Starting phenix.real_space_refine on Thu Feb 22 02:47:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l7e_0843/02_2024/6l7e_0843_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l7e_0843/02_2024/6l7e_0843.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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l7e_0843/02_2024/6l7e_0843.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l7e_0843/02_2024/6l7e_0843.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l7e_0843/02_2024/6l7e_0843_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6l7e_0843/02_2024/6l7e_0843_neut.pdb" } 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= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 305 5.16 5 C 61665 2.51 5 N 16555 2.21 5 O 18875 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 1250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1430": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1616": "NH1" <-> "NH2" Residue "A PHE 1711": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1430": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1616": "NH1" <-> "NH2" Residue "B PHE 1711": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1430": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 1616": "NH1" <-> "NH2" Residue "C PHE 1711": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1430": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 1616": "NH1" <-> "NH2" Residue "D PHE 1711": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1430": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 1616": "NH1" <-> "NH2" Residue "E PHE 1711": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.27s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 97400 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 19480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2454, 19480 Classifications: {'peptide': 2454} Link IDs: {'PTRANS': 88, 'TRANS': 2365} Chain breaks: 2 Chain: "B" Number of atoms: 19480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2454, 19480 Classifications: {'peptide': 2454} Link IDs: {'PTRANS': 88, 'TRANS': 2365} Chain breaks: 2 Chain: "C" Number of atoms: 19480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2454, 19480 Classifications: {'peptide': 2454} Link IDs: {'PTRANS': 88, 'TRANS': 2365} Chain breaks: 2 Chain: "D" Number of atoms: 19480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2454, 19480 Classifications: {'peptide': 2454} Link IDs: {'PTRANS': 88, 'TRANS': 2365} Chain breaks: 2 Chain: "E" Number of atoms: 19480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2454, 19480 Classifications: {'peptide': 2454} Link IDs: {'PTRANS': 88, 'TRANS': 2365} Chain breaks: 2 Time building chain proxies: 39.56, per 1000 atoms: 0.41 Number of scatterers: 97400 At special positions: 0 Unit cell: (202.038, 189.996, 262.248, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 305 16.00 O 18875 8.00 N 16555 7.00 C 61665 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 28.16 Conformation dependent library (CDL) restraints added in 14.1 seconds 24480 Ramachandran restraints generated. 12240 Oldfield, 0 Emsley, 12240 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 23260 Finding SS restraints... Secondary structure from input PDB file: 435 helices and 105 sheets defined 47.2% alpha, 13.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 10.93 Creating SS restraints... Processing helix chain 'A' and resid 42 through 70 removed outlier: 3.646A pdb=" N HIS A 50 " --> pdb=" O HIS A 46 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG A 69 " --> pdb=" O ARG A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 77 removed outlier: 4.155A pdb=" N ALA A 77 " --> pdb=" O GLN A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 81 Processing helix chain 'A' and resid 87 through 96 removed outlier: 4.140A pdb=" N GLY A 91 " --> pdb=" O ALA A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 127 removed outlier: 3.522A pdb=" N GLU A 121 " --> pdb=" O ALA A 117 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG A 127 " --> pdb=" O TYR A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 142 Processing helix chain 'A' and resid 151 through 157 removed outlier: 3.573A pdb=" N MET A 155 " --> pdb=" O SER A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 177 Processing helix chain 'A' and resid 181 through 192 removed outlier: 3.846A pdb=" N THR A 191 " --> pdb=" O GLU A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 215 removed outlier: 3.808A pdb=" N VAL A 210 " --> pdb=" O ASN A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 224 Processing helix chain 'A' and resid 224 through 229 Processing helix chain 'A' and resid 232 through 241 removed outlier: 3.951A pdb=" N GLY A 238 " --> pdb=" O ALA A 234 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ILE A 239 " --> pdb=" O SER A 235 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASN A 240 " --> pdb=" O LEU A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 252 removed outlier: 3.551A pdb=" N ASN A 249 " --> pdb=" O PRO A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 269 removed outlier: 3.660A pdb=" N LYS A 265 " --> pdb=" O GLU A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 277 Processing helix chain 'A' and resid 278 through 286 removed outlier: 3.633A pdb=" N ARG A 284 " --> pdb=" O GLU A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 294 Processing helix chain 'A' and resid 398 through 403 removed outlier: 3.640A pdb=" N ILE A 402 " --> pdb=" O ASN A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 451 Processing helix chain 'A' and resid 453 through 465 removed outlier: 3.540A pdb=" N VAL A 464 " --> pdb=" O ILE A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 488 removed outlier: 3.582A pdb=" N LYS A 477 " --> pdb=" O ASP A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 498 removed outlier: 3.503A pdb=" N LEU A 498 " --> pdb=" O THR A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 520 Processing helix chain 'A' and resid 523 through 527 removed outlier: 3.706A pdb=" N GLY A 526 " --> pdb=" O LEU A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 556 removed outlier: 3.722A pdb=" N THR A 549 " --> pdb=" O ASP A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 570 Processing helix chain 'A' and resid 581 through 597 removed outlier: 3.548A pdb=" N GLY A 591 " --> pdb=" O ASN A 587 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU A 594 " --> pdb=" O ILE A 590 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA A 595 " --> pdb=" O GLY A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 613 Processing helix chain 'A' and resid 623 through 645 removed outlier: 3.524A pdb=" N SER A 639 " --> pdb=" O ASN A 635 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N THR A 643 " --> pdb=" O SER A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 656 removed outlier: 3.583A pdb=" N ILE A 653 " --> pdb=" O PHE A 649 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N MET A 654 " --> pdb=" O GLN A 650 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 678 removed outlier: 3.604A pdb=" N LEU A 670 " --> pdb=" O GLU A 666 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 698 removed outlier: 3.580A pdb=" N VAL A 691 " --> pdb=" O ASP A 687 " (cutoff:3.500A) Proline residue: A 694 - end of helix Processing helix chain 'A' and resid 704 through 719 removed outlier: 3.698A pdb=" N ALA A 708 " --> pdb=" O SER A 704 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LYS A 717 " --> pdb=" O LEU A 713 " (cutoff:3.500A) Processing helix chain 'A' and resid 726 through 737 removed outlier: 3.534A pdb=" N ASP A 732 " --> pdb=" O GLU A 728 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N THR A 736 " --> pdb=" O ASP A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 748 through 769 removed outlier: 3.676A pdb=" N ILE A 752 " --> pdb=" O THR A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 772 through 782 removed outlier: 3.685A pdb=" N ARG A 777 " --> pdb=" O GLU A 773 " (cutoff:3.500A) Processing helix chain 'A' and resid 783 through 787 removed outlier: 3.739A pdb=" N GLY A 787 " --> pdb=" O GLU A 784 " (cutoff:3.500A) Processing helix chain 'A' and resid 797 through 813 removed outlier: 3.542A pdb=" N ILE A 802 " --> pdb=" O ALA A 798 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N MET A 803 " --> pdb=" O LEU A 799 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 816 No H-bonds generated for 'chain 'A' and resid 814 through 816' Processing helix chain 'A' and resid 817 through 827 removed outlier: 3.603A pdb=" N ALA A 827 " --> pdb=" O ALA A 823 " (cutoff:3.500A) Processing helix chain 'A' and resid 831 through 839 removed outlier: 3.527A pdb=" N ALA A 838 " --> pdb=" O GLN A 834 " (cutoff:3.500A) Processing helix chain 'A' and resid 842 through 855 removed outlier: 3.701A pdb=" N LEU A 846 " --> pdb=" O ASP A 842 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLN A 854 " --> pdb=" O SER A 850 " (cutoff:3.500A) Processing helix chain 'A' and resid 870 through 885 Processing helix chain 'A' and resid 890 through 899 removed outlier: 3.576A pdb=" N LEU A 897 " --> pdb=" O GLY A 893 " (cutoff:3.500A) Processing helix chain 'A' and resid 903 through 907 removed outlier: 3.648A pdb=" N LYS A 907 " --> pdb=" O GLN A 904 " (cutoff:3.500A) Processing helix chain 'A' and resid 911 through 924 removed outlier: 3.603A pdb=" N LEU A 922 " --> pdb=" O ALA A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 927 through 954 removed outlier: 3.557A pdb=" N ASN A 932 " --> pdb=" O SER A 928 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU A 940 " --> pdb=" O ALA A 936 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA A 944 " --> pdb=" O GLU A 940 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA A 945 " --> pdb=" O SER A 941 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N THR A 948 " --> pdb=" O ALA A 944 " (cutoff:3.500A) Processing helix chain 'A' and resid 963 through 972 Processing helix chain 'A' and resid 984 through 1001 removed outlier: 3.525A pdb=" N ARG A 999 " --> pdb=" O LEU A 995 " (cutoff:3.500A) Processing helix chain 'A' and resid 1009 through 1014 Processing helix chain 'A' and resid 1015 through 1020 Processing helix chain 'A' and resid 1027 through 1040 removed outlier: 3.625A pdb=" N GLY A1033 " --> pdb=" O SER A1029 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLN A1036 " --> pdb=" O ALA A1032 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N VAL A1038 " --> pdb=" O VAL A1034 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N TYR A1039 " --> pdb=" O SER A1035 " (cutoff:3.500A) Processing helix chain 'A' and resid 1041 through 1044 Processing helix chain 'A' and resid 1054 through 1064 Processing helix chain 'A' and resid 1070 through 1090 removed outlier: 3.557A pdb=" N VAL A1074 " --> pdb=" O ASN A1070 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER A1084 " --> pdb=" O SER A1080 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN A1087 " --> pdb=" O THR A1083 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL A1088 " --> pdb=" O SER A1084 " (cutoff:3.500A) Processing helix chain 'A' and resid 1217 through 1224 Processing helix chain 'A' and resid 1255 through 1261 removed outlier: 3.711A pdb=" N SER A1258 " --> pdb=" O THR A1255 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TYR A1259 " --> pdb=" O LEU A1256 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS A1260 " --> pdb=" O ASP A1257 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ASN A1261 " --> pdb=" O SER A1258 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1255 through 1261' Processing helix chain 'A' and resid 1279 through 1289 removed outlier: 3.949A pdb=" N VAL A1285 " --> pdb=" O GLU A1281 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASN A1289 " --> pdb=" O VAL A1285 " (cutoff:3.500A) Processing helix chain 'A' and resid 1290 through 1294 Processing helix chain 'A' and resid 1325 through 1329 removed outlier: 3.656A pdb=" N LEU A1329 " --> pdb=" O ASP A1326 " (cutoff:3.500A) Processing helix chain 'A' and resid 1368 through 1378 removed outlier: 3.668A pdb=" N LEU A1374 " --> pdb=" O ASN A1370 " (cutoff:3.500A) Processing helix chain 'A' and resid 1463 through 1467 Processing helix chain 'A' and resid 1608 through 1613 removed outlier: 3.655A pdb=" N GLN A1612 " --> pdb=" O LEU A1608 " (cutoff:3.500A) Processing helix chain 'A' and resid 1620 through 1625 Processing helix chain 'A' and resid 1626 through 1631 removed outlier: 3.807A pdb=" N GLN A1630 " --> pdb=" O SER A1626 " (cutoff:3.500A) Processing helix chain 'A' and resid 1764 through 1773 Processing helix chain 'A' and resid 1773 through 1786 Processing helix chain 'A' and resid 1788 through 1797 removed outlier: 3.808A pdb=" N ARG A1794 " --> pdb=" O ASP A1790 " (cutoff:3.500A) Processing helix chain 'A' and resid 1818 through 1823 Processing helix chain 'A' and resid 1836 through 1844 removed outlier: 3.521A pdb=" N VAL A1840 " --> pdb=" O ASP A1836 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA A1841 " --> pdb=" O PRO A1837 " (cutoff:3.500A) Processing helix chain 'A' and resid 1845 through 1869 Processing helix chain 'A' and resid 1872 through 1886 removed outlier: 3.653A pdb=" N LEU A1876 " --> pdb=" O GLU A1872 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASN A1877 " --> pdb=" O ARG A1873 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA A1886 " --> pdb=" O TRP A1882 " (cutoff:3.500A) Processing helix chain 'A' and resid 1886 through 1891 removed outlier: 3.617A pdb=" N LEU A1890 " --> pdb=" O ALA A1886 " (cutoff:3.500A) Processing helix chain 'A' and resid 1906 through 1911 Processing helix chain 'A' and resid 1912 through 1928 Processing helix chain 'A' and resid 1953 through 1972 removed outlier: 3.807A pdb=" N TYR A1959 " --> pdb=" O VAL A1955 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N TRP A1960 " --> pdb=" O MET A1956 " (cutoff:3.500A) Processing helix chain 'A' and resid 2018 through 2105 removed outlier: 3.900A pdb=" N GLU A2024 " --> pdb=" O PRO A2020 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN A2032 " --> pdb=" O GLY A2028 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU A2033 " --> pdb=" O MET A2029 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLN A2035 " --> pdb=" O SER A2031 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU A2062 " --> pdb=" O ASN A2058 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE A2064 " --> pdb=" O ALA A2060 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N LEU A2065 " --> pdb=" O ALA A2061 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N THR A2066 " --> pdb=" O GLU A2062 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASP A2072 " --> pdb=" O LEU A2068 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N THR A2083 " --> pdb=" O ASP A2079 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER A2094 " --> pdb=" O ALA A2090 " (cutoff:3.500A) Processing helix chain 'A' and resid 2108 through 2121 removed outlier: 3.714A pdb=" N GLN A2113 " --> pdb=" O ALA A2109 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N MET A2115 " --> pdb=" O GLU A2111 " (cutoff:3.500A) Processing helix chain 'A' and resid 2124 through 2139 Processing helix chain 'A' and resid 2155 through 2244 removed outlier: 3.692A pdb=" N ASN A2170 " --> pdb=" O GLU A2166 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA A2199 " --> pdb=" O GLN A2195 " (cutoff:3.500A) Processing helix chain 'A' and resid 2247 through 2284 removed outlier: 3.704A pdb=" N TYR A2251 " --> pdb=" O ASN A2247 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA A2260 " --> pdb=" O GLY A2256 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU A2268 " --> pdb=" O GLN A2264 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA A2271 " --> pdb=" O ASP A2267 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ARG A2272 " --> pdb=" O LEU A2268 " (cutoff:3.500A) Processing helix chain 'A' and resid 2305 through 2323 removed outlier: 3.541A pdb=" N LEU A2312 " --> pdb=" O GLU A2308 " (cutoff:3.500A) Processing helix chain 'A' and resid 2337 through 2342 Processing helix chain 'A' and resid 2352 through 2363 removed outlier: 3.721A pdb=" N ASP A2358 " --> pdb=" O ALA A2354 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N SER A2362 " --> pdb=" O ASP A2358 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLN A2363 " --> pdb=" O LYS A2359 " (cutoff:3.500A) Processing helix chain 'A' and resid 2398 through 2402 removed outlier: 3.600A pdb=" N TYR A2402 " --> pdb=" O ARG A2399 " (cutoff:3.500A) Processing helix chain 'A' and resid 2499 through 2503 Processing helix chain 'B' and resid 43 through 70 removed outlier: 3.645A pdb=" N HIS B 50 " --> pdb=" O HIS B 46 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ARG B 69 " --> pdb=" O ARG B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 77 removed outlier: 4.155A pdb=" N ALA B 77 " --> pdb=" O GLN B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 81 Processing helix chain 'B' and resid 87 through 96 removed outlier: 4.141A pdb=" N GLY B 91 " --> pdb=" O ALA B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 127 removed outlier: 3.523A pdb=" N GLU B 121 " --> pdb=" O ALA B 117 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG B 127 " --> pdb=" O TYR B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 142 Processing helix chain 'B' and resid 151 through 157 removed outlier: 3.574A pdb=" N MET B 155 " --> pdb=" O SER B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 177 Processing helix chain 'B' and resid 181 through 192 removed outlier: 3.847A pdb=" N THR B 191 " --> pdb=" O GLU B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 215 removed outlier: 3.807A pdb=" N VAL B 210 " --> pdb=" O ASN B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 224 Processing helix chain 'B' and resid 224 through 229 Processing helix chain 'B' and resid 232 through 241 removed outlier: 3.950A pdb=" N GLY B 238 " --> pdb=" O ALA B 234 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ILE B 239 " --> pdb=" O SER B 235 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASN B 240 " --> pdb=" O LEU B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 252 removed outlier: 3.552A pdb=" N ASN B 249 " --> pdb=" O PRO B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 269 removed outlier: 3.662A pdb=" N LYS B 265 " --> pdb=" O GLU B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 277 Processing helix chain 'B' and resid 278 through 286 removed outlier: 3.633A pdb=" N ARG B 284 " --> pdb=" O GLU B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 294 Processing helix chain 'B' and resid 398 through 403 removed outlier: 3.639A pdb=" N ILE B 402 " --> pdb=" O ASN B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 451 Processing helix chain 'B' and resid 453 through 465 removed outlier: 3.539A pdb=" N VAL B 464 " --> pdb=" O ILE B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 471 through 488 removed outlier: 3.583A pdb=" N LYS B 477 " --> pdb=" O ASP B 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 491 through 498 removed outlier: 3.503A pdb=" N LEU B 498 " --> pdb=" O THR B 494 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 520 Processing helix chain 'B' and resid 523 through 527 removed outlier: 3.706A pdb=" N GLY B 526 " --> pdb=" O LEU B 523 " (cutoff:3.500A) Processing helix chain 'B' and resid 545 through 556 removed