASP M 302 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N VAL M 66 " --> pdb=" O PHE M 329 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N SER M 331 " --> pdb=" O VAL M 66 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N LEU M 68 " --> pdb=" O SER M 331 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ALA M 65 " --> pdb=" O MET M 359 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N ILE M 361 " --> pdb=" O ALA M 65 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N LEU M 67 " --> pdb=" O ILE M 361 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'M' and resid 237 through 239 Processing sheet with id=AC3, first strand: chain 'M' and resid 129 through 131 Processing sheet with id=AC4, first strand: chain 'M' and resid 166 through 171 removed outlier: 6.500A pdb=" N HIS M 156 " --> pdb=" O PRO M 140 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ILE M 158 " --> pdb=" O LEU M 138 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N LEU M 138 " --> pdb=" O ILE M 158 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N GLY M 160 " --> pdb=" O THR M 136 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLY M 133 " --> pdb=" O ILE M 191 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE M 191 " --> pdb=" O GLY M 133 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ASP M 189 " --> pdb=" O VAL M 135 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N TYR M 192 " --> pdb=" O ARG M 202 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N ARG M 202 " --> pdb=" O TYR M 192 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'M' and resid 336 through 337 Processing sheet with id=AC6, first strand: chain 'N' and resid 42 through 43 Processing sheet with id=AC7, first strand: chain 'N' and resid 100 through 104 removed outlier: 6.300A pdb=" N LEU N 296 " --> pdb=" O ILE N 325 " (cutoff:3.500A) removed outlier: 8.449A pdb=" N ALA N 327 " --> pdb=" O LEU N 296 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N ILE N 298 " --> pdb=" O ALA N 327 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N ALA N 72 " --> pdb=" O LEU N 355 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N VAL N 357 " --> pdb=" O ALA N 72 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N LEU N 74 " --> pdb=" O VAL N 357 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N THR N 359 " --> pdb=" O LEU N 74 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N ALA N 76 " --> pdb=" O THR N 359 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'N' and resid 238 through 243 Processing sheet with id=AC9, first strand: chain 'N' and resid 136 through 145 removed outlier: 6.613A pdb=" N THR N 162 " --> pdb=" O VAL N 143 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N ILE N 145 " --> pdb=" O LYS N 160 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N LYS N 160 " --> pdb=" O ILE N 145 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLY N 159 " --> pdb=" O LEU N 174 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 169 through 174 current: chain 'N' and resid 202 through 204 Processing sheet with id=AD1, first strand: chain 'N' and resid 332 through 334 Processing sheet with id=AD2, first strand: chain 'O' and resid 35 through 36 Processing sheet with id=AD3, first strand: chain 'O' and resid 93 through 97 removed outlier: 6.521A pdb=" N LEU O 299 " --> pdb=" O ILE O 328 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N ALA O 330 " --> pdb=" O LEU O 299 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N VAL O 301 " --> pdb=" O ALA O 330 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N VAL O 66 " --> pdb=" O PHE O 329 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N SER O 331 " --> pdb=" O VAL O 66 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N LEU O 68 " --> pdb=" O SER O 331 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N ALA O 65 " --> pdb=" O MET O 359 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N ILE O 361 " --> pdb=" O ALA O 65 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N LEU O 67 " --> pdb=" O ILE O 361 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'O' and resid 121 through 142 removed outlier: 6.667A pdb=" N GLY O 160 " --> pdb=" O THR O 136 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N LEU O 138 " --> pdb=" O ILE O 158 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ILE O 158 " --> pdb=" O LEU O 138 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N HIS O 156 " --> pdb=" O PRO O 140 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N GLU O 142 " --> pdb=" O ILE O 154 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N ILE O 154 " --> pdb=" O GLU O 142 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL O 157 " --> pdb=" O LEU O 172 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 167 through 172 current: chain 'O' and resid 200 through 206 removed outlier: 5.301A pdb=" N VAL O 221 " --> pdb=" O GLN O 203 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N ARG O 205 " --> pdb=" O VAL O 221 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'O' and resid 335 through 337 removed outlier: 3.639A pdb=" N CYS O 336 " --> pdb=" O SER O 346 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'P' and resid 100 through 104 removed outlier: 3.663A pdb=" N ALA P 327 " --> pdb=" O ILE P 298 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLY P 77 " --> pdb=" O THR P 328 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N ALA P 72 " --> pdb=" O LEU P 355 " (cutoff:3.500A) removed outlier: 8.327A pdb=" N VAL P 357 " --> pdb=" O ALA P 72 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N LEU P 74 " --> pdb=" O VAL P 357 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N THR P 359 " --> pdb=" O LEU P 74 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N ALA P 76 " --> pdb=" O THR P 359 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'P' and resid 238 through 243 removed outlier: 3.543A pdb=" N ILE P 292 " --> pdb=" O GLY P 128 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'P' and resid 333 through 334 removed outlier: 3.555A pdb=" N THR P 333 " --> pdb=" O SER P 342 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER P 342 " --> pdb=" O THR P 333 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'Q' and resid 35 through 36 Processing sheet with id=AE1, first strand: chain 'Q' and resid 93 through 97 removed outlier: 7.228A pdb=" N LEU Q 299 " --> pdb=" O ILE Q 328 " (cutoff:3.500A) removed outlier: 8.174A pdb=" N ALA Q 330 " --> pdb=" O LEU Q 299 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N VAL Q 301 " --> pdb=" O ALA Q 330 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N ALA Q 65 " --> pdb=" O MET Q 359 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N ILE Q 361 " --> pdb=" O ALA Q 65 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N LEU Q 67 " --> pdb=" O ILE Q 361 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'Q' and resid 234 through 239 Processing sheet with id=AE3, first strand: chain 'Q' and resid 437 through 438 removed outlier: 7.508A pdb=" N VAL R 357 " --> pdb=" O ALA R 72 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N LEU R 74 " --> pdb=" O VAL R 357 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N THR R 359 " --> pdb=" O LEU R 74 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ALA R 76 " --> pdb=" O THR R 359 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLY R 77 " --> pdb=" O THR R 328 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ALA R 327 " --> pdb=" O ILE R 298 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N THR R 101 " --> pdb=" O PHE R 297 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N ASP R 299 " --> pdb=" O THR R 101 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ILE R 103 " --> pdb=" O ASP R 299 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'R' and resid 42 through 43 Processing sheet with id=AE5, first strand: chain 'R' and resid 127 through 145 removed outlier: 6.839A pdb=" N THR R 162 " --> pdb=" O VAL R 143 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N ILE R 145 " --> pdb=" O LYS R 160 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N LYS R 160 " --> pdb=" O ILE R 145 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 169 through 173 current: chain 'R' and resid 202 through 205 Processing sheet with id=AE6, first strand: chain 'R' and resid 332 through 334 Processing sheet with id=AE7, first strand: chain 'S' and resid 29 through 32 removed outlier: 6.536A pdb=" N LEU S 8 " --> pdb=" O LEU S 104 " (cutoff:3.500A) removed outlier: 8.127A pdb=" N THR S 106 " --> pdb=" O LEU S 8 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N VAL S 10 " --> pdb=" O THR S 106 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'S' and resid 53 through 54 Processing sheet with id=AE9, first strand: chain 'S' and resid 71 through 72 Processing sheet with id=AF1, first strand: chain 'S' and resid 150 through 155 WARNING: can't find start of bonding for strands! previous: chain 'S' and resid 169 through 170 current: chain 'S' and resid 329 through 330 Processing sheet with id=AF2, first strand: chain 'S' and resid 238 through 241 Processing sheet with id=AF3, first strand: chain 'T' and resid 35 through 38 removed outlier: 6.411A pdb=" N LEU T 14 " --> pdb=" O LEU T 121 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N SER T 123 " --> pdb=" O LEU T 14 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N PHE T 16 " --> pdb=" O SER T 123 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'T' and resid 67 through 69 removed outlier: 4.127A pdb=" N GLY T 42 " --> pdb=" O TYR T 69 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'T' and resid 88 through 89 Processing sheet with id=AF6, first strand: chain 'T' and resid 167 through 172 Processing sheet with id=AF7, first strand: chain 'T' and resid 223 through 227 removed outlier: 6.583A pdb=" N LYS T 238 " --> pdb=" O ALA T 224 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N LYS T 226 " --> pdb=" O ASN T 236 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N ASN T 236 " --> pdb=" O LYS T 226 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'T' and resid 285 through 288 removed outlier: 3.608A pdb=" N TYR T 287 " --> pdb=" O CYS T 295 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'U' and resid 8 through 11 removed outlier: 3.500A pdb=" N VAL U 9 " --> pdb=" O GLY U 20 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE U 31 " --> pdb=" O CYS U 17 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA U 19 " --> pdb=" O ALA U 29 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA U 29 " --> pdb=" O ALA U 19 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'U' and resid 35 through 36 Processing sheet with id=AG2, first strand: chain 'U' and resid 71 through 72 Processing sheet with id=AG3, first strand: chain 'U' and resid 104 through 107 removed outlier: 3.597A pdb=" N LEU U 105 " --> pdb=" O TYR U 133 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N ALA U 135 " --> pdb=" O LEU U 105 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLU U 107 " --> pdb=" O ALA U 135 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG3 Processing sheet with id=AG4, first strand: chain 'U' and resid 149 through 150 Processing sheet with id=AG5, first strand: chain 'U' and resid 160 through 161 Processing sheet with id=AG6, first strand: chain 'V' and resid 96 through 101 removed outlier: 3.658A pdb=" N LYS V 96 " --> pdb=" O ARG V 115 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ARG V 115 " --> pdb=" O LYS V 96 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'W' and resid 87 through 92 Processing sheet with id=AG8, first strand: chain 'W' and resid 78 through 81 2217 hydrogen bonds defined for protein. 6273 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 335 hydrogen bonds 670 hydrogen bond angles 0 basepair planarities 130 basepair parallelities 249 stacking parallelities Total time for adding SS restraints: 27.98 Time building geometry restraints manager: 13.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 14881 1.33 - 1.46: 16498 1.46 - 1.59: 25769 1.59 - 1.72: 581 1.72 - 1.84: 424 Bond restraints: 58153 Sorted by residual: bond pdb=" C3' DC X 21 " pdb=" C2' DC X 21 " ideal model delta sigma weight residual 1.525 1.844 -0.319 2.00e-02 2.50e+03 2.54e+02 bond pdb=" O3' DA X 60 " pdb=" P DA X 61 " ideal model delta sigma weight residual 1.607 1.427 0.180 1.50e-02 4.44e+03 1.44e+02 bond pdb=" C4 ATP T 501 " pdb=" C5 ATP T 501 " ideal model delta sigma weight residual 1.388 1.469 -0.081 1.00e-02 1.00e+04 6.62e+01 bond pdb=" C4 ATP U 401 " pdb=" C5 ATP U 401 " ideal model delta sigma weight residual 1.388 1.469 -0.081 1.00e-02 1.00e+04 6.62e+01 bond pdb=" C4 ATP K 401 " pdb=" C5 ATP K 401 " ideal model delta sigma weight residual 1.388 1.469 -0.081 1.00e-02 1.00e+04 6.55e+01 ... (remaining 58148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.88: 79306 4.88 - 9.76: 468 9.76 - 14.64: 49 14.64 - 19.51: 5 19.51 - 24.39: 3 Bond angle restraints: 79831 Sorted by residual: angle pdb=" PB ATP U 401 " pdb=" O3B ATP U 401 " pdb=" PG ATP U 401 " ideal model delta sigma weight residual 139.87 120.03 19.84 1.00e+00 1.00e+00 3.94e+02 angle pdb=" PB ATP T 501 " pdb=" O3B ATP T 501 " pdb=" PG ATP T 501 " ideal model delta sigma weight residual 139.87 120.74 19.13 1.00e+00 1.00e+00 3.66e+02 angle pdb=" PB ATP K 401 " pdb=" O3B ATP K 401 " pdb=" PG ATP K 401 " ideal model delta sigma weight residual 139.87 120.85 19.02 1.00e+00 1.00e+00 3.62e+02 angle pdb=" PA ATP T 501 " pdb=" O3A ATP T 501 " pdb=" PB ATP T 501 " ideal model delta sigma weight residual 136.83 120.68 16.15 1.00e+00 1.00e+00 2.61e+02 angle pdb=" PA ATP K 401 " pdb=" O3A ATP K 401 " pdb=" PB ATP K 401 " ideal model delta sigma weight residual 136.83 121.37 15.46 1.00e+00 1.00e+00 2.39e+02 ... (remaining 79826 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.38: 32442 33.38 - 66.75: 2214 66.75 - 100.13: 86 100.13 - 133.50: 8 133.50 - 166.88: 6 Dihedral angle restraints: 34756 sinusoidal: 16380 harmonic: 18376 Sorted by residual: dihedral pdb=" CA GLU Q 278 " pdb=" C GLU Q 278 " pdb=" N ILE Q 279 " pdb=" CA ILE Q 279 " ideal model delta harmonic sigma weight residual 180.00 -132.44 -47.56 0 5.00e+00 4.00e-02 9.05e+01 dihedral pdb=" CD ARG J 260 " pdb=" NE ARG J 260 " pdb=" CZ ARG J 260 " pdb=" NH1 ARG J 260 " ideal model delta sinusoidal sigma weight residual 0.00 84.08 -84.08 1 1.00e+01 1.00e-02 8.61e+01 dihedral pdb=" CA CYS U 257 " pdb=" C CYS U 257 " pdb=" N PRO U 258 " pdb=" CA PRO U 258 " ideal model delta harmonic sigma weight residual 180.00 133.86 46.14 0 5.00e+00 4.00e-02 8.52e+01 ... (remaining 34753 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.108: 8514 0.108 - 0.216: 282 0.216 - 0.323: 16 0.323 - 0.431: 44 0.431 - 0.539: 137 Chirality restraints: 8993 Sorted by residual: chirality pdb=" P DT Y-138 " pdb=" OP1 DT Y-138 " pdb=" OP2 DT Y-138 " pdb=" O5' DT Y-138 " both_signs ideal model delta sigma weight residual True 2.35 -2.88 -0.54 2.00e-01 2.50e+01 7.26e+00 chirality pdb=" P DA X 89 " pdb=" OP1 DA X 89 " pdb=" OP2 DA X 89 " pdb=" O5' DA X 89 " both_signs ideal model delta sigma weight residual True 2.35 -2.88 -0.54 2.00e-01 2.50e+01 7.20e+00 chirality pdb=" P DG X 37 " pdb=" OP1 DG X 37 " pdb=" OP2 DG X 37 " pdb=" O5' DG X 37 " both_signs ideal model delta sigma weight residual True 2.35 -2.87 -0.53 2.00e-01 2.50e+01 6.93e+00 ... (remaining 8990 not shown) Planarity restraints: 9191 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG J 260 " 1.078 9.50e-02 1.11e+02 4.83e-01 1.41e+02 pdb=" NE ARG J 260 " -0.066 2.00e-02 2.50e+03 pdb=" CZ ARG J 260 " -0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG J 260 " 0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG J 260 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG J 263 " -1.077 9.50e-02 1.11e+02 4.83e-01 1.41e+02 pdb=" NE ARG J 263 " 0.064 2.00e-02 2.50e+03 pdb=" CZ ARG J 263 " 0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG J 263 " -0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG J 263 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG I2029 " 0.985 9.50e-02 1.11e+02 4.41e-01 1.18e+02 pdb=" NE ARG I2029 " -0.059 2.00e-02 2.50e+03 pdb=" CZ ARG I2029 " -0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG I2029 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG I2029 " 0.023 2.00e-02 2.50e+03 ... (remaining 9188 not shown) Histogram of nonbonded interaction distances: 1.05 - 1.82: 14 1.82 - 2.59: 736 2.59 - 3.36: 75434 3.36 - 4.13: 145642 4.13 - 4.90: 256952 Nonbonded interactions: 478778 Sorted by model distance: nonbonded pdb=" N GLU W 40 " pdb=" OP1 DA Y -82 " model vdw 1.051 3.120 nonbonded pdb=" OD1 ASN I 902 " pdb=" OD2 ASP I2137 " model vdw 1.075 3.040 nonbonded pdb=" NH2 ARG I 898 " pdb=" OE1 GLN I2067 " model vdw 1.168 3.120 nonbonded pdb=" OH TYR F 37 " pdb=" OP1 DG X 121 " model vdw 1.299 3.040 nonbonded pdb=" NH2 ARG E 32 " pdb=" OP1 DA Y-117 " model vdw 1.366 3.120 ... (remaining 478773 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 14 through 118) selection = chain 'E' } ncs_group { reference = (chain 'B' and resid 28 through 121) selection = chain 'F' } ncs_group { reference = (chain 'C' and resid 41 through 134) selection = (chain 'G' and resid 41 through 134) } ncs_group { reference = (chain 'D' and resid 23 through 102) selection = chain 'H' } ncs_group { reference = (chain 'M' and (resid 15 through 451 or resid 501)) selection = (chain 'O' and (resid 15 through 141 or resid 153 through 451 or resid 501)) selection = (chain 'Q' and (resid 15 through 141 or resid 153 through 451 or resid 501)) } ncs_group { reference = (chain 'N' and (resid 18 through 148 or resid 157 through 210 or (resid 223 and \ (name N or name CA or name C or name O or name CB )) or resid 224 through 447 or \ resid 501)) selection = (chain 'P' and (resid 18 through 148 or resid 157 through 210 or resid 223 throu \ gh 447 or resid 501)) selection = (chain 'R' and (resid 18 through 210 or (resid 223 and (name N or name CA or nam \ e C or name O or name CB )) or resid 224 through 447 or resid 501)) } ncs_group { reference = (chain 'S' and (resid 2 through 40 or resid 52 through 371)) selection = (chain 'U' and resid 2 through 371) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.01 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: 4.930 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: 0.050 Extract box with map and model: 1.570 Check model and map are aligned: 0.310 Set scattering table: 0.400 Process input model: 113.460 Find NCS groups from input model: 2.020 Set up NCS constraints: 0.330 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 125.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5327 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 : 0.005 0.319 58153 Z= 0.288 Angle : 0.894 24.392 79831 Z= 0.533 Chirality : 0.077 0.539 8993 Planarity : 0.009 0.483 9191 Dihedral : 18.429 166.879 22892 Min Nonbonded Distance : 1.051 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.37 % Allowed : 4.45 % Favored : 95.18 % Rotamer: Outliers : 5.29 % Allowed : 7.09 % Favored : 87.62 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.37 % Twisted General : 0.03 % 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: -2.42 (0.10), residues: 6271 helix: -0.98 (0.09), residues: 2812 sheet: -1.54 (0.18), residues: 760 loop : -2.23 (0.11), residues: 2699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP I 206 HIS 0.004 0.001 HIS K 194 PHE 0.013 0.001 PHE P 257 TYR 0.011 0.001 TYR W 86 ARG 0.004 0.000 ARG J 260 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12542 Ramachandran restraints generated. 6271 Oldfield, 0 Emsley, 6271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12542 Ramachandran restraints generated. 6271 Oldfield, 0 Emsley, 6271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1357 residues out of total 5462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 288 poor density : 1069 time to evaluate : 4.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 TYR cc_start: 0.6244 (m-80) cc_final: 0.6027 (m-80) REVERT: E 118 LYS cc_start: 0.3843 (tmmm) cc_final: 0.3642 (tttm) REVERT: I 120 SER cc_start: 0.0672 (OUTLIER) cc_final: 0.0347 (p) REVERT: I 144 MET cc_start: -0.0067 (OUTLIER) cc_final: -0.0671 (ttt) REVERT: I 225 ARG cc_start: 0.7059 (tpp-160) cc_final: 0.6762 (ttm-80) REVERT: I 227 LYS cc_start: 0.5460 (tttt) cc_final: 0.5135 (ttpt) REVERT: I 784 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.7219 (mp0) REVERT: I 943 MET cc_start: 0.8740 (mmp) cc_final: 0.8254 (mmt) REVERT: I 1936 ILE cc_start: 0.8687 (OUTLIER) cc_final: 0.8347 (pt) REVERT: I 2015 TRP cc_start: 0.7698 (OUTLIER) cc_final: 0.6616 (m-90) REVERT: I 2051 LEU cc_start: 0.7272 (tp) cc_final: 0.6920 (tp) REVERT: I 2126 ASN cc_start: 0.4150 (m-40) cc_final: 0.3900 (t0) REVERT: K 71 GLN cc_start: 0.7563 (OUTLIER) cc_final: 0.6738 (tm-30) REVERT: K 88 PHE cc_start: 0.6992 (OUTLIER) cc_final: 0.6544 (t80) REVERT: K 106 GLN cc_start: 0.6439 (mt0) cc_final: 0.5749 (tt0) REVERT: L 35 LEU cc_start: 0.8025 (mt) cc_final: 0.7499 (mt) REVERT: M 192 TYR cc_start: 0.5087 (m-80) cc_final: 0.4857 (m-10) REVERT: N 88 MET cc_start: 0.7481 (mmm) cc_final: 0.7273 (mmt) REVERT: N 209 PHE cc_start: 0.4845 (OUTLIER) cc_final: 0.4062 (m-80) REVERT: N 269 LYS cc_start: 0.8068 (tptt) cc_final: 0.6924 (tptt) REVERT: N 274 GLU cc_start: 0.7291 (pt0) cc_final: 0.6711 (pt0) REVERT: N 338 THR cc_start: 0.6866 (p) cc_final: 0.6648 (p) REVERT: O 55 LEU cc_start: 0.7732 (OUTLIER) cc_final: 0.7328 (tp) REVERT: O 171 LYS cc_start: 0.7110 (mttt) cc_final: 0.6570 (tttt) REVERT: O 272 THR cc_start: 0.8081 (m) cc_final: 0.7776 (p) REVERT: O 371 MET cc_start: 0.8244 (ttp) cc_final: 0.7982 (ttp) REVERT: O 455 MET cc_start: 0.6929 (tpt) cc_final: 0.6455 (tpt) REVERT: P 269 LYS cc_start: 0.8610 (tttm) cc_final: 0.7842 (tttm) REVERT: P 441 GLN cc_start: 0.8988 (tt0) cc_final: 0.8633 (tp40) REVERT: P 448 ASP cc_start: 0.7114 (OUTLIER) cc_final: 0.6144 (t0) REVERT: Q 129 GLU cc_start: 0.7453 (pm20) cc_final: 0.6758 (pm20) REVERT: Q 196 ASN cc_start: 0.7594 (OUTLIER) cc_final: 0.7366 (m-40) REVERT: Q 228 VAL cc_start: 0.9077 (p) cc_final: 0.8795 (t) REVERT: Q 259 MET cc_start: 0.6489 (tpp) cc_final: 0.6061 (tpp) REVERT: Q 289 GLN cc_start: 0.7561 (tt0) cc_final: 0.7274 (mt0) REVERT: Q 362 ARG cc_start: 0.7863 (ttp80) cc_final: 0.7571 (ptm-80) REVERT: Q 431 GLU cc_start: 0.8019 (mm-30) cc_final: 0.7697 (mt-10) REVERT: Q 450 GLN cc_start: 0.7797 (OUTLIER) cc_final: 0.6488 (pt0) REVERT: R 88 MET cc_start: 0.7741 (mmm) cc_final: 0.7172 (mmt) REVERT: R 90 MET cc_start: 0.8467 (mtp) cc_final: 0.8094 (mtp) REVERT: R 117 GLU cc_start: 0.5485 (mm-30) cc_final: 0.5188 (mt-10) REVERT: R 171 ILE cc_start: 0.8578 (mt) cc_final: 0.8361 (tt) REVERT: R 193 ILE cc_start: 0.8233 (tp) cc_final: 0.7726 (pt) REVERT: R 253 ARG cc_start: 0.7821 (ttm170) cc_final: 0.7498 (ttp-170) REVERT: R 269 LYS cc_start: 0.7876 (mptt) cc_final: 0.7241 (mtmt) REVERT: S 1 MET cc_start: 0.0376 (mtt) cc_final: -0.1340 (tpt) REVERT: S 44 MET cc_start: -0.2109 (mtt) cc_final: -0.2811 (ptt) REVERT: T 10 GLU cc_start: 0.0196 (OUTLIER) cc_final: -0.1222 (pp20) REVERT: T 77 VAL cc_start: 0.1326 (OUTLIER) cc_final: 0.1037 (t) REVERT: T 79 ARG cc_start: -0.0674 (OUTLIER) cc_final: -0.0992 (mtt90) REVERT: T 399 ILE cc_start: 0.4265 (OUTLIER) cc_final: 0.3944 (tt) REVERT: U 78 ASN cc_start: 0.1331 (OUTLIER) cc_final: 0.0967 (p0) REVERT: U 165 ILE cc_start: 0.1373 (OUTLIER) cc_final: 0.0859 (tt) REVERT: U 175 ILE cc_start: 0.1369 (OUTLIER) cc_final: 0.0817 (mt) REVERT: U 270 GLU cc_start: 0.1826 (OUTLIER) cc_final: 0.0450 (tt0) REVERT: U 359 LYS cc_start: 0.3138 (OUTLIER) cc_final: 0.2258 (tttp) REVERT: V 229 GLN cc_start: 0.1874 (OUTLIER) cc_final: 0.1477 (pt0) REVERT: V 255 GLU cc_start: 0.3251 (OUTLIER) cc_final: 0.2227 (mt-10) REVERT: W 98 ILE cc_start: 0.1994 (mt) cc_final: 0.1162 (pt) REVERT: W 151 MET cc_start: 0.0289 (tpt) cc_final: 0.0030 (mmm) outliers start: 288 outliers final: 46 residues processed: 1301 average time/residue: 0.6018 time to fit residues: 1254.6010 Evaluate side-chains 595 residues out of total 5462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 526 time to evaluate : 4.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain C residue 42 ARG Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain I residue 120 SER Chi-restraints excluded: chain I residue 138 ASP Chi-restraints excluded: chain I residue 144 MET Chi-restraints excluded: chain I residue 726 LYS Chi-restraints excluded: chain I residue 732 HIS Chi-restraints excluded: chain I residue 784 GLU Chi-restraints excluded: chain I residue 864 ARG Chi-restraints excluded: chain I residue 966 ARG Chi-restraints excluded: chain I residue 988 LYS Chi-restraints excluded: chain I residue 1936 ILE Chi-restraints excluded: chain I residue 2015 TRP Chi-restraints excluded: chain I residue 2176 ILE Chi-restraints excluded: chain I residue 2177 LEU Chi-restraints excluded: chain J residue 131 LYS Chi-restraints excluded: chain J residue 177 LYS Chi-restraints excluded: chain J residue 216 SER Chi-restraints excluded: chain J residue 261 CYS Chi-restraints excluded: chain J residue 267 THR Chi-restraints excluded: chain K residue 71 GLN Chi-restraints excluded: chain K residue 88 PHE Chi-restraints excluded: chain K residue 124 ARG Chi-restraints excluded: chain K residue 202 ILE Chi-restraints excluded: chain K residue 289 ILE Chi-restraints excluded: chain M residue 170 LEU Chi-restraints excluded: chain M residue 256 ILE Chi-restraints excluded: chain M residue 271 ILE Chi-restraints excluded: chain M residue 433 ILE Chi-restraints excluded: chain N residue 209 PHE Chi-restraints excluded: chain N residue 325 ILE Chi-restraints excluded: chain N residue 426 ILE Chi-restraints excluded: chain O residue 55 LEU Chi-restraints excluded: chain O residue 269 THR Chi-restraints excluded: chain O residue 273 ASP Chi-restraints excluded: chain O residue 274 LYS Chi-restraints excluded: chain O residue 353 ASP Chi-restraints excluded: chain P residue 59 VAL Chi-restraints excluded: chain P residue 68 ILE Chi-restraints excluded: chain P residue 261 PHE Chi-restraints excluded: chain P residue 429 VAL Chi-restraints excluded: chain P residue 448 ASP Chi-restraints excluded: chain Q residue 185 VAL Chi-restraints excluded: chain Q residue 196 ASN Chi-restraints excluded: chain Q residue 450 GLN Chi-restraints excluded: chain R residue 21 ARG Chi-restraints excluded: chain R residue 68 ILE Chi-restraints excluded: chain R residue 205 LEU Chi-restraints excluded: chain R residue 250 ILE Chi-restraints excluded: chain R residue 444 LYS Chi-restraints excluded: chain T residue 10 GLU Chi-restraints excluded: chain T residue 77 VAL Chi-restraints excluded: chain T residue 79 ARG Chi-restraints excluded: chain T residue 399 ILE Chi-restraints excluded: chain U residue 78 ASN Chi-restraints excluded: chain U residue 85 ILE Chi-restraints excluded: chain U residue 165 ILE Chi-restraints excluded: chain U residue 175 ILE Chi-restraints excluded: chain U residue 192 ILE Chi-restraints excluded: chain U residue 270 GLU Chi-restraints excluded: chain U residue 330 ILE Chi-restraints excluded: chain U residue 359 LYS Chi-restraints excluded: chain V residue 229 GLN Chi-restraints excluded: chain V residue 245 GLU Chi-restraints excluded: chain V residue 247 LEU Chi-restraints excluded: chain V residue 255 GLU Chi-restraints excluded: chain W residue 38 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 652 random chunks: chunk 550 optimal weight: 4.9990 chunk 494 optimal weight: 7.9990 chunk 274 optimal weight: 5.9990 chunk 168 optimal weight: 3.9990 chunk 333 optimal weight: 4.9990 chunk 264 optimal weight: 4.9990 chunk 511 optimal weight: 9.9990 chunk 197 optimal weight: 4.9990 chunk 310 optimal weight: 0.5980 chunk 380 optimal weight: 1.9990 chunk 592 optimal weight: 5.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 46 HIS D 25 ASN ** E 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 46 HIS G 39 HIS G 108 ASN ** I 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 252 ASN I 652 GLN I 702 GLN ** I 732 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 790 HIS I 800 HIS I 819 GLN I1896 GLN ** I1945 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I2084 HIS ** I2153 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I2175 ASN ** K 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 214 GLN K 304 ASN K 310 GLN M 203 GLN M 236 GLN ** M 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 280 ASN M 408 GLN M 414 ASN N 240 HIS N 245 HIS N 275 GLN N 277 ASN N 302 HIS N 447 GLN O 18 HIS O 20 HIS O 34 GLN O 203 GLN O 348 HIS O 393 HIS P 25 HIS P 27 HIS P 44 GLN P 313 ASN P 422 GLN P 447 GLN Q 18 HIS Q 20 HIS Q 203 GLN Q 229 HIS Q 236 GLN Q 393 HIS ** Q 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 221 GLN R 233 GLN R 302 HIS R 313 ASN ** S 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 251 HIS U 78 ASN Total number of N/Q/H flips: 52 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5730 moved from start: 0.3691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.156 58153 Z= 0.468 Angle : 0.834 13.545 79831 Z= 0.433 Chirality : 0.051 0.340 8993 Planarity : 0.007 0.112 9191 Dihedral : 22.137 176.216 10488 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.76 % Favored : 94.12 % Rotamer: Outliers : 4.10 % Allowed : 12.97 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.37 % Twisted General : 0.07 % 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: -1.33 (0.10), residues: 6271 helix: -0.09 (0.09), residues: 2882 sheet: -1.09 (0.18), residues: 816 loop : -1.64 (0.12), residues: 2573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP K 68 HIS 0.016 0.002 HIS T 251 PHE 0.034 0.003 PHE D 61 TYR 0.041 0.003 TYR C 54 ARG 0.024 0.001 ARG R 235 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12542 Ramachandran restraints generated. 6271 Oldfield, 0 Emsley, 6271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12542 Ramachandran restraints generated. 6271 Oldfield, 0 Emsley, 6271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 772 residues out of total 5462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 223 poor density : 549 time to evaluate : 4.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 77 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.7976 (mt) REVERT: E 118 LYS cc_start: 0.4473 (tmmm) cc_final: 0.3801 (tttm) REVERT: I 225 ARG cc_start: 0.7093 (tpp-160) cc_final: 0.6743 (ttm-80) REVERT: I 227 LYS cc_start: 0.6006 (tttt) cc_final: 0.5667 (ttpt) REVERT: I 613 LEU cc_start: 0.7146 (OUTLIER) cc_final: 0.6473 (tt) REVERT: I 784 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.7870 (mp0) REVERT: I 861 LEU cc_start: 0.8206 (OUTLIER) cc_final: 0.7797 (mp) REVERT: I 864 ARG cc_start: 0.8512 (OUTLIER) cc_final: 0.8104 (ttt180) REVERT: I 943 MET cc_start: 0.8800 (mmp) cc_final: 0.8338 (mmt) REVERT: I 2144 MET cc_start: 0.7092 (mmm) cc_final: 0.6769 (mmm) REVERT: J 131 LYS cc_start: 0.7253 (OUTLIER) cc_final: 0.6667 (mttp) REVERT: K 3 THR cc_start: 0.3936 (OUTLIER) cc_final: 0.3673 (m) REVERT: K 88 PHE cc_start: 0.7128 (OUTLIER) cc_final: 0.6885 (t80) REVERT: K 109 MET cc_start: 0.5245 (mtm) cc_final: 0.5036 (mtp) REVERT: K 118 GLN cc_start: 0.3032 (OUTLIER) cc_final: 0.1913 (mp10) REVERT: K 124 ARG cc_start: 0.5771 (OUTLIER) cc_final: 0.5393 (ptm-80) REVERT: K 196 MET cc_start: 0.7248 (ppp) cc_final: 0.6307 (ptm) REVERT: L 35 LEU cc_start: 0.8258 (mt) cc_final: 0.7904 (mt) REVERT: M 26 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8559 (mp) REVERT: M 106 ILE cc_start: 0.6935 (mm) cc_final: 0.6629 (tt) REVERT: M 182 LYS cc_start: 0.8865 (tppt) cc_final: 0.8647 (mtpt) REVERT: M 264 MET cc_start: 0.5777 (OUTLIER) cc_final: 0.5437 (mpp) REVERT: M 293 GLU cc_start: 0.8136 (tp30) cc_final: 0.7845 (tp30) REVERT: M 323 ILE cc_start: 0.8901 (pt) cc_final: 0.8585 (mt) REVERT: M 359 MET cc_start: 0.8161 (OUTLIER) cc_final: 0.7737 (mtt) REVERT: M 410 LEU cc_start: 0.8486 (tt) cc_final: 0.8249 (tt) REVERT: N 46 MET cc_start: 0.7218 (mtp) cc_final: 0.7007 (tpp) REVERT: N 88 MET cc_start: 0.7640 (mmm) cc_final: 0.7290 (mmt) REVERT: N 178 MET cc_start: 0.8713 (mmp) cc_final: 0.8323 (mmt) REVERT: N 209 PHE cc_start: 0.5634 (OUTLIER) cc_final: 0.4398 (m-80) REVERT: N 319 ASP cc_start: 0.8132 (OUTLIER) cc_final: 0.7736 (m-30) REVERT: O 18 HIS cc_start: 0.7573 (OUTLIER) cc_final: 0.5906 (t70) REVERT: O 100 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.6702 (mp0) REVERT: O 171 LYS cc_start: 0.7510 (mttt) cc_final: 0.7022 (tttt) REVERT: P 112 GLU cc_start: 0.7188 (pm20) cc_final: 0.6960 (pm20) REVERT: P 269 LYS cc_start: 0.8480 (tttm) cc_final: 0.8219 (tttm) REVERT: P 286 GLU cc_start: 0.6231 (OUTLIER) cc_final: 0.5846 (mt-10) REVERT: P 441 GLN cc_start: 0.9001 (tt0) cc_final: 0.8570 (tp40) REVERT: Q 61 MET cc_start: 0.7838 (mmm) cc_final: 0.7419 (mmm) REVERT: Q 236 GLN cc_start: 0.8573 (OUTLIER) cc_final: 0.8223 (tt0) REVERT: Q 345 THR cc_start: 0.7332 (OUTLIER) cc_final: 0.7035 (t) REVERT: Q 346 SER cc_start: 0.8524 (p) cc_final: 0.8218 (t) REVERT: Q 362 ARG cc_start: 0.8662 (ttp80) cc_final: 0.8068 (ttt90) REVERT: R 90 MET cc_start: 0.8777 (mtp) cc_final: 0.8422 (mtp) REVERT: R 178 MET cc_start: 0.7701 (tpp) cc_final: 0.7308 (tpp) REVERT: R 234 LYS cc_start: 0.7469 (mtpt) cc_final: 0.7207 (mttt) REVERT: R 246 GLU cc_start: 0.5551 (OUTLIER) cc_final: 0.5214 (pt0) REVERT: R 253 ARG cc_start: 0.8123 (ttm170) cc_final: 0.7914 (ttm170) REVERT: R 257 PHE cc_start: 0.7983 (p90) cc_final: 0.7654 (p90) REVERT: R 261 PHE cc_start: 0.5466 (p90) cc_final: 0.5107 (p90) REVERT: R 269 LYS cc_start: 0.8227 (mptt) cc_final: 0.7650 (ttmt) REVERT: R 273 ARG cc_start: 0.7024 (mpt180) cc_final: 0.6809 (mmt-90) REVERT: R 444 LYS cc_start: 0.7619 (OUTLIER) cc_final: 0.7333 (ptpp) REVERT: S 1 MET cc_start: 0.0253 (mtt) cc_final: -0.1367 (tpt) REVERT: S 47 MET cc_start: 0.2261 (tmm) cc_final: 0.1972 (tmt) REVERT: S 82 MET cc_start: 0.4033 (mmm) cc_final: 0.3760 (tpp) REVERT: S 123 MET cc_start: 0.6013 (ttm) cc_final: 0.5792 (ttm) REVERT: S 161 HIS cc_start: 0.2760 (OUTLIER) cc_final: 0.2241 (t-90) REVERT: S 227 MET cc_start: 0.2500 (mmm) cc_final: 0.2225 (mmp) REVERT: S 239 SER cc_start: 0.2799 (OUTLIER) cc_final: 0.2590 (t) REVERT: S 305 MET cc_start: 0.4712 (mmm) cc_final: 0.4153 (mmp) REVERT: T 77 VAL cc_start: 0.1496 (OUTLIER) cc_final: 0.0950 (t) REVERT: T 79 ARG cc_start: 0.0541 (OUTLIER) cc_final: 0.0138 (ttm-80) REVERT: T 376 MET cc_start: 0.0001 (mtm) cc_final: -0.0289 (mtm) REVERT: T 399 ILE cc_start: 0.4291 (OUTLIER) cc_final: 0.4089 (tt) REVERT: U 190 MET cc_start: 0.0590 (ttt) cc_final: 0.0272 (ttp) REVERT: U 359 LYS cc_start: 0.2936 (OUTLIER) cc_final: 0.1946 (tttp) REVERT: V 53 MET cc_start: 0.3015 (ttm) cc_final: 0.2420 (ttm) REVERT: V 62 TYR cc_start: 0.3319 (t80) cc_final: 0.2984 (t80) REVERT: V 98 MET cc_start: 0.1307 (ppp) cc_final: 0.0743 (ttp) REVERT: V 154 LYS cc_start: 0.3875 (tttm) cc_final: 0.3597 (tmtt) REVERT: V 248 LEU cc_start: 0.3311 (OUTLIER) cc_final: 0.2555 (tp) REVERT: V 255 GLU cc_start: 0.4113 (OUTLIER) cc_final: 0.3188 (mt-10) REVERT: W 151 MET cc_start: 0.0443 (tpt) cc_final: 0.0163 (mmm) outliers start: 223 outliers final: 100 residues processed: 735 average time/residue: 0.5499 time to fit residues: 678.5722 Evaluate side-chains 557 residues out of total 5462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 427 time to evaluate : 4.