outlier: 3.722A pdb=" N THR B 549 " --> pdb=" O ASP B 545 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 570 Processing helix chain 'B' and resid 581 through 597 removed outlier: 3.549A pdb=" N GLY B 591 " --> pdb=" O ASN B 587 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU B 594 " --> pdb=" O ILE B 590 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA B 595 " --> pdb=" O GLY B 591 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 613 Processing helix chain 'B' and resid 623 through 645 removed outlier: 3.524A pdb=" N SER B 639 " --> pdb=" O ASN B 635 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N THR B 643 " --> pdb=" O SER B 639 " (cutoff:3.500A) Processing helix chain 'B' and resid 647 through 656 removed outlier: 3.584A pdb=" N ILE B 653 " --> pdb=" O PHE B 649 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N MET B 654 " --> pdb=" O GLN B 650 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 678 removed outlier: 3.604A pdb=" N LEU B 670 " --> pdb=" O GLU B 666 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 698 removed outlier: 3.580A pdb=" N VAL B 691 " --> pdb=" O ASP B 687 " (cutoff:3.500A) Proline residue: B 694 - end of helix Processing helix chain 'B' and resid 704 through 719 removed outlier: 3.698A pdb=" N ALA B 708 " --> pdb=" O SER B 704 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LYS B 717 " --> pdb=" O LEU B 713 " (cutoff:3.500A) Processing helix chain 'B' and resid 726 through 737 removed outlier: 3.534A pdb=" N ASP B 732 " --> pdb=" O GLU B 728 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR B 736 " --> pdb=" O ASP B 732 " (cutoff:3.500A) Processing helix chain 'B' and resid 748 through 769 removed outlier: 3.676A pdb=" N ILE B 752 " --> pdb=" O THR B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 772 through 782 removed outlier: 3.686A pdb=" N ARG B 777 " --> pdb=" O GLU B 773 " (cutoff:3.500A) Processing helix chain 'B' and resid 783 through 787 removed outlier: 3.740A pdb=" N GLY B 787 " --> pdb=" O GLU B 784 " (cutoff:3.500A) Processing helix chain 'B' and resid 797 through 813 removed outlier: 3.542A pdb=" N ILE B 802 " --> pdb=" O ALA B 798 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N MET B 803 " --> pdb=" O LEU B 799 " (cutoff:3.500A) Processing helix chain 'B' and resid 814 through 816 No H-bonds generated for 'chain 'B' and resid 814 through 816' Processing helix chain 'B' and resid 817 through 827 removed outlier: 3.604A pdb=" N ALA B 827 " --> pdb=" O ALA B 823 " (cutoff:3.500A) Processing helix chain 'B' and resid 831 through 839 removed outlier: 3.526A pdb=" N ALA B 838 " --> pdb=" O GLN B 834 " (cutoff:3.500A) Processing helix chain 'B' and resid 842 through 855 removed outlier: 3.700A pdb=" N LEU B 846 " --> pdb=" O ASP B 842 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLN B 854 " --> pdb=" O SER B 850 " (cutoff:3.500A) Processing helix chain 'B' and resid 870 through 885 Processing helix chain 'B' and resid 890 through 899 removed outlier: 3.577A pdb=" N LEU B 897 " --> pdb=" O GLY B 893 " (cutoff:3.500A) Processing helix chain 'B' and resid 903 through 907 removed outlier: 3.648A pdb=" N LYS B 907 " --> pdb=" O GLN B 904 " (cutoff:3.500A) Processing helix chain 'B' and resid 911 through 924 removed outlier: 3.604A pdb=" N LEU B 922 " --> pdb=" O ALA B 918 " (cutoff:3.500A) Processing helix chain 'B' and resid 927 through 954 removed outlier: 3.558A pdb=" N ASN B 932 " --> pdb=" O SER B 928 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU B 940 " --> pdb=" O ALA B 936 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA B 944 " --> pdb=" O GLU B 940 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA B 945 " --> pdb=" O SER B 941 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N THR B 948 " --> pdb=" O ALA B 944 " (cutoff:3.500A) Processing helix chain 'B' and resid 963 through 972 Processing helix chain 'B' and resid 984 through 1001 removed outlier: 3.525A pdb=" N ARG B 999 " --> pdb=" O LEU B 995 " (cutoff:3.500A) Processing helix chain 'B' and resid 1009 through 1014 Processing helix chain 'B' and resid 1015 through 1020 Processing helix chain 'B' and resid 1027 through 1040 removed outlier: 3.624A pdb=" N GLY B1033 " --> pdb=" O SER B1029 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLN B1036 " --> pdb=" O ALA B1032 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N VAL B1038 " --> pdb=" O VAL B1034 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N TYR B1039 " --> pdb=" O SER B1035 " (cutoff:3.500A) Processing helix chain 'B' and resid 1041 through 1044 Processing helix chain 'B' and resid 1054 through 1064 Processing helix chain 'B' and resid 1070 through 1090 removed outlier: 3.556A pdb=" N VAL B1074 " --> pdb=" O ASN B1070 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER B1084 " --> pdb=" O SER B1080 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN B1087 " --> pdb=" O THR B1083 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL B1088 " --> pdb=" O SER B1084 " (cutoff:3.500A) Processing helix chain 'B' and resid 1217 through 1224 Processing helix chain 'B' and resid 1255 through 1261 removed outlier: 3.711A pdb=" N SER B1258 " --> pdb=" O THR B1255 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TYR B1259 " --> pdb=" O LEU B1256 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS B1260 " --> pdb=" O ASP B1257 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ASN B1261 " --> pdb=" O SER B1258 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1255 through 1261' Processing helix chain 'B' and resid 1279 through 1289 removed outlier: 3.950A pdb=" N VAL B1285 " --> pdb=" O GLU B1281 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASN B1289 " --> pdb=" O VAL B1285 " (cutoff:3.500A) Processing helix chain 'B' and resid 1290 through 1294 Processing helix chain 'B' and resid 1325 through 1329 removed outlier: 3.656A pdb=" N LEU B1329 " --> pdb=" O ASP B1326 " (cutoff:3.500A) Processing helix chain 'B' and resid 1368 through 1378 removed outlier: 3.668A pdb=" N LEU B1374 " --> pdb=" O ASN B1370 " (cutoff:3.500A) Processing helix chain 'B' and resid 1463 through 1467 Processing helix chain 'B' and resid 1608 through 1613 removed outlier: 3.654A pdb=" N GLN B1612 " --> pdb=" O LEU B1608 " (cutoff:3.500A) Processing helix chain 'B' and resid 1620 through 1625 Processing helix chain 'B' and resid 1626 through 1631 removed outlier: 3.807A pdb=" N GLN B1630 " --> pdb=" O SER B1626 " (cutoff:3.500A) Processing helix chain 'B' and resid 1764 through 1773 Processing helix chain 'B' and resid 1773 through 1786 Processing helix chain 'B' and resid 1788 through 1797 removed outlier: 3.808A pdb=" N ARG B1794 " --> pdb=" O ASP B1790 " (cutoff:3.500A) Processing helix chain 'B' and resid 1818 through 1823 Processing helix chain 'B' and resid 1836 through 1844 removed outlier: 3.522A pdb=" N VAL B1840 " --> pdb=" O ASP B1836 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA B1841 " --> pdb=" O PRO B1837 " (cutoff:3.500A) Processing helix chain 'B' and resid 1845 through 1869 Processing helix chain 'B' and resid 1872 through 1886 removed outlier: 3.653A pdb=" N LEU B1876 " --> pdb=" O GLU B1872 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASN B1877 " --> pdb=" O ARG B1873 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA B1886 " --> pdb=" O TRP B1882 " (cutoff:3.500A) Processing helix chain 'B' and resid 1886 through 1891 removed outlier: 3.616A pdb=" N LEU B1890 " --> pdb=" O ALA B1886 " (cutoff:3.500A) Processing helix chain 'B' and resid 1906 through 1911 Processing helix chain 'B' and resid 1912 through 1928 Processing helix chain 'B' and resid 1953 through 1972 removed outlier: 3.807A pdb=" N TYR B1959 " --> pdb=" O VAL B1955 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N TRP B1960 " --> pdb=" O MET B1956 " (cutoff:3.500A) Processing helix chain 'B' and resid 2018 through 2105 removed outlier: 3.901A pdb=" N GLU B2024 " --> pdb=" O PRO B2020 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLN B2032 " --> pdb=" O GLY B2028 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU B2033 " --> pdb=" O MET B2029 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLN B2035 " --> pdb=" O SER B2031 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU B2062 " --> pdb=" O ASN B2058 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE B2064 " --> pdb=" O ALA B2060 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N LEU B2065 " --> pdb=" O ALA B2061 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N THR B2066 " --> pdb=" O GLU B2062 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASP B2072 " --> pdb=" O LEU B2068 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N THR B2083 " --> pdb=" O ASP B2079 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER B2094 " --> pdb=" O ALA B2090 " (cutoff:3.500A) Processing helix chain 'B' and resid 2108 through 2121 removed outlier: 3.715A pdb=" N GLN B2113 " --> pdb=" O ALA B2109 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N MET B2115 " --> pdb=" O GLU B2111 " (cutoff:3.500A) Processing helix chain 'B' and resid 2124 through 2139 Processing helix chain 'B' and resid 2155 through 2244 removed outlier: 3.690A pdb=" N ASN B2170 " --> pdb=" O GLU B2166 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA B2199 " --> pdb=" O GLN B2195 " (cutoff:3.500A) Processing helix chain 'B' and resid 2247 through 2284 removed outlier: 3.704A pdb=" N TYR B2251 " --> pdb=" O ASN B2247 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA B2260 " --> pdb=" O GLY B2256 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU B2268 " --> pdb=" O GLN B2264 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA B2271 " --> pdb=" O ASP B2267 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG B2272 " --> pdb=" O LEU B2268 " (cutoff:3.500A) Processing helix chain 'B' and resid 2305 through 2323 removed outlier: 3.541A pdb=" N LEU B2312 " --> pdb=" O GLU B2308 " (cutoff:3.500A) Processing helix chain 'B' and resid 2337 through 2342 Processing helix chain 'B' and resid 2352 through 2363 removed outlier: 3.720A pdb=" N ASP B2358 " --> pdb=" O ALA B2354 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER B2362 " --> pdb=" O ASP B2358 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLN B2363 " --> pdb=" O LYS B2359 " (cutoff:3.500A) Processing helix chain 'B' and resid 2398 through 2402 removed outlier: 3.600A pdb=" N TYR B2402 " --> pdb=" O ARG B2399 " (cutoff:3.500A) Processing helix chain 'B' and resid 2499 through 2503 Processing helix chain 'C' and resid 43 through 70 removed outlier: 3.645A pdb=" N HIS C 50 " --> pdb=" O HIS C 46 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG C 69 " --> pdb=" O ARG C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 77 removed outlier: 4.154A pdb=" N ALA C 77 " --> pdb=" O GLN C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 81 Processing helix chain 'C' and resid 87 through 96 removed outlier: 4.141A pdb=" N GLY C 91 " --> pdb=" O ALA C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 127 removed outlier: 3.522A pdb=" N GLU C 121 " --> pdb=" O ALA C 117 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG C 127 " --> pdb=" O TYR C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 142 Processing helix chain 'C' and resid 151 through 157 removed outlier: 3.574A pdb=" N MET C 155 " --> pdb=" O SER C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 161 through 177 Processing helix chain 'C' and resid 181 through 192 removed outlier: 3.847A pdb=" N THR C 191 " --> pdb=" O GLU C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 215 removed outlier: 3.806A pdb=" N VAL C 210 " --> pdb=" O ASN C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 219 through 224 Processing helix chain 'C' and resid 224 through 229 Processing helix chain 'C' and resid 232 through 241 removed outlier: 3.951A pdb=" N GLY C 238 " --> pdb=" O ALA C 234 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ILE C 239 " --> pdb=" O SER C 235 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASN C 240 " --> pdb=" O LEU C 236 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 252 removed outlier: 3.552A pdb=" N ASN C 249 " --> pdb=" O PRO C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 269 removed outlier: 3.661A pdb=" N LYS C 265 " --> pdb=" O GLU C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 277 Processing helix chain 'C' and resid 278 through 286 removed outlier: 3.634A pdb=" N ARG C 284 " --> pdb=" O GLU C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 294 Processing helix chain 'C' and resid 398 through 403 removed outlier: 3.638A pdb=" N ILE C 402 " --> pdb=" O ASN C 398 " (cutoff:3.500A) Processing helix chain 'C' and resid 433 through 451 Processing helix chain 'C' and resid 453 through 465 removed outlier: 3.540A pdb=" N VAL C 464 " --> pdb=" O ILE C 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 471 through 488 removed outlier: 3.583A pdb=" N LYS C 477 " --> pdb=" O ASP C 473 " (cutoff:3.500A) Processing helix chain 'C' and resid 491 through 498 removed outlier: 3.503A pdb=" N LEU C 498 " --> pdb=" O THR C 494 " (cutoff:3.500A) Processing helix chain 'C' and resid 513 through 520 Processing helix chain 'C' and resid 523 through 527 removed outlier: 3.706A pdb=" N GLY C 526 " --> pdb=" O LEU C 523 " (cutoff:3.500A) Processing helix chain 'C' and resid 545 through 556 removed outlier: 3.723A pdb=" N THR C 549 " --> pdb=" O ASP C 545 " (cutoff:3.500A) Processing helix chain 'C' and resid 558 through 570 Processing helix chain 'C' and resid 581 through 597 removed outlier: 3.548A pdb=" N GLY C 591 " --> pdb=" O ASN C 587 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU C 594 " --> pdb=" O ILE C 590 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA C 595 " --> pdb=" O GLY C 591 " (cutoff:3.500A) Processing helix chain 'C' and resid 601 through 613 Processing helix chain 'C' and resid 623 through 645 removed outlier: 3.524A pdb=" N SER C 639 " --> pdb=" O ASN C 635 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N THR C 643 " --> pdb=" O SER C 639 " (cutoff:3.500A) Processing helix chain 'C' and resid 647 through 656 removed outlier: 3.584A pdb=" N ILE C 653 " --> pdb=" O PHE C 649 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N MET C 654 " --> pdb=" O GLN C 650 " (cutoff:3.500A) Processing helix chain 'C' and resid 664 through 678 removed outlier: 3.604A pdb=" N LEU C 670 " --> pdb=" O GLU C 666 " (cutoff:3.500A) Processing helix chain 'C' and resid 687 through 698 removed outlier: 3.580A pdb=" N VAL C 691 " --> pdb=" O ASP C 687 " (cutoff:3.500A) Proline residue: C 694 - end of helix Processing helix chain 'C' and resid 704 through 719 removed outlier: 3.698A pdb=" N ALA C 708 " --> pdb=" O SER C 704 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LYS C 717 " --> pdb=" O LEU C 713 " (cutoff:3.500A) Processing helix chain 'C' and resid 726 through 737 removed outlier: 3.534A pdb=" N ASP C 732 " --> pdb=" O GLU C 728 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR C 736 " --> pdb=" O ASP C 732 " (cutoff:3.500A) Processing helix chain 'C' and resid 748 through 769 removed outlier: 3.675A pdb=" N ILE C 752 " --> pdb=" O THR C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 772 through 782 removed outlier: 3.686A pdb=" N ARG C 777 " --> pdb=" O GLU C 773 " (cutoff:3.500A) Processing helix chain 'C' and resid 783 through 787 removed outlier: 3.739A pdb=" N GLY C 787 " --> pdb=" O GLU C 784 " (cutoff:3.500A) Processing helix chain 'C' and resid 797 through 813 removed outlier: 3.543A pdb=" N ILE C 802 " --> pdb=" O ALA C 798 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N MET C 803 " --> pdb=" O LEU C 799 " (cutoff:3.500A) Processing helix chain 'C' and resid 814 through 816 No H-bonds generated for 'chain 'C' and resid 814 through 816' Processing helix chain 'C' and resid 817 through 827 removed outlier: 3.603A pdb=" N ALA C 827 " --> pdb=" O ALA C 823 " (cutoff:3.500A) Processing helix chain 'C' and resid 831 through 839 removed outlier: 3.527A pdb=" N ALA C 838 " --> pdb=" O GLN C 834 " (cutoff:3.500A) Processing helix chain 'C' and resid 842 through 855 removed outlier: 3.702A pdb=" N LEU C 846 " --> pdb=" O ASP C 842 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLN C 854 " --> pdb=" O SER C 850 " (cutoff:3.500A) Processing helix chain 'C' and resid 870 through 885 Processing helix chain 'C' and resid 890 through 899 removed outlier: 3.577A pdb=" N LEU C 897 " --> pdb=" O GLY C 893 " (cutoff:3.500A) Processing helix chain 'C' and resid 903 through 907 removed outlier: 3.649A pdb=" N LYS C 907 " --> pdb=" O GLN C 904 " (cutoff:3.500A) Processing helix chain 'C' and resid 911 through 924 removed outlier: 3.604A pdb=" N LEU C 922 " --> pdb=" O ALA C 918 " (cutoff:3.500A) Processing helix chain 'C' and resid 927 through 954 removed outlier: 3.558A pdb=" N ASN C 932 " --> pdb=" O SER C 928 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU C 940 " --> pdb=" O ALA C 936 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA C 944 " --> pdb=" O GLU C 940 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA C 945 " --> pdb=" O SER C 941 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N THR C 948 " --> pdb=" O ALA C 944 " (cutoff:3.500A) Processing helix chain 'C' and resid 963 through 972 Processing helix chain 'C' and resid 984 through 1001 removed outlier: 3.525A pdb=" N ARG C 999 " --> pdb=" O LEU C 995 " (cutoff:3.500A) Processing helix chain 'C' and resid 1009 through 1014 Processing helix chain 'C' and resid 1015 through 1020 Processing helix chain 'C' and resid 1027 through 1040 removed outlier: 3.625A pdb=" N GLY C1033 " --> pdb=" O SER C1029 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLN C1036 " --> pdb=" O ALA C1032 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N VAL C1038 " --> pdb=" O VAL C1034 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N TYR C1039 " --> pdb=" O SER C1035 " (cutoff:3.500A) Processing helix chain 'C' and resid 1041 through 1044 Processing helix chain 'C' and resid 1054 through 1064 Processing helix chain 'C' and resid 1070 through 1090 removed outlier: 3.556A pdb=" N VAL C1074 " --> pdb=" O ASN C1070 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER C1084 " --> pdb=" O SER C1080 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLN C1087 " --> pdb=" O THR C1083 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL C1088 " --> pdb=" O SER C1084 " (cutoff:3.500A) Processing helix chain 'C' and resid 1217 through 1224 Processing helix chain 'C' and resid 1255 through 1261 removed outlier: 3.711A pdb=" N SER C1258 " --> pdb=" O THR C1255 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TYR C1259 " --> pdb=" O LEU C1256 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS C1260 " --> pdb=" O ASP C1257 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ASN C1261 " --> pdb=" O SER C1258 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1255 through 1261' Processing helix chain 'C' and resid 1279 through 1289 removed outlier: 3.948A pdb=" N VAL C1285 " --> pdb=" O GLU C1281 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ASN C1289 " --> pdb=" O VAL C1285 " (cutoff:3.500A) Processing helix chain 'C' and resid 1290 through 1294 Processing helix chain 'C' and resid 1325 through 1329 removed outlier: 3.656A pdb=" N LEU C1329 " --> pdb=" O ASP C1326 " (cutoff:3.500A) Processing helix chain 'C' and resid 