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 46 HIS Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain E residue 54 VAL Chi-restraints excluded: chain F residue 49 THR Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain G residue 84 PHE Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain H residue 53 GLU Chi-restraints excluded: chain I residue 211 LYS Chi-restraints excluded: chain I residue 613 LEU Chi-restraints excluded: chain I residue 660 LEU Chi-restraints excluded: chain I residue 742 TYR Chi-restraints excluded: chain I residue 784 GLU Chi-restraints excluded: chain I residue 861 LEU Chi-restraints excluded: chain I residue 864 ARG Chi-restraints excluded: chain I residue 921 ILE Chi-restraints excluded: chain I residue 1936 ILE Chi-restraints excluded: chain I residue 1947 THR Chi-restraints excluded: chain I residue 2015 TRP Chi-restraints excluded: chain I residue 2068 MET Chi-restraints excluded: chain I residue 2074 VAL Chi-restraints excluded: chain I residue 2115 ILE Chi-restraints excluded: chain I residue 2120 SER Chi-restraints excluded: chain I residue 2177 LEU Chi-restraints excluded: chain I residue 2189 MET Chi-restraints excluded: chain J residue 131 LYS Chi-restraints excluded: chain J residue 177 LYS Chi-restraints excluded: chain J residue 261 CYS Chi-restraints excluded: chain J residue 267 THR Chi-restraints excluded: chain J residue 275 GLU Chi-restraints excluded: chain J residue 306 THR Chi-restraints excluded: chain K residue 3 THR Chi-restraints excluded: chain K residue 6 LEU Chi-restraints excluded: chain K residue 88 PHE Chi-restraints excluded: chain K residue 113 LEU Chi-restraints excluded: chain K residue 118 GLN Chi-restraints excluded: chain K residue 124 ARG Chi-restraints excluded: chain K residue 125 VAL Chi-restraints excluded: chain K residue 161 CYS Chi-restraints excluded: chain K residue 179 LEU Chi-restraints excluded: chain K residue 226 LYS Chi-restraints excluded: chain K residue 289 ILE Chi-restraints excluded: chain K residue 356 ILE Chi-restraints excluded: chain L residue 151 LYS Chi-restraints excluded: chain M residue 26 LEU Chi-restraints excluded: chain M residue 135 VAL Chi-restraints excluded: chain M residue 176 ILE Chi-restraints excluded: chain M residue 264 MET Chi-restraints excluded: chain M residue 271 ILE Chi-restraints excluded: chain M residue 295 VAL Chi-restraints excluded: chain M residue 317 ARG Chi-restraints excluded: chain M residue 359 MET Chi-restraints excluded: chain M residue 406 SER Chi-restraints excluded: chain M residue 408 GLN Chi-restraints excluded: chain M residue 419 ILE Chi-restraints excluded: chain M residue 433 ILE Chi-restraints excluded: chain N residue 60 LEU Chi-restraints excluded: chain N residue 163 LEU Chi-restraints excluded: chain N residue 192 VAL Chi-restraints excluded: chain N residue 209 PHE Chi-restraints excluded: chain N residue 210 THR Chi-restraints excluded: chain N residue 283 TRP Chi-restraints excluded: chain N residue 301 VAL Chi-restraints excluded: chain N residue 319 ASP Chi-restraints excluded: chain N residue 325 ILE Chi-restraints excluded: chain N residue 326 MET Chi-restraints excluded: chain N residue 413 CYS Chi-restraints excluded: chain N residue 426 ILE Chi-restraints excluded: chain O residue 18 HIS Chi-restraints excluded: chain O residue 96 MET Chi-restraints excluded: chain O residue 100 GLU Chi-restraints excluded: chain O residue 273 ASP Chi-restraints excluded: chain O residue 274 LYS Chi-restraints excluded: chain O residue 345 THR Chi-restraints excluded: chain O residue 353 ASP Chi-restraints excluded: chain P residue 68 ILE Chi-restraints excluded: chain P residue 255 GLN Chi-restraints excluded: chain P residue 257 PHE Chi-restraints excluded: chain P residue 261 PHE Chi-restraints excluded: chain P residue 286 GLU Chi-restraints excluded: chain P residue 292 ILE Chi-restraints excluded: chain P residue 305 ASP Chi-restraints excluded: chain P residue 355 LEU Chi-restraints excluded: chain P residue 429 VAL Chi-restraints excluded: chain Q residue 124 ILE Chi-restraints excluded: chain Q residue 168 LYS Chi-restraints excluded: chain Q residue 185 VAL Chi-restraints excluded: chain Q residue 209 TYR Chi-restraints excluded: chain Q residue 236 GLN Chi-restraints excluded: chain Q residue 313 THR Chi-restraints excluded: chain Q residue 345 THR Chi-restraints excluded: chain Q residue 416 LEU Chi-restraints excluded: chain R residue 19 ILE Chi-restraints excluded: chain R residue 21 ARG Chi-restraints excluded: chain R residue 205 LEU Chi-restraints excluded: chain R residue 225 VAL Chi-restraints excluded: chain R residue 246 GLU Chi-restraints excluded: chain R residue 247 ILE Chi-restraints excluded: chain R residue 250 ILE Chi-restraints excluded: chain R residue 323 VAL Chi-restraints excluded: chain R residue 333 THR Chi-restraints excluded: chain R residue 346 ILE Chi-restraints excluded: chain R residue 429 VAL Chi-restraints excluded: chain R residue 434 LEU Chi-restraints excluded: chain R residue 444 LYS Chi-restraints excluded: chain S residue 66 THR Chi-restraints excluded: chain S residue 161 HIS Chi-restraints excluded: chain S residue 235 SER Chi-restraints excluded: chain S residue 239 SER Chi-restraints excluded: chain T residue 77 VAL Chi-restraints excluded: chain T residue 79 ARG Chi-restraints excluded: chain T residue 399 ILE Chi-restraints excluded: chain U residue 78 ASN Chi-restraints excluded: chain U residue 85 ILE Chi-restraints excluded: chain U residue 165 ILE Chi-restraints excluded: chain U residue 330 ILE Chi-restraints excluded: chain U residue 351 THR Chi-restraints excluded: chain U residue 359 LYS Chi-restraints excluded: chain V residue 58 TYR Chi-restraints excluded: chain V residue 247 LEU Chi-restraints excluded: chain V residue 248 LEU Chi-restraints excluded: chain V residue 255 GLU Chi-restraints excluded: chain W residue 38 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 652 random chunks: chunk 329 optimal weight: 0.9980 chunk 183 optimal weight: 0.9990 chunk 492 optimal weight: 20.0000 chunk 403 optimal weight: 0.9990 chunk 163 optimal weight: 0.0020 chunk 593 optimal weight: 0.0470 chunk 640 optimal weight: 6.9990 chunk 528 optimal weight: 10.0000 chunk 588 optimal weight: 5.9990 chunk 202 optimal weight: 4.9990 chunk 475 optimal weight: 30.0000 overall best weight: 0.6090 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 104 GLN G 85 GLN ** I 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 702 GLN ** I 967 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1945 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I1991 HIS I2067 GLN I2153 HIS J 200 GLN ** K 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 133 HIS ** K 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 283 ASN ** M 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 408 GLN O 18 HIS ** O 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 392 ASN O 408 GLN Q 236 GLN Q 316 HIS Q 348 HIS Q 380 GLN ** Q 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 173 HIS ** S 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 327 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 354 ASN ** U 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5679 moved from start: 0.3992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 58153 Z= 0.194 Angle : 0.637 10.197 79831 Z= 0.331 Chirality : 0.042 0.226 8993 Planarity : 0.005 0.079 9191 Dihedral : 21.720 179.524 10421 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.93 % Favored : 94.98 % Rotamer: Outliers : 3.33 % Allowed : 14.64 % Favored : 82.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.37 % Twisted General : 0.07 % 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: -0.79 (0.11), residues: 6271 helix: 0.37 (0.10), residues: 2913 sheet: -0.94 (0.18), residues: 821 loop : -1.36 (0.12), residues: 2537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP S 356 HIS 0.016 0.001 HIS B 46 PHE 0.035 0.001 PHE N 261 TYR 0.022 0.001 TYR V 124 ARG 0.016 0.001 ARG T 79 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12542 Ramachandran restraints generated. 6271 Oldfield, 0 Emsley, 6271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12542 Ramachandran restraints generated. 6271 Oldfield, 0 Emsley, 6271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 654 residues out of total 5462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 181 poor density : 473 time to evaluate : 4.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 118 LYS cc_start: 0.4775 (tmmm) cc_final: 0.3988 (mttm) REVERT: F 37 TYR cc_start: 0.7730 (m-80) cc_final: 0.7490 (m-80) REVERT: I 225 ARG cc_start: 0.7044 (tpp-160) cc_final: 0.6769 (ttm-80) REVERT: I 227 LYS cc_start: 0.5931 (tttt) cc_final: 0.5694 (ttpt) REVERT: I 613 LEU cc_start: 0.7190 (OUTLIER) cc_final: 0.6616 (tt) REVERT: I 679 MET cc_start: 0.8557 (OUTLIER) cc_final: 0.8344 (ttm) REVERT: I 784 GLU cc_start: 0.7959 (OUTLIER) cc_final: 0.7571 (mp0) REVERT: I 861 LEU cc_start: 0.8023 (OUTLIER) cc_final: 0.7465 (mp) REVERT: I 864 ARG cc_start: 0.8496 (OUTLIER) cc_final: 0.8122 (ttt180) REVERT: I 930 LEU cc_start: 0.8553 (mp) cc_final: 0.8330 (mp) REVERT: I 943 MET cc_start: 0.8770 (mmp) cc_final: 0.8279 (mmt) REVERT: J 131 LYS cc_start: 0.7185 (OUTLIER) cc_final: 0.6639 (mttp) REVERT: K 3 THR cc_start: 0.4599 (OUTLIER) cc_final: 0.4199 (m) REVERT: K 118 GLN cc_start: 0.2767 (OUTLIER) cc_final: 0.1599 (mp10) REVERT: K 124 ARG cc_start: 0.5391 (OUTLIER) cc_final: 0.5045 (ptm-80) REVERT: K 196 MET cc_start: 0.6710 (ppp) cc_final: 0.5633 (ptm) REVERT: L 35 LEU cc_start: 0.8312 (mt) cc_final: 0.7910 (mt) REVERT: M 113 MET cc_start: 0.7171 (tpt) cc_final: 0.6916 (tpt) REVERT: M 182 LYS cc_start: 0.8863 (tppt) cc_final: 0.8658 (mtpt) REVERT: M 264 MET cc_start: 0.5588 (OUTLIER) cc_final: 0.5343 (mpp) REVERT: M 293 GLU cc_start: 0.8148 (tp30) cc_final: 0.7596 (tm-30) REVERT: M 323 ILE cc_start: 0.8829 (pt) cc_final: 0.8520 (mt) REVERT: M 359 MET cc_start: 0.7944 (OUTLIER) cc_final: 0.7643 (mtm) REVERT: N 88 MET cc_start: 0.7647 (mmm) cc_final: 0.7361 (mmt) REVERT: N 209 PHE cc_start: 0.5705 (OUTLIER) cc_final: 0.4507 (m-80) REVERT: N 258 LEU cc_start: 0.4127 (mt) cc_final: 0.3866 (mp) REVERT: N 442 TYR cc_start: 0.8214 (m-80) cc_final: 0.7736 (m-10) REVERT: O 18 HIS cc_start: 0.7411 (OUTLIER) cc_final: 0.5760 (t70) REVERT: O 171 LYS cc_start: 0.7388 (mttt) cc_final: 0.7026 (tmmt) REVERT: O 244 ASP cc_start: 0.7722 (m-30) cc_final: 0.7504 (m-30) REVERT: P 46 MET cc_start: 0.8495 (mmm) cc_final: 0.8080 (mmm) REVERT: P 168 MET cc_start: 0.8602 (ptm) cc_final: 0.8396 (ptp) REVERT: P 183 THR cc_start: 0.9419 (m) cc_final: 0.9123 (p) REVERT: P 269 LYS cc_start: 0.8480 (tttm) cc_final: 0.8168 (tttm) REVERT: P 441 GLN cc_start: 0.9003 (tt0) cc_final: 0.8538 (tp40) REVERT: Q 61 MET cc_start: 0.7730 (mmm) cc_final: 0.7409 (mmm) REVERT: Q 168 LYS cc_start: 0.6424 (OUTLIER) cc_final: 0.5913 (tttt) REVERT: Q 346 SER cc_start: 0.8411 (p) cc_final: 0.8136 (t) REVERT: R 90 MET cc_start: 0.8732 (mtp) cc_final: 0.8468 (mtp) REVERT: R 253 ARG cc_start: 0.8009 (ttm170) cc_final: 0.7652 (mtm-85) REVERT: R 269 LYS cc_start: 0.8206 (mptt) cc_final: 0.7481 (tmtt) REVERT: R 273 ARG cc_start: 0.6851 (mpt180) cc_final: 0.6519 (mmt-90) REVERT: R 444 LYS cc_start: 0.7495 (OUTLIER) cc_final: 0.7184 (mmmt) REVERT: S 1 MET cc_start: 0.0927 (mtt) cc_final: -0.0952 (tpt) REVERT: S 119 MET cc_start: 0.3435 (OUTLIER) cc_final: 0.2123 (ptp) REVERT: S 161 HIS cc_start: 0.2727 (OUTLIER) cc_final: 0.2224 (t-90) REVERT: S 227 MET cc_start: 0.2995 (mmm) cc_final: 0.2264 (mmp) REVERT: S 313 MET cc_start: 0.5367 (tpt) cc_final: 0.5079 (tpp) REVERT: T 79 ARG cc_start: 0.0850 (OUTLIER) cc_final: -0.0843 (mmt-90) REVERT: U 359 LYS cc_start: 0.2880 (OUTLIER) cc_final: 0.1981 (tttp) REVERT: V 53 MET cc_start: 0.2978 (ttm) cc_final: 0.2494 (ttm) REVERT: V 62 TYR cc_start: 0.3290 (t80) cc_final: 0.3043 (t80) REVERT: V 98 MET cc_start: 0.1445 (ppp) cc_final: 0.0888 (ttp) REVERT: V 124 TYR cc_start: 0.0116 (t80) cc_final: -0.0505 (t80) REVERT: V 248 LEU cc_start: 0.3033 (OUTLIER) cc_final: 0.2306 (tp) REVERT: V 255 GLU cc_start: 0.3727 (OUTLIER) cc_final: 0.2883 (mt-10) REVERT: W 151 MET cc_start: 0.0463 (tpt) cc_final: 0.0187 (mmm) outliers start: 181 outliers final: 88 residues processed: 617 average time/residue: 0.5677 time to fit residues: 592.3380 Evaluate side-chains 520 residues out of total 5462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 411 time to evaluate : 4.