1368 through 1378 removed outlier: 3.668A pdb=" N LEU C1374 " --> pdb=" O ASN C1370 " (cutoff:3.500A) Processing helix chain 'C' and resid 1463 through 1467 Processing helix chain 'C' and resid 1608 through 1613 removed outlier: 3.655A pdb=" N GLN C1612 " --> pdb=" O LEU C1608 " (cutoff:3.500A) Processing helix chain 'C' and resid 1620 through 1625 Processing helix chain 'C' and resid 1626 through 1631 removed outlier: 3.807A pdb=" N GLN C1630 " --> pdb=" O SER C1626 " (cutoff:3.500A) Processing helix chain 'C' and resid 1764 through 1773 Processing helix chain 'C' and resid 1773 through 1786 Processing helix chain 'C' and resid 1788 through 1797 removed outlier: 3.808A pdb=" N ARG C1794 " --> pdb=" O ASP C1790 " (cutoff:3.500A) Processing helix chain 'C' and resid 1818 through 1823 Processing helix chain 'C' and resid 1836 through 1844 removed outlier: 3.522A pdb=" N VAL C1840 " --> pdb=" O ASP C1836 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA C1841 " --> pdb=" O PRO C1837 " (cutoff:3.500A) Processing helix chain 'C' and resid 1845 through 1869 Processing helix chain 'C' and resid 1872 through 1886 removed outlier: 3.654A pdb=" N LEU C1876 " --> pdb=" O GLU C1872 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASN C1877 " --> pdb=" O ARG C1873 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA C1886 " --> pdb=" O TRP C1882 " (cutoff:3.500A) Processing helix chain 'C' and resid 1886 through 1891 removed outlier: 3.616A pdb=" N LEU C1890 " --> pdb=" O ALA C1886 " (cutoff:3.500A) Processing helix chain 'C' and resid 1906 through 1911 Processing helix chain 'C' and resid 1912 through 1928 Processing helix chain 'C' and resid 1953 through 1972 removed outlier: 3.807A pdb=" N TYR C1959 " --> pdb=" O VAL C1955 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N TRP C1960 " --> pdb=" O MET C1956 " (cutoff:3.500A) Processing helix chain 'C' and resid 2018 through 2105 removed outlier: 3.900A pdb=" N GLU C2024 " --> pdb=" O PRO C2020 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLN C2032 " --> pdb=" O GLY C2028 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU C2033 " --> pdb=" O MET C2029 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLN C2035 " --> pdb=" O SER C2031 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU C2062 " --> pdb=" O ASN C2058 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE C2064 " --> pdb=" O ALA C2060 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N LEU C2065 " --> pdb=" O ALA C2061 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N THR C2066 " --> pdb=" O GLU C2062 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASP C2072 " --> pdb=" O LEU C2068 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N THR C2083 " --> pdb=" O ASP C2079 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER C2094 " --> pdb=" O ALA C2090 " (cutoff:3.500A) Processing helix chain 'C' and resid 2108 through 2121 removed outlier: 3.714A pdb=" N GLN C2113 " --> pdb=" O ALA C2109 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N MET C2115 " --> pdb=" O GLU C2111 " (cutoff:3.500A) Processing helix chain 'C' and resid 2124 through 2139 Processing helix chain 'C' and resid 2155 through 2244 removed outlier: 3.691A pdb=" N ASN C2170 " --> pdb=" O GLU C2166 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA C2199 " --> pdb=" O GLN C2195 " (cutoff:3.500A) Processing helix chain 'C' and resid 2247 through 2284 removed outlier: 3.704A pdb=" N TYR C2251 " --> pdb=" O ASN C2247 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA C2260 " --> pdb=" O GLY C2256 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU C2268 " --> pdb=" O GLN C2264 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA C2271 " --> pdb=" O ASP C2267 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ARG C2272 " --> pdb=" O LEU C2268 " (cutoff:3.500A) Processing helix chain 'C' and resid 2305 through 2323 removed outlier: 3.540A pdb=" N LEU C2312 " --> pdb=" O GLU C2308 " (cutoff:3.500A) Processing helix chain 'C' and resid 2337 through 2342 Processing helix chain 'C' and resid 2352 through 2363 removed outlier: 3.721A pdb=" N ASP C2358 " --> pdb=" O ALA C2354 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N SER C2362 " --> pdb=" O ASP C2358 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLN C2363 " --> pdb=" O LYS C2359 " (cutoff:3.500A) Processing helix chain 'C' and resid 2398 through 2402 removed outlier: 3.600A pdb=" N TYR C2402 " --> pdb=" O ARG C2399 " (cutoff:3.500A) Processing helix chain 'C' and resid 2499 through 2503 Processing helix chain 'D' and resid 43 through 70 removed outlier: 3.645A pdb=" N HIS D 50 " --> pdb=" O HIS D 46 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG D 69 " --> pdb=" O ARG D 65 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 77 removed outlier: 4.155A pdb=" N ALA D 77 " --> pdb=" O GLN D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 81 Processing helix chain 'D' and resid 87 through 96 removed outlier: 4.141A pdb=" N GLY D 91 " --> pdb=" O ALA D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 127 removed outlier: 3.521A pdb=" N GLU D 121 " --> pdb=" O ALA D 117 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG D 127 " --> pdb=" O TYR D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 142 Processing helix chain 'D' and resid 151 through 157 removed outlier: 3.574A pdb=" N MET D 155 " --> pdb=" O SER D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 177 Processing helix chain 'D' and resid 181 through 192 removed outlier: 3.847A pdb=" N THR D 191 " --> pdb=" O GLU D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 201 through 215 removed outlier: 3.807A pdb=" N VAL D 210 " --> pdb=" O ASN D 206 " (cutoff:3.500A) Processing helix chain 'D' and resid 219 through 224 Processing helix chain 'D' and resid 224 through 229 Processing helix chain 'D' and resid 232 through 241 removed outlier: 3.951A pdb=" N GLY D 238 " --> pdb=" O ALA D 234 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ILE D 239 " --> pdb=" O SER D 235 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASN D 240 " --> pdb=" O LEU D 236 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 252 removed outlier: 3.552A pdb=" N ASN D 249 " --> pdb=" O PRO D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 269 removed outlier: 3.662A pdb=" N LYS D 265 " --> pdb=" O GLU D 261 " (cutoff:3.500A) Processing helix chain 'D' and resid 272 through 277 Processing helix chain 'D' and resid 278 through 286 removed outlier: 3.634A pdb=" N ARG D 284 " --> pdb=" O GLU D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 289 through 294 Processing helix chain 'D' and resid 398 through 403 removed outlier: 3.639A pdb=" N ILE D 402 " --> pdb=" O ASN D 398 " (cutoff:3.500A) Processing helix chain 'D' and resid 433 through 451 Processing helix chain 'D' and resid 453 through 465 removed outlier: 3.540A pdb=" N VAL D 464 " --> pdb=" O ILE D 460 " (cutoff:3.500A) Processing helix chain 'D' and resid 471 through 488 removed outlier: 3.583A pdb=" N LYS D 477 " --> pdb=" O ASP D 473 " (cutoff:3.500A) Processing helix chain 'D' and resid 491 through 498 removed outlier: 3.503A pdb=" N LEU D 498 " --> pdb=" O THR D 494 " (cutoff:3.500A) Processing helix chain 'D' and resid 513 through 520 Processing helix chain 'D' and resid 523 through 527 removed outlier: 3.705A pdb=" N GLY D 526 " --> pdb=" O LEU D 523 " (cutoff:3.500A) Processing helix chain 'D' and resid 545 through 556 removed outlier: 3.723A pdb=" N THR D 549 " --> pdb=" O ASP D 545 " (cutoff:3.500A) Processing helix chain 'D' and resid 558 through 570 Processing helix chain 'D' and resid 581 through 597 removed outlier: 3.548A pdb=" N GLY D 591 " --> pdb=" O ASN D 587 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU D 594 " --> pdb=" O ILE D 590 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA D 595 " --> pdb=" O GLY D 591 " (cutoff:3.500A) Processing helix chain 'D' and resid 601 through 613 Processing helix chain 'D' and resid 623 through 645 removed outlier: 3.525A pdb=" N SER D 639 " --> pdb=" O ASN D 635 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N THR D 643 " --> pdb=" O SER D 639 " (cutoff:3.500A) Processing helix chain 'D' and resid 647 through 656 removed outlier: 3.583A pdb=" N ILE D 653 " --> pdb=" O PHE D 649 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N MET D 654 " --> pdb=" O GLN D 650 " (cutoff:3.500A) Processing helix chain 'D' and resid 664 through 678 removed outlier: 3.604A pdb=" N LEU D 670 " --> pdb=" O GLU D 666 " (cutoff:3.500A) Processing helix chain 'D' and resid 687 through 698 removed outlier: 3.580A pdb=" N VAL D 691 " --> pdb=" O ASP D 687 " (cutoff:3.500A) Proline residue: D 694 - end of helix Processing helix chain 'D' and resid 704 through 719 removed outlier: 3.698A pdb=" N ALA D 708 " --> pdb=" O SER D 704 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LYS D 717 " --> pdb=" O LEU D 713 " (cutoff:3.500A) Processing helix chain 'D' and resid 726 through 737 removed outlier: 3.534A pdb=" N ASP D 732 " --> pdb=" O GLU D 728 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR D 736 " --> pdb=" O ASP D 732 " (cutoff:3.500A) Processing helix chain 'D' and resid 748 through 769 removed outlier: 3.676A pdb=" N ILE D 752 " --> pdb=" O THR D 748 " (cutoff:3.500A) Processing helix chain 'D' and resid 772 through 782 removed outlier: 3.686A pdb=" N ARG D 777 " --> pdb=" O GLU D 773 " (cutoff:3.500A) Processing helix chain 'D' and resid 783 through 787 removed outlier: 3.738A pdb=" N GLY D 787 " --> pdb=" O GLU D 784 " (cutoff:3.500A) Processing helix chain 'D' and resid 797 through 813 removed outlier: 3.542A pdb=" N ILE D 802 " --> pdb=" O ALA D 798 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N MET D 803 " --> pdb=" O LEU D 799 " (cutoff:3.500A) Processing helix chain 'D' and resid 814 through 816 No H-bonds generated for 'chain 'D' and resid 814 through 816' Processing helix chain 'D' and resid 817 through 827 removed outlier: 3.603A pdb=" N ALA D 827 " --> pdb=" O ALA D 823 " (cutoff:3.500A) Processing helix chain 'D' and resid 831 through 839 removed outlier: 3.526A pdb=" N ALA D 838 " --> pdb=" O GLN D 834 " (cutoff:3.500A) Processing helix chain 'D' and resid 842 through 855 removed outlier: 3.702A pdb=" N LEU D 846 " --> pdb=" O ASP D 842 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLN D 854 " --> pdb=" O SER D 850 " (cutoff:3.500A) Processing helix chain 'D' and resid 870 through 885 Processing helix chain 'D' and resid 890 through 899 removed outlier: 3.577A pdb=" N LEU D 897 " --> pdb=" O GLY D 893 " (cutoff:3.500A) Processing helix chain 'D' and resid 903 through 907 removed outlier: 3.648A pdb=" N LYS D 907 " --> pdb=" O GLN D 904 " (cutoff:3.500A) Processing helix chain 'D' and resid 911 through 924 removed outlier: 3.603A pdb=" N LEU D 922 " --> pdb=" O ALA D 918 " (cutoff:3.500A) Processing helix chain 'D' and resid 927 through 954 removed outlier: 3.557A pdb=" N ASN D 932 " --> pdb=" O SER D 928 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU D 940 " --> pdb=" O ALA D 936 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ALA D 944 " --> pdb=" O GLU D 940 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA D 945 " --> pdb=" O SER D 941 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N THR D 948 " --> pdb=" O ALA D 944 " (cutoff:3.500A) Processing helix chain 'D' and resid 963 through 972 Processing helix chain 'D' and resid 984 through 1001 removed outlier: 3.524A pdb=" N ARG D 999 " --> pdb=" O LEU D 995 " (cutoff:3.500A) Processing helix chain 'D' and resid 1009 through 1014 Processing helix chain 'D' and resid 1015 through 1020 Processing helix chain 'D' and resid 1027 through 1040 removed outlier: 3.625A pdb=" N GLY D1033 " --> pdb=" O SER D1029 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLN D1036 " --> pdb=" O ALA D1032 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N VAL D1038 " --> pdb=" O VAL D1034 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N TYR D1039 " --> pdb=" O SER D1035 " (cutoff:3.500A) Processing helix chain 'D' and resid 1041 through 1044 Processing helix chain 'D' and resid 1054 through 1064 Processing helix chain 'D' and resid 1070 through 1090 removed outlier: 3.556A pdb=" N VAL D1074 " --> pdb=" O ASN D1070 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER D1084 " --> pdb=" O SER D1080 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN D1087 " --> pdb=" O THR D1083 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL D1088 " --> pdb=" O SER D1084 " (cutoff:3.500A) Processing helix chain 'D' and resid 1217 through 1224 Processing helix chain 'D' and resid 1255 through 1261 removed outlier: 3.711A pdb=" N SER D1258 " --> pdb=" O THR D1255 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR D1259 " --> pdb=" O LEU D1256 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS D1260 " --> pdb=" O ASP D1257 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ASN D1261 " --> pdb=" O SER D1258 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1255 through 1261' Processing helix chain 'D' and resid 1279 through 1289 removed outlier: 3.948A pdb=" N VAL D1285 " --> pdb=" O GLU D1281 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ASN D1289 " --> pdb=" O VAL D1285 " (cutoff:3.500A) Processing helix chain 'D' and resid 1290 through 1294 Processing helix chain 'D' and resid 1325 through 1329 removed outlier: 3.655A pdb=" N LEU D1329 " --> pdb=" O ASP D1326 " (cutoff:3.500A) Processing helix chain 'D' and resid 1368 through 1378 removed outlier: 3.669A pdb=" N LEU D1374 " --> pdb=" O ASN D1370 " (cutoff:3.500A) Processing helix chain 'D' and resid 1463 through 1467 Processing helix chain 'D' and resid 1608 through 1613 removed outlier: 3.655A pdb=" N GLN D1612 " --> pdb=" O LEU D1608 " (cutoff:3.500A) Processing helix chain 'D' and resid 1620 through 1625 Processing helix chain 'D' and resid 1626 through 1631 removed outlier: 3.806A pdb=" N GLN D1630 " --> pdb=" O SER D1626 " (cutoff:3.500A) Processing helix chain 'D' and resid 1764 through 1773 Processing helix chain 'D' and resid 1773 through 1786 Processing helix chain 'D' and resid 1788 through 1797 removed outlier: 3.808A pdb=" N ARG D1794 " --> pdb=" O ASP D1790 " (cutoff:3.500A) Processing helix chain 'D' and resid 1818 through 1823 Processing helix chain 'D' and resid 1836 through 1844 removed outlier: 3.522A pdb=" N VAL D1840 " --> pdb=" O ASP D1836 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA D1841 " --> pdb=" O PRO D1837 " (cutoff:3.500A) Processing helix chain 'D' and resid 1845 through 1869 Processing helix chain 'D' and resid 1872 through 1886 removed outlier: 3.653A pdb=" N LEU D1876 " --> pdb=" O GLU D1872 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASN D1877 " --> pdb=" O ARG D1873 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA D1886 " --> pdb=" O TRP D1882 " (cutoff:3.500A) Processing helix chain 'D' and resid 1886 through 1891 removed outlier: 3.617A pdb=" N LEU D1890 " --> pdb=" O ALA D1886 " (cutoff:3.500A) Processing helix chain 'D' and resid 1906 through 1911 Processing helix chain 'D' and resid 1912 through 1928 Processing helix chain 'D' and resid 1953 through 1972 removed outlier: 3.808A pdb=" N TYR D1959 " --> pdb=" O VAL D1955 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N TRP D1960 " --> pdb=" O MET D1956 " (cutoff:3.500A) Processing helix chain 'D' and resid 2018 through 2105 removed outlier: 3.901A pdb=" N GLU D2024 " --> pdb=" O PRO D2020 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLN D2032 " --> pdb=" O GLY D2028 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU D2033 " --> pdb=" O MET D2029 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLN D2035 " --> pdb=" O SER D2031 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU D2062 " --> pdb=" O ASN D2058 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE D2064 " --> pdb=" O ALA D2060 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N LEU D2065 " --> pdb=" O ALA D2061 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N THR D2066 " --> pdb=" O GLU D2062 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ASP D2072 " --> pdb=" O LEU D2068 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N THR D2083 " --> pdb=" O ASP D2079 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER D2094 " --> pdb=" O ALA D2090 " (cutoff:3.500A) Processing helix chain 'D' and resid 2108 through 2121 removed outlier: 3.715A pdb=" N GLN D2113 " --> pdb=" O ALA D2109 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N MET D2115 " --> pdb=" O GLU D2111 " (cutoff:3.500A) Processing helix chain 'D' and resid 2124 through 2139 Processing helix chain 'D' and resid 2155 through 2244 removed outlier: 3.691A pdb=" N ASN D2170 " --> pdb=" O GLU D2166 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA D2199 " --> pdb=" O GLN D2195 " (cutoff:3.500A) Processing helix chain 'D' and resid 2247 through 2284 removed outlier: 3.703A pdb=" N TYR D2251 " --> pdb=" O ASN D2247 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ALA D2260 " --> pdb=" O GLY D2256 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU D2268 " --> pdb=" O GLN D2264 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA D2271 " --> pdb=" O ASP D2267 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ARG D2272 " --> pdb=" O LEU D2268 " (cutoff:3.500A) Processing helix chain 'D' and resid 2305 through 2323 removed outlier: 3.541A pdb=" N LEU D2312 " --> pdb=" O GLU D2308 " (cutoff:3.500A) Processing helix chain 'D' and resid 2337 through 2342 Processing helix chain 'D' and resid 2352 through 2363 removed outlier: 3.721A pdb=" N ASP D2358 " --> pdb=" O ALA D2354 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N SER D2362 " --> pdb=" O ASP D2358 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLN D2363 " --> pdb=" O LYS D2359 " (cutoff:3.500A) Processing helix chain 'D' and resid 2398 through 2402 removed outlier: 3.601A pdb=" N TYR D2402 " --> pdb=" O ARG D2399 " (cutoff:3.500A) Processing helix chain 'D' and resid 2499 through 2503 Processing helix chain 'E' and resid 43 through 70 removed outlier: 3.646A pdb=" N HIS E 50 " --> pdb=" O HIS E 46 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ARG E 69 " --> pdb=" O ARG E 65 " (cutoff:3.500A) Processing helix chain 'E' and resid 71 through 77 removed outlier: 4.154A pdb=" N ALA E 77 " --> pdb=" O GLN E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 78 through 81 Processing helix chain 'E' and resid 87 through 96 removed outlier: 4.140A pdb=" N GLY E 91 " --> pdb=" O ALA E 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 114 through 127 removed outlier: 3.522A pdb=" N GLU E 121 " --> pdb=" O ALA E 117 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG E 127 " --> pdb=" O TYR E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 142 Processing helix chain 'E' and resid 151 through 157 removed outlier: 3.575A pdb=" N MET E 155 " --> pdb=" O SER E 151 " (cutoff:3.500A) Processing helix chain 'E' and resid 161 through 177 Processing helix chain 'E' and resid 181 through 192 removed outlier: 3.846A pdb=" N THR E 191 " --> pdb=" O GLU E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 201 through 215 removed outlier: 3.807A pdb=" N VAL E 210 " --> pdb=" O ASN E 206 " (cutoff:3.500A) Processing helix chain 'E' and resid 219 through 224 Processing helix chain 'E' and resid 224 through 229 Processing helix chain 'E' and resid 232 through 