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain G residue 84 PHE Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain H residue 93 GLN Chi-restraints excluded: chain I residue 610 ILE Chi-restraints excluded: chain I residue 613 LEU Chi-restraints excluded: chain I residue 660 LEU Chi-restraints excluded: chain I residue 679 MET Chi-restraints excluded: chain I residue 742 TYR Chi-restraints excluded: chain I residue 784 GLU Chi-restraints excluded: chain I residue 859 CYS Chi-restraints excluded: chain I residue 861 LEU Chi-restraints excluded: chain I residue 864 ARG Chi-restraints excluded: chain I residue 921 ILE Chi-restraints excluded: chain I residue 1947 THR Chi-restraints excluded: chain I residue 1959 VAL Chi-restraints excluded: chain I residue 2062 VAL Chi-restraints excluded: chain I residue 2074 VAL Chi-restraints excluded: chain I residue 2177 LEU Chi-restraints excluded: chain I residue 2189 MET Chi-restraints excluded: chain J residue 131 LYS Chi-restraints excluded: chain J residue 177 LYS Chi-restraints excluded: chain J residue 216 SER Chi-restraints excluded: chain J residue 261 CYS Chi-restraints excluded: chain J residue 267 THR Chi-restraints excluded: chain K residue 3 THR Chi-restraints excluded: chain K residue 6 LEU Chi-restraints excluded: chain K residue 113 LEU Chi-restraints excluded: chain K residue 118 GLN Chi-restraints excluded: chain K residue 124 ARG Chi-restraints excluded: chain K residue 161 CYS Chi-restraints excluded: chain K residue 289 ILE Chi-restraints excluded: chain K residue 292 MET Chi-restraints excluded: chain K residue 356 ILE Chi-restraints excluded: chain L residue 18 VAL Chi-restraints excluded: chain L residue 93 LEU Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain M residue 157 VAL Chi-restraints excluded: chain M residue 262 GLN Chi-restraints excluded: chain M residue 264 MET Chi-restraints excluded: chain M residue 271 ILE Chi-restraints excluded: chain M residue 295 VAL Chi-restraints excluded: chain M residue 317 ARG Chi-restraints excluded: chain M residue 359 MET Chi-restraints excluded: chain M residue 406 SER Chi-restraints excluded: chain M residue 419 ILE Chi-restraints excluded: chain M residue 433 ILE Chi-restraints excluded: chain N residue 163 LEU Chi-restraints excluded: chain N residue 192 VAL Chi-restraints excluded: chain N residue 209 PHE Chi-restraints excluded: chain N residue 210 THR Chi-restraints excluded: chain N residue 325 ILE Chi-restraints excluded: chain N residue 326 MET Chi-restraints excluded: chain N residue 395 LEU Chi-restraints excluded: chain N residue 413 CYS Chi-restraints excluded: chain N residue 426 ILE Chi-restraints excluded: chain O residue 18 HIS Chi-restraints excluded: chain O residue 40 VAL Chi-restraints excluded: chain O residue 124 ILE Chi-restraints excluded: chain O residue 273 ASP Chi-restraints excluded: chain O residue 274 LYS Chi-restraints excluded: chain O residue 342 GLU Chi-restraints excluded: chain O residue 353 ASP Chi-restraints excluded: chain P residue 68 ILE Chi-restraints excluded: chain P residue 261 PHE Chi-restraints excluded: chain P residue 355 LEU Chi-restraints excluded: chain P residue 429 VAL Chi-restraints excluded: chain Q residue 124 ILE Chi-restraints excluded: chain Q residue 168 LYS Chi-restraints excluded: chain Q residue 185 VAL Chi-restraints excluded: chain Q residue 192 TYR Chi-restraints excluded: chain Q residue 228 VAL Chi-restraints excluded: chain Q residue 235 ILE Chi-restraints excluded: chain Q residue 407 VAL Chi-restraints excluded: chain Q residue 416 LEU Chi-restraints excluded: chain R residue 19 ILE Chi-restraints excluded: chain R residue 21 ARG Chi-restraints excluded: chain R residue 62 MET Chi-restraints excluded: chain R residue 171 ILE Chi-restraints excluded: chain R residue 205 LEU Chi-restraints excluded: chain R residue 214 ASP Chi-restraints excluded: chain R residue 247 ILE Chi-restraints excluded: chain R residue 250 ILE Chi-restraints excluded: chain R residue 292 ILE Chi-restraints excluded: chain R residue 429 VAL Chi-restraints excluded: chain R residue 444 LYS Chi-restraints excluded: chain S residue 66 THR Chi-restraints excluded: chain S residue 119 MET Chi-restraints excluded: chain S residue 161 HIS Chi-restraints excluded: chain T residue 77 VAL Chi-restraints excluded: chain T residue 79 ARG Chi-restraints excluded: chain T residue 110 HIS Chi-restraints excluded: chain U residue 78 ASN Chi-restraints excluded: chain U residue 159 VAL Chi-restraints excluded: chain U residue 165 ILE Chi-restraints excluded: chain U residue 330 ILE Chi-restraints excluded: chain U residue 359 LYS Chi-restraints excluded: chain V residue 58 TYR Chi-restraints excluded: chain V residue 247 LEU Chi-restraints excluded: chain V residue 248 LEU Chi-restraints excluded: chain V residue 255 GLU Chi-restraints excluded: chain W residue 38 ARG Chi-restraints excluded: chain W residue 157 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 652 random chunks: chunk 586 optimal weight: 20.0000 chunk 445 optimal weight: 0.9990 chunk 307 optimal weight: 2.9990 chunk 65 optimal weight: 0.2980 chunk 283 optimal weight: 0.0870 chunk 398 optimal weight: 1.9990 chunk 595 optimal weight: 30.0000 chunk 630 optimal weight: 7.9990 chunk 311 optimal weight: 2.9990 chunk 564 optimal weight: 9.9990 chunk 169 optimal weight: 9.9990 overall best weight: 1.2764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 GLN ** E 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 113 HIS ** I 967 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1945 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1991 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 332 ASN M 429 HIS O 229 HIS ** O 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 408 GLN P 255 GLN P 404 GLN Q 203 GLN Q 429 HIS R 25 HIS ** S 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 327 HIS ** U 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5732 moved from start: 0.4441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 58153 Z= 0.231 Angle : 0.630 11.215 79831 Z= 0.325 Chirality : 0.043 0.229 8993 Planarity : 0.005 0.079 9191 Dihedral : 21.476 174.853 10411 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.49 % Favored : 94.42 % Rotamer: Outliers : 3.73 % Allowed : 14.62 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.37 % Twisted General : 0.07 % 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: -0.51 (0.11), residues: 6271 helix: 0.61 (0.10), residues: 2908 sheet: -0.85 (0.18), residues: 848 loop : -1.21 (0.12), residues: 2515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP K 68 HIS 0.029 0.001 HIS O 18 PHE 0.026 0.002 PHE R 261 TYR 0.018 0.001 TYR J 190 ARG 0.029 0.001 ARG R 207 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12542 Ramachandran restraints generated. 6271 Oldfield, 0 Emsley, 6271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12542 Ramachandran restraints generated. 6271 Oldfield, 0 Emsley, 6271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 641 residues out of total 5462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 203 poor density : 438 time to evaluate : 4.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 101 THR cc_start: 0.8677 (OUTLIER) cc_final: 0.8404 (p) REVERT: E 118 LYS cc_start: 0.4730 (tmmm) cc_final: 0.3945 (mttm) REVERT: I 225 ARG cc_start: 0.7078 (tpp-160) cc_final: 0.6837 (ttm-80) REVERT: I 227 LYS cc_start: 0.5831 (tttt) cc_final: 0.5629 (ttpt) REVERT: I 613 LEU cc_start: 0.7253 (OUTLIER) cc_final: 0.6596 (tt) REVERT: I 679 MET cc_start: 0.8578 (OUTLIER) cc_final: 0.8367 (ttm) REVERT: I 784 GLU cc_start: 0.8120 (OUTLIER) cc_final: 0.7746 (mp0) REVERT: I 861 LEU cc_start: 0.7981 (OUTLIER) cc_final: 0.7370 (mp) REVERT: I 943 MET cc_start: 0.8776 (mmp) cc_final: 0.8223 (mmt) REVERT: J 131 LYS cc_start: 0.6973 (OUTLIER) cc_final: 0.6699 (mttp) REVERT: J 187 LEU cc_start: 0.8251 (OUTLIER) cc_final: 0.7854 (mm) REVERT: K 3 THR cc_start: 0.4896 (OUTLIER) cc_final: 0.4567 (m) REVERT: K 118 GLN cc_start: 0.2155 (OUTLIER) cc_final: 0.1796 (mp10) REVERT: K 196 MET cc_start: 0.6713 (ppp) cc_final: 0.5678 (ptm) REVERT: K 279 GLU cc_start: 0.7585 (OUTLIER) cc_final: 0.7195 (tp30) REVERT: L 35 LEU cc_start: 0.8099 (mt) cc_final: 0.7687 (mt) REVERT: M 113 MET cc_start: 0.7119 (tpt) cc_final: 0.6916 (tpt) REVERT: M 182 LYS cc_start: 0.8867 (tppt) cc_final: 0.8639 (mtpt) REVERT: M 293 GLU cc_start: 0.8171 (tp30) cc_final: 0.7653 (tm-30) REVERT: M 323 ILE cc_start: 0.8769 (pt) cc_final: 0.8532 (mt) REVERT: M 359 MET cc_start: 0.7885 (OUTLIER) cc_final: 0.7667 (mtm) REVERT: N 88 MET cc_start: 0.7531 (mmm) cc_final: 0.7197 (mmt) REVERT: N 209 PHE cc_start: 0.5383 (OUTLIER) cc_final: 0.4030 (m-80) REVERT: N 381 GLU cc_start: 0.5569 (OUTLIER) cc_final: 0.5306 (mp0) REVERT: N 442 TYR cc_start: 0.8029 (m-80) cc_final: 0.7278 (m-10) REVERT: O 100 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.7120 (mp0) REVERT: O 171 LYS cc_start: 0.7443 (mttt) cc_final: 0.7129 (tmmt) REVERT: O 249 ARG cc_start: 0.6396 (tpt90) cc_final: 0.5657 (mtp-110) REVERT: O 362 ARG cc_start: 0.8720 (OUTLIER) cc_final: 0.8353 (ttt180) REVERT: O 364 MET cc_start: 0.7358 (mmm) cc_final: 0.7029 (mmm) REVERT: P 46 MET cc_start: 0.8473 (mmm) cc_final: 0.7694 (mmm) REVERT: P 168 MET cc_start: 0.8617 (ptm) cc_final: 0.8415 (ptp) REVERT: P 269 LYS cc_start: 0.8539 (tttm) cc_final: 0.8219 (tttm) REVERT: P 441 GLN cc_start: 0.8859 (tt0) cc_final: 0.8459 (tp40) REVERT: Q 168 LYS cc_start: 0.6731 (OUTLIER) cc_final: 0.6244 (tttt) REVERT: Q 172 LEU cc_start: 0.7764 (OUTLIER) cc_final: 0.7538 (mt) REVERT: Q 249 ARG cc_start: 0.6149 (mtm180) cc_final: 0.5690 (mtm180) REVERT: Q 345 THR cc_start: 0.7826 (OUTLIER) cc_final: 0.7382 (t) REVERT: Q 346 SER cc_start: 0.8402 (p) cc_final: 0.8125 (t) REVERT: R 253 ARG cc_start: 0.8052 (ttm170) cc_final: 0.7560 (mtm-85) REVERT: R 269 LYS cc_start: 0.8167 (mptt) cc_final: 0.7355 (tmtt) REVERT: R 273 ARG cc_start: 0.6889 (mpt180) cc_final: 0.6565 (mmt-90) REVERT: R 346 ILE cc_start: 0.8283 (OUTLIER) cc_final: 0.8062 (pt) REVERT: R 444 LYS cc_start: 0.7484 (OUTLIER) cc_final: 0.7164 (mmmt) REVERT: S 1 MET cc_start: 0.0800 (mtt) cc_final: -0.1021 (tpt) REVERT: S 161 HIS cc_start: 0.2804 (OUTLIER) cc_final: 0.2379 (t-90) REVERT: S 227 MET cc_start: 0.3594 (mmm) cc_final: 0.2785 (mmp) REVERT: S 313 MET cc_start: 0.5145 (tpt) cc_final: 0.4802 (tpp) REVERT: T 79 ARG cc_start: 0.0892 (OUTLIER) cc_final: -0.1002 (tpp80) REVERT: U 175 ILE cc_start: 0.1148 (OUTLIER) cc_final: 0.0738 (mt) REVERT: U 283 MET cc_start: 0.3893 (mtp) cc_final: 0.3523 (mtp) REVERT: U 359 LYS cc_start: 0.2772 (OUTLIER) cc_final: 0.1919 (tttp) REVERT: V 98 MET cc_start: 0.1583 (ppp) cc_final: 0.1021 (ttp) REVERT: V 248 LEU cc_start: 0.2969 (OUTLIER) cc_final: 0.2320 (tp) REVERT: V 255 GLU cc_start: 0.4107 (OUTLIER) cc_final: 0.2873 (mt-10) REVERT: W 151 MET cc_start: 0.0521 (tpt) cc_final: -0.0007 (mmm) outliers start: 203 outliers final: 113 residues processed: 597 average time/residue: 0.5379 time to fit residues: 543.3523 Evaluate side-chains 538 residues out of total 5462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 399 time to evaluate : 4.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain F residue 49 THR Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 91 ILE Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain G residue 84 PHE Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain H residue 49 LEU Chi-restraints excluded: chain H residue 52 GLU Chi-restraints excluded: chain I residue 211 LYS Chi-restraints excluded: chain I residue 610 ILE Chi-restraints excluded: chain I residue 613 LEU Chi-restraints excluded: chain I residue 679 MET Chi-restraints excluded: chain I residue 742 TYR Chi-restraints excluded: chain I residue 778 LEU Chi-restraints excluded: chain I residue 784 GLU Chi-restraints excluded: chain I residue 859 CYS Chi-restraints excluded: chain I residue 861 LEU Chi-restraints excluded: chain I residue 918 THR Chi-restraints excluded: chain I residue 921 ILE Chi-restraints excluded: chain I residue 928 LEU Chi-restraints excluded: chain I residue 1921 GLU Chi-restraints excluded: chain I residue 1947 THR Chi-restraints excluded: chain I residue 1959 VAL Chi-restraints excluded: chain I residue 2062 VAL Chi-restraints excluded: chain I residue 2074 VAL Chi-restraints excluded: chain I residue 2177 LEU Chi-restraints excluded: chain I residue 2189 MET Chi-restraints excluded: chain J residue 131 LYS Chi-restraints excluded: chain J residue 177 LYS Chi-restraints excluded: chain J residue 187 LEU Chi-restraints excluded: chain J residue 216 SER Chi-restraints excluded: chain J residue 261 CYS Chi-restraints excluded: chain J residue 267 THR Chi-restraints excluded: chain K residue 3 THR Chi-restraints excluded: chain K residue 6 LEU Chi-restraints excluded: chain K residue 70 VAL Chi-restraints excluded: chain K residue 83 MET Chi-restraints excluded: chain K residue 113 LEU Chi-restraints excluded: chain K residue 118 GLN Chi-restraints excluded: chain K residue 125 VAL Chi-restraints excluded: chain K residue 161 CYS Chi-restraints excluded: chain K residue 279 GLU Chi-restraints excluded: chain K residue 289 ILE Chi-restraints excluded: chain K residue 292 MET Chi-restraints excluded: chain K residue 356 ILE Chi-restraints excluded: chain K residue 378 THR Chi-restraints excluded: chain L residue 92 ASN Chi-restraints excluded: chain L residue 93 LEU Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain M residue 157 VAL Chi-restraints excluded: chain M residue 262 GLN Chi-restraints excluded: chain M residue 271 ILE Chi-restraints excluded: chain M residue 295 VAL Chi-restraints excluded: chain M residue 317 ARG Chi-restraints excluded: chain M residue 332 ASN Chi-restraints excluded: chain M residue 359 MET Chi-restraints excluded: chain M residue 406 SER Chi-restraints excluded: chain M residue 433 ILE Chi-restraints excluded: chain N residue 60 LEU Chi-restraints excluded: chain N residue 163 LEU Chi-restraints excluded: chain N residue 192 VAL Chi-restraints excluded: chain N residue 209 PHE Chi-restraints excluded: chain N residue 210 THR Chi-restraints excluded: chain N residue 301 VAL Chi-restraints excluded: chain N residue 325 ILE Chi-restraints excluded: chain N residue 326 MET Chi-restraints excluded: chain N residue 354 LEU Chi-restraints excluded: chain N residue 381 GLU Chi-restraints excluded: chain N residue 395 LEU Chi-restraints excluded: chain N residue 413 CYS Chi-restraints excluded: chain N residue 426 ILE Chi-restraints excluded: chain O residue 40 VAL Chi-restraints excluded: chain O residue 100 GLU Chi-restraints excluded: chain O residue 124 ILE Chi-restraints excluded: chain O residue 256 ILE Chi-restraints excluded: chain O residue 274 LYS Chi-restraints excluded: chain O residue 342 GLU Chi-restraints excluded: chain O residue 353 ASP Chi-restraints excluded: chain O residue 362 ARG Chi-restraints excluded: chain P residue 68 ILE Chi-restraints excluded: chain P residue 239 VAL Chi-restraints excluded: chain P residue 255 GLN Chi-restraints excluded: chain P residue 261 PHE Chi-restraints excluded: chain P residue 305 ASP Chi-restraints excluded: chain P residue 355 LEU Chi-restraints excluded: chain P residue 429 VAL Chi-restraints excluded: chain Q residue 40 VAL Chi-restraints excluded: chain Q residue 124 ILE Chi-restraints excluded: chain Q residue 168 LYS Chi-restraints excluded: chain Q residue 172 LEU Chi-restraints excluded: chain Q residue 185 VAL Chi-restraints excluded: chain Q residue 192 TYR Chi-restraints excluded: chain Q residue 197 SER Chi-restraints excluded: chain Q residue 228 VAL Chi-restraints excluded: chain Q residue 235 ILE Chi-restraints excluded: chain Q residue 313 THR Chi-restraints excluded: chain Q residue 345 THR Chi-restraints excluded: chain Q residue 407 VAL Chi-restraints excluded: chain Q residue 416 LEU Chi-restraints excluded: chain R residue 19 ILE Chi-restraints excluded: chain R residue 21 ARG Chi-restraints excluded: chain R residue 62 MET Chi-restraints excluded: chain R residue 116 THR Chi-restraints excluded: chain R residue 171 ILE Chi-restraints excluded: chain R residue 205 LEU Chi-restraints excluded: chain R residue 214 ASP Chi-restraints excluded: chain R residue 250 ILE Chi-restraints excluded: chain R residue 346 ILE Chi-restraints excluded: chain R residue 434 LEU Chi-restraints excluded: chain R residue 444 LYS Chi-restraints excluded: chain S residue 66 THR Chi-restraints excluded: chain S residue 161 HIS Chi-restraints excluded: chain T residue 77 VAL Chi-restraints excluded: chain T residue 79 ARG Chi-restraints excluded: chain T residue 110 HIS Chi-restraints excluded: chain U residue 78 ASN Chi-restraints excluded: chain U residue 159 VAL Chi-restraints excluded: chain U residue 175 ILE Chi-restraints excluded: chain U residue 330 ILE Chi-restraints excluded: chain U residue 349 LEU Chi-restraints excluded: chain U residue 351 THR Chi-restraints excluded: chain U residue 359 LYS Chi-restraints excluded: chain V residue 58 TYR Chi-restraints excluded: chain V residue 247 LEU Chi-restraints excluded: chain V residue 248 LEU Chi-restraints excluded: chain V residue 255 GLU Chi-restraints excluded: chain W residue 38 ARG Chi-restraints excluded: chain W residue 81 VAL Chi-restraints excluded: chain W residue 157 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 652 random chunks: chunk 524 optimal weight: 5.9990 chunk 357 optimal weight: 6.9990 chunk 9 optimal weight: 0.2980 chunk 469 optimal weight: 0.9990 chunk 260 optimal weight: 0.0470 chunk 537 optimal weight: 1.9990 chunk 435 optimal weight: 1.9990 chunk 0 optimal weight: 40.0000 chunk 321 optimal weight: 3.9990 chunk 565 optimal weight: 30.0000 chunk 159 optimal weight: 0.9990 overall best weight: 0.8684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 GLN E 38 ASN ** E 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 830 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 967 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1945 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I1964 GLN ** I1991 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 200 HIS ** K 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 31 GLN ** M 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 408 GLN ** S 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 296 ASN T 81 ASN ** U 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5727 moved from start: 0.4684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 58153 Z= 0.190 Angle : 0.609 10.755 79831 Z= 0.314 Chirality : 0.041 0.235 8993 Planarity : 0.004 0.080 9191 Dihedral : 21.289 169.471 10399 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.49 % Favored : 94.43 % Rotamer: Outliers : 3.16 % Allowed : 15.58 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.37 % Twisted General : 0.07 % 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: -0.34 (0.11), residues: 6271 helix: 0.74 (0.10), residues: 2902 sheet: -0.75 (0.18), residues: 854 loop : -1.09 (0.12), residues: 2515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP K 68 HIS 0.009 0.001 HIS Q 316 PHE 0.023 0.001 PHE P 257 TYR 0.025 0.001 TYR K 77 ARG 0.011 0.000 ARG R 207 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12542 Ramachandran restraints generated. 