241 removed outlier: 3.951A pdb=" N GLY E 238 " --> pdb=" O ALA E 234 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ILE E 239 " --> pdb=" O SER E 235 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASN E 240 " --> pdb=" O LEU E 236 " (cutoff:3.500A) Processing helix chain 'E' and resid 244 through 252 removed outlier: 3.552A pdb=" N ASN E 249 " --> pdb=" O PRO E 245 " (cutoff:3.500A) Processing helix chain 'E' and resid 259 through 269 removed outlier: 3.662A pdb=" N LYS E 265 " --> pdb=" O GLU E 261 " (cutoff:3.500A) Processing helix chain 'E' and resid 272 through 277 Processing helix chain 'E' and resid 278 through 286 removed outlier: 3.633A pdb=" N ARG E 284 " --> pdb=" O GLU E 280 " (cutoff:3.500A) Processing helix chain 'E' and resid 289 through 294 Processing helix chain 'E' and resid 398 through 403 removed outlier: 3.638A pdb=" N ILE E 402 " --> pdb=" O ASN E 398 " (cutoff:3.500A) Processing helix chain 'E' and resid 433 through 451 Processing helix chain 'E' and resid 453 through 465 removed outlier: 3.540A pdb=" N VAL E 464 " --> pdb=" O ILE E 460 " (cutoff:3.500A) Processing helix chain 'E' and resid 471 through 488 removed outlier: 3.584A pdb=" N LYS E 477 " --> pdb=" O ASP E 473 " (cutoff:3.500A) Processing helix chain 'E' and resid 491 through 498 removed outlier: 3.503A pdb=" N LEU E 498 " --> pdb=" O THR E 494 " (cutoff:3.500A) Processing helix chain 'E' and resid 513 through 520 Processing helix chain 'E' and resid 523 through 527 removed outlier: 3.707A pdb=" N GLY E 526 " --> pdb=" O LEU E 523 " (cutoff:3.500A) Processing helix chain 'E' and resid 545 through 556 removed outlier: 3.722A pdb=" N THR E 549 " --> pdb=" O ASP E 545 " (cutoff:3.500A) Processing helix chain 'E' and resid 558 through 570 Processing helix chain 'E' and resid 581 through 597 removed outlier: 3.548A pdb=" N GLY E 591 " --> pdb=" O ASN E 587 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU E 594 " --> pdb=" O ILE E 590 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA E 595 " --> pdb=" O GLY E 591 " (cutoff:3.500A) Processing helix chain 'E' and resid 601 through 613 Processing helix chain 'E' and resid 623 through 645 removed outlier: 3.525A pdb=" N SER E 639 " --> pdb=" O ASN E 635 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N THR E 643 " --> pdb=" O SER E 639 " (cutoff:3.500A) Processing helix chain 'E' and resid 647 through 656 removed outlier: 3.584A pdb=" N ILE E 653 " --> pdb=" O PHE E 649 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N MET E 654 " --> pdb=" O GLN E 650 " (cutoff:3.500A) Processing helix chain 'E' and resid 664 through 678 removed outlier: 3.605A pdb=" N LEU E 670 " --> pdb=" O GLU E 666 " (cutoff:3.500A) Processing helix chain 'E' and resid 687 through 698 removed outlier: 3.579A pdb=" N VAL E 691 " --> pdb=" O ASP E 687 " (cutoff:3.500A) Proline residue: E 694 - end of helix Processing helix chain 'E' and resid 704 through 719 removed outlier: 3.698A pdb=" N ALA E 708 " --> pdb=" O SER E 704 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LYS E 717 " --> pdb=" O LEU E 713 " (cutoff:3.500A) Processing helix chain 'E' and resid 726 through 737 removed outlier: 3.534A pdb=" N ASP E 732 " --> pdb=" O GLU E 728 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N THR E 736 " --> pdb=" O ASP E 732 " (cutoff:3.500A) Processing helix chain 'E' and resid 748 through 769 removed outlier: 3.676A pdb=" N ILE E 752 " --> pdb=" O THR E 748 " (cutoff:3.500A) Processing helix chain 'E' and resid 772 through 782 removed outlier: 3.686A pdb=" N ARG E 777 " --> pdb=" O GLU E 773 " (cutoff:3.500A) Processing helix chain 'E' and resid 783 through 787 removed outlier: 3.739A pdb=" N GLY E 787 " --> pdb=" O GLU E 784 " (cutoff:3.500A) Processing helix chain 'E' and resid 797 through 813 removed outlier: 3.542A pdb=" N ILE E 802 " --> pdb=" O ALA E 798 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N MET E 803 " --> pdb=" O LEU E 799 " (cutoff:3.500A) Processing helix chain 'E' and resid 814 through 816 No H-bonds generated for 'chain 'E' and resid 814 through 816' Processing helix chain 'E' and resid 817 through 827 removed outlier: 3.604A pdb=" N ALA E 827 " --> pdb=" O ALA E 823 " (cutoff:3.500A) Processing helix chain 'E' and resid 831 through 839 removed outlier: 3.526A pdb=" N ALA E 838 " --> pdb=" O GLN E 834 " (cutoff:3.500A) Processing helix chain 'E' and resid 842 through 855 removed outlier: 3.701A pdb=" N LEU E 846 " --> pdb=" O ASP E 842 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLN E 854 " --> pdb=" O SER E 850 " (cutoff:3.500A) Processing helix chain 'E' and resid 870 through 885 Processing helix chain 'E' and resid 890 through 899 removed outlier: 3.577A pdb=" N LEU E 897 " --> pdb=" O GLY E 893 " (cutoff:3.500A) Processing helix chain 'E' and resid 903 through 907 removed outlier: 3.648A pdb=" N LYS E 907 " --> pdb=" O GLN E 904 " (cutoff:3.500A) Processing helix chain 'E' and resid 911 through 924 removed outlier: 3.603A pdb=" N LEU E 922 " --> pdb=" O ALA E 918 " (cutoff:3.500A) Processing helix chain 'E' and resid 927 through 954 removed outlier: 3.558A pdb=" N ASN E 932 " --> pdb=" O SER E 928 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU E 940 " --> pdb=" O ALA E 936 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA E 944 " --> pdb=" O GLU E 940 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA E 945 " --> pdb=" O SER E 941 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N THR E 948 " --> pdb=" O ALA E 944 " (cutoff:3.500A) Processing helix chain 'E' and resid 963 through 972 Processing helix chain 'E' and resid 984 through 1001 removed outlier: 3.525A pdb=" N ARG E 999 " --> pdb=" O LEU E 995 " (cutoff:3.500A) Processing helix chain 'E' and resid 1009 through 1014 Processing helix chain 'E' and resid 1015 through 1020 Processing helix chain 'E' and resid 1027 through 1040 removed outlier: 3.625A pdb=" N GLY E1033 " --> pdb=" O SER E1029 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLN E1036 " --> pdb=" O ALA E1032 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N VAL E1038 " --> pdb=" O VAL E1034 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N TYR E1039 " --> pdb=" O SER E1035 " (cutoff:3.500A) Processing helix chain 'E' and resid 1041 through 1044 Processing helix chain 'E' and resid 1054 through 1064 Processing helix chain 'E' and resid 1070 through 1090 removed outlier: 3.556A pdb=" N VAL E1074 " --> pdb=" O ASN E1070 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER E1084 " --> pdb=" O SER E1080 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLN E1087 " --> pdb=" O THR E1083 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL E1088 " --> pdb=" O SER E1084 " (cutoff:3.500A) Processing helix chain 'E' and resid 1217 through 1224 Processing helix chain 'E' and resid 1255 through 1261 removed outlier: 3.711A pdb=" N SER E1258 " --> pdb=" O THR E1255 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR E1259 " --> pdb=" O LEU E1256 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS E1260 " --> pdb=" O ASP E1257 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ASN E1261 " --> pdb=" O SER E1258 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 1255 through 1261' Processing helix chain 'E' and resid 1279 through 1289 removed outlier: 3.950A pdb=" N VAL E1285 " --> pdb=" O GLU E1281 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASN E1289 " --> pdb=" O VAL E1285 " (cutoff:3.500A) Processing helix chain 'E' and resid 1290 through 1294 Processing helix chain 'E' and resid 1325 through 1329 removed outlier: 3.656A pdb=" N LEU E1329 " --> pdb=" O ASP E1326 " (cutoff:3.500A) Processing helix chain 'E' and resid 1368 through 1378 removed outlier: 3.668A pdb=" N LEU E1374 " --> pdb=" O ASN E1370 " (cutoff:3.500A) Processing helix chain 'E' and resid 1463 through 1467 Processing helix chain 'E' and resid 1608 through 1613 removed outlier: 3.655A pdb=" N GLN E1612 " --> pdb=" O LEU E1608 " (cutoff:3.500A) Processing helix chain 'E' and resid 1620 through 1625 Processing helix chain 'E' and resid 1626 through 1631 removed outlier: 3.806A pdb=" N GLN E1630 " --> pdb=" O SER E1626 " (cutoff:3.500A) Processing helix chain 'E' and resid 1764 through 1773 Processing helix chain 'E' and resid 1773 through 1786 Processing helix chain 'E' and resid 1788 through 1797 removed outlier: 3.808A pdb=" N ARG E1794 " --> pdb=" O ASP E1790 " (cutoff:3.500A) Processing helix chain 'E' and resid 1818 through 1823 Processing helix chain 'E' and resid 1836 through 1844 removed outlier: 3.522A pdb=" N VAL E1840 " --> pdb=" O ASP E1836 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA E1841 " --> pdb=" O PRO E1837 " (cutoff:3.500A) Processing helix chain 'E' and resid 1845 through 1869 Processing helix chain 'E' and resid 1872 through 1886 removed outlier: 3.653A pdb=" N LEU E1876 " --> pdb=" O GLU E1872 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASN E1877 " --> pdb=" O ARG E1873 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA E1886 " --> pdb=" O TRP E1882 " (cutoff:3.500A) Processing helix chain 'E' and resid 1886 through 1891 removed outlier: 3.616A pdb=" N LEU E1890 " --> pdb=" O ALA E1886 " (cutoff:3.500A) Processing helix chain 'E' and resid 1906 through 1911 Processing helix chain 'E' and resid 1912 through 1928 Processing helix chain 'E' and resid 1953 through 1972 removed outlier: 3.807A pdb=" N TYR E1959 " --> pdb=" O VAL E1955 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N TRP E1960 " --> pdb=" O MET E1956 " (cutoff:3.500A) Processing helix chain 'E' and resid 2018 through 2105 removed outlier: 3.901A pdb=" N GLU E2024 " --> pdb=" O PRO E2020 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLN E2032 " --> pdb=" O GLY E2028 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU E2033 " --> pdb=" O MET E2029 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLN E2035 " --> pdb=" O SER E2031 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU E2062 " --> pdb=" O ASN E2058 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE E2064 " --> pdb=" O ALA E2060 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N LEU E2065 " --> pdb=" O ALA E2061 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N THR E2066 " --> pdb=" O GLU E2062 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASP E2072 " --> pdb=" O LEU E2068 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N THR E2083 " --> pdb=" O ASP E2079 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER E2094 " --> pdb=" O ALA E2090 " (cutoff:3.500A) Processing helix chain 'E' and resid 2108 through 2121 removed outlier: 3.714A pdb=" N GLN E2113 " --> pdb=" O ALA E2109 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N MET E2115 " --> pdb=" O GLU E2111 " (cutoff:3.500A) Processing helix chain 'E' and resid 2124 through 2139 Processing helix chain 'E' and resid 2155 through 2244 removed outlier: 3.691A pdb=" N ASN E2170 " --> pdb=" O GLU E2166 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA E2199 " --> pdb=" O GLN E2195 " (cutoff:3.500A) Processing helix chain 'E' and resid 2247 through 2284 removed outlier: 3.704A pdb=" N TYR E2251 " --> pdb=" O ASN E2247 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ALA E2260 " --> pdb=" O GLY E2256 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU E2268 " --> pdb=" O GLN E2264 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA E2271 " --> pdb=" O ASP E2267 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ARG E2272 " --> pdb=" O LEU E2268 " (cutoff:3.500A) Processing helix chain 'E' and resid 2305 through 2323 removed outlier: 3.541A pdb=" N LEU E2312 " --> pdb=" O GLU E2308 " (cutoff:3.500A) Processing helix chain 'E' and resid 2337 through 2342 Processing helix chain 'E' and resid 2352 through 2363 removed outlier: 3.720A pdb=" N ASP E2358 " --> pdb=" O ALA E2354 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N SER E2362 " --> pdb=" O ASP E2358 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLN E2363 " --> pdb=" O LYS E2359 " (cutoff:3.500A) Processing helix chain 'E' and resid 2398 through 2402 removed outlier: 3.601A pdb=" N TYR E2402 " --> pdb=" O ARG E2399 " (cutoff:3.500A) Processing helix chain 'E' and resid 2499 through 2503 Processing sheet with id=AA1, first strand: chain 'A' and resid 159 through 160 Processing sheet with id=AA2, first strand: chain 'A' and resid 299 through 300 removed outlier: 4.210A pdb=" N LYS A 299 " --> pdb=" O GLU A 307 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU A 307 " --> pdb=" O LYS A 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 312 through 318 removed outlier: 3.598A pdb=" N THR A 315 " --> pdb=" O TYR A 328 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA A 423 " --> pdb=" O THR A 335 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N TYR A 367 " --> pdb=" O VAL A 413 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N LEU A 368 " --> pdb=" O ARG A 380 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ARG A 380 " --> pdb=" O LEU A 368 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ILE A 370 " --> pdb=" O LEU A 378 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 341 through 347 Processing sheet with id=AA5, first strand: chain 'A' and resid 1096 through 1098 Processing sheet with id=AA6, first strand: chain 'A' and resid 1122 through 1123 Processing sheet with id=AA7, first strand: chain 'A' and resid 1131 through 1132 removed outlier: 3.568A pdb=" N LYS A1135 " --> pdb=" O ASN A1132 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1158 through 1162 removed outlier: 3.509A pdb=" N VAL A1161 " --> pdb=" O TYR A1168 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1233 through 1239 removed outlier: 3.664A pdb=" N TYR A1239 " --> pdb=" O THR A1244 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N THR A1244 " --> pdb=" O TYR A1239 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1300 through 1302 removed outlier: 4.282A pdb=" N ARG A1300 " --> pdb=" O LEU A1586 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N LEU A1584 " --> pdb=" O VAL A1302 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR A1585 " --> pdb=" O GLN A1597 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1310 through 1311 removed outlier: 3.928A pdb=" N ALA A1557 " --> pdb=" O GLY A1566 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N GLY A1566 " --> pdb=" O ALA A1557 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1310 through 1311 Processing sheet with id=AB4, first strand: chain 'A' and resid 1331 through 1332 Processing sheet with id=AB5, first strand: chain 'A' and resid 1340 through 1345 removed outlier: 3.527A pdb=" N LYS A1343 " --> pdb=" O LYS A1350 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASP A1348 " --> pdb=" O ALA A1345 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE A1353 " --> pdb=" O LEU A1535 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1443 through 1450 removed outlier: 3.755A pdb=" N ASN A1449 " --> pdb=" O SER A1432 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N SER A1432 " --> pdb=" O ASN A1449 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N TYR A1388 " --> pdb=" O PRO A1486 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N GLU A1488 " --> pdb=" O ILE A1386 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ILE A1386 " --> pdb=" O GLU A1488 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ASN A1490 " --> pdb=" O LYS A1384 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N LYS A1384 " --> pdb=" O ASN A1490 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1633 through 1635 Processing sheet with id=AB8, first strand: chain 'A' and resid 1686 through 1693 removed outlier: 3.521A pdb=" N ILE A1686 " --> pdb=" O ILE A1647 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N TYR A1642 " --> pdb=" O LEU A1750 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N SER A1746 " --> pdb=" O VAL A1646 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1673 through 1680 removed outlier: 6.377A pdb=" N LEU A1663 " --> pdb=" O ILE A1676 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N SER A1678 " --> pdb=" O PHE A1661 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N PHE A1661 " --> pdb=" O SER A1678 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 2144 through 2146 Processing sheet with id=AC2, first strand: chain 'A' and resid 2148 through 2150 Processing sheet with id=AC3, first strand: chain 'A' and resid 2329 through 2336 removed outlier: 6.704A pdb=" N ILE A2508 " --> pdb=" O VAL A2417 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N VAL A2417 " --> pdb=" O ILE A2508 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N HIS A2510 " --> pdb=" O ILE A2415 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ILE A2415 " --> pdb=" O HIS A2510 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ARG A2512 " --> pdb=" O LYS A2413 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 2369 through 2370 removed outlier: 3.717A pdb=" N SER A2370 " --> pdb=" O ASN A2373 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASN A2373 " --> pdb=" O SER A2370 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ASN A2374 " --> pdb=" O SER A2390 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA A2431 " --> pdb=" O VAL A2450 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 159 through 160 Processing sheet with id=AC6, first strand: chain 'B' and resid 299 through 300 removed outlier: 4.210A pdb=" N LYS B 299 " --> pdb=" O GLU B 307 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU B 307 " --> pdb=" O LYS B 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'B' and resid 312 through 318 removed outlier: 3.598A pdb=" N THR B 315 " --> pdb=" O TYR B 328 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA B 423 " --> pdb=" O THR B 335 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N TYR B 367 " --> pdb=" O VAL B 413 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N LEU B 368 " --> pdb=" O ARG B 380 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ARG B 380 " --> pdb=" O LEU B 368 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ILE B 370 " --> pdb=" O LEU B 378 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 341 through 347 Processing sheet with id=AC9, first strand: chain 'B' and resid 1096 through 1098 Processing sheet with id=AD1, first strand: chain 'B' and resid 1122 through 1123 Processing sheet with id=AD2, first strand: chain 'B' and resid 1131 through 1132 removed outlier: 3.567A pdb=" N LYS B1135 " --> pdb=" O ASN B1132 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1158 through 1162 removed outlier: 3.509A pdb=" N VAL B1161 " --> pdb=" O TYR B1168 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1233 through 1239 removed outlier: 3.663A pdb=" N TYR B1239 " --> pdb=" O THR B1244 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N THR B1244 " --> pdb=" O TYR B1239 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1300 through 1302 removed outlier: 4.282A pdb=" N ARG B1300 " --> pdb=" O LEU B1586 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N LEU B1584 " --> pdb=" O VAL B1302 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR B1585 " --> pdb=" O GLN B1597 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 1310 through 1311 removed outlier: 3.927A pdb=" N ALA B1557 " --> pdb=" O GLY B1566 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N GLY B1566 " --> pdb=" O ALA B1557 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 1310 through 1311 Processing sheet with id=AD8, first strand: chain 'B' and resid 1331 through 1332 Processing sheet with id=AD9, first strand: chain 'B' and resid 1340 through 1345 removed outlier: 3.526A pdb=" N LYS B1343 " --> pdb=" O LYS B1350 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASP B1348 " --> pdb=" O ALA B1345 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE B1353 " --> pdb=" O LEU B1535 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 1443 through 1450 removed outlier: 3.755A pdb=" N ASN B1449 " --> pdb=" O SER B1432 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N SER B1432 " --> pdb=" O ASN B1449 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N TYR B1388 " --> pdb=" O PRO B1486 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N GLU B1488 " --> pdb=" O ILE B1386 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ILE B1386 " --> pdb=" O GLU B1488 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ASN B1490 " --> pdb=" O LYS B1384 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N LYS B1384 " --> pdb=" O ASN B1490 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 1633 through 1635 Processing sheet with id=AE3, first strand: chain 'B' and resid 1686 through 1693 removed outlier: 3.522A pdb=" N ILE B1686 " --> pdb=" O ILE B1647 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N TYR B1642 " --> pdb=" O LEU B1750 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N SER B1746 " --> pdb=" O VAL B1646 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 1673 through 1680 removed outlier: 6.376A pdb=" N LEU B1663 " --> pdb=" O ILE B1676 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N SER B1678 " --> pdb=" O PHE B1661 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N PHE B1661 " --> pdb=" O SER B1678 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 2148 through 2150 Processing sheet with id=AE6, first strand: chain 'B' and resid 2329 through 2336 removed outlier: 6.704A pdb=" N ILE B2508 " --> pdb=" O VAL B2417 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N VAL B2417 " --> pdb=" O ILE B2508 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N HIS B2510 " --> pdb=" O ILE B2415 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ILE B2415 " --> pdb=" O HIS B2510 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ARG B2512 " --> pdb=" O LYS B2413 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'B' and resid 2369 through 2370 removed outlier: 3.719A pdb=" N SER B2370 " --> pdb=" O ASN B2373 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASN B2373 " --> pdb=" O SER B2370 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ASN B2374 " --> pdb=" O SER B2390 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA B2431 " --> pdb=" O VAL B2450 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 159 through 160 Processing sheet with id=AE9, first strand: chain 'C' and resid 299 through 300 removed outlier: 4.210A pdb=" N LYS C 299 " --> pdb=" O GLU C 307 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU C 307 " --> pdb=" O LYS C 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE9 Processing sheet with id=AF1, first strand: chain 'C' and resid 312 through 318 removed outlier: 3.598A pdb=" N THR C 315 " --> pdb=" O TYR C 328 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA C 423 " --> pdb=" O THR C 335 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N TYR C 367 " --> pdb=" O VAL C 413 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N LEU C 368 " --> pdb=" O ARG C 380 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ARG C 380 " --> pdb=" O LEU C 368 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ILE C 370 " --> pdb=" O LEU C 378 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 341 through 347 Processing sheet with id=AF3, first strand: chain 'C' and resid 1096 through 1098 Processing sheet with id=AF4, first strand: chain 'C' and resid 1122 through 1123 Processing sheet with id=AF5, first strand: chain 'C' and resid 1131 through 1132 removed outlier: 3.568A pdb=" N LYS C1135 " --> pdb=" O ASN C1132 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 1158 through 1162 removed outlier: 3.509A pdb=" N VAL C1161 " --> pdb=" O TYR C1168 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 1233 through 1239 removed outlier: 3.664A pdb=" N TYR C1239 " --> pdb=" O THR C1244 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N THR C1244 " --> pdb=" O TYR C1239 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 1300 through 1302 removed outlier: 4.282A pdb=" N ARG C1300 " --> pdb=" O LEU C1586 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N LEU C1584 " --> pdb=" O VAL C1302 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR C1585 " --> pdb=" O GLN C1597 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 1310 through 1311 removed outlier: 3.927A pdb=" N ALA C1557 " --> pdb=" O GLY C1566 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N GLY C1566 " --> pdb=" O ALA C1557 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'C' and resid 1310 through 1311 Processing sheet with id=AG2, first strand: chain 'C' and resid 1331 through 1332 Processing sheet with id=AG3, first strand: chain 'C' and resid 1340 through 1345 removed outlier: 3.526A pdb=" N LYS C1343 " --> pdb=" O LYS C1350 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASP C1348 " --> pdb=" O ALA C1345 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE C1353 " --> pdb=" O LEU C1535 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'C' and resid 1443 through 1450 removed outlier: 3.757A pdb=" N ASN C1449 " --> pdb=" O SER C1432 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N SER C1432 " --> pdb=" O ASN C1449 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N TYR C1388 " --> pdb=" O PRO C1486 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N GLU C1488 " --> pdb=" O ILE C1386 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ILE C1386 " --> pdb=" O GLU C1488 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ASN C1490 " --> pdb=" O LYS C1384 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N LYS C1384 " --> pdb=" O ASN C1490 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'C' and resid 1633 through 1635 Processing sheet with id=AG6, first strand: chain 'C' and resid 1686 through 1693 removed outlier: 3.521A pdb=" N ILE C1686 " --> pdb=" O ILE C1647 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N TYR C1642 " --> pdb=" O LEU C1750 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N SER C1746 " --> pdb=" O VAL C1646 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'C' and resid 1673 through 1680 removed outlier: 6.376A pdb=" N LEU C1663 " --> pdb=" O ILE C1676 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N SER C1678 " --> pdb=" O PHE C1661 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N PHE C1661 " --> pdb=" O SER C1678 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'C' and resid 2148 through 2150 Processing sheet with id=AG9, first strand: chain 'C' and resid 2329 through 2336 removed outlier: 6.704A pdb=" N ILE C2508 " --> pdb=" O VAL C2417 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N VAL C2417 " --> pdb=" O ILE C2508 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N HIS C2510 " --> pdb=" O ILE C2415 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ILE C2415 " --> pdb=" O HIS C2510 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ARG C2512 " --> pdb=" O LYS C2413 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'C' and resid 2369 through 2370 removed outlier: 3.717A pdb=" N SER C2370 " --> pdb=" O ASN C2373 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASN C2373 " --> pdb=" O SER C2370 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ASN C2374 " --> pdb=" O SER C2390 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA C2431 " --> pdb=" O VAL C2450 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'D' and resid 159 through 160 Processing sheet with id=AH3, first strand: chain 'D' and resid 299 through 300 removed outlier: 4.209A pdb=" N LYS D 299 " --> pdb=" O GLU D 307 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU D 307 " --> pdb=" O LYS D 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH3 Processing sheet with id=AH4, first strand: chain 'D' and resid 312 through 318 removed outlier: 3.598A pdb=" N THR D 315 " --> pdb=" O TYR D 328 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA D 423 " --> pdb=" O THR D 335 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N TYR D 367 " --> pdb=" O VAL D 413 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N LEU D 368 " --> pdb=" O ARG D 380 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ARG D 380 " --> pdb=" O LEU D 368 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ILE D 370 " --> pdb=" O LEU D 378 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'D' and resid 341 through 347 Processing sheet with id=AH6, first strand: chain 'D' and resid 1096 through 1098 Processing sheet with id=AH7, first strand: chain 'D' and resid 1122 through 1123 Processing sheet with id=AH8, first strand: chain 'D' and resid 1131 through 1132 removed outlier: 3.568A pdb=" N LYS D1135 " --> pdb=" O ASN D1132 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'D' and resid 1158 through 1162 removed outlier: 3.509A pdb=" N VAL D1161 " --> pdb=" O TYR D1168 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'D' and resid 1233 through 1239 removed outlier: 3.663A pdb=" N TYR D1239 " --> pdb=" O THR D1244 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N THR D1244 " --> pdb=" O TYR D1239 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'D' and resid 1300 through 1302 removed outlier: 4.282A pdb=" N ARG D1300 " --> pdb=" O LEU D1586 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N LEU D1584 " --> pdb=" O VAL D1302 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR D1585 " --> pdb=" O GLN D1597 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'D' and resid 1310 through 1311 removed outlier: 3.927A pdb=" N ALA D1557 " --> pdb=" O GLY D1566 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N GLY D1566 " --> pdb=" O ALA D1557 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'D' and resid 1310 through 1311 Processing sheet with id=AI5, first strand: chain 'D' and resid 1331 through 1332 Processing sheet with id=AI6, first strand: chain 'D' and resid 1340 through 1345 removed outlier: 3.526A pdb=" N LYS D1343 " --> pdb=" O LYS D1350 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASP D1348 " --> pdb=" O ALA D1345 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE D1353 " --> pdb=" O LEU D1535 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'D' and resid 1443 through 1450 removed outlier: 3.756A pdb=" N ASN D1449 " --> pdb=" O SER D1432 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N SER D1432 " --> pdb=" O ASN D1449 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N TYR D1388 " --> pdb=" O PRO D1486 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N GLU D1488 " --> pdb=" O ILE D1386 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ILE D1386 " --> pdb=" O GLU D1488 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ASN D1490 " --> pdb=" O LYS D1384 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N LYS D1384 " --> pdb=" O ASN D1490 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'D' and resid 1633 through 1635 Processing sheet with id=AI9, first strand: chain 'D' and resid 1686 through 1693 removed outlier: 3.522A pdb=" N ILE D1686 " --> pdb=" O ILE D1647 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N TYR D1642 " --> pdb=" O LEU D1750 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N SER D1746 " --> pdb=" O VAL D1646 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'D' and resid 1673 through 1680 removed outlier: 6.375A pdb=" N LEU D1663 " --> pdb=" O ILE D1676 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N SER D1678 " --> pdb=" O PHE D1661 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N PHE D1661 " --> pdb=" O SER D1678 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'D' and resid 2148 through 2150 Processing sheet with id=AJ3, first strand: chain 'D' and resid 2329 through 2336 removed outlier: 6.705A pdb=" N ILE D2508 " --> pdb=" O VAL D2417 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N VAL D2417 " --> pdb=" O ILE D2508 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N HIS D2510 " --> pdb=" O ILE D2415 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ILE D2415 " --> pdb=" O HIS D2510 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ARG D2512 " --> pdb=" O LYS D2413 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'D' and resid 2369 through 2370 removed outlier: 3.718A pdb=" N SER D2370 " --> pdb=" O ASN D2373 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASN D2373 " --> pdb=" O SER D2370 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ASN D2374 " --> pdb=" O SER D2390 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA D2431 " --> pdb=" O VAL D2450 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'E' and resid 159 through 160 Processing sheet with id=AJ6, first strand: chain 'E' and resid 299 through 300 removed outlier: 4.210A pdb=" N LYS E 299 " --> pdb=" O GLU E 307 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU E 307 " --> pdb=" O LYS E 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AJ6 Processing sheet with id=AJ7, first strand: chain 'E' and resid 312 through 318 removed outlier: 3.598A pdb=" N THR E 315 " --> pdb=" O TYR E 328 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA E 423 " --> pdb=" O THR E 335 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N TYR E 367 " --> pdb=" O VAL E 413 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N LEU E 368 " --> pdb=" O ARG E 380 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ARG E 380 " --> pdb=" O LEU E 368 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ILE E 370 " --> pdb=" O LEU E 378 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'E' and resid 341 through 347 Processing sheet with id=AJ9, first strand: chain 'E' and resid 1096 through 1098 Processing sheet with id=AK1, first strand: chain 'E' and resid 1122 through 1123 Processing sheet with id=AK2, first strand: chain 'E' and resid 1131 through 1132 removed outlier: 3.568A pdb=" N LYS E1135 " --> pdb=" O ASN E1132 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'E' and resid 1158 through 1162 removed outlier: 3.509A pdb=" N VAL E1161 " --> pdb=" O TYR E1168 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'E' and resid 1233 through 1239 removed outlier: 3.664A pdb=" N TYR E1239 " --> pdb=" O THR E1244 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N THR E1244 " --> pdb=" O TYR E1239 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'E' and resid 1300 through 1302 removed outlier: 4.282A pdb=" N ARG E1300 " --> pdb=" O LEU E1586 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N LEU E1584 " --> pdb=" O VAL E1302 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR E1585 " --> pdb=" O GLN E1597 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'E' and resid 1310 through 1311 removed outlier: 3.927A pdb=" N ALA E1557 " --> pdb=" O GLY E1566 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N GLY E1566 " --> pdb=" O ALA E1557 " (cutoff:3.500A) Processing sheet with id=AK7, first strand: chain 'E' and resid 1310 through 1311 Processing sheet with id=AK8, first strand: chain 'E' and resid 1331 through 1332 Processing sheet with id=AK9, first strand: chain 'E' and resid 1340 through 1345 removed outlier: 3.526A pdb=" N LYS E1343 " --> pdb=" O LYS E1350 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASP E1348 " --> pdb=" O ALA E1345 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE E1353 " --> pdb=" O LEU E1535 " (cutoff:3.500A) Processing sheet with id=AL1, first strand: chain 'E' and resid 1443 through 1450 removed outlier: 3.756A pdb=" N ASN E1449 " --> pdb=" O SER E1432 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N SER E1432 " --> pdb=" O ASN E1449 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N TYR E1388 " --> pdb=" O PRO E1486 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N GLU E1488 " --> pdb=" O ILE E1386 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ILE E1386 " --> pdb=" O GLU E1488 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ASN E1490 " --> pdb=" O LYS E1384 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N LYS E1384 " --> pdb=" O ASN E1490 " (cutoff:3.500A) Processing sheet with id=AL2, first strand: chain 'E' and resid 1633 through 1635 Processing sheet with id=AL3, first strand: chain 'E' and resid 1686 through 1693 removed outlier: 3.521A pdb=" N ILE E1686 " --> pdb=" O ILE E1647 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N TYR E1642 " --> pdb=" O LEU E1750 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N SER E1746 " --> pdb=" O VAL E1646 " (cutoff:3.500A) Processing sheet with id=AL4, first strand: chain 'E' and resid 1673 through 1680 removed outlier: 6.376A pdb=" N LEU E1663 " --> pdb=" O ILE E1676 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N SER E1678 " --> pdb=" O PHE E1661 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N PHE E1661 " --> pdb=" O SER E1678 " (cutoff:3.500A) Processing sheet with id=AL5, first strand: chain 'E' and resid 2329 through 2336 removed outlier: 6.705A pdb=" N ILE E2508 " --> pdb=" O VAL E2417 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N VAL E2417 " --> pdb=" O ILE E2508 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N HIS E2510 " --> pdb=" O ILE E2415 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ILE E2415 " --> pdb=" O HIS E2510 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ARG E2512 " --> pdb=" O LYS E2413 " (cutoff:3.500A) Processing sheet with id=AL6, first strand: chain 'E' and resid 2369 through 2370 removed outlier: 3.718A pdb=" N SER E2370 " --> pdb=" O ASN E2373 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASN E2373 " --> pdb=" O SER E2370 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASN E2374 " --> pdb=" O SER E2390 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA E2431 " --> pdb=" O VAL E2450 " (cutoff:3.500A) 4646 hydrogen bonds defined for protein. 13383 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 67.81 Time building geometry restraints manager: 31.