6271 Oldfield, 0 Emsley, 6271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12542 Ramachandran restraints generated. 6271 Oldfield, 0 Emsley, 6271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 595 residues out of total 5462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 172 poor density : 423 time to evaluate : 4.540 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: B 77 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.8067 (mt) REVERT: E 101 THR cc_start: 0.8675 (OUTLIER) cc_final: 0.8429 (p) REVERT: E 118 LYS cc_start: 0.4704 (tmmm) cc_final: 0.3990 (mttm) REVERT: F 37 TYR cc_start: 0.7885 (m-80) cc_final: 0.7671 (m-80) REVERT: F 80 TYR cc_start: 0.7025 (m-10) cc_final: 0.6421 (m-80) REVERT: I 225 ARG cc_start: 0.7080 (tpp-160) cc_final: 0.6864 (ttm-80) REVERT: I 227 LYS cc_start: 0.5815 (tttt) cc_final: 0.5588 (ttpt) REVERT: I 613 LEU cc_start: 0.7126 (OUTLIER) cc_final: 0.6466 (tt) REVERT: I 679 MET cc_start: 0.8598 (OUTLIER) cc_final: 0.8368 (ttm) REVERT: I 784 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.7611 (mp0) REVERT: I 861 LEU cc_start: 0.7901 (OUTLIER) cc_final: 0.7236 (mp) REVERT: I 864 ARG cc_start: 0.8685 (OUTLIER) cc_final: 0.8387 (ttt-90) REVERT: I 943 MET cc_start: 0.8746 (mmp) cc_final: 0.8219 (mmt) REVERT: K 1 MET cc_start: 0.5850 (tmm) cc_final: 0.5116 (tmm) REVERT: K 196 MET cc_start: 0.6949 (ppp) cc_final: 0.6284 (ptm) REVERT: K 279 GLU cc_start: 0.7750 (OUTLIER) cc_final: 0.7381 (tp30) REVERT: L 35 LEU cc_start: 0.8045 (mt) cc_final: 0.7711 (mt) REVERT: M 182 LYS cc_start: 0.8854 (tppt) cc_final: 0.8640 (mtpt) REVERT: M 293 GLU cc_start: 0.8157 (tp30) cc_final: 0.7693 (tm-30) REVERT: M 323 ILE cc_start: 0.8770 (pt) cc_final: 0.8532 (mt) REVERT: M 332 ASN cc_start: 0.8673 (OUTLIER) cc_final: 0.8396 (t0) REVERT: M 359 MET cc_start: 0.7768 (OUTLIER) cc_final: 0.7525 (mtt) REVERT: M 410 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8312 (tt) REVERT: N 88 MET cc_start: 0.7586 (mmm) cc_final: 0.7249 (mmt) REVERT: N 168 MET cc_start: 0.8865 (ptp) cc_final: 0.8645 (ptp) REVERT: N 209 PHE cc_start: 0.5630 (OUTLIER) cc_final: 0.4087 (m-80) REVERT: N 320 MET cc_start: 0.8767 (mmt) cc_final: 0.8212 (mmt) REVERT: N 381 GLU cc_start: 0.5599 (OUTLIER) cc_final: 0.5340 (mp0) REVERT: N 442 TYR cc_start: 0.7976 (m-80) cc_final: 0.7297 (m-10) REVERT: O 100 GLU cc_start: 0.8246 (OUTLIER) cc_final: 0.7005 (mp0) REVERT: P 168 MET cc_start: 0.8629 (ptm) cc_final: 0.8417 (ptp) REVERT: P 183 THR cc_start: 0.9311 (m) cc_final: 0.9082 (p) REVERT: P 269 LYS cc_start: 0.8550 (tttm) cc_final: 0.8232 (tttm) REVERT: P 441 GLN cc_start: 0.8861 (tt0) cc_final: 0.8434 (tp40) REVERT: Q 168 LYS cc_start: 0.6600 (OUTLIER) cc_final: 0.6129 (tttt) REVERT: Q 249 ARG cc_start: 0.6089 (mtm180) cc_final: 0.5679 (mtm180) REVERT: Q 345 THR cc_start: 0.7941 (OUTLIER) cc_final: 0.7458 (t) REVERT: Q 346 SER cc_start: 0.8383 (p) cc_final: 0.8135 (t) REVERT: R 253 ARG cc_start: 0.8042 (ttm170) cc_final: 0.7766 (mtm-85) REVERT: R 269 LYS cc_start: 0.8175 (mptt) cc_final: 0.7358 (tmtt) REVERT: R 273 ARG cc_start: 0.6865 (mpt180) cc_final: 0.6550 (mmt-90) REVERT: R 444 LYS cc_start: 0.7448 (OUTLIER) cc_final: 0.7143 (mmmt) REVERT: S 1 MET cc_start: 0.0616 (mtt) cc_final: -0.1140 (tpt) REVERT: S 161 HIS cc_start: 0.2877 (OUTLIER) cc_final: 0.2362 (t-90) REVERT: S 227 MET cc_start: 0.3720 (mmm) cc_final: 0.3443 (mmt) REVERT: S 313 MET cc_start: 0.5075 (tpt) cc_final: 0.4798 (tpp) REVERT: T 79 ARG cc_start: 0.0862 (OUTLIER) cc_final: -0.0932 (tpp80) REVERT: U 221 LEU cc_start: 0.0524 (OUTLIER) cc_final: 0.0253 (mt) REVERT: U 283 MET cc_start: 0.4689 (mtp) cc_final: 0.4394 (mtp) REVERT: U 359 LYS cc_start: 0.2906 (OUTLIER) cc_final: 0.2064 (tttp) REVERT: V 248 LEU cc_start: 0.2846 (OUTLIER) cc_final: 0.2288 (tp) REVERT: V 255 GLU cc_start: 0.4121 (OUTLIER) cc_final: 0.2867 (mt-10) REVERT: W 151 MET cc_start: 0.0581 (tpt) cc_final: 0.0046 (mmm) outliers start: 172 outliers final: 96 residues processed: 560 average time/residue: 0.5491 time to fit residues: 517.9198 Evaluate side-chains 506 residues out of total 5462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 387 time to evaluate : 4.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain H residue 49 LEU Chi-restraints excluded: chain H residue 93 GLN Chi-restraints excluded: chain I residue 211 LYS Chi-restraints excluded: chain I residue 610 ILE Chi-restraints excluded: chain I residue 613 LEU Chi-restraints excluded: chain I residue 660 LEU Chi-restraints excluded: chain I residue 679 MET Chi-restraints excluded: chain I residue 742 TYR Chi-restraints excluded: chain I residue 778 LEU Chi-restraints excluded: chain I residue 784 GLU Chi-restraints excluded: chain I residue 859 CYS Chi-restraints excluded: chain I residue 861 LEU Chi-restraints excluded: chain I residue 864 ARG Chi-restraints excluded: chain I residue 921 ILE Chi-restraints excluded: chain I residue 928 LEU Chi-restraints excluded: chain I residue 1921 GLU Chi-restraints excluded: chain I residue 1959 VAL Chi-restraints excluded: chain I residue 2062 VAL Chi-restraints excluded: chain I residue 2189 MET Chi-restraints excluded: chain J residue 194 GLU Chi-restraints excluded: chain J residue 261 CYS Chi-restraints excluded: chain J residue 267 THR Chi-restraints excluded: chain J residue 275 GLU Chi-restraints excluded: chain J residue 300 LEU Chi-restraints excluded: chain K residue 6 LEU Chi-restraints excluded: chain K residue 70 VAL Chi-restraints excluded: chain K residue 83 MET Chi-restraints excluded: chain K residue 114 PHE Chi-restraints excluded: chain K residue 125 VAL Chi-restraints excluded: chain K residue 161 CYS Chi-restraints excluded: chain K residue 279 GLU Chi-restraints excluded: chain K residue 289 ILE Chi-restraints excluded: chain K residue 292 MET Chi-restraints excluded: chain K residue 356 ILE Chi-restraints excluded: chain K residue 378 THR Chi-restraints excluded: chain L residue 92 ASN Chi-restraints excluded: chain L residue 93 LEU Chi-restraints excluded: chain L residue 151 LYS Chi-restraints excluded: chain M residue 157 VAL Chi-restraints excluded: chain M residue 262 GLN Chi-restraints excluded: chain M residue 271 ILE Chi-restraints excluded: chain M residue 295 VAL Chi-restraints excluded: chain M residue 317 ARG Chi-restraints excluded: chain M residue 332 ASN Chi-restraints excluded: chain M residue 359 MET Chi-restraints excluded: chain M residue 406 SER Chi-restraints excluded: chain M residue 410 LEU Chi-restraints excluded: chain M residue 419 ILE Chi-restraints excluded: chain M residue 433 ILE Chi-restraints excluded: chain N residue 163 LEU Chi-restraints excluded: chain N residue 192 VAL Chi-restraints excluded: chain N residue 209 PHE Chi-restraints excluded: chain N residue 301 VAL Chi-restraints excluded: chain N residue 326 MET Chi-restraints excluded: chain N residue 354 LEU Chi-restraints excluded: chain N residue 381 GLU Chi-restraints excluded: chain N residue 395 LEU Chi-restraints excluded: chain N residue 413 CYS Chi-restraints excluded: chain O residue 40 VAL Chi-restraints excluded: chain O residue 100 GLU Chi-restraints excluded: chain O residue 124 ILE Chi-restraints excluded: chain O residue 274 LYS Chi-restraints excluded: chain O residue 342 GLU Chi-restraints excluded: chain O residue 353 ASP Chi-restraints excluded: chain P residue 68 ILE Chi-restraints excluded: chain P residue 261 PHE Chi-restraints excluded: chain P residue 305 ASP Chi-restraints excluded: chain P residue 355 LEU Chi-restraints excluded: chain P residue 429 VAL Chi-restraints excluded: chain Q residue 40 VAL Chi-restraints excluded: chain Q residue 124 ILE Chi-restraints excluded: chain Q residue 168 LYS Chi-restraints excluded: chain Q residue 192 TYR Chi-restraints excluded: chain Q residue 228 VAL Chi-restraints excluded: chain Q residue 235 ILE Chi-restraints excluded: chain Q residue 345 THR Chi-restraints excluded: chain Q residue 407 VAL Chi-restraints excluded: chain Q residue 416 LEU Chi-restraints excluded: chain R residue 21 ARG Chi-restraints excluded: chain R residue 62 MET Chi-restraints excluded: chain R residue 171 ILE Chi-restraints excluded: chain R residue 205 LEU Chi-restraints excluded: chain R residue 214 ASP Chi-restraints excluded: chain R residue 250 ILE Chi-restraints excluded: chain R residue 429 VAL Chi-restraints excluded: chain R residue 434 LEU Chi-restraints excluded: chain R residue 444 LYS Chi-restraints excluded: chain S residue 66 THR Chi-restraints excluded: chain S residue 161 HIS Chi-restraints excluded: chain T residue 77 VAL Chi-restraints excluded: chain T residue 79 ARG Chi-restraints excluded: chain T residue 110 HIS Chi-restraints excluded: chain U residue 78 ASN Chi-restraints excluded: chain U residue 159 VAL Chi-restraints excluded: chain U residue 221 LEU Chi-restraints excluded: chain U residue 330 ILE Chi-restraints excluded: chain U residue 349 LEU Chi-restraints excluded: chain U residue 359 LYS Chi-restraints excluded: chain V residue 58 TYR Chi-restraints excluded: chain V residue 208 VAL Chi-restraints excluded: chain V residue 247 LEU Chi-restraints excluded: chain V residue 248 LEU Chi-restraints excluded: chain V residue 255 GLU Chi-restraints excluded: chain W residue 38 ARG Chi-restraints excluded: chain W residue 81 VAL Chi-restraints excluded: chain W residue 157 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 652 random chunks: chunk 212 optimal weight: 20.0000 chunk 567 optimal weight: 20.0000 chunk 124 optimal weight: 0.2980 chunk 370 optimal weight: 0.2980 chunk 155 optimal weight: 0.6980 chunk 630 optimal weight: 7.9990 chunk 523 optimal weight: 0.0070 chunk 292 optimal weight: 2.9990 chunk 52 optimal weight: 8.9990 chunk 208 optimal weight: 0.0870 chunk 331 optimal weight: 0.7980 overall best weight: 0.2776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 830 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 967 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1945 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1991 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 92 ASN ** K 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 31 GLN ** M 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 305 HIS M 332 ASN ** O 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 408 GLN ** S 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 111 ASN ** S 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5707 moved from start: 0.4843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 58153 Z= 0.159 Angle : 0.591 10.817 79831 Z= 0.304 Chirality : 0.041 0.317 8993 Planarity : 0.004 0.086 9191 Dihedral : 21.095 171.593 10384 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.41 % Favored : 94.51 % Rotamer: Outliers : 2.87 % Allowed : 15.86 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.37 % Twisted General : 0.08 % 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: -0.17 (0.11), residues: 6271 helix: 0.87 (0.10), residues: 2902 sheet: -0.69 (0.18), residues: 840 loop : -1.00 (0.12), residues: 2529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP S 86 HIS 0.008 0.001 HIS M 316 PHE 0.018 0.001 PHE D 61 TYR 0.024 0.001 TYR I 821 ARG 0.008 0.000 ARG F 96 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12542 Ramachandran restraints generated. 6271 Oldfield, 0 Emsley, 6271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12542 Ramachandran restraints generated. 6271 Oldfield, 0 Emsley, 6271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 576 residues out of total 5462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 420 time to evaluate : 4.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 77 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.8082 (mt) REVERT: C 120 MET cc_start: 0.7275 (OUTLIER) cc_final: 0.7059 (mtp) REVERT: E 118 LYS cc_start: 0.4690 (tmmm) cc_final: 0.3963 (mttm) REVERT: I 225 ARG cc_start: 0.7077 (tpp-160) cc_final: 0.6861 (ttm-80) REVERT: I 227 LYS cc_start: 0.5848 (tttt) cc_final: 0.5640 (ttpt) REVERT: I 613 LEU cc_start: 0.7142 (OUTLIER) cc_final: 0.6491 (tt) REVERT: I 679 MET cc_start: 0.8589 (OUTLIER) cc_final: 0.7956 (ttm) REVERT: I 784 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.7571 (mp0) REVERT: I 803 PHE cc_start: 0.6094 (t80) cc_final: 0.5860 (t80) REVERT: I 861 LEU cc_start: 0.7800 (OUTLIER) cc_final: 0.7184 (mp) REVERT: I 864 ARG cc_start: 0.8680 (OUTLIER) cc_final: 0.8423 (ttt-90) REVERT: K 1 MET cc_start: 0.5843 (tmm) cc_final: 0.5254 (tmm) REVERT: K 196 MET cc_start: 0.6848 (ppp) cc_final: 0.6186 (ptm) REVERT: K 279 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.7481 (tp30) REVERT: L 35 LEU cc_start: 0.8161 (mt) cc_final: 0.7771 (mt) REVERT: M 293 GLU cc_start: 0.8110 (tp30) cc_final: 0.7544 (tm-30) REVERT: M 323 ILE cc_start: 0.8716 (pt) cc_final: 0.8472 (mt) REVERT: M 410 LEU cc_start: 0.8457 (OUTLIER) cc_final: 0.8237 (tt) REVERT: N 88 MET cc_start: 0.7588 (mmm) cc_final: 0.7236 (mmt) REVERT: N 168 MET cc_start: 0.8843 (ptp) cc_final: 0.8539 (ptp) REVERT: N 381 GLU cc_start: 0.5602 (OUTLIER) cc_final: 0.5333 (mp0) REVERT: N 442 TYR cc_start: 0.7931 (m-80) cc_final: 0.7490 (m-10) REVERT: O 100 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.6948 (mp0) REVERT: P 46 MET cc_start: 0.8297 (mmm) cc_final: 0.7562 (mmm) REVERT: P 183 THR cc_start: 0.9308 (m) cc_final: 0.9066 (p) REVERT: P 269 LYS cc_start: 0.8536 (tttm) cc_final: 0.8230 (tttm) REVERT: P 441 GLN cc_start: 0.8828 (tt0) cc_final: 0.8406 (tp40) REVERT: Q 61 MET cc_start: 0.8174 (mmm) cc_final: 0.7608 (mmm) REVERT: Q 168 LYS cc_start: 0.6574 (OUTLIER) cc_final: 0.6113 (tttt) REVERT: Q 249 ARG cc_start: 0.6066 (mtm180) cc_final: 0.5685 (mtm180) REVERT: Q 302 ASP cc_start: 0.7493 (p0) cc_final: 0.7223 (p0) REVERT: Q 345 THR cc_start: 0.7968 (OUTLIER) cc_final: 0.7496 (t) REVERT: Q 346 SER cc_start: 0.8360 (p) cc_final: 0.8126 (t) REVERT: R 253 ARG cc_start: 0.8028 (ttm170) cc_final: 0.7760 (mtm-85) REVERT: R 269 LYS cc_start: 0.8129 (mptt) cc_final: 0.7340 (tmtt) REVERT: R 273 ARG cc_start: 0.6880 (mpt180) cc_final: 0.6673 (mpt180) REVERT: R 401 TYR cc_start: 0.8034 (t80) cc_final: 0.7563 (t80) REVERT: R 444 LYS cc_start: 0.7389 (OUTLIER) cc_final: 0.7100 (mmmt) REVERT: S 1 MET cc_start: 0.0549 (mtt) cc_final: -0.1188 (tpt) REVERT: S 161 HIS cc_start: 0.3039 (OUTLIER) cc_final: 0.2229 (t-90) REVERT: S 305 MET cc_start: 0.4468 (mmp) cc_final: 0.3955 (ptt) REVERT: S 313 MET cc_start: 0.5129 (tpt) cc_final: 0.4868 (tpp) REVERT: S 325 MET cc_start: 0.4818 (tpp) cc_final: 0.4498 (tpt) REVERT: T 79 ARG cc_start: 0.0648 (OUTLIER) cc_final: -0.1166 (tpp80) REVERT: U 221 LEU cc_start: 0.0394 (OUTLIER) cc_final: 0.0140 (mt) REVERT: U 269 MET cc_start: -0.0240 (ppp) cc_final: -0.1235 (ppp) REVERT: U 359 LYS cc_start: 0.2914 (OUTLIER) cc_final: 0.2099 (tttp) REVERT: V 154 LYS cc_start: 0.3419 (tttm) cc_final: 0.3173 (tmtt) REVERT: V 248 LEU cc_start: 0.2827 (OUTLIER) cc_final: 0.2290 (tp) REVERT: V 255 GLU cc_start: 0.4137 (OUTLIER) cc_final: 0.2860 (mt-10) REVERT: W 151 MET cc_start: 0.0572 (tpt) cc_final: 0.0041 (mmm) outliers start: 156 outliers final: 95 residues processed: 544 average time/residue: 0.5434 time to fit residues: 506.5971 Evaluate side-chains 502 residues out of total 5462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 387 time to evaluate : 4.