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 31887 1.34 - 1.46: 17934 1.46 - 1.58: 49104 1.58 - 1.69: 0 1.69 - 1.81: 570 Bond restraints: 99495 Sorted by residual: bond pdb=" C THR B 198 " pdb=" N PRO B 199 " ideal model delta sigma weight residual 1.334 1.402 -0.068 2.34e-02 1.83e+03 8.51e+00 bond pdb=" C THR D 198 " pdb=" N PRO D 199 " ideal model delta sigma weight residual 1.334 1.402 -0.068 2.34e-02 1.83e+03 8.38e+00 bond pdb=" C THR E 198 " pdb=" N PRO E 199 " ideal model delta sigma weight residual 1.334 1.402 -0.068 2.34e-02 1.83e+03 8.35e+00 bond pdb=" C THR A 198 " pdb=" N PRO A 199 " ideal model delta sigma weight residual 1.334 1.401 -0.068 2.34e-02 1.83e+03 8.34e+00 bond pdb=" C THR C 198 " pdb=" N PRO C 199 " ideal model delta sigma weight residual 1.334 1.401 -0.067 2.34e-02 1.83e+03 8.20e+00 ... (remaining 99490 not shown) Histogram of bond angle deviations from ideal: 98.53 - 105.63: 1790 105.63 - 112.74: 51061 112.74 - 119.84: 34597 119.84 - 126.95: 46476 126.95 - 134.06: 1216 Bond angle restraints: 135140 Sorted by residual: angle pdb=" C THR A2381 " pdb=" N ASP A2382 " pdb=" CA ASP A2382 " ideal model delta sigma weight residual 121.54 131.39 -9.85 1.91e+00 2.74e-01 2.66e+01 angle pdb=" C THR C2381 " pdb=" N ASP C2382 " pdb=" CA ASP C2382 " ideal model delta sigma weight residual 121.54 131.39 -9.85 1.91e+00 2.74e-01 2.66e+01 angle pdb=" C THR D2381 " pdb=" N ASP D2382 " pdb=" CA ASP D2382 " ideal model delta sigma weight residual 121.54 131.34 -9.80 1.91e+00 2.74e-01 2.63e+01 angle pdb=" C THR B2381 " pdb=" N ASP B2382 " pdb=" CA ASP B2382 " ideal model delta sigma weight residual 121.54 131.34 -9.80 1.91e+00 2.74e-01 2.63e+01 angle pdb=" C THR E2381 " pdb=" N ASP E2382 " pdb=" CA ASP E2382 " ideal model delta sigma weight residual 121.54 131.31 -9.77 1.91e+00 2.74e-01 2.62e+01 ... (remaining 135135 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.07: 58164 17.07 - 34.15: 1160 34.15 - 51.22: 261 51.22 - 68.30: 15 68.30 - 85.37: 45 Dihedral angle restraints: 59645 sinusoidal: 23510 harmonic: 36135 Sorted by residual: dihedral pdb=" CA THR A 521 " pdb=" C THR A 521 " pdb=" N PRO A 522 " pdb=" CA PRO A 522 " ideal model delta harmonic sigma weight residual 180.00 137.07 42.93 0 5.00e+00 4.00e-02 7.37e+01 dihedral pdb=" CA THR C 521 " pdb=" C THR C 521 " pdb=" N PRO C 522 " pdb=" CA PRO C 522 " ideal model delta harmonic sigma weight residual 180.00 137.11 42.89 0 5.00e+00 4.00e-02 7.36e+01 dihedral pdb=" CA THR E 521 " pdb=" C THR E 521 " pdb=" N PRO E 522 " pdb=" CA PRO E 522 " ideal model delta harmonic sigma weight residual 180.00 137.12 42.88 0 5.00e+00 4.00e-02 7.36e+01 ... (remaining 59642 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 12819 0.065 - 0.131: 1922 0.131 - 0.196: 169 0.196 - 0.262: 42 0.262 - 0.327: 8 Chirality restraints: 14960 Sorted by residual: chirality pdb=" CB THR B 521 " pdb=" CA THR B 521 " pdb=" OG1 THR B 521 " pdb=" CG2 THR B 521 " both_signs ideal model delta sigma weight residual False 2.55 2.22 0.33 2.00e-01 2.50e+01 2.67e+00 chirality pdb=" CB THR E 521 " pdb=" CA THR E 521 " pdb=" OG1 THR E 521 " pdb=" CG2 THR E 521 " both_signs ideal model delta sigma weight residual False 2.55 2.23 0.33 2.00e-01 2.50e+01 2.65e+00 chirality pdb=" CB THR C 521 " pdb=" CA THR C 521 " pdb=" OG1 THR C 521 " pdb=" CG2 THR C 521 " both_signs ideal model delta sigma weight residual False 2.55 2.23 0.32 2.00e-01 2.50e+01 2.64e+00 ... (remaining 14957 not shown) Planarity restraints: 17580 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 521 " 0.058 5.00e-02 4.00e+02 8.83e-02 1.25e+01 pdb=" N PRO B 522 " -0.153 5.00e-02 4.00e+02 pdb=" CA PRO B 522 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO B 522 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR D 521 " -0.058 5.00e-02 4.00e+02 8.83e-02 1.25e+01 pdb=" N PRO D 522 " 0.153 5.00e-02 4.00e+02 pdb=" CA PRO D 522 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO D 522 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 521 " -0.058 5.00e-02 4.00e+02 8.82e-02 1.25e+01 pdb=" N PRO C 522 " 0.153 5.00e-02 4.00e+02 pdb=" CA PRO C 522 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO C 522 " -0.049 5.00e-02 4.00e+02 ... (remaining 17577 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 11611 2.75 - 3.29: 89861 3.29 - 3.83: 159845 3.83 - 4.36: 199333 4.36 - 4.90: 340218 Nonbonded interactions: 800868 Sorted by model distance: nonbonded pdb=" O PRO B 194 " pdb=" OH TYR B 285 " model vdw 2.217 2.440 nonbonded pdb=" O PRO D 194 " pdb=" OH TYR D 285 " model vdw 2.217 2.440 nonbonded pdb=" O PRO A 194 " pdb=" OH TYR A 285 " model vdw 2.217 2.440 nonbonded pdb=" O PRO E 194 " pdb=" OH TYR E 285 " model vdw 2.217 2.440 nonbonded pdb=" O PRO C 194 " pdb=" OH TYR C 285 " model vdw 2.217 2.440 ... (remaining 800863 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.080 Extract box with map and model: 14.730 Check model and map are aligned: 1.120 Set scattering table: 0.720 Process input model: 232.100 Find NCS groups from input model: 5.080 Set up NCS constraints: 0.450 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:2.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 259.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 99495 Z= 0.253 Angle : 0.778 13.778 135140 Z= 0.432 Chirality : 0.048 0.327 14960 Planarity : 0.006 0.088 17580 Dihedral : 8.537 85.369 36385 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 0.05 % Allowed : 0.86 % Favored : 99.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.27 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.72 (0.06), residues: 12240 helix: -4.32 (0.03), residues: 5410 sheet: -1.24 (0.11), residues: 2005 loop : -2.20 (0.07), residues: 4825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP B1827 HIS 0.012 0.002 HIS E1888 PHE 0.036 0.002 PHE D1532 TYR 0.043 0.003 TYR E1239 ARG 0.008 0.001 ARG A2189 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 24480 Ramachandran restraints generated. 12240 Oldfield, 0 Emsley, 12240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 24480 Ramachandran restraints generated. 12240 Oldfield, 0 Emsley, 12240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2681 residues out of total 10500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 2676 time to evaluate : 8.692 Fit side-chains REVERT: A 231 MET cc_start: 0.8178 (mmm) cc_final: 0.7969 (mmm) REVERT: A 287 ASN cc_start: 0.8417 (t0) cc_final: 0.8141 (t0) REVERT: A 333 GLU cc_start: 0.8127 (mt-10) cc_final: 0.7777 (mt-10) REVERT: A 356 ASP cc_start: 0.7910 (m-30) cc_final: 0.7573 (m-30) REVERT: A 803 MET cc_start: 0.8008 (tmm) cc_final: 0.7762 (tmm) REVERT: A 1003 ASN cc_start: 0.8459 (t0) cc_final: 0.8053 (t0) REVERT: A 1115 GLU cc_start: 0.6672 (mm-30) cc_final: 0.6274 (tp30) REVERT: A 1162 ILE cc_start: 0.8463 (mm) cc_final: 0.8168 (mm) REVERT: A 1321 ASP cc_start: 0.7797 (t70) cc_final: 0.7404 (t0) REVERT: A 1341 ASN cc_start: 0.8317 (m-40) cc_final: 0.8116 (m110) REVERT: A 1369 ARG cc_start: 0.8385 (tpp80) cc_final: 0.8137 (ttm110) REVERT: A 1454 ASP cc_start: 0.8314 (m-30) cc_final: 0.7899 (m-30) REVERT: A 1508 GLU cc_start: 0.7292 (tt0) cc_final: 0.7071 (tt0) REVERT: A 1726 VAL cc_start: 0.8825 (t) cc_final: 0.8586 (m) REVERT: A 2021 HIS cc_start: 0.8141 (m90) cc_final: 0.7919 (m90) REVERT: A 2029 MET cc_start: 0.8924 (tpt) cc_final: 0.8690 (tpt) REVERT: A 2045 GLU cc_start: 0.7901 (mt-10) cc_final: 0.7686 (mt-10) REVERT: A 2204 LYS cc_start: 0.8761 (mttt) cc_final: 0.8486 (mtpt) REVERT: A 2456 ASP cc_start: 0.7855 (t0) cc_final: 0.7606 (t0) REVERT: A 2468 LYS cc_start: 0.8849 (mttt) cc_final: 0.8483 (mttp) REVERT: B 136 TYR cc_start: 0.8595 (m-80) cc_final: 0.7848 (m-80) REVERT: B 264 TYR cc_start: 0.8603 (t80) cc_final: 0.8002 (t80) REVERT: B 309 SER cc_start: 0.8734 (t) cc_final: 0.8329 (p) REVERT: B 348 PHE cc_start: 0.6332 (m-10) cc_final: 0.5969 (m-10) REVERT: B 453 SER cc_start: 0.8676 (t) cc_final: 0.8312 (m) REVERT: B 543 THR cc_start: 0.7875 (p) cc_final: 0.7611 (p) REVERT: B 1015 ARG cc_start: 0.8238 (mtt180) cc_final: 0.7795 (mmp-170) REVERT: B 1255 THR cc_start: 0.9144 (p) cc_final: 0.8917 (p) REVERT: B 1898 LEU cc_start: 0.7926 (tm) cc_final: 0.7703 (mt) REVERT: B 1945 THR cc_start: 0.8022 (t) cc_final: 0.7702 (m) REVERT: B 2022 MET cc_start: 0.8045 (tpp) cc_final: 0.7739 (tpp) REVERT: B 2035 GLN cc_start: 0.8431 (mt0) cc_final: 0.8184 (mt0) REVERT: B 2177 ASP cc_start: 0.7805 (m-30) cc_final: 0.7499 (m-30) REVERT: B 2281 ARG cc_start: 0.8537 (mtt180) cc_final: 0.7949 (mtt90) REVERT: B 2351 PHE cc_start: 0.7056 (p90) cc_final: 0.6638 (p90) REVERT: C 97 SER cc_start: 0.8643 (m) cc_final: 0.8370 (t) REVERT: C 183 THR cc_start: 0.8812 (m) cc_final: 0.8599 (m) REVERT: C 572 ASP cc_start: 0.7062 (m-30) cc_final: 0.6814 (m-30) REVERT: C 635 ASN cc_start: 0.7913 (t0) cc_final: 0.7619 (t0) REVERT: C 904 GLN cc_start: 0.6797 (mm110) cc_final: 0.6541 (mm-40) REVERT: C 973 ILE cc_start: 0.8857 (tt) cc_final: 0.8641 (tt) REVERT: C 1015 ARG cc_start: 0.7679 (mtt180) cc_final: 0.7272 (mmp-170) REVERT: C 1273 MET cc_start: 0.8804 (mmp) cc_final: 0.8479 (mmp) REVERT: C 1278 MET cc_start: 0.9287 (mtt) cc_final: 0.8900 (mtt) REVERT: C 1596 MET cc_start: 0.9076 (ttp) cc_final: 0.8595 (ttp) REVERT: C 1619 THR cc_start: 0.8766 (m) cc_final: 0.8512 (p) REVERT: C 1680 GLN cc_start: 0.8093 (mm-40) cc_final: 0.7710 (mm-40) REVERT: C 1810 GLN cc_start: 0.7981 (tt0) cc_final: 0.7692 (tt0) REVERT: C 1913 ILE cc_start: 0.8883 (pt) cc_final: 0.8661 (mt) REVERT: C 1920 ASP cc_start: 0.8446 (m-30) cc_final: 0.8212 (m-30) REVERT: C 2165 MET cc_start: 0.8500 (mtm) cc_final: 0.8241 (mtp) REVERT: C 2177 ASP cc_start: 0.8085 (m-30) cc_final: 0.7691 (m-30) REVERT: C 2218 GLU cc_start: 0.7866 (mt-10) cc_final: 0.7598 (mt-10) REVERT: C 2263 PHE cc_start: 0.8627 (t80) cc_final: 0.8369 (t80) REVERT: C 2386 SER cc_start: 0.8977 (m) cc_final: 0.8573 (p) REVERT: C 2494 LYS cc_start: 0.8213 (mttt) cc_final: 0.8010 (ttpp) REVERT: D 136 TYR cc_start: 0.8554 (m-80) cc_final: 0.8325 (m-80) REVERT: D 407 GLU cc_start: 0.7923 (tt0) cc_final: 0.7608 (tt0) REVERT: D 683 LYS cc_start: 0.7514 (ttpp) cc_final: 0.7143 (tptt) REVERT: D 2022 MET cc_start: 0.8389 (tpp) cc_final: 0.8116 (tpp) REVERT: D 2264 GLN cc_start: 0.8577 (mt0) cc_final: 0.8376 (mt0) REVERT: D 2422 LEU cc_start: 0.8497 (mp) cc_final: 0.8228 (mt) REVERT: E 51 ASP cc_start: 0.8154 (m-30) cc_final: 0.7844 (m-30) REVERT: E 186 MET cc_start: 0.9108 (mmt) cc_final: 0.8817 (mmp) REVERT: E 290 ASP cc_start: 0.7601 (m-30) cc_final: 0.7400 (m-30) REVERT: E 524 LEU cc_start: 0.8709 (tp) cc_final: 0.8489 (tt) REVERT: E 774 ASN cc_start: 0.8681 (t0) cc_final: 0.8471 (t0) REVERT: E 805 THR cc_start: 0.8851 (m) cc_final: 0.8011 (p) REVERT: E 1020 ASP cc_start: 0.8067 (m-30) cc_final: 0.7716 (m-30) REVERT: E 1463 LYS cc_start: 0.8429 (mttt) cc_final: 0.8062 (mmtt) REVERT: E 1884 MET cc_start: 0.8931 (mmt) cc_final: 0.8149 (mmt) REVERT: E 1920 ASP cc_start: 0.8077 (m-30) cc_final: 0.7731 (m-30) REVERT: E 2022 MET cc_start: 0.8109 (tpp) cc_final: 0.7726 (tpp) REVERT: E 2042 ASN cc_start: 0.8141 (t160) cc_final: 0.7270 (m-40) REVERT: E 2104 ASP cc_start: 0.7897 (m-30) cc_final: 0.7598 (m-30) REVERT: E 2125 THR cc_start: 0.9051 (m) cc_final: 0.8755 (p) REVERT: E 2311 MET cc_start: 0.8722 (tpp) cc_final: 0.8178 (tpt) REVERT: E 2317 MET cc_start: 0.8695 (ttm) cc_final: 0.8489 (ttm) REVERT: E 2385 THR cc_start: 0.8981 (p) cc_final: 0.8774 (t) outliers start: 5 outliers final: 0 residues processed: 2681 average time/residue: 0.9922 time to fit residues: 4461.6087 Evaluate side-chains 1317 residues out of total 10500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1317 time to evaluate : 8.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1225 random chunks: chunk 1034 optimal weight: 0.5980 chunk 928 optimal weight: 3.9990 chunk 515 optimal weight: 5.9990 chunk 317 optimal weight: 2.9990 chunk 626 optimal weight: 0.8980 chunk 496 optimal weight: 4.9990 chunk 960 optimal weight: 0.8980 chunk 371 optimal weight: 0.1980 chunk 583 optimal weight: 0.7980 chunk 714 optimal weight: 3.9990 chunk 1112 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN ** A 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 130 HIS A 340 GLN A 511 GLN A 587 ASN A 618 ASN ** A 749 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 834 GLN A 858 HIS A 875 ASN A 914 GLN A1043 ASN A1189 GLN A1229 ASN A1240 GLN A1293 GLN A1304 ASN A1373 ASN A1531 GLN A1543 ASN A1630 GLN A1674 HIS A1843 HIS ** A2047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2285 ASN A2348 ASN A2452 HIS A2459 GLN B 56 GLN ** B 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 ASN B 102 GLN B 130 HIS B 587 ASN B 875 ASN B1090 ASN B1180 GLN B1293 GLN B1304 ASN B1373 ASN B1531 GLN ** B1547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1630 GLN B1843 HIS B1919 HIS B2285 ASN B2348 ASN B2373 ASN B2459 GLN B2497 GLN C 94 ASN C 102 GLN C 130 HIS C 302 ASN C 556 ASN C 587 ASN ** C 749 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 834 GLN C 858 HIS C 875 ASN C1090 ASN C1180 GLN C1289 ASN C1293 GLN C1304 ASN C1373 ASN C1413 ASN ** C1462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1531 GLN C1543 ASN C1630 GLN C1674 HIS C1764 ASN C1785 HIS C1815 GLN C1843 HIS C2042 ASN ** C2047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2205 GLN C2242 GLN ** C2252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C2285 ASN C2348 ASN C2459 GLN ** C2497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2505 ASN D 130 HIS D 206 ASN D 373 ASN D 587 ASN D 618 ASN D 709 HIS D 834 GLN D 858 HIS D1103 ASN D1189 GLN D1293 GLN D1304 ASN D1373 ASN D1509 GLN D1531 GLN D1701 GLN D1764 ASN D1972 HIS D2035 GLN D2278 GLN D2348 ASN D2452 HIS D2459 GLN E 130 HIS E 514 GLN ** E 581 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 618 ASN E 761 GLN E 772 ASN E 834 GLN E 858 HIS E 875 ASN E1180 GLN E1293 GLN E1304 ASN E1373 ASN ** E1394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1418 ASN E1425 HIS E1531 GLN E1543 ASN E1589 ASN E1674 HIS E1787 GLN E1808 HIS E1810 GLN E1843 HIS E1928 GLN E1951 GLN E2035 GLN E2042 ASN ** E2047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E2230 GLN ** E2252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 127 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.2555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 99495 Z= 0.168 Angle : 0.522 8.660 135140 Z= 0.281 Chirality : 0.041 0.321 14960 Planarity : 0.005 0.076 17580 Dihedral : 4.687 39.277 13370 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.30 % Allowed : 6.31 % Favored : 92.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.91 % Twisted General : 0.00 % 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: -2.05 (0.07), residues: 12240 helix: -1.25 (0.06), residues: 5530 sheet: -0.67 (0.11), residues: 2000 loop : -1.60 (0.08), residues: 4710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 731 HIS 0.005 0.001 HIS A 767 PHE 0.017 0.001 PHE E 937 TYR 0.021 0.001 TYR B1239 ARG 0.006 0.000 ARG C 462 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 24480 Ramachandran restraints generated. 12240 Oldfield, 0 Emsley, 12240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 24480 Ramachandran restraints generated. 12240 Oldfield, 0 Emsley, 12240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1501 residues out of total 10500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 1365 time to evaluate : 8.768 Fit side-chains revert: symmetry clash REVERT: A 157 ILE cc_start: 0.9288 (mt) cc_final: 0.9058 (mm) REVERT: A 262 GLU cc_start: 0.8034 (tm-30) cc_final: 0.7492 (tm-30) REVERT: A 287 ASN cc_start: 0.8695 (t0) cc_final: 0.8332 (t0) REVERT: A 333 GLU cc_start: 0.8203 (mt-10) cc_final: 0.7816 (mt-10) REVERT: A 356 ASP cc_start: 0.8255 (m-30) cc_final: 0.7983 (m-30) REVERT: A 803 MET cc_start: 0.8477 (tmm) cc_final: 0.7981 (tmm) REVERT: A 1003 ASN cc_start: 0.8322 (t0) cc_final: 0.7861 (t0) REVERT: A 1079 MET cc_start: 0.8972 (mmp) cc_final: 0.8730 (mmt) REVERT: A 1162 ILE cc_start: 0.8745 (mm) cc_final: 0.8396 (mm) REVERT: A 1321 ASP cc_start: 0.7393 (t70) cc_final: 0.6917 (t0) REVERT: A 1454 ASP cc_start: 0.8703 (m-30) cc_final: 0.8220 (m-30) REVERT: A 1508 GLU cc_start: 0.7187 (tt0) cc_final: 0.6972 (tt0) REVERT: A 1746 SER cc_start: 0.8101 (t) cc_final: 0.7797 (m) REVERT: A 1898 LEU cc_start: 0.7862 (OUTLIER) cc_final: 0.7654 (pp) REVERT: A 1927 ARG cc_start: 0.9056 (OUTLIER) cc_final: 0.8686 (ttp-110) REVERT: A 2029 MET cc_start: 0.8874 (tpt) cc_final: 0.8528 (tpt) REVERT: A 2311 MET cc_start: 0.8585 (tpp) cc_final: 0.8063 (mmm) REVERT: A 2422 LEU cc_start: 0.8678 (mm) cc_final: 0.8318 (mm) REVERT: A 2456 ASP cc_start: 0.7747 (t0) cc_final: 0.7468 (t0) REVERT: A 2468 LYS cc_start: 0.8829 (mttt) cc_final: 0.8616 (mttp) REVERT: B 264 TYR cc_start: 0.8462 (t80) cc_final: 0.8147 (t80) REVERT: B 280 GLU cc_start: 0.8182 (tp30) cc_final: 0.7858 (mm-30) REVERT: B 348 PHE cc_start: 0.6454 (m-10) cc_final: 0.5906 (m-10) REVERT: B 448 ARG cc_start: 0.8233 (mtm110) cc_final: 0.7914 (mtm-85) REVERT: B 521 THR cc_start: 0.7237 (OUTLIER) cc_final: 0.6997 (m) REVERT: B 570 ASP cc_start: 0.8099 (t0) cc_final: 0.7867 (t0) REVERT: B 574 LYS cc_start: 0.8486 (mmtt) cc_final: 0.7842 (ttmm) REVERT: B 1015 ARG cc_start: 0.8236 (mtt180) cc_final: 0.7701 (mmp-170) REVERT: B 1870 GLN cc_start: 0.8997 (mp10) cc_final: 0.8778 (mp10) REVERT: B 2022 MET cc_start: 0.8628 (tpp) cc_final: 0.8236 (tpp) REVERT: B 2105 GLU cc_start: 0.7945 (tm-30) cc_final: 0.7643 (tm-30) REVERT: B 2132 ARG cc_start: 0.8073 (mmt180) cc_final: 0.7739 (mmt-90) REVERT: B 2242 GLN cc_start: 0.8330 (mt0) cc_final: 0.7967 (mt0) REVERT: B 2351 PHE cc_start: 0.7585 (p90) cc_final: 0.7178 (p90) REVERT: B 2496 LYS cc_start: 0.8815 (ptmt) cc_final: 0.8557 (ptmm) REVERT: C 148 MET cc_start: 0.8535 (ptm) cc_final: 0.7877 (ptm) REVERT: C 351 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7950 (tt0) REVERT: C 572 ASP cc_start: 0.7205 (m-30) cc_final: 0.6972 (m-30) REVERT: C 797 ASP cc_start: 0.8127 (p0) cc_final: 0.7878 (p0) REVERT: C 1015 ARG cc_start: 0.7592 (mtt180) cc_final: 0.6980 (mmp-170) REVERT: C 1020 ASP cc_start: 0.7758 (m-30) cc_final: 0.7550 (m-30) REVERT: C 1175 LYS cc_start: 0.7974 (mttt) cc_final: 0.7768 (mttp) REVERT: C 1278 MET cc_start: 0.9195 (mtt) cc_final: 0.8958 (mtt) REVERT: C 1596 MET cc_start: 0.8971 (ttp) cc_final: 0.8526 (ttp) REVERT: C 1913 ILE cc_start: 0.8752 (pt) cc_final: 0.8405 (mt) REVERT: C 1920 ASP cc_start: 0.8450 (m-30) cc_final: 0.8170 (m-30) REVERT: C 1961 GLN cc_start: 0.8356 (mt0) cc_final: 0.8050 (mt0) REVERT: C 2263 PHE cc_start: 0.8491 (t80) cc_final: 0.8231 (t80) REVERT: C 2386 SER cc_start: 0.9085 (m) cc_final: 0.8672 (p) REVERT: C 2494 LYS cc_start: 0.8288 (mttt) cc_final: 0.8007 (ttpp) REVERT: D 153 GLN cc_start: 0.8091 (mp10) cc_final: 0.7696 (mp10) REVERT: D 334 TYR cc_start: 0.8535 (m-80) cc_final: 0.8251 (m-80) REVERT: D 363 TYR cc_start: 0.6852 (m-10) cc_final: 0.6525 (m-80) REVERT: D 407 GLU cc_start: 0.8116 (tt0) cc_final: 0.7770 (tt0) REVERT: D 683 LYS cc_start: 0.7553 (ttpp) cc_final: 0.7137 (tptt) REVERT: D 725 MET cc_start: 0.8775 (tpp) cc_final: 0.8561 (tpp) REVERT: D 1079 MET cc_start: 0.9335 (mmt) cc_final: 0.8780 (mmp) REVERT: D 1437 TRP cc_start: 0.8589 (t-100) cc_final: 0.8285 (t-100) REVERT: D 1732 ILE cc_start: 0.8712 (mm) cc_final: 0.8447 (mp) REVERT: D 1857 LEU cc_start: 0.9158 (mt) cc_final: 0.8796 (mt) REVERT: D 2022 MET cc_start: 0.8716 (tpp) cc_final: 0.8436 (tpt) REVERT: D 2311 MET cc_start: 0.8743 (tpp) cc_final: 0.8366 (mmt) REVERT: D 2491 MET cc_start: 0.7925 (OUTLIER) cc_final: 0.7555 (mtp) REVERT: D 2496 LYS cc_start: 0.8304 (ptpp) cc_final: 0.8017 (ptmm) REVERT: E 51 ASP cc_start: 0.8000 (m-30) cc_final: 0.7505 (m-30) REVERT: E 56 GLN cc_start: 0.8228 (tm-30) cc_final: 0.7910 (tt0) REVERT: E 94 ASN cc_start: 0.7924 (m-40) cc_final: 0.7499 (m-40) REVERT: E 171 GLU cc_start: 0.7945 (tp30) cc_final: 0.7647 (tp30) REVERT: E 186 MET cc_start: 0.8922 (mmt) cc_final: 0.8642 (mmp) REVERT: E 276 LEU cc_start: 0.8905 (tp) cc_final: 0.8684 (tp) REVERT: E 431 TYR cc_start: 0.8605 (m-80) cc_final: 0.8282 (m-80) REVERT: E 805 THR cc_start: 0.8888 (m) cc_final: 0.8655 (m) REVERT: E 1020 ASP cc_start: 0.7836 (m-30) cc_final: 0.7458 (m-30) REVERT: E 1079 MET cc_start: 0.8979 (mmm) cc_final: 0.8429 (mmp) REVERT: E 1228 LYS cc_start: 0.8254 (tppt) cc_final: 0.7855 (mmmt) REVERT: E 1463 LYS cc_start: 0.8393 (mttt) cc_final: 0.7897 (mmtt) REVERT: E 1488 GLU cc_start: 0.7210 (tm-30) cc_final: 0.6942 (tm-30) REVERT: E 2042 ASN cc_start: 0.8176 (t0) cc_final: 0.7405 (m-40) REVERT: E 2104 ASP cc_start: 0.8047 (m-30) cc_final: 0.7766 (m-30) REVERT: E 2232 GLU cc_start: 0.7959 (OUTLIER) cc_final: 0.7389 (mp0) REVERT: E 2356 GLU cc_start: 0.8501 (OUTLIER) cc_final: 0.8085 (mm-30) REVERT: E 2385 THR cc_start: 0.8989 (p) cc_final: 0.8764 (t) REVERT: E 2505 ASN cc_start: 0.8378 (t0) cc_final: 0.7630 (t0) outliers start: 136 outliers final: 79 residues processed: 1456 average time/residue: 0.9159 time to fit residues: 2287.6117 Evaluate side-chains 1172 residues out of total 10500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 1086 time to evaluate : 9.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 558 ASP Chi-restraints excluded: chain A residue 572 ASP Chi-restraints excluded: chain A residue 603 ASP Chi-restraints excluded: chain A residue 816 GLU Chi-restraints excluded: chain A residue 1087 GLN Chi-restraints excluded: chain A residue 1139 ASN Chi-restraints excluded: chain A residue 1242 GLU Chi-restraints excluded: chain A residue 1446 THR Chi-restraints excluded: chain A residue 1461 LEU Chi-restraints excluded: chain A residue 1465 ASP Chi-restraints excluded: chain A residue 1576 LEU Chi-restraints excluded: chain A residue 1700 ASN Chi-restraints excluded: chain A residue 1898 LEU Chi-restraints excluded: chain A residue 1927 ARG Chi-restraints excluded: chain A residue 2228 LYS Chi-restraints excluded: chain B residue 240 ASN Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 521 THR Chi-restraints excluded: chain B residue 524 LEU Chi-restraints excluded: chain B residue 601 THR Chi-restraints excluded: chain B residue 603 ASP Chi-restraints excluded: chain B residue 1103 ASN Chi-restraints excluded: chain B residue 1156 SER Chi-restraints excluded: chain B residue 1321 ASP Chi-restraints excluded: chain B residue 1364 TYR Chi-restraints excluded: chain B residue 1459 ASP Chi-restraints excluded: chain B residue 1528 MET Chi-restraints excluded: chain B residue 1675 ILE Chi-restraints excluded: chain B residue 1684 THR Chi-restraints excluded: chain B residue 1719 THR Chi-restraints excluded: chain B residue 1874 ASP Chi-restraints excluded: chain B residue 1898 LEU Chi-restraints excluded: chain B residue 2325 ASP Chi-restraints excluded: chain B residue 2352 SER Chi-restraints excluded: chain B residue 2353 LEU Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 351 GLU Chi-restraints excluded: chain C residue 648 VAL Chi-restraints excluded: chain C residue 928 SER Chi-restraints excluded: chain C residue 1156 SER Chi-restraints excluded: chain C residue 1626 SER Chi-restraints excluded: chain C residue 1830 ASP Chi-restraints excluded: chain C residue 1946 ASP Chi-restraints excluded: chain C residue 2108 ASN Chi-restraints excluded: chain C residue 2434 SER Chi-restraints excluded: chain C residue 2493 GLU Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 163 SER Chi-restraints excluded: chain D residue 195 SER Chi-restraints excluded: chain D residue 275 SER Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 496 LEU Chi-restraints excluded: chain D residue 559 ASP Chi-restraints excluded: chain D residue 603 ASP Chi-restraints excluded: chain D residue 710 SER Chi-restraints excluded: chain D residue 748 THR Chi-restraints excluded: chain D residue 1364 TYR Chi-restraints excluded: chain D residue 1419 GLN Chi-restraints excluded: chain D residue 1461 LEU Chi-restraints excluded: chain D residue 1524 SER Chi-restraints excluded: chain D residue 1652 LEU Chi-restraints excluded: chain D residue 1657 ASP Chi-restraints excluded: chain D residue 2002 THR Chi-restraints excluded: chain D residue 2225 THR Chi-restraints excluded: chain D residue 2390 SER Chi-restraints excluded: chain D residue 2446 GLU Chi-restraints excluded: chain D residue 2491 MET Chi-restraints excluded: chain E residue 101 SER Chi-restraints excluded: chain E residue 468 LEU Chi-restraints excluded: chain E residue 603 ASP Chi-restraints excluded: chain E residue 639 SER Chi-restraints excluded: chain E residue 762 LEU Chi-restraints excluded: chain E residue 1087 GLN Chi-restraints excluded: chain E residue 1139 ASN Chi-restraints excluded: chain E residue 1243 ASP Chi-restraints excluded: chain E residue 1252 GLN Chi-restraints excluded: chain E residue 1396 ASN Chi-restraints excluded: chain E residue 1461 LEU Chi-restraints excluded: chain E residue 1465 ASP Chi-restraints excluded: chain E residue 1652 LEU Chi-restraints excluded: chain E residue 1734 THR Chi-restraints excluded: chain E residue 2232 GLU Chi-restraints excluded: chain E residue 2337 LEU Chi-restraints excluded: chain E residue 2356 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1225 random chunks: chunk 618 optimal weight: 6.9990 chunk 345 optimal weight: 0.6980 chunk 925 optimal weight: 3.9990 chunk 757 optimal weight: 2.9990 chunk 306 optimal weight: 0.0270 chunk 1114 optimal weight: 2.9990 chunk 1203 optimal weight: 5.9990 chunk 992 optimal weight: 0.7980 chunk 1105 optimal weight: 4.9990 chunk 379 optimal weight: 0.2980 chunk 894 optimal weight: 3.9990 overall best weight: 0.9640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 HIS ** A 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 749 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1293 GLN A1304 ASN A1781 GLN A1916 GLN ** B 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 ASN B 709 HIS B1132 ASN ** B1547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1630 GLN B1781 GLN B1812 GLN C 94 ASN C 302 ASN C 709 HIS ** C1293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1304 ASN C1334 ASN ** C1462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 94 ASN D 206 ASN D 834 GLN D1152 ASN D1367 GLN D1397 ASN D1701 GLN D1781 GLN D1785 HIS D1843 HIS ** D2047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2285 ASN E 222 ASN ** E 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 761 GLN ** E1394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1764 ASN E1810 GLN E1812 GLN E1958 ASN ** E2497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.3132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 99495 Z= 0.198 Angle : 0.500 8.226 135140 Z= 0.263 Chirality : 0.041 0.309 14960 Planarity : 0.004 0.074 17580 Dihedral : 4.391 35.481 13370 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.56 % Allowed : 7.37 % Favored : 91.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.00 % 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: -0.53 (0.07), residues: 12240 helix: 0.52 (0.07), residues: 5535 sheet: -0.38 (0.11), residues: 2105 loop : -1.31 (0.08), residues: 4600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 731 HIS 0.007 0.001 HIS D1888 PHE 0.020 0.001 PHE B 937 TYR 0.021 0.001 TYR E 103 ARG 0.006 0.000 ARG D 806 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 24480 Ramachandran restraints generated. 12240 Oldfield, 0 Emsley, 12240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 24480 Ramachandran restraints generated. 12240 Oldfield, 0 Emsley, 12240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1313 residues out of total 10500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 1149 time to evaluate : 8.668 Fit side-chains REVERT: A 262 GLU cc_start: 0.8039 (tm-30) cc_final: 0.7742 (tp30) REVERT: A 287 ASN cc_start: 0.8773 (t0) cc_final: 0.8273 (t0) REVERT: A 356 ASP cc_start: 0.8509 (m-30) cc_final: 0.8277 (m-30) REVERT: A 666 GLU cc_start: 0.8004 (mp0) cc_final: 0.7663 (pm20) REVERT: A 764 MET cc_start: 0.8212 (ttm) cc_final: 0.7789 (ttt) REVERT: A 803 MET cc_start: 0.8572 (tmm) cc_final: 0.8033 (tmm) REVERT: A 839 MET cc_start: 0.9146 (mtp) cc_final: 0.8651 (mtp) REVERT: A 1321 ASP cc_start: 0.7582 (t70) cc_final: 0.7328 (t0) REVERT: A 1454 ASP cc_start: 0.8777 (m-30) cc_final: 0.8372 (m-30) REVERT: A 1627 MET cc_start: 0.8729 (mmm) cc_final: 0.8400 (mmm) REVERT: A 1746 SER cc_start: 0.8073 (t) cc_final: 0.7804 (m) REVERT: A 1927 ARG cc_start: 0.9019 (OUTLIER) cc_final: 0.8630 (ttp-110) REVERT: A 2422 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8276 (mm) REVERT: A 2427 GLN cc_start: 0.7370 (mm110) cc_final: 0.7166 (mm-40) REVERT: A 2456 ASP cc_start: 0.7884 (t0) cc_final: 0.7655 (t0) REVERT: A 2468 LYS cc_start: 0.8901 (mttt) cc_final: 0.8545 (mttt) REVERT: B 309 SER cc_start: 0.8694 (t) cc_final: 0.8333 (p) REVERT: B 348 PHE cc_start: 0.6532 (m-10) cc_final: 0.5970 (m-10) REVERT: B 448 ARG cc_start: 0.8188 (mtm110) cc_final: 0.7761 (mtm-85) REVERT: B 570 ASP cc_start: 0.8276 (t0) cc_final: 0.7983 (t0) REVERT: B 601 THR cc_start: 0.8877 (OUTLIER) cc_final: 0.8496 (p) REVERT: B 733 TRP cc_start: 0.9344 (t60) cc_final: 0.8961 (t60) REVERT: B 1015 ARG cc_start: 0.8249 (mtt180) cc_final: 0.7719 (mmp-170) REVERT: B 1224 LEU cc_start: 0.8279 (mt) cc_final: 0.7783 (mt) REVERT: B 1295 ASP cc_start: 0.7953 (m-30) cc_final: 0.7645 (m-30) REVERT: B 1461 LEU cc_start: 0.6067 (OUTLIER) cc_final: 0.5765 (pp) REVERT: B 1870 GLN cc_start: 0.8931 (OUTLIER) cc_final: 0.8248 (mp10) REVERT: B 2029 MET cc_start: 0.8585 (tpp) cc_final: 0.8294 (tpp) REVERT: B 2165 MET cc_start: 0.8778 (mtp) cc_final: 0.8563 (mtp) REVERT: B 2351 PHE cc_start: 0.7652 (p90) cc_final: 0.7241 (p90) REVERT: B 2463 ASP cc_start: 0.8238 (t0) cc_final: 0.7808 (t70) REVERT: C 148 MET cc_start: 0.8734 (ptm) cc_final: 0.8108 (ptm) REVERT: C 231 MET cc_start: 0.7844 (mmm) cc_final: 0.7591 (mtp) REVERT: C 904 GLN cc_start: 0.6410 (mp10) cc_final: 0.6108 (mp10) REVERT: C 973 ILE cc_start: 0.8789 (tt) cc_final: 0.8505 (tt) REVERT: C 1015 ARG cc_start: 0.7697 (mtt180) cc_final: 0.7039 (mmp-170) REVERT: C 1364 TYR cc_start: 0.5542 (OUTLIER) cc_final: 0.5210 (m-80) REVERT: C 1596 MET cc_start: 0.8957 (ttp) cc_final: 0.8574 (ttp) REVERT: C 1657 ASP cc_start: 0.7863 (OUTLIER) cc_final: 0.7581 (p0) REVERT: C 1913 ILE cc_start: 0.8800 (pt) cc_final: 0.8511 (mt) REVERT: C 2218 GLU cc_start: 0.7770 (mt-10) cc_final: 0.7546 (mt-10) REVERT: C 2263 PHE cc_start: 0.8607 (t80) cc_final: 0.8356 (t80) REVERT: C 2386 SER cc_start: 0.9186 (m) cc_final: 0.8779 (p) REVERT: C 2473 GLU cc_start: 0.7961 (tt0) cc_final: 0.7751 (tt0) REVERT: C 2478 ASP cc_start: 0.8084 (m-30) cc_final: 0.7880 (m-30) REVERT: C 2494 LYS cc_start: 0.8383 (mttt) cc_final: 0.8055 (ttpp) REVERT: D 153 GLN cc_start: 0.8220 (mp10) cc_final: 0.7964 (mp10) REVERT: D 299 LYS cc_start: 0.8610 (OUTLIER) cc_final: 0.8259 (mmtp) REVERT: D 363 TYR cc_start: 0.7022 (m-10) cc_final: 0.6697 (m-80) REVERT: D 407 GLU cc_start: 0.8106 (tt0) cc_final: 0.7730 (tt0) REVERT: D 683 LYS cc_start: 0.7771 (ttpp) cc_final: 0.7303 (tptt) REVERT: D 1020 ASP cc_start: 0.7901 (m-30) cc_final: 0.7635 (m-30) REVERT: D 1079 MET cc_start: 0.9322 (mmt) cc_final: 0.8842 (mmp) REVERT: D 1101 ILE cc_start: 0.8737 (mm) cc_final: 0.8394 (tt) REVERT: D 1300 ARG cc_start: 0.8495 (ttp80) cc_final: 0.8036 (ttp80) REVERT: D 1367 GLN cc_start: 0.6834 (OUTLIER) cc_final: 0.6341 (tm130) REVERT: D 1419 GLN cc_start: 0.7997 (OUTLIER) cc_final: 0.7583 (pt0) REVERT: D 1437 TRP cc_start: 0.8544 (t-100) cc_final: 0.8277 (t-100) REVERT: D 2022 MET cc_start: 0.8643 (tpp) cc_final: 0.8279 (mmt) REVERT: D 2311 MET cc_start: 0.8759 (tpp) cc_final: 0.8361 (mmt) REVERT: E 51 ASP cc_start: 0.7890 (m-30) cc_final: 0.7567 (m-30) REVERT: E 56 GLN cc_start: 0.8126 (tm-30) cc_final: 0.7805 (tt0) REVERT: E 94 ASN cc_start: 0.7982 (m-40) cc_final: 0.7692 (m-40) REVERT: E 186 MET cc_start: 0.8926 (mmt) cc_final: 0.8670 (mmp) REVERT: E 299 LYS cc_start: 0.8493 (mmtm) cc_final: 0.8029 (mttm) REVERT: E 462 ARG cc_start: 0.8172 (ttm170) cc_final: 0.7794 (mmt90) REVERT: E 1003 ASN cc_start: 0.8131 (t0) cc_final: 0.7908 (t0) REVERT: E 1020 ASP cc_start: 0.7801 (m-30) cc_final: 0.7456 (m-30) REVERT: E 1463 LYS cc_start: 0.8555 (mttt) cc_final: 0.8048 (mmtt) REVERT: E 2042 ASN cc_start: 0.8144 (t0) cc_final: 0.7445 (m-40) REVERT: E 2104 ASP cc_start: 0.8295 (m-30) cc_final: 0.7867 (m-30) REVERT: E 2232 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7514 (mp0) REVERT: E 2348 ASN cc_start: 0.8305 (m110) cc_final: 0.8075 (m-40) REVERT: E 2385 THR cc_start: 0.8982 (p) cc_final: 0.8748 (t) REVERT: E 2505 ASN cc_start: 0.8426 (t0) cc_final: 0.7805 (t0) outliers start: 164 outliers final: 109 residues processed: 1262 average time/residue: 0.8892 time to fit residues: 1931.3829 Evaluate side-chains 1152 residues out of total 10500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 1032 time to evaluate : 8.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 533 ASP Chi-restraints excluded: chain A residue 558 ASP Chi-restraints excluded: chain A residue 572 ASP Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 816 GLU Chi-restraints excluded: chain A residue 869 SER Chi-restraints excluded: chain A residue 1087 GLN Chi-restraints excluded: chain A residue 1139 ASN Chi-restraints excluded: chain A residue 1242 GLU Chi-restraints excluded: chain A residue 1423 LEU Chi-restraints excluded: chain A residue 1446 THR Chi-restraints excluded: chain A residue 1461 LEU Chi-restraints excluded: chain A residue 1484 SER Chi-restraints excluded: chain A residue 1683 ASP Chi-restraints excluded: chain A residue 1927 ARG Chi-restraints excluded: chain A residue 2228 LYS Chi-restraints excluded: chain A residue 2422 LEU Chi-restraints excluded: chain A residue 2483 THR Chi-restraints excluded: chain B residue 240 ASN Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 455 THR Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 511 GLN Chi-restraints excluded: chain B residue 601 THR Chi-restraints excluded: chain B residue 603 ASP Chi-restraints excluded: chain B residue 928 SER Chi-restraints excluded: chain B residue 1103 ASN Chi-restraints excluded: chain B residue 1132 ASN Chi-restraints excluded: chain B residue 1139 ASN Chi-restraints excluded: chain B residue 1156 SER Chi-restraints excluded: chain B residue 1165 SER Chi-restraints excluded: chain B residue 1192 THR Chi-restraints excluded: chain B residue 1364 TYR Chi-restraints excluded: chain B residue 1459 ASP Chi-restraints excluded: chain B residue 1461 LEU Chi-restraints excluded: chain B residue 1477 LYS Chi-restraints excluded: chain B residue 1528 MET Chi-restraints excluded: chain B residue 1675 ILE Chi-restraints excluded: chain B residue 1684 THR Chi-restraints excluded: chain B residue 1719 THR Chi-restraints excluded: chain B residue 1870 GLN Chi-restraints excluded: chain B residue 1898 LEU Chi-restraints excluded: chain B residue 1957 MET Chi-restraints excluded: chain B residue 2287 ASP Chi-restraints excluded: chain B residue 2325 ASP Chi-restraints excluded: chain B residue 2352 SER Chi-restraints excluded: chain B residue 2353 LEU Chi-restraints excluded: chain B residue 2427 GLN Chi-restraints excluded: chain B residue 2428 ASP Chi-restraints excluded: chain C residue 291 GLU Chi-restraints excluded: chain C residue 458 GLU Chi-restraints excluded: chain C residue 534 GLU Chi-restraints excluded: chain C residue 648 VAL Chi-restraints excluded: chain C residue 1014 SER Chi-restraints excluded: chain C residue 1101 ILE Chi-restraints excluded: chain C residue 1156 SER Chi-restraints excluded: chain C residue 1364 TYR Chi-restraints excluded: chain C residue 1518 SER Chi-restraints excluded: chain C residue 1657 ASP Chi-restraints excluded: chain C residue 1830 ASP Chi-restraints excluded: chain C residue 1946 ASP Chi-restraints excluded: chain C residue 2330 GLU Chi-restraints excluded: chain C residue 2434 SER Chi-restraints excluded: chain C residue 2493 GLU Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 195 SER Chi-restraints excluded: chain D residue 275 SER Chi-restraints excluded: chain D residue 299 LYS Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 496 LEU Chi-restraints excluded: chain D residue 603 ASP Chi-restraints excluded: chain D residue 748 THR Chi-restraints excluded: chain D residue 1056 MET Chi-restraints excluded: chain D residue 1317 SER Chi-restraints excluded: chain D residue 1318 SER Chi-restraints excluded: chain D residue 1364 TYR Chi-restraints excluded: chain D residue 1367 GLN Chi-restraints excluded: chain D residue 1419 GLN Chi-restraints excluded: chain D residue 1423 LEU Chi-restraints excluded: chain D residue 1461 LEU Chi-restraints excluded: chain D residue 1524 SER Chi-restraints excluded: chain D residue 1652 LEU Chi-restraints excluded: chain D residue 1657 ASP Chi-restraints excluded: chain D residue 1811 ILE Chi-restraints excluded: chain D residue 2002 THR Chi-restraints excluded: chain D residue 2225 THR Chi-restraints excluded: chain D residue 2390 SER Chi-restraints excluded: chain E residue 88 GLU Chi-restraints excluded: chain E residue 101 SER Chi-restraints excluded: chain E residue 222 ASN Chi-restraints excluded: chain E residue 331 THR Chi-restraints excluded: chain E residue 358 LYS Chi-restraints excluded: chain E residue 468 LEU Chi-restraints excluded: chain E residue 603 ASP Chi-restraints excluded: chain E residue 666 GLU Chi-restraints excluded: chain E residue 763 GLU Chi-restraints excluded: chain E residue 881 VAL Chi-restraints excluded: chain E residue 909 THR Chi-restraints excluded: chain E residue 1139 ASN Chi-restraints excluded: chain E residue 1296 THR Chi-restraints excluded: chain E residue 1309 ASP Chi-restraints excluded: chain E residue 1396 ASN Chi-restraints excluded: chain E residue 1429 THR Chi-restraints excluded: chain E residue 1460 SER Chi-restraints excluded: chain E residue 1465 ASP Chi-restraints excluded: chain E residue 1578 VAL Chi-restraints excluded: chain E residue 1652 LEU Chi-restraints excluded: chain E residue 1683 ASP Chi-restraints excluded: chain E residue 1684 THR Chi-restraints excluded: chain E residue 1695 ASP Chi-restraints excluded: chain E residue 1730 LYS Chi-restraints excluded: chain E residue 1734 THR Chi-restraints excluded: chain E residue 1913 ILE Chi-restraints excluded: chain E residue 2232 GLU Chi-restraints excluded: chain E residue 2330 GLU Chi-restraints excluded: chain E residue 2337 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1225 random chunks: chunk 1101 optimal weight: 4.9990 chunk 837 optimal weight: 1.9990 chunk 578 optimal weight: 0.4980 chunk 123 optimal weight: 0.9980 chunk 531 optimal weight: 1.9990 chunk 748 optimal weight: 0.3980 chunk 1118 optimal weight: 2.9990 chunk 1184 optimal weight: 0.8980 chunk 584 optimal weight: 4.9990 chunk 1060 optimal weight: 3.9990 chunk 319 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 305 GLN ** A 749 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 834 GLN A1068 GLN A1240 GLN A1373 ASN ** B 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 102 GLN B 520 ASN B 749 GLN B1373 ASN ** B1547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 302 ASN ** C1293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1334 ASN ** C1462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 206 ASN ** D 749 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 834 GLN D1152 ASN D1367 GLN D1413 ASN D1588 HIS ** D2047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2452 HIS ** E 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E2230 GLN ** E2497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.3399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 99495 Z= 0.191 Angle : 0.481 10.131 135140 Z= 0.252 Chirality : 0.041 0.298 14960 Planarity : 0.003 0.074 17580 Dihedral : 4.256 35.086 13370 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.82 % Allowed : 7.86 % Favored : 90.