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 120 MET Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain F residue 91 ILE Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain H residue 49 LEU Chi-restraints excluded: chain H residue 93 GLN Chi-restraints excluded: chain I residue 610 ILE Chi-restraints excluded: chain I residue 613 LEU Chi-restraints excluded: chain I residue 660 LEU Chi-restraints excluded: chain I residue 679 MET Chi-restraints excluded: chain I residue 742 TYR Chi-restraints excluded: chain I residue 784 GLU Chi-restraints excluded: chain I residue 859 CYS Chi-restraints excluded: chain I residue 861 LEU Chi-restraints excluded: chain I residue 864 ARG Chi-restraints excluded: chain I residue 918 THR Chi-restraints excluded: chain I residue 921 ILE Chi-restraints excluded: chain I residue 928 LEU Chi-restraints excluded: chain I residue 1921 GLU Chi-restraints excluded: chain I residue 1999 LEU Chi-restraints excluded: chain I residue 2062 VAL Chi-restraints excluded: chain I residue 2189 MET Chi-restraints excluded: chain J residue 194 GLU Chi-restraints excluded: chain J residue 213 THR Chi-restraints excluded: chain J residue 261 CYS Chi-restraints excluded: chain J residue 300 LEU Chi-restraints excluded: chain K residue 6 LEU Chi-restraints excluded: chain K residue 70 VAL Chi-restraints excluded: chain K residue 83 MET Chi-restraints excluded: chain K residue 125 VAL Chi-restraints excluded: chain K residue 161 CYS Chi-restraints excluded: chain K residue 279 GLU Chi-restraints excluded: chain K residue 289 ILE Chi-restraints excluded: chain K residue 292 MET Chi-restraints excluded: chain K residue 356 ILE Chi-restraints excluded: chain K residue 378 THR Chi-restraints excluded: chain L residue 93 LEU Chi-restraints excluded: chain L residue 151 LYS Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain M residue 135 VAL Chi-restraints excluded: chain M residue 157 VAL Chi-restraints excluded: chain M residue 170 LEU Chi-restraints excluded: chain M residue 262 GLN Chi-restraints excluded: chain M residue 271 ILE Chi-restraints excluded: chain M residue 295 VAL Chi-restraints excluded: chain M residue 406 SER Chi-restraints excluded: chain M residue 410 LEU Chi-restraints excluded: chain M residue 419 ILE Chi-restraints excluded: chain M residue 433 ILE Chi-restraints excluded: chain N residue 163 LEU Chi-restraints excluded: chain N residue 192 VAL Chi-restraints excluded: chain N residue 209 PHE Chi-restraints excluded: chain N residue 210 THR Chi-restraints excluded: chain N residue 242 VAL Chi-restraints excluded: chain N residue 301 VAL Chi-restraints excluded: chain N residue 326 MET Chi-restraints excluded: chain N residue 354 LEU Chi-restraints excluded: chain N residue 381 GLU Chi-restraints excluded: chain N residue 395 LEU Chi-restraints excluded: chain N residue 413 CYS Chi-restraints excluded: chain N residue 435 ASP Chi-restraints excluded: chain O residue 40 VAL Chi-restraints excluded: chain O residue 100 GLU Chi-restraints excluded: chain O residue 274 LYS Chi-restraints excluded: chain O residue 342 GLU Chi-restraints excluded: chain O residue 353 ASP Chi-restraints excluded: chain P residue 68 ILE Chi-restraints excluded: chain P residue 261 PHE Chi-restraints excluded: chain P residue 355 LEU Chi-restraints excluded: chain P residue 429 VAL Chi-restraints excluded: chain Q residue 40 VAL Chi-restraints excluded: chain Q residue 91 VAL Chi-restraints excluded: chain Q residue 124 ILE Chi-restraints excluded: chain Q residue 168 LYS Chi-restraints excluded: chain Q residue 192 TYR Chi-restraints excluded: chain Q residue 235 ILE Chi-restraints excluded: chain Q residue 345 THR Chi-restraints excluded: chain Q residue 416 LEU Chi-restraints excluded: chain R residue 21 ARG Chi-restraints excluded: chain R residue 62 MET Chi-restraints excluded: chain R residue 171 ILE Chi-restraints excluded: chain R residue 205 LEU Chi-restraints excluded: chain R residue 214 ASP Chi-restraints excluded: chain R residue 250 ILE Chi-restraints excluded: chain R residue 260 LEU Chi-restraints excluded: chain R residue 429 VAL Chi-restraints excluded: chain R residue 444 LYS Chi-restraints excluded: chain S residue 66 THR Chi-restraints excluded: chain S residue 161 HIS Chi-restraints excluded: chain T residue 77 VAL Chi-restraints excluded: chain T residue 79 ARG Chi-restraints excluded: chain T residue 110 HIS Chi-restraints excluded: chain U residue 78 ASN Chi-restraints excluded: chain U residue 159 VAL Chi-restraints excluded: chain U residue 221 LEU Chi-restraints excluded: chain U residue 330 ILE Chi-restraints excluded: chain U residue 349 LEU Chi-restraints excluded: chain U residue 351 THR Chi-restraints excluded: chain U residue 359 LYS Chi-restraints excluded: chain V residue 58 TYR Chi-restraints excluded: chain V residue 208 VAL Chi-restraints excluded: chain V residue 247 LEU Chi-restraints excluded: chain V residue 248 LEU Chi-restraints excluded: chain V residue 255 GLU Chi-restraints excluded: chain W residue 81 VAL Chi-restraints excluded: chain W residue 157 THR Chi-restraints excluded: chain W residue 183 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 652 random chunks: chunk 608 optimal weight: 0.0970 chunk 71 optimal weight: 7.9990 chunk 359 optimal weight: 0.1980 chunk 460 optimal weight: 0.6980 chunk 356 optimal weight: 0.6980 chunk 531 optimal weight: 0.0030 chunk 352 optimal weight: 1.9990 chunk 628 optimal weight: 10.0000 chunk 393 optimal weight: 0.7980 chunk 383 optimal weight: 5.9990 chunk 290 optimal weight: 4.9990 overall best weight: 0.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 830 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1945 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1991 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 332 ASN ** O 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 408 GLN P 121 GLN ** S 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 173 HIS ** T 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5701 moved from start: 0.5030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.060 58153 Z= 0.155 Angle : 0.589 11.292 79831 Z= 0.302 Chirality : 0.040 0.269 8993 Planarity : 0.004 0.095 9191 Dihedral : 20.896 173.346 10379 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.21 % Favored : 94.71 % Rotamer: Outliers : 2.77 % Allowed : 16.17 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.37 % 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: -0.06 (0.11), residues: 6271 helix: 0.95 (0.10), residues: 2909 sheet: -0.61 (0.18), residues: 853 loop : -0.93 (0.13), residues: 2509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP S 86 HIS 0.008 0.001 HIS M 316 PHE 0.028 0.001 PHE R 257 TYR 0.033 0.001 TYR F 80 ARG 0.011 0.000 ARG C 42 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12542 Ramachandran restraints generated. 6271 Oldfield, 0 Emsley, 6271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12542 Ramachandran restraints generated. 6271 Oldfield, 0 Emsley, 6271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 572 residues out of total 5462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 421 time to evaluate : 4.577 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: C 120 MET cc_start: 0.7327 (OUTLIER) cc_final: 0.7097 (mtp) REVERT: E 118 LYS cc_start: 0.4637 (tmmm) cc_final: 0.3965 (mttm) REVERT: I 227 LYS cc_start: 0.5797 (tttt) cc_final: 0.5558 (ttpt) REVERT: I 613 LEU cc_start: 0.7174 (OUTLIER) cc_final: 0.6514 (tt) REVERT: I 679 MET cc_start: 0.8614 (OUTLIER) cc_final: 0.7934 (ttm) REVERT: I 784 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.7508 (mp0) REVERT: I 803 PHE cc_start: 0.6490 (t80) cc_final: 0.6234 (t80) REVERT: I 861 LEU cc_start: 0.7656 (OUTLIER) cc_final: 0.7049 (mp) REVERT: J 274 PHE cc_start: 0.5208 (OUTLIER) cc_final: 0.4409 (t80) REVERT: K 1 MET cc_start: 0.5863 (tmm) cc_final: 0.5104 (tmm) REVERT: K 279 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.7494 (tp30) REVERT: L 35 LEU cc_start: 0.8133 (mt) cc_final: 0.7853 (mt) REVERT: M 178 GLU cc_start: 0.7356 (mp0) cc_final: 0.7048 (mp0) REVERT: M 293 GLU cc_start: 0.7926 (tp30) cc_final: 0.7530 (tm-30) REVERT: M 323 ILE cc_start: 0.8715 (pt) cc_final: 0.8476 (mt) REVERT: M 410 LEU cc_start: 0.8530 (OUTLIER) cc_final: 0.8301 (tt) REVERT: N 88 MET cc_start: 0.7603 (mmm) cc_final: 0.7229 (mmt) REVERT: N 168 MET cc_start: 0.8756 (ptp) cc_final: 0.8444 (ptp) REVERT: N 202 ILE cc_start: 0.8490 (OUTLIER) cc_final: 0.8170 (mp) REVERT: N 381 GLU cc_start: 0.5616 (OUTLIER) cc_final: 0.5328 (mp0) REVERT: N 442 TYR cc_start: 0.7921 (m-80) cc_final: 0.7479 (m-10) REVERT: O 100 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.6932 (mp0) REVERT: P 46 MET cc_start: 0.8219 (mmm) cc_final: 0.7535 (mmm) REVERT: P 183 THR cc_start: 0.9295 (m) cc_final: 0.9053 (p) REVERT: P 269 LYS cc_start: 0.8506 (tttm) cc_final: 0.8190 (tttm) REVERT: P 414 ARG cc_start: 0.7666 (ttm-80) cc_final: 0.7190 (ttp-170) REVERT: P 441 GLN cc_start: 0.8828 (tt0) cc_final: 0.8387 (tp40) REVERT: Q 61 MET cc_start: 0.8166 (mmm) cc_final: 0.7765 (mmm) REVERT: Q 168 LYS cc_start: 0.6576 (OUTLIER) cc_final: 0.6113 (tttt) REVERT: Q 249 ARG cc_start: 0.5935 (mtm180) cc_final: 0.5610 (mtm180) REVERT: Q 345 THR cc_start: 0.8065 (OUTLIER) cc_final: 0.7541 (t) REVERT: Q 346 SER cc_start: 0.8349 (p) cc_final: 0.8138 (t) REVERT: R 253 ARG cc_start: 0.8025 (ttm170) cc_final: 0.7756 (mtm-85) REVERT: R 257 PHE cc_start: 0.7407 (p90) cc_final: 0.7136 (p90) REVERT: R 269 LYS cc_start: 0.8122 (mptt) cc_final: 0.7293 (tmtt) REVERT: R 273 ARG cc_start: 0.6861 (mpt180) cc_final: 0.6560 (mmt-90) REVERT: R 401 TYR cc_start: 0.8005 (t80) cc_final: 0.7621 (t80) REVERT: R 444 LYS cc_start: 0.7612 (OUTLIER) cc_final: 0.7278 (mmmt) REVERT: S 1 MET cc_start: 0.0282 (mtt) cc_final: -0.1340 (tpt) REVERT: S 153 MET cc_start: 0.3512 (tpp) cc_final: 0.2466 (ttt) REVERT: S 227 MET cc_start: 0.1673 (mmm) cc_final: 0.1128 (mmp) REVERT: S 305 MET cc_start: 0.4113 (mmp) cc_final: 0.3876 (ptt) REVERT: S 313 MET cc_start: 0.4998 (tpt) cc_final: 0.4467 (tpp) REVERT: S 325 MET cc_start: 0.4767 (tpp) cc_final: 0.4400 (tpt) REVERT: T 79 ARG cc_start: -0.0087 (OUTLIER) cc_final: -0.1395 (ttm-80) REVERT: T 82 MET cc_start: -0.0607 (ttt) cc_final: -0.1108 (ttt) REVERT: T 320 ASN cc_start: 0.3601 (m110) cc_final: 0.3252 (m110) REVERT: U 221 LEU cc_start: 0.0503 (OUTLIER) cc_final: 0.0245 (mt) REVERT: U 269 MET cc_start: -0.1538 (ppp) cc_final: -0.2107 (ppp) REVERT: U 359 LYS cc_start: 0.2513 (OUTLIER) cc_final: 0.1834 (tttp) REVERT: V 248 LEU cc_start: 0.2930 (OUTLIER) cc_final: 0.2372 (tp) REVERT: V 255 GLU cc_start: 0.4161 (OUTLIER) cc_final: 0.2859 (mt-10) REVERT: W 128 MET cc_start: 0.2968 (mmm) cc_final: 0.2139 (mtt) REVERT: W 151 MET cc_start: 0.0589 (tpt) cc_final: 0.0036 (mmm) outliers start: 151 outliers final: 102 residues processed: 547 average time/residue: 0.5260 time to fit residues: 492.7308 Evaluate side-chains 510 residues out of total 5462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 389 time to evaluate : 4.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 120 MET Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain F residue 91 ILE Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain H residue 49 LEU Chi-restraints excluded: chain I residue 211 LYS Chi-restraints excluded: chain I residue 610 ILE Chi-restraints excluded: chain I residue 613 LEU Chi-restraints excluded: chain I residue 679 MET Chi-restraints excluded: chain I residue 742 TYR Chi-restraints excluded: chain I residue 784 GLU Chi-restraints excluded: chain I residue 859 CYS Chi-restraints excluded: chain I residue 861 LEU Chi-restraints excluded: chain I residue 918 THR Chi-restraints excluded: chain I residue 921 ILE Chi-restraints excluded: chain I residue 928 LEU Chi-restraints excluded: chain I residue 1921 GLU Chi-restraints excluded: chain I residue 1999 LEU Chi-restraints excluded: chain I residue 2062 VAL Chi-restraints excluded: chain I residue 2141 ASN Chi-restraints excluded: chain I residue 2189 MET Chi-restraints excluded: chain J residue 177 LYS Chi-restraints excluded: chain J residue 194 GLU Chi-restraints excluded: chain J residue 213 THR Chi-restraints excluded: chain J residue 261 CYS Chi-restraints excluded: chain J residue 267 THR Chi-restraints excluded: chain J residue 274 PHE Chi-restraints excluded: chain J residue 300 LEU Chi-restraints excluded: chain K residue 6 LEU Chi-restraints excluded: chain K residue 70 VAL Chi-restraints excluded: chain K residue 83 MET Chi-restraints excluded: chain K residue 125 VAL Chi-restraints excluded: chain K residue 161 CYS Chi-restraints excluded: chain K residue 279 GLU Chi-restraints excluded: chain K residue 289 ILE Chi-restraints excluded: chain K residue 356 ILE Chi-restraints excluded: chain K residue 378 THR Chi-restraints excluded: chain L residue 93 LEU Chi-restraints excluded: chain L residue 129 VAL Chi-restraints excluded: chain L residue 151 LYS Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain M residue 135 VAL Chi-restraints excluded: chain M residue 157 VAL Chi-restraints excluded: chain M residue 170 LEU Chi-restraints excluded: chain M residue 262 GLN Chi-restraints excluded: chain M residue 271 ILE Chi-restraints excluded: chain M residue 295 VAL Chi-restraints excluded: chain M residue 317 ARG Chi-restraints excluded: chain M residue 406 SER Chi-restraints excluded: chain M residue 410 LEU Chi-restraints excluded: chain M residue 433 ILE Chi-restraints excluded: chain N residue 163 LEU Chi-restraints excluded: chain N residue 192 VAL Chi-restraints excluded: chain N residue 202 ILE Chi-restraints excluded: chain N residue 205 LEU Chi-restraints excluded: chain N residue 209 PHE Chi-restraints excluded: chain N residue 238 VAL Chi-restraints excluded: chain N residue 242 VAL Chi-restraints excluded: chain N residue 272 VAL Chi-restraints excluded: chain N residue 276 ILE Chi-restraints excluded: chain N residue 301 VAL Chi-restraints excluded: chain N residue 326 MET Chi-restraints excluded: chain N residue 354 LEU Chi-restraints excluded: chain N residue 381 GLU Chi-restraints excluded: chain N residue 413 CYS Chi-restraints excluded: chain N residue 435 ASP Chi-restraints excluded: chain O residue 40 VAL Chi-restraints excluded: chain O residue 100 GLU Chi-restraints excluded: chain O residue 124 ILE Chi-restraints excluded: chain O residue 274 LYS Chi-restraints excluded: chain O residue 342 GLU Chi-restraints excluded: chain O residue 353 ASP Chi-restraints excluded: chain P residue 68 ILE Chi-restraints excluded: chain P residue 239 VAL Chi-restraints excluded: chain P residue 261 PHE Chi-restraints excluded: chain P residue 355 LEU Chi-restraints excluded: chain P residue 429 VAL Chi-restraints excluded: chain Q residue 40 VAL Chi-restraints excluded: chain Q residue 91 VAL Chi-restraints excluded: chain Q residue 124 ILE Chi-restraints excluded: chain Q residue 168 LYS Chi-restraints excluded: chain Q residue 235 ILE Chi-restraints excluded: chain Q residue 345 THR Chi-restraints excluded: chain Q residue 407 VAL Chi-restraints excluded: chain Q residue 416 LEU Chi-restraints excluded: chain R residue 21 ARG Chi-restraints excluded: chain R residue 62 MET Chi-restraints excluded: chain R residue 171 ILE Chi-restraints excluded: chain R residue 205 LEU Chi-restraints excluded: chain R residue 250 ILE Chi-restraints excluded: chain R residue 429 VAL Chi-restraints excluded: chain R residue 444 LYS Chi-restraints excluded: chain S residue 66 THR Chi-restraints excluded: chain S residue 355 MET Chi-restraints excluded: chain T residue 77 VAL Chi-restraints excluded: chain T residue 79 ARG Chi-restraints excluded: chain T residue 110 HIS Chi-restraints excluded: chain U residue 78 ASN Chi-restraints excluded: chain U residue 159 VAL Chi-restraints excluded: chain U residue 221 LEU Chi-restraints excluded: chain U residue 330 ILE Chi-restraints excluded: chain U residue 349 LEU Chi-restraints excluded: chain U residue 351 THR Chi-restraints excluded: chain U residue 359 LYS Chi-restraints excluded: chain V residue 58 TYR Chi-restraints excluded: chain V residue 208 VAL Chi-restraints excluded: chain V residue 247 LEU Chi-restraints excluded: chain V residue 248 LEU Chi-restraints excluded: chain V residue 255 GLU Chi-restraints excluded: chain W residue 81 VAL Chi-restraints excluded: chain W residue 157 THR Chi-restraints excluded: chain W residue 183 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 652 random chunks: chunk 388 optimal weight: 6.9990 chunk 250 optimal weight: 0.6980 chunk 375 optimal weight: 0.9990 chunk 189 optimal weight: 6.9990 chunk 123 optimal weight: 2.9990 chunk 121 optimal weight: 0.9980 chunk 399 optimal weight: 0.8980 chunk 428 optimal weight: 0.8980 chunk 310 optimal weight: 4.9990 chunk 58 optimal weight: 0.8980 chunk 493 optimal weight: 3.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 GLN ** E 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 830 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1945 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1991 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 332 ASN ** O 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 408 GLN P 121 GLN ** S 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 111 ASN ** T 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 407 GLN ** U 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5730 moved from start: 0.5227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 58153 Z= 0.184 Angle : 0.598 16.743 79831 Z= 0.306 Chirality : 0.041 0.261 8993 Planarity : 0.004 0.091 9191 Dihedral : 20.802 174.478 10379 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.55 % Favored : 94.37 % Rotamer: Outliers : 2.74 % Allowed : 16.42 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.37 % 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: 0.00 (0.11), residues: 6271 helix: 0.99 (0.10), residues: 2904 sheet: -0.57 (0.18), residues: 860 loop : -0.89 (0.13), residues: 2507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP S 79 HIS 0.009 0.001 HIS Q 316 PHE 0.019 0.001 PHE D 61 TYR 0.036 0.001 TYR F 80 ARG 0.015 0.000 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12542 Ramachandran restraints generated. 6271 Oldfield, 0 Emsley, 6271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12542 Ramachandran restraints generated. 6271 Oldfield, 0 Emsley, 6271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 550 residues out of total 5462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 401 time to evaluate : 4.659 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: E 118 LYS cc_start: 0.4688 (tmmm) cc_final: 0.4054 (mttm) REVERT: H 93 GLN cc_start: 0.7523 (mm-40) cc_final: 0.7212 (mm-40) REVERT: I 227 LYS cc_start: 0.5790 (tttt) cc_final: 0.5548 (ttpt) REVERT: I 613 LEU cc_start: 0.7318 (OUTLIER) cc_final: 0.6651 (tt) REVERT: I 679 MET cc_start: 0.8664 (OUTLIER) cc_final: 0.7962 (ttm) REVERT: I 784 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7537 (mp0) REVERT: I 803 PHE cc_start: 0.6537 (t80) cc_final: 0.6278 (t80) REVERT: I 861 LEU cc_start: 0.7737 (OUTLIER) cc_final: 0.7119 (mp) REVERT: J 274 PHE cc_start: 0.5266 (OUTLIER) cc_final: 0.4539 (t80) REVERT: K 1 MET cc_start: 0.5632 (tmm) cc_final: 0.5191 (tmm) REVERT: K 196 MET cc_start: 0.7216 (ppp) cc_final: 0.5853 (ptm) REVERT: K 273 GLU cc_start: 0.7372 (pm20) cc_final: 0.7053 (pm20) REVERT: K 279 GLU cc_start: 0.7752 (OUTLIER) cc_final: 0.7422 (tp30) REVERT: L 35 LEU cc_start: 0.8124 (mt) cc_final: 0.7830 (mt) REVERT: M 293 GLU cc_start: 0.8021 (tp30) cc_final: 0.7644 (tm-30) REVERT: M 323 ILE cc_start: 0.8739 (pt) cc_final: 0.8513 (mt) REVERT: M 410 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8342 (tt) REVERT: N 88 MET cc_start: 0.7596 (mmm) cc_final: 0.7231 (mmt) REVERT: N 168 MET cc_start: 0.8764 (ptp) cc_final: 0.8398 (ptp) REVERT: N 381 GLU cc_start: 0.5683 (OUTLIER) cc_final: 0.5464 (mp0) REVERT: N 442 TYR cc_start: 0.8029 (m-80) cc_final: 0.7553 (m-10) REVERT: O 100 GLU cc_start: 0.8223 (OUTLIER) cc_final: 0.6899 (mp0) REVERT: P 183 THR cc_start: 0.9297 (m) cc_final: 0.9052 (p) REVERT: P 269 LYS cc_start: 0.8519 (tttm) cc_final: 0.8053 (tptp) REVERT: P 414 ARG cc_start: 0.7771 (ttm-80) cc_final: 0.7306 (ttp-170) REVERT: P 441 GLN cc_start: 0.8823 (tt0) cc_final: 0.8379 (tp40) REVERT: Q 61 MET cc_start: 0.8220 (mmm) cc_final: 0.7861 (mmm) REVERT: Q 168 LYS cc_start: 0.6770 (OUTLIER) cc_final: 0.6275 (tttt) REVERT: Q 249 ARG cc_start: 0.5958 (mtm180) cc_final: 0.5667 (mtm180) REVERT: Q 270 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.7445 (mm-30) REVERT: R 139 GLU cc_start: 0.7873 (pt0) cc_final: 0.7185 (pp20) REVERT: R 253 ARG cc_start: 0.8020 (ttm170) cc_final: 0.7750 (mtm-85) REVERT: R 269 LYS cc_start: 0.8058 (mptt) cc_final: 0.7294 (tmtt) REVERT: R 273 ARG cc_start: 0.6951 (mpt180) cc_final: 0.6624 (mmt-90) REVERT: R 401 TYR cc_start: 0.8091 (t80) cc_final: 0.7617 (t80) REVERT: R 444 LYS cc_start: 0.7545 (OUTLIER) cc_final: 0.7343 (ptpp) REVERT: S 1 MET cc_start: 0.0495 (mtt) cc_final: -0.1005 (tpt) REVERT: S 153 MET cc_start: 0.3907 (tpp) cc_final: 0.2682 (ttt) REVERT: S 227 MET cc_start: 0.1634 (mmm) cc_final: 0.1075 (mmp) REVERT: S 313 MET cc_start: 0.5147 (tpt) cc_final: 0.4625 (tpp) REVERT: S 325 MET cc_start: 0.4774 (tpp) cc_final: 0.4448 (tpt) REVERT: T 79 ARG cc_start: -0.0041 (OUTLIER) cc_final: -0.1484 (ttm-80) REVERT: T 320 ASN cc_start: 0.3419 (m110) cc_final: 0.3056 (m110) REVERT: U 191 LYS cc_start: 0.2162 (OUTLIER) cc_final: 0.1509 (mmpt) REVERT: U 221 LEU cc_start: 0.0446 (OUTLIER) cc_final: 0.0157 (mt) REVERT: U 227 MET cc_start: 0.3699 (tpp) cc_final: 0.2690 (mpp) REVERT: U 269 MET cc_start: -0.1174 (ppp) cc_final: -0.1870 (ppp) REVERT: U 355 MET cc_start: 0.0285 (mtm) cc_final: -0.0491 (mtm) REVERT: U 359 LYS cc_start: 0.2507 (OUTLIER) cc_final: 0.1785 (tttm) REVERT: V 154 LYS cc_start: 0.3498 (tttm) cc_final: 0.3242 (tmtt) REVERT: V 235 ASN cc_start: 0.0700 (OUTLIER) cc_final: -0.0044 (t0) REVERT: V 248 LEU cc_start: 0.2905 (OUTLIER) cc_final: 0.2347 (tp) REVERT: V 255 GLU cc_start: 0.4177 (OUTLIER) cc_final: 0.2896 (mt-10) REVERT: W 128 MET cc_start: 0.2971 (mmm) cc_final: 0.2153 (mtt) REVERT: W 151 MET cc_start: 0.0596 (tpt) cc_final: 0.0043 (mmm) outliers start: 149 outliers final: 104 residues processed: 520 average time/residue: 0.5443 time to fit residues: 486.2912 Evaluate side-chains 511 residues out of total 5462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 388 time to evaluate : 4.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain F residue 91 ILE Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain H residue 49 LEU Chi-restraints excluded: chain I residue 177 ARG Chi-restraints excluded: chain I residue 211 LYS Chi-restraints excluded: chain I residue 610 ILE Chi-restraints excluded: chain I residue 613 LEU Chi-restraints excluded: chain I residue 679 MET Chi-restraints excluded: chain I residue 784 GLU Chi-restraints excluded: chain I residue 859 CYS Chi-restraints excluded: chain I residue 861 LEU Chi-restraints excluded: chain I residue 918 THR Chi-restraints excluded: chain I residue 921 ILE Chi-restraints excluded: chain I residue 928 LEU Chi-restraints excluded: chain I residue 964 LEU Chi-restraints excluded: chain I residue 1921 GLU Chi-restraints excluded: chain I residue 1959 VAL Chi-restraints excluded: chain I residue 1999 LEU Chi-restraints excluded: chain I residue 2062 VAL Chi-restraints excluded: chain I residue 2074 VAL Chi-restraints excluded: chain J residue 177 LYS Chi-restraints excluded: chain J residue 194 GLU Chi-restraints excluded: chain J residue 213 THR Chi-restraints excluded: chain J residue 274 PHE Chi-restraints excluded: chain K residue 6 LEU Chi-restraints excluded: chain K residue 70 VAL Chi-restraints excluded: chain K residue 83 MET Chi-restraints excluded: chain K residue 114 PHE Chi-restraints excluded: chain K residue 125 VAL Chi-restraints excluded: chain K residue 161 CYS Chi-restraints excluded: chain K residue 279 GLU Chi-restraints excluded: chain K residue 289 ILE Chi-restraints excluded: chain K residue 292 MET Chi-restraints excluded: chain K residue 356 ILE Chi-restraints excluded: chain L residue 92 ASN Chi-restraints excluded: chain L residue 93 LEU Chi-restraints excluded: chain L residue 129 VAL Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain M residue 157 VAL Chi-restraints excluded: chain M residue 170 LEU Chi-restraints excluded: chain M residue 262 GLN Chi-restraints excluded: chain M residue 271 ILE Chi-restraints excluded: chain M residue 295 VAL Chi-restraints excluded: chain M residue 317 ARG Chi-restraints excluded: chain M residue 406 SER Chi-restraints excluded: chain M residue 410 LEU Chi-restraints excluded: chain M residue 433 ILE Chi-restraints excluded: chain N residue 163 LEU Chi-restraints excluded: chain N residue 192 VAL Chi-restraints excluded: chain N residue 205 LEU Chi-restraints excluded: chain N residue 209 PHE Chi-restraints excluded: chain N residue 210 THR Chi-restraints excluded: chain N residue 238 VAL Chi-restraints excluded: chain N residue 242 VAL Chi-restraints excluded: chain N residue 258 LEU Chi-restraints excluded: chain N residue 301 VAL Chi-restraints excluded: chain N residue 326 MET Chi-restraints excluded: chain N residue 354 LEU Chi-restraints excluded: chain N residue 381 GLU Chi-restraints excluded: chain N residue 413 CYS Chi-restraints excluded: chain N residue 435 ASP Chi-restraints excluded: chain O residue 40 VAL Chi-restraints excluded: chain O residue 100 GLU Chi-restraints excluded: chain O residue 124 ILE Chi-restraints excluded: chain O residue 274 LYS Chi-restraints excluded: chain O residue 342 GLU Chi-restraints excluded: chain O residue 353 ASP Chi-restraints excluded: chain P residue 68 ILE Chi-restraints excluded: chain P residue 239 VAL Chi-restraints excluded: chain P residue 261 PHE Chi-restraints excluded: chain P residue 305 ASP Chi-restraints excluded: chain P residue 355 LEU Chi-restraints excluded: chain P residue 429 VAL Chi-restraints excluded: chain Q residue 40 VAL Chi-restraints excluded: chain Q residue 91 VAL Chi-restraints excluded: chain Q residue 124 ILE Chi-restraints excluded: chain Q residue 168 LYS Chi-restraints excluded: chain Q residue 192 TYR Chi-restraints excluded: chain Q residue 197 SER Chi-restraints excluded: chain Q residue 235 ILE Chi-restraints excluded: chain Q residue 270 GLU Chi-restraints excluded: chain Q residue 407 VAL Chi-restraints excluded: chain Q residue 416 LEU Chi-restraints excluded: chain R residue 21 ARG Chi-restraints excluded: chain R residue 62 MET Chi-restraints excluded: chain R residue 171 ILE Chi-restraints excluded: chain R residue 205 LEU Chi-restraints excluded: chain R residue 250 ILE Chi-restraints excluded: chain R residue 429 VAL Chi-restraints excluded: chain R residue 444 LYS Chi-restraints excluded: chain S residue 66 THR Chi-restraints excluded: chain S residue 355 MET Chi-restraints excluded: chain T residue 77 VAL Chi-restraints excluded: chain T residue 79 ARG Chi-restraints excluded: chain T residue 110 HIS Chi-restraints excluded: chain U residue 78 ASN Chi-restraints excluded: chain U residue 159 VAL Chi-restraints excluded: chain U residue 191 LYS Chi-restraints excluded: chain U residue 221 LEU Chi-restraints excluded: chain U residue 330 ILE Chi-restraints excluded: chain U residue 349 LEU Chi-restraints excluded: chain U residue 351 THR Chi-restraints excluded: chain U residue 359 LYS Chi-restraints excluded: chain V residue 58 TYR Chi-restraints excluded: chain V residue 208 VAL Chi-restraints excluded: chain V residue 235 ASN Chi-restraints excluded: chain V residue 247 LEU Chi-restraints excluded: chain V residue 248 LEU Chi-restraints excluded: chain V residue 255 GLU Chi-restraints excluded: chain W residue 81 VAL Chi-restraints excluded: chain W residue 157 THR Chi-restraints excluded: chain W residue 183 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 652 random chunks: chunk 571 optimal weight: 0.6980 chunk 602 optimal weight: 10.0000 chunk 549 optimal weight: 30.0000 chunk 585 optimal weight: 8.9990 chunk 601 optimal weight: 8.9990 chunk 352 optimal weight: 0.9990 chunk 255 optimal weight: 2.9990 chunk 459 optimal weight: 0.0060 chunk 179 optimal weight: 10.0000 chunk 529 optimal weight: 3.9990 chunk 553 optimal weight: 20.0000 overall best weight: 1.7402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 GLN ** E 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 HIS I 902 ASN ** I 967 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1945 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 44 ASN ** M 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 332 ASN P 344 HIS ** U 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5797 moved from start: 0.5598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.131 58153 Z= 0.264 Angle : 0.639 10.951 79831 Z= 0.328 Chirality : 0.043 0.218 8993 Planarity : 0.005 0.091 9191 Dihedral : 20.863 173.652 10378 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.92 % Favored : 94.00 % Rotamer: Outliers : 2.50 % Allowed : 16.66 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.37 % Twisted General : 0.08 % 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: -0.09 (0.11), residues: 6271 helix: 0.93 (0.10), residues: 2897 sheet: -0.63 (0.18), residues: 877 loop : -0.96 (0.13), residues: 2497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP S 79 HIS 0.011 0.001 HIS Q 316 PHE 0.026 0.002 PHE N 261 TYR 0.032 0.002 TYR F 80 ARG 0.007 0.001 ARG I 931 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12542 Ramachandran restraints generated. 6271 Oldfield, 0 Emsley, 6271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12542 Ramachandran restraints generated. 6271 Oldfield, 0 Emsley, 6271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 535 residues out of total 5462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 399 time to evaluate : 4.570 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: E 118 LYS cc_start: 0.4886 (tmmm) cc_final: 0.4283 (mttm) REVERT: F 39 TYR cc_start: 0.8216 (t80) cc_final: 0.8010 (t80) REVERT: I 227 LYS cc_start: 0.5742 (tttt) cc_final: 0.5484 (ttpt) REVERT: I 613 LEU cc_start: 0.7238 (OUTLIER) cc_final: 0.6557 (tt) REVERT: I 679 MET cc_start: 0.8781 (OUTLIER) cc_final: 0.8151 (ttm) REVERT: I 784 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7635 (mp0) REVERT: I 861 LEU cc_start: 0.7980 (OUTLIER) cc_final: 0.7283 (mp) REVERT: J 274 PHE cc_start: 0.5544 (OUTLIER) cc_final: 0.4828 (t80) REVERT: K 1 MET cc_start: 0.5704 (tmm) cc_final: 0.5333 (tmm) REVERT: K 196 MET cc_start: 0.7361 (ppp) cc_final: 0.6027 (ptm) REVERT: K 273 GLU cc_start: 0.7302 (pm20) cc_final: 0.6964 (pm20) REVERT: K 279 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.7511 (tp30) REVERT: L 35 LEU cc_start: 0.8008 (mt) cc_final: 0.7574 (mt) REVERT: M 293 GLU cc_start: 0.8017 (tp30) cc_final: 0.7675 (tm-30) REVERT: M 323 ILE cc_start: 0.8783 (pt) cc_final: 0.8568 (mt) REVERT: M 410 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8564 (tt) REVERT: N 88 MET cc_start: 0.7557 (mmm) cc_final: 0.7198 (mmt) REVERT: N 168 MET cc_start: 0.8808 (ptp) cc_final: 0.8461 (ptp) REVERT: N 178 MET cc_start: 0.8816 (tpp) cc_final: 0.8523 (tpp) REVERT: N 179 ILE cc_start: 0.8569 (tt) cc_final: 0.8342 (tp) REVERT: N 320 MET cc_start: 0.8765 (mmt) cc_final: 0.8174 (mmt) REVERT: N 381 GLU cc_start: 0.5846 (OUTLIER) cc_final: 0.5615 (mp0) REVERT: N 382 MET cc_start: 0.7233 (OUTLIER) cc_final: 0.6769 (ttp) REVERT: N 411 LEU cc_start: 0.8301 (mt) cc_final: 0.8008 (mt) REVERT: O 100 GLU cc_start: 0.8333 (OUTLIER) cc_final: 0.6922 (mp0) REVERT: P 183 THR cc_start: 0.9380 (m) cc_final: 0.9132 (p) REVERT: P 269 LYS cc_start: 0.8504 (tttm) cc_final: 0.7973 (tptp) REVERT: P 414 ARG cc_start: 0.7798 (ttm-80) cc_final: 0.7337 (ttp-170) REVERT: P 441 GLN cc_start: 0.8878 (tt0) cc_final: 0.8401 (tp40) REVERT: Q 168 LYS cc_start: 0.7290 (OUTLIER) cc_final: 0.6968 (tttt) REVERT: Q 249 ARG cc_start: 0.6219 (mtm180) cc_final: 0.5883 (mtm180) REVERT: Q 270 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.7949 (mm-30) REVERT: R 269 LYS cc_start: 0.8214 (mptt) cc_final: 0.7580 (tmtt) REVERT: R 273 ARG cc_start: 0.7048 (mpt180) cc_final: 0.6788 (mpt180) REVERT: R 444 LYS cc_start: 0.7576 (OUTLIER) cc_final: 0.7230 (ptpp) REVERT: S 1 MET cc_start: 0.0515 (mtt) cc_final: -0.0698 (tpt) REVERT: S 153 MET cc_start: 0.4063 (tpp) cc_final: 0.2719 (ttt) REVERT: S 227 MET cc_start: 0.1667 (mmm) cc_final: 0.1318 (mmp) REVERT: S 325 MET cc_start: 0.5439 (tpp) cc_final: 0.5203 (tpt) REVERT: T 79 ARG cc_start: -0.0075 (OUTLIER) cc_final: -0.1636 (ttm-80) REVERT: T 82 MET cc_start: -0.1041 (ttt) cc_final: -0.1774 (ttt) REVERT: U 132 MET cc_start: 0.0318 (tpt) cc_final: 0.0084 (tpt) REVERT: U 191 LYS cc_start: 0.1967 (pttt) cc_final: 0.1492 (mmpt) REVERT: U 269 MET cc_start: -0.1178 (ppp) cc_final: -0.1860 (ppp) REVERT: U 355 MET cc_start: 0.0087 (mtm) cc_final: -0.0786 (mtm) REVERT: U 359 LYS cc_start: 0.2440 (OUTLIER) cc_final: 0.1715 (tttm) REVERT: V 154 LYS cc_start: 0.3461 (tttm) cc_final: 0.3193 (tmtt) REVERT: V 248 LEU cc_start: 0.2847 (OUTLIER) cc_final: 0.2226 (tp) REVERT: V 255 GLU cc_start: 0.4223 (OUTLIER) cc_final: 0.2960 (mt-10) REVERT: W 151 MET cc_start: 0.0361 (tpt) cc_final: -0.0273 (mmm) outliers start: 136 outliers final: 102 residues processed: 507 average time/residue: 0.5465 time to fit residues: 474.0896 Evaluate side-chains 499 residues out of total 5462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 380 time to evaluate : 4.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain F residue 91 ILE Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain I residue 211 LYS Chi-restraints excluded: chain I residue 610 ILE Chi-restraints excluded: chain I residue 613 LEU Chi-restraints excluded: chain I residue 679 MET Chi-restraints excluded: chain I residue 742 TYR Chi-restraints excluded: chain I residue 784 GLU Chi-restraints excluded: chain I residue 859 CYS Chi-restraints excluded: chain I residue 861 LEU Chi-restraints excluded: chain I residue 918 THR Chi-restraints excluded: chain I residue 921 ILE Chi-restraints excluded: chain I residue 928 LEU Chi-restraints excluded: chain I residue 964 LEU Chi-restraints excluded: chain I residue 1921 GLU Chi-restraints excluded: chain I residue 1959 VAL Chi-restraints excluded: chain I residue 1979 VAL Chi-restraints excluded: chain I residue 1999 LEU Chi-restraints excluded: chain I residue 2062 VAL Chi-restraints excluded: chain I residue 2074 VAL Chi-restraints excluded: chain J residue 177 LYS Chi-restraints excluded: chain J residue 213 THR Chi-restraints excluded: chain J residue 266 ILE Chi-restraints excluded: chain J residue 274 PHE Chi-restraints excluded: chain J residue 275 GLU Chi-restraints excluded: chain K residue 6 LEU Chi-restraints excluded: chain K residue 83 MET Chi-restraints excluded: chain K residue 125 VAL Chi-restraints excluded: chain K residue 161 CYS Chi-restraints excluded: chain K residue 279 GLU Chi-restraints excluded: chain K residue 289 ILE Chi-restraints excluded: chain K residue 292 MET Chi-restraints excluded: chain K residue 325 LEU Chi-restraints excluded: chain K residue 356 ILE Chi-restraints excluded: chain K residue 378 THR Chi-restraints excluded: chain L residue 92 ASN Chi-restraints excluded: chain L residue 93 LEU Chi-restraints excluded: chain L residue 101 TYR Chi-restraints excluded: chain L residue 129 VAL Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain M residue 135 VAL Chi-restraints excluded: chain M residue 157 VAL Chi-restraints excluded: chain M residue 170 LEU Chi-restraints excluded: chain M residue 262 GLN Chi-restraints excluded: chain M residue 271 ILE Chi-restraints excluded: chain M residue 295 VAL Chi-restraints excluded: chain M residue 317 ARG Chi-restraints excluded: chain M residue 406 SER Chi-restraints excluded: chain M residue 410 LEU Chi-restraints excluded: chain M residue 419 ILE Chi-restraints excluded: chain N residue 163 LEU Chi-restraints excluded: chain N residue 192 VAL Chi-restraints excluded: chain N residue 205 LEU Chi-restraints excluded: chain N residue 209 PHE Chi-restraints excluded: chain N residue 210 THR Chi-restraints excluded: chain N residue 238 VAL Chi-restraints excluded: chain N residue 242 VAL Chi-restraints excluded: chain N residue 258 LEU Chi-restraints excluded: chain N residue 272 VAL Chi-restraints excluded: chain N residue 301 VAL Chi-restraints excluded: chain N residue 326 MET Chi-restraints excluded: chain N residue 354 LEU Chi-restraints excluded: chain N residue 381 GLU Chi-restraints excluded: chain N residue 382 MET Chi-restraints excluded: chain N residue 413 CYS Chi-restraints excluded: chain O residue 40 VAL Chi-restraints excluded: chain O residue 100 GLU Chi-restraints excluded: chain O residue 124 ILE Chi-restraints excluded: chain O residue 274 LYS Chi-restraints excluded: chain O residue 342 GLU Chi-restraints excluded: chain O residue 353 ASP Chi-restraints excluded: chain P residue 68 ILE Chi-restraints excluded: chain P residue 187 VAL Chi-restraints excluded: chain P residue 239 VAL Chi-restraints excluded: chain P residue 305 ASP Chi-restraints excluded: chain P residue 429 VAL Chi-restraints excluded: chain Q residue 40 VAL Chi-restraints excluded: chain Q residue 91 VAL Chi-restraints excluded: chain Q residue 124 ILE Chi-restraints excluded: chain Q residue 168 LYS Chi-restraints excluded: chain Q residue 197 SER Chi-restraints excluded: chain Q residue 235 ILE Chi-restraints excluded: chain Q residue 270 GLU Chi-restraints excluded: chain Q residue 416 LEU Chi-restraints excluded: chain R residue 21 ARG Chi-restraints excluded: chain R residue 62 MET Chi-restraints excluded: chain R residue 171 ILE Chi-restraints excluded: chain R residue 205 LEU Chi-restraints excluded: chain R residue 250 ILE Chi-restraints excluded: chain R residue 429 VAL Chi-restraints excluded: chain R residue 444 LYS Chi-restraints excluded: chain S residue 66 THR Chi-restraints excluded: chain S residue 355 MET Chi-restraints excluded: chain T residue 77 VAL Chi-restraints excluded: chain T residue 79 ARG Chi-restraints excluded: chain T residue 110 HIS Chi-restraints excluded: chain U residue 78 ASN Chi-restraints excluded: chain U residue 159 VAL Chi-restraints excluded: chain U residue 330 ILE Chi-restraints excluded: chain U residue 349 LEU Chi-restraints excluded: chain U residue 351 THR Chi-restraints excluded: chain U residue 359 LYS Chi-restraints excluded: chain V residue 208 VAL Chi-restraints excluded: chain V residue 248 LEU Chi-restraints excluded: chain V residue 255 GLU Chi-restraints excluded: chain W residue 81 VAL Chi-restraints excluded: chain W residue 157 THR Chi-restraints excluded: chain W residue 183 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 652 random chunks: chunk 583 optimal weight: 10.0000 chunk 384 optimal weight: 0.5980 chunk 619 optimal weight: 20.0000 chunk 377 optimal weight: 0.9980 chunk 293 optimal weight: 0.4980 chunk 430 optimal weight: 2.9990 chunk 649 optimal weight: 10.0000 chunk 597 optimal weight: 7.9990 chunk 517 optimal weight: 0.7980 chunk 53 optimal weight: 0.9980 chunk 399 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 830 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1945 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1991 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 332 ASN O 408 GLN R 404 GLN ** T 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 235 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5767 moved from start: 0.5706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 58153 Z= 0.182 Angle : 0.607 11.480 79831 Z= 0.312 Chirality : 0.041 0.191 8993 Planarity : 0.004 0.091 9191 Dihedral : 20.772 177.037 10372 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.61 % Favored : 94.31 % Rotamer: Outliers : 2.19 % Allowed : 17.27 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.37 % 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: 0.00 (0.11), residues: 6271 helix: 0.98 (0.10), residues: 2897 sheet: -0.53 (0.18), residues: 849 loop : -0.89 (0.13), residues: 2525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP S 79 HIS 0.008 0.001 HIS Q 316 PHE 0.026 0.001 PHE P 261 TYR 0.028 0.001 TYR I 821 ARG 0.018 0.000 ARG R 207 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12542 Ramachandran restraints generated. 6271 Oldfield, 0 Emsley, 6271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12542 Ramachandran restraints generated. 6271 Oldfield, 0 Emsley, 6271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 509 residues out of total 5462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 390 time to evaluate : 4.936 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: B 77 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.7890 (mm) REVERT: E 118 LYS cc_start: 0.4888 (tmmm) cc_final: 0.4318 (mttm) REVERT: H 93 GLN cc_start: 0.7422 (mm-40) cc_final: 0.7218 (tp40) REVERT: I 206 TRP cc_start: 0.4151 (m100) cc_final: 0.3244 (m100) REVERT: I 227 LYS cc_start: 0.5710 (tttt) cc_final: 0.5486 (ttpt) REVERT: I 613 LEU cc_start: 0.7189 (OUTLIER) cc_final: 0.6507 (tt) REVERT: I 679 MET cc_start: 0.8732 (OUTLIER) cc_final: 0.8042 (ttm) REVERT: I 784 GLU cc_start: 0.7956 (OUTLIER) cc_final: 0.7637 (mp0) REVERT: I 861 LEU cc_start: 0.7831 (OUTLIER) cc_final: 0.7152 (mp) REVERT: I 2141 ASN cc_start: 0.6932 (OUTLIER) cc_final: 0.6567 (t0) REVERT: J 274 PHE cc_start: 0.5481 (OUTLIER) cc_final: 0.4808 (t80) REVERT: K 1 MET cc_start: 0.5668 (tmm) cc_final: 0.5293 (tmm) REVERT: K 196 MET cc_start: 0.7371 (ppp) cc_final: 0.5986 (ptm) REVERT: K 273 GLU cc_start: 0.7041 (pm20) cc_final: 0.6772 (pm20) REVERT: K 279 GLU cc_start: 0.7838 (OUTLIER) cc_final: 0.7458 (tp30) REVERT: L 35 LEU cc_start: 0.7961 (mt) cc_final: 0.7535 (mt) REVERT: M 293 GLU cc_start: 0.7949 (tp30) cc_final: 0.7679 (tm-30) REVERT: M 323 ILE cc_start: 0.8739 (pt) cc_final: 0.8529 (mt) REVERT: N 88 MET cc_start: 0.7576 (mmm) cc_final: 0.7199 (mmt) REVERT: N 168 MET cc_start: 0.8775 (ptp) cc_final: 0.8431 (ptp) REVERT: N 178 MET cc_start: 0.8822 (tpp) cc_final: 0.8549 (tpp) REVERT: N 320 MET cc_start: 0.8851 (mmt) cc_final: 0.8235 (mmt) REVERT: N 381 GLU cc_start: 0.5759 (OUTLIER) cc_final: 0.5500 (mp0) REVERT: N 382 MET cc_start: 0.7199 (OUTLIER) cc_final: 0.6734 (ttp) REVERT: N 411 LEU cc_start: 0.8263 (mt) cc_final: 0.8012 (mt) REVERT: N 442 TYR cc_start: 0.8127 (m-80) cc_final: 0.7830 (m-80) REVERT: O 100 GLU cc_start: 0.8302 (OUTLIER) cc_final: 0.6924 (mp0) REVERT: P 183 THR cc_start: 0.9382 (m) cc_final: 0.9126 (p) REVERT: P 269 LYS cc_start: 0.8314 (tttm) cc_final: 0.8034 (ttpt) REVERT: P 414 ARG cc_start: 0.7774 (ttm-80) cc_final: 0.7307 (ttp-170) REVERT: P 441 GLN cc_start: 0.8865 (tt0) cc_final: 0.8407 (tp40) REVERT: Q 168 LYS cc_start: 0.7184 (OUTLIER) cc_final: 0.6541 (mppt) REVERT: Q 249 ARG cc_start: 0.6035 (mtm180) cc_final: 0.5736 (mtm180) REVERT: Q 270 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7716 (mm-30) REVERT: R 113 MET cc_start: 0.7254 (mtm) cc_final: 0.6860 (mtm) REVERT: R 269 LYS cc_start: 0.8156 (mptt) cc_final: 0.7378 (tmtt) REVERT: R 273 ARG cc_start: 0.7016 (mpt180) cc_final: 0.6681 (mmt-90) REVERT: R 401 TYR cc_start: 0.8130 (t80) cc_final: 0.7624 (t80) REVERT: R 444 LYS cc_start: 0.7587 (OUTLIER) cc_final: 0.7226 (ptpp) REVERT: S 1 MET cc_start: 0.0492 (mtt) cc_final: -0.0689 (tpt) REVERT: S 153 MET cc_start: 0.3938 (tpp) cc_final: 0.2619 (ttt) REVERT: S 227 MET cc_start: 0.1796 (mmm) cc_final: 0.1515 (mmp) REVERT: T 79 ARG cc_start: -0.0137 (OUTLIER) cc_final: -0.1621 (ttm-80) REVERT: T 82 MET cc_start: -0.1002 (ttt) cc_final: -0.1689 (ttt) REVERT: U 132 MET cc_start: -0.0031 (tpt) cc_final: -0.0232 (tpt) REVERT: U 191 LYS cc_start: 0.2031 (pttt) cc_final: 0.1594 (mmpt) REVERT: U 269 MET cc_start: -0.1247 (ppp) cc_final: -0.1917 (ppp) REVERT: U 355 MET cc_start: 0.0097 (mtm) cc_final: -0.0656 (mtt) REVERT: U 359 LYS cc_start: 0.2369 (OUTLIER) cc_final: 0.1701 (tttm) REVERT: V 154 LYS cc_start: 0.3452 (tttm) cc_final: 0.3183 (tmtt) REVERT: V 248 LEU cc_start: 0.2758 (OUTLIER) cc_final: 0.2166 (tp) REVERT: V 255 GLU cc_start: 0.4215 (OUTLIER) cc_final: 0.2950 (mt-10) REVERT: W 128 MET cc_start: 0.2875 (mmm) cc_final: 0.2133 (mtt) REVERT: W 151 MET cc_start: 0.0351 (tpt) cc_final: -0.0272 (mmm) outliers start: 119 outliers final: 92 residues processed: 490 average time/residue: 0.5453 time to fit residues: 457.9564 Evaluate side-chains 489 residues out of total 5462 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 379 time to evaluate : 4.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain C residue 46 VAL Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain D residue 49 LEU Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 91 ILE Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain I residue 211 LYS Chi-restraints excluded: chain I residue 610 ILE Chi-restraints excluded: chain I residue 613 LEU Chi-restraints excluded: chain I residue 679 MET Chi-restraints excluded: chain I residue 742 TYR Chi-restraints excluded: chain I residue 784 GLU Chi-restraints excluded: chain I residue 859 CYS Chi-restraints excluded: chain I residue 861 LEU Chi-restraints excluded: chain I residue 918 THR Chi-restraints excluded: chain I residue 921 ILE Chi-restraints excluded: chain I residue 928 LEU Chi-restraints excluded: chain I residue 1921 GLU Chi-restraints excluded: chain I residue 1959 VAL Chi-restraints excluded: chain I residue 1979 VAL Chi-restraints excluded: chain I residue 1999 LEU Chi-restraints excluded: chain I residue 2062 VAL Chi-restraints excluded: chain I residue 2074 VAL Chi-restraints excluded: chain I residue 2141 ASN Chi-restraints excluded: chain J residue 177 LYS Chi-restraints excluded: chain J residue 213 THR Chi-restraints excluded: chain J residue 274 PHE Chi-restraints excluded: chain J residue 300 LEU Chi-restraints excluded: chain K residue 6 LEU Chi-restraints excluded: chain K residue 83 MET Chi-restraints excluded: chain K residue 114 PHE Chi-restraints excluded: chain K residue 125 VAL Chi-restraints excluded: chain K residue 161 CYS Chi-restraints excluded: chain K residue 279 GLU Chi-restraints excluded: chain K residue 289 ILE Chi-restraints excluded: chain K residue 325 LEU Chi-restraints excluded: chain K residue 356 ILE Chi-restraints excluded: chain K residue 378 THR Chi-restraints excluded: chain L residue 93 LEU Chi-restraints excluded: chain L residue 129 VAL Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain M residue 135 VAL Chi-restraints excluded: chain M residue 157 VAL Chi-restraints excluded: chain M residue 170 LEU Chi-restraints excluded: chain M residue 262 GLN Chi-restraints excluded: chain M residue 271 ILE Chi-restraints excluded: chain M residue 295 VAL Chi-restraints excluded: chain M residue 317 ARG Chi-restraints excluded: chain M residue 406 SER Chi-restraints excluded: chain M residue 419 ILE Chi-restraints excluded: chain N residue 163 LEU Chi-restraints excluded: chain N residue 192 VAL Chi-restraints excluded: chain N residue 205 LEU Chi-restraints excluded: chain N residue 209 PHE Chi-restraints excluded: chain N residue 210 THR Chi-restraints excluded: chain N residue 238 VAL Chi-restraints excluded: chain N residue 242 VAL Chi-restraints excluded: chain N residue 258 LEU Chi-restraints excluded: chain N residue 301 VAL Chi-restraints excluded: chain N residue 326 MET Chi-restraints excluded: chain N residue 381 GLU Chi-restraints excluded: chain N residue 382 MET Chi-restraints excluded: chain N residue 413 CYS Chi-restraints excluded: chain O residue 40 VAL Chi-restraints excluded: chain O residue 100 GLU Chi-restraints excluded: chain O residue 274 LYS Chi-restraints excluded: chain O residue 342 GLU Chi-restraints excluded: chain O residue 353 ASP Chi-restraints excluded: chain P residue 68 ILE Chi-restraints excluded: chain P residue 187 VAL Chi-restraints excluded: chain P residue 239 VAL Chi-restraints excluded: chain P residue 429 VAL Chi-restraints excluded: chain Q residue 40 VAL Chi-restraints excluded: chain Q residue 91 VAL Chi-restraints excluded: chain Q residue 124 ILE Chi-restraints excluded: chain Q residue 168 LYS Chi-restraints excluded: chain Q residue 235 ILE Chi-restraints excluded: chain Q residue 270 GLU Chi-restraints excluded: chain Q residue 416 LEU Chi-restraints excluded: chain R residue 21 ARG Chi-restraints excluded: chain R residue 62 MET Chi-restraints excluded: chain R residue 171 ILE Chi-restraints excluded: chain R residue 250 ILE Chi-restraints excluded: chain R residue 429 VAL Chi-restraints excluded: chain R residue 444 LYS Chi-restraints excluded: chain S residue 66 THR Chi-restraints excluded: chain S residue 355 MET Chi-restraints excluded: chain T residue 77 VAL Chi-restraints excluded: chain T residue 79 ARG Chi-restraints excluded: chain T residue 110 HIS Chi-restraints excluded: chain U residue 78 ASN Chi-restraints excluded: chain U residue 159 VAL Chi-restraints excluded: chain U residue 330 ILE Chi-restraints excluded: chain U residue 349 LEU Chi-restraints excluded: chain U residue 351 THR Chi-restraints excluded: chain U residue 359 LYS Chi-restraints excluded: chain V residue 208 VAL Chi-restraints excluded: chain V residue 235 ASN Chi-restraints excluded: chain V residue 248 LEU Chi-restraints excluded: chain V residue 255 GLU Chi-restraints excluded: chain W residue 81 VAL Chi-restraints excluded: chain W residue 157 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 652 random chunks: chunk 317 optimal weight: 3.9990 chunk 410 optimal weight: 3.9990 chunk 550 optimal weight: 6.9990 chunk 158 optimal weight: 0.0020 chunk 476 optimal weight: 0.0980 chunk 76 optimal weight: 7.9990 chunk 143 optimal weight: 3.9990 chunk 518 optimal weight: 20.0000 chunk 216 optimal weight: 2.9990 chunk 531 optimal weight: 8.9990 chunk 65 optimal weight: 0.8980 overall best weight: 1.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 830 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1945 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1991 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.132307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.090211 restraints weight = 151252.883| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 3.26 r_work: 0.3228 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3228 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3228 r_free = 0.3228 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3228 r_free = 0.3228 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3228 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.5716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.214 58153 Z= 0.219 Angle : 0.664 59.200 79831 Z= 0.355 Chirality : 0.042 0.895 8993 Planarity : 0.004 0.092 9191 Dihedral : 20.767 176.968 10370 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.65 % Favored : 94.26 % Rotamer: Outliers : 2.22 % Allowed : 17.14 % Favored : 80.64 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.37 % 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: 0.00 (0.11), residues: 6271 helix: 0.98 (0.10), residues: 2896 sheet: -0.53 (0.18), residues: 849 loop : -0.88 (0.13), residues: 2526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP S 79 HIS 0.008 0.001 HIS Q 316 PHE 0.023 0.001 PHE P 261 TYR 0.028 0.001 TYR I 821 ARG 0.012 0.000 ARG R 207 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11443.25 seconds wall clock time: 201 minutes 59.97 seconds (12119.97 seconds total)