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.00 % 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: 0.15 (0.08), residues: 12240 helix: 1.23 (0.07), residues: 5535 sheet: -0.27 (0.11), residues: 2150 loop : -1.07 (0.09), residues: 4555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E1960 HIS 0.008 0.001 HIS C2452 PHE 0.018 0.001 PHE B 937 TYR 0.017 0.001 TYR D2262 ARG 0.008 0.000 ARG D 806 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 24480 Ramachandran restraints generated. 12240 Oldfield, 0 Emsley, 12240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 24480 Ramachandran restraints generated. 12240 Oldfield, 0 Emsley, 12240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1285 residues out of total 10500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 191 poor density : 1094 time to evaluate : 9.400 Fit side-chains REVERT: A 262 GLU cc_start: 0.8047 (tm-30) cc_final: 0.7715 (tp30) REVERT: A 287 ASN cc_start: 0.8750 (t0) cc_final: 0.8298 (t0) REVERT: A 307 GLU cc_start: 0.7168 (mm-30) cc_final: 0.6913 (mm-30) REVERT: A 764 MET cc_start: 0.8248 (ttm) cc_final: 0.7819 (ttt) REVERT: A 803 MET cc_start: 0.8610 (tmm) cc_final: 0.8048 (tmm) REVERT: A 806 ARG cc_start: 0.8072 (mmt90) cc_final: 0.7619 (mtp85) REVERT: A 839 MET cc_start: 0.9142 (mtp) cc_final: 0.8667 (mtp) REVERT: A 1101 ILE cc_start: 0.8654 (OUTLIER) cc_final: 0.8249 (tt) REVERT: A 1321 ASP cc_start: 0.7542 (t70) cc_final: 0.7161 (t0) REVERT: A 1746 SER cc_start: 0.8057 (t) cc_final: 0.7803 (m) REVERT: A 1898 LEU cc_start: 0.7886 (OUTLIER) cc_final: 0.7680 (pp) REVERT: A 1927 ARG cc_start: 0.9031 (OUTLIER) cc_final: 0.8664 (ttp-110) REVERT: A 2076 GLU cc_start: 0.8324 (mt-10) cc_final: 0.8036 (mt-10) REVERT: A 2422 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8407 (mm) REVERT: A 2427 GLN cc_start: 0.7320 (mm110) cc_final: 0.7075 (mm-40) REVERT: A 2456 ASP cc_start: 0.7882 (t0) cc_final: 0.7656 (t0) REVERT: B 309 SER cc_start: 0.8706 (t) cc_final: 0.8357 (p) REVERT: B 348 PHE cc_start: 0.6737 (m-10) cc_final: 0.6193 (m-10) REVERT: B 448 ARG cc_start: 0.8178 (mtm110) cc_final: 0.7740 (mtm-85) REVERT: B 570 ASP cc_start: 0.8326 (t0) cc_final: 0.8100 (t0) REVERT: B 601 THR cc_start: 0.8870 (OUTLIER) cc_final: 0.8523 (p) REVERT: B 733 TRP cc_start: 0.9377 (t60) cc_final: 0.8927 (t60) REVERT: B 1015 ARG cc_start: 0.8223 (mtt180) cc_final: 0.7681 (mmp-170) REVERT: B 1224 LEU cc_start: 0.8262 (mt) cc_final: 0.8032 (mt) REVERT: B 1295 ASP cc_start: 0.7877 (m-30) cc_final: 0.7575 (m-30) REVERT: B 1461 LEU cc_start: 0.6187 (OUTLIER) cc_final: 0.5889 (pp) REVERT: B 1870 GLN cc_start: 0.8935 (OUTLIER) cc_final: 0.7633 (mp10) REVERT: B 1872 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.6861 (mp0) REVERT: B 2216 ARG cc_start: 0.7611 (mtm-85) cc_final: 0.7371 (mtm-85) REVERT: B 2242 GLN cc_start: 0.8558 (mt0) cc_final: 0.8195 (mt0) REVERT: B 2351 PHE cc_start: 0.7784 (p90) cc_final: 0.7392 (p90) REVERT: B 2463 ASP cc_start: 0.8211 (t0) cc_final: 0.7754 (t0) REVERT: C 148 MET cc_start: 0.8781 (ptm) cc_final: 0.8174 (ptm) REVERT: C 162 LEU cc_start: 0.8986 (tp) cc_final: 0.8727 (tp) REVERT: C 231 MET cc_start: 0.7772 (mmm) cc_final: 0.7569 (mtp) REVERT: C 904 GLN cc_start: 0.6595 (mp10) cc_final: 0.6215 (mp10) REVERT: C 973 ILE cc_start: 0.8869 (tt) cc_final: 0.8597 (tt) REVERT: C 1015 ARG cc_start: 0.7715 (mtt180) cc_final: 0.6936 (mmp-170) REVERT: C 1461 LEU cc_start: 0.7952 (OUTLIER) cc_final: 0.7410 (pp) REVERT: C 1596 MET cc_start: 0.8928 (ttp) cc_final: 0.8548 (ttp) REVERT: C 1657 ASP cc_start: 0.7940 (OUTLIER) cc_final: 0.7668 (p0) REVERT: C 1884 MET cc_start: 0.8394 (mmm) cc_final: 0.8175 (mmm) REVERT: C 1913 ILE cc_start: 0.8769 (pt) cc_final: 0.8524 (mt) REVERT: C 2263 PHE cc_start: 0.8583 (t80) cc_final: 0.8338 (t80) REVERT: C 2386 SER cc_start: 0.9201 (m) cc_final: 0.8794 (p) REVERT: C 2473 GLU cc_start: 0.7850 (tt0) cc_final: 0.7597 (tt0) REVERT: C 2494 LYS cc_start: 0.8390 (mttt) cc_final: 0.8087 (ttpp) REVERT: D 299 LYS cc_start: 0.8614 (OUTLIER) cc_final: 0.8248 (mmtp) REVERT: D 363 TYR cc_start: 0.7046 (m-10) cc_final: 0.6741 (m-80) REVERT: D 407 GLU cc_start: 0.7977 (tt0) cc_final: 0.7656 (tt0) REVERT: D 683 LYS cc_start: 0.7797 (ttpp) cc_final: 0.7326 (tptt) REVERT: D 916 GLU cc_start: 0.8083 (tt0) cc_final: 0.7820 (tt0) REVERT: D 1079 MET cc_start: 0.9312 (mmt) cc_final: 0.8872 (mmp) REVERT: D 1101 ILE cc_start: 0.8770 (mm) cc_final: 0.8464 (tt) REVERT: D 1300 ARG cc_start: 0.8546 (ttp80) cc_final: 0.8000 (ttp80) REVERT: D 1367 GLN cc_start: 0.6393 (OUTLIER) cc_final: 0.6170 (tm-30) REVERT: D 1419 GLN cc_start: 0.7970 (OUTLIER) cc_final: 0.7548 (pt0) REVERT: D 1437 TRP cc_start: 0.8551 (t-100) cc_final: 0.8277 (t-100) REVERT: D 1758 MET cc_start: 0.8720 (ptm) cc_final: 0.8506 (ptm) REVERT: D 1830 ASP cc_start: 0.7808 (t70) cc_final: 0.7598 (t70) REVERT: D 2022 MET cc_start: 0.8644 (tpp) cc_final: 0.8322 (mmt) REVERT: D 2311 MET cc_start: 0.8761 (tpp) cc_final: 0.8363 (mmt) REVERT: D 2491 MET cc_start: 0.7661 (OUTLIER) cc_final: 0.7291 (mtp) REVERT: E 51 ASP cc_start: 0.7963 (m-30) cc_final: 0.7560 (m-30) REVERT: E 56 GLN cc_start: 0.8100 (tm-30) cc_final: 0.7791 (tt0) REVERT: E 94 ASN cc_start: 0.7908 (m-40) cc_final: 0.7554 (m-40) REVERT: E 186 MET cc_start: 0.8956 (mmt) cc_final: 0.8730 (mmp) REVERT: E 299 LYS cc_start: 0.8534 (mmtm) cc_final: 0.8191 (mttm) REVERT: E 462 ARG cc_start: 0.8223 (ttm170) cc_final: 0.7805 (mmt90) REVERT: E 1003 ASN cc_start: 0.8170 (t0) cc_final: 0.7936 (t0) REVERT: E 1020 ASP cc_start: 0.7789 (m-30) cc_final: 0.7454 (m-30) REVERT: E 1321 ASP cc_start: 0.6976 (t70) cc_final: 0.6755 (t0) REVERT: E 1463 LYS cc_start: 0.8557 (mttt) cc_final: 0.8026 (mmtt) REVERT: E 1869 ARG cc_start: 0.8084 (mtt90) cc_final: 0.7683 (mtt90) REVERT: E 2042 ASN cc_start: 0.8148 (t0) cc_final: 0.7415 (m-40) REVERT: E 2232 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7493 (mp0) REVERT: E 2340 VAL cc_start: 0.8587 (m) cc_final: 0.8316 (t) REVERT: E 2348 ASN cc_start: 0.8454 (m110) cc_final: 0.8253 (m-40) REVERT: E 2385 THR cc_start: 0.8988 (p) cc_final: 0.8760 (t) REVERT: E 2505 ASN cc_start: 0.8465 (t0) cc_final: 0.7840 (t0) outliers start: 191 outliers final: 133 residues processed: 1217 average time/residue: 0.8870 time to fit residues: 1858.3725 Evaluate side-chains 1170 residues out of total 10500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 1022 time to evaluate : 8.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 ASN Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 533 ASP Chi-restraints excluded: chain A residue 558 ASP Chi-restraints excluded: chain A residue 572 ASP Chi-restraints excluded: chain A residue 603 ASP Chi-restraints excluded: chain A residue 713 LEU Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 816 GLU Chi-restraints excluded: chain A residue 869 SER Chi-restraints excluded: chain A residue 983 THR Chi-restraints excluded: chain A residue 1101 ILE Chi-restraints excluded: chain A residue 1139 ASN Chi-restraints excluded: chain A residue 1242 GLU Chi-restraints excluded: chain A residue 1446 THR Chi-restraints excluded: chain A residue 1461 LEU Chi-restraints excluded: chain A residue 1465 ASP Chi-restraints excluded: chain A residue 1683 ASP Chi-restraints excluded: chain A residue 1898 LEU Chi-restraints excluded: chain A residue 1927 ARG Chi-restraints excluded: chain A residue 1956 MET Chi-restraints excluded: chain A residue 2228 LYS Chi-restraints excluded: chain A residue 2367 SER Chi-restraints excluded: chain A residue 2381 THR Chi-restraints excluded: chain A residue 2422 LEU Chi-restraints excluded: chain A residue 2483 THR Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 240 ASN Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 352 ASN Chi-restraints excluded: chain B residue 455 THR Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 601 THR Chi-restraints excluded: chain B residue 603 ASP Chi-restraints excluded: chain B residue 625 LYS Chi-restraints excluded: chain B residue 1103 ASN Chi-restraints excluded: chain B residue 1132 ASN Chi-restraints excluded: chain B residue 1139 ASN Chi-restraints excluded: chain B residue 1156 SER Chi-restraints excluded: chain B residue 1165 SER Chi-restraints excluded: chain B residue 1192 THR Chi-restraints excluded: chain B residue 1364 TYR Chi-restraints excluded: chain B residue 1423 LEU Chi-restraints excluded: chain B residue 1459 ASP Chi-restraints excluded: chain B residue 1461 LEU Chi-restraints excluded: chain B residue 1477 LYS Chi-restraints excluded: chain B residue 1528 MET Chi-restraints excluded: chain B residue 1684 THR Chi-restraints excluded: chain B residue 1719 THR Chi-restraints excluded: chain B residue 1811 ILE Chi-restraints excluded: chain B residue 1870 GLN Chi-restraints excluded: chain B residue 1872 GLU Chi-restraints excluded: chain B residue 1898 LEU Chi-restraints excluded: chain B residue 1957 MET Chi-restraints excluded: chain B residue 1977 ASP Chi-restraints excluded: chain B residue 2128 VAL Chi-restraints excluded: chain B residue 2182 SER Chi-restraints excluded: chain B residue 2325 ASP Chi-restraints excluded: chain B residue 2352 SER Chi-restraints excluded: chain B residue 2428 ASP Chi-restraints excluded: chain C residue 291 GLU Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 458 GLU Chi-restraints excluded: chain C residue 534 GLU Chi-restraints excluded: chain C residue 648 VAL Chi-restraints excluded: chain C residue 1014 SER Chi-restraints excluded: chain C residue 1101 ILE Chi-restraints excluded: chain C residue 1156 SER Chi-restraints excluded: chain C residue 1204 ARG Chi-restraints excluded: chain C residue 1243 ASP Chi-restraints excluded: chain C residue 1461 LEU Chi-restraints excluded: chain C residue 1518 SER Chi-restraints excluded: chain C residue 1657 ASP Chi-restraints excluded: chain C residue 1830 ASP Chi-restraints excluded: chain C residue 1946 ASP Chi-restraints excluded: chain C residue 1977 ASP Chi-restraints excluded: chain C residue 2330 GLU Chi-restraints excluded: chain C residue 2331 VAL Chi-restraints excluded: chain C residue 2357 ILE Chi-restraints excluded: chain C residue 2434 SER Chi-restraints excluded: chain C residue 2477 ILE Chi-restraints excluded: chain C residue 2493 GLU Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 195 SER Chi-restraints excluded: chain D residue 206 ASN Chi-restraints excluded: chain D residue 275 SER Chi-restraints excluded: chain D residue 299 LYS Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 496 LEU Chi-restraints excluded: chain D residue 601 THR Chi-restraints excluded: chain D residue 603 ASP Chi-restraints excluded: chain D residue 664 THR Chi-restraints excluded: chain D residue 710 SER Chi-restraints excluded: chain D residue 748 THR Chi-restraints excluded: chain D residue 1056 MET Chi-restraints excluded: chain D residue 1073 THR Chi-restraints excluded: chain D residue 1139 ASN Chi-restraints excluded: chain D residue 1285 VAL Chi-restraints excluded: chain D residue 1317 SER Chi-restraints excluded: chain D residue 1318 SER Chi-restraints excluded: chain D residue 1364 TYR Chi-restraints excluded: chain D residue 1367 GLN Chi-restraints excluded: chain D residue 1419 GLN Chi-restraints excluded: chain D residue 1423 LEU Chi-restraints excluded: chain D residue 1461 LEU Chi-restraints excluded: chain D residue 1524 SER Chi-restraints excluded: chain D residue 1652 LEU Chi-restraints excluded: chain D residue 1657 ASP Chi-restraints excluded: chain D residue 1811 ILE Chi-restraints excluded: chain D residue 2002 THR Chi-restraints excluded: chain D residue 2031 SER Chi-restraints excluded: chain D residue 2225 THR Chi-restraints excluded: chain D residue 2340 VAL Chi-restraints excluded: chain D residue 2347 ASP Chi-restraints excluded: chain D residue 2390 SER Chi-restraints excluded: chain D residue 2416 SER Chi-restraints excluded: chain D residue 2491 MET Chi-restraints excluded: chain E residue 331 THR Chi-restraints excluded: chain E residue 381 THR Chi-restraints excluded: chain E residue 468 LEU Chi-restraints excluded: chain E residue 666 GLU Chi-restraints excluded: chain E residue 763 GLU Chi-restraints excluded: chain E residue 881 VAL Chi-restraints excluded: chain E residue 909 THR Chi-restraints excluded: chain E residue 1139 ASN Chi-restraints excluded: chain E residue 1148 ASP Chi-restraints excluded: chain E residue 1296 THR Chi-restraints excluded: chain E residue 1309 ASP Chi-restraints excluded: chain E residue 1396 ASN Chi-restraints excluded: chain E residue 1429 THR Chi-restraints excluded: chain E residue 1461 LEU Chi-restraints excluded: chain E residue 1465 ASP Chi-restraints excluded: chain E residue 1578 VAL Chi-restraints excluded: chain E residue 1652 LEU Chi-restraints excluded: chain E residue 1683 ASP Chi-restraints excluded: chain E residue 1695 ASP Chi-restraints excluded: chain E residue 1730 LYS Chi-restraints excluded: chain E residue 1734 THR Chi-restraints excluded: chain E residue 1790 ASP Chi-restraints excluded: chain E residue 1913 ILE Chi-restraints excluded: chain E residue 1977 ASP Chi-restraints excluded: chain E residue 2125 THR Chi-restraints excluded: chain E residue 2232 GLU Chi-restraints excluded: chain E residue 2330 GLU Chi-restraints excluded: chain E residue 2337 LEU Chi-restraints excluded: chain E residue 2409 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1225 random chunks: chunk 986 optimal weight: 0.6980 chunk 672 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 881 optimal weight: 0.7980 chunk 488 optimal weight: 1.9990 chunk 1010 optimal weight: 3.9990 chunk 818 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 604 optimal weight: 0.5980 chunk 1062 optimal weight: 5.9990 chunk 298 optimal weight: 6.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN ** A 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 305 GLN A1808 HIS ** B 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 102 GLN B 749 GLN ** B1547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 302 ASN C1003 ASN ** C1293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1413 ASN ** C2047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 749 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 834 GLN D1152 ASN D1701 GLN ** D2047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1373 ASN ** E1394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E2230 GLN E2321 HIS E2452 HIS ** E2497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.3568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 99495 Z= 0.168 Angle : 0.463 9.543 135140 Z= 0.243 Chirality : 0.040 0.368 14960 Planarity : 0.003 0.073 17580 Dihedral : 4.136 35.419 13370 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.88 % Allowed : 8.02 % Favored : 90.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.00 % 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: 0.56 (0.08), residues: 12240 helix: 1.65 (0.07), residues: 5530 sheet: -0.07 (0.11), residues: 2125 loop : -0.96 (0.09), residues: 4585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C1171 HIS 0.006 0.001 HIS D1888 PHE 0.022 0.001 PHE E 937 TYR 0.016 0.001 TYR A1868 ARG 0.006 0.000 ARG D1659 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 24480 Ramachandran restraints generated. 12240 Oldfield, 0 Emsley, 12240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 24480 Ramachandran restraints generated. 12240 Oldfield, 0 Emsley, 12240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1278 residues out of total 10500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 197 poor density : 1081 time to evaluate : 8.579 Fit side-chains REVERT: A 262 GLU cc_start: 0.8049 (tm-30) cc_final: 0.7723 (tp30) REVERT: A 287 ASN cc_start: 0.8777 (t0) cc_final: 0.8354 (t0) REVERT: A 374 ASP cc_start: 0.7353 (t0) cc_final: 0.6819 (t0) REVERT: A 666 GLU cc_start: 0.8198 (mp0) cc_final: 0.7892 (pm20) REVERT: A 764 MET cc_start: 0.8197 (ttm) cc_final: 0.7910 (ttt) REVERT: A 803 MET cc_start: 0.8625 (tmm) cc_final: 0.8075 (tmm) REVERT: A 806 ARG cc_start: 0.8060 (mmt90) cc_final: 0.7556 (mtp85) REVERT: A 839 MET cc_start: 0.9161 (mtp) cc_final: 0.8812 (mtt) REVERT: A 902 TYR cc_start: 0.8665 (m-10) cc_final: 0.8415 (m-10) REVERT: A 1101 ILE cc_start: 0.8725 (OUTLIER) cc_final: 0.8344 (tt) REVERT: A 1746 SER cc_start: 0.8066 (t) cc_final: 0.7786 (m) REVERT: A 1898 LEU cc_start: 0.7850 (OUTLIER) cc_final: 0.7617 (pp) REVERT: A 1927 ARG cc_start: 0.9051 (OUTLIER) cc_final: 0.8694 (ttp-110) REVERT: A 2076 GLU cc_start: 0.8295 (mt-10) cc_final: 0.8010 (mt-10) REVERT: A 2081 GLU cc_start: 0.8119 (mm-30) cc_final: 0.7896 (mm-30) REVERT: A 2422 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8438 (mm) REVERT: A 2427 GLN cc_start: 0.7317 (mm110) cc_final: 0.7052 (mm-40) REVERT: B 136 TYR cc_start: 0.9150 (m-80) cc_final: 0.8815 (m-80) REVERT: B 309 SER cc_start: 0.8670 (t) cc_final: 0.8320 (p) REVERT: B 348 PHE cc_start: 0.6768 (m-10) cc_final: 0.6237 (m-10) REVERT: B 448 ARG cc_start: 0.8168 (mtm110) cc_final: 0.7953 (mtm-85) REVERT: B 462 ARG cc_start: 0.8655 (mmt-90) cc_final: 0.8427 (mmt-90) REVERT: B 570 ASP cc_start: 0.8312 (t0) cc_final: 0.8089 (t0) REVERT: B 601 THR cc_start: 0.8756 (OUTLIER) cc_final: 0.8435 (p) REVERT: B 1015 ARG cc_start: 0.8232 (mtt180) cc_final: 0.7661 (mmp-170) REVERT: B 1051 ILE cc_start: 0.9292 (mp) cc_final: 0.8963 (mt) REVERT: B 1388 TYR cc_start: 0.9104 (m-80) cc_final: 0.8705 (m-80) REVERT: B 1423 LEU cc_start: 0.9072 (OUTLIER) cc_final: 0.8826 (mt) REVERT: B 1461 LEU cc_start: 0.6216 (OUTLIER) cc_final: 0.5963 (pp) REVERT: B 1499 GLN cc_start: 0.8490 (OUTLIER) cc_final: 0.8260 (pm20) REVERT: B 1870 GLN cc_start: 0.8879 (OUTLIER) cc_final: 0.7585 (mp10) REVERT: B 1872 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.6819 (mp0) REVERT: B 2022 MET cc_start: 0.8690 (tpp) cc_final: 0.8348 (tpp) REVERT: B 2242 GLN cc_start: 0.8658 (mt0) cc_final: 0.8327 (mt0) REVERT: B 2351 PHE cc_start: 0.7755 (p90) cc_final: 0.7370 (p90) REVERT: B 2463 ASP cc_start: 0.8167 (t0) cc_final: 0.7702 (t0) REVERT: C 148 MET cc_start: 0.8787 (ptm) cc_final: 0.8158 (ptm) REVERT: C 162 LEU cc_start: 0.9059 (tp) cc_final: 0.8839 (tp) REVERT: C 280 GLU cc_start: 0.7600 (tp30) cc_final: 0.7362 (tt0) REVERT: C 904 GLN cc_start: 0.6537 (mp10) cc_final: 0.6151 (mp10) REVERT: C 1015 ARG cc_start: 0.7707 (mtt180) cc_final: 0.6926 (mmp-170) REVERT: C 1252 GLN cc_start: 0.9343 (OUTLIER) cc_final: 0.8987 (mt0) REVERT: C 1334 ASN cc_start: 0.8657 (m-40) cc_final: 0.8168 (m110) REVERT: C 1461 LEU cc_start: 0.7938 (OUTLIER) cc_final: 0.7402 (pp) REVERT: C 1596 MET cc_start: 0.8905 (ttp) cc_final: 0.8552 (ttp) REVERT: C 1884 MET cc_start: 0.8375 (mmm) cc_final: 0.8089 (mmm) REVERT: C 1913 ILE cc_start: 0.8744 (pt) cc_final: 0.8497 (mt) REVERT: C 1961 GLN cc_start: 0.8439 (mt0) cc_final: 0.8155 (mt0) REVERT: C 2263 PHE cc_start: 0.8604 (t80) cc_final: 0.8381 (t80) REVERT: C 2386 SER cc_start: 0.9194 (m) cc_final: 0.8858 (p) REVERT: C 2427 GLN cc_start: 0.7266 (mt0) cc_final: 0.7056 (tt0) REVERT: C 2494 LYS cc_start: 0.8394 (mttt) cc_final: 0.8111 (ttpp) REVERT: D 299 LYS cc_start: 0.8621 (OUTLIER) cc_final: 0.8258 (mmtp) REVERT: D 363 TYR cc_start: 0.7112 (m-10) cc_final: 0.6792 (m-80) REVERT: D 683 LYS cc_start: 0.7808 (ttpp) cc_final: 0.7308 (tptt) REVERT: D 1101 ILE cc_start: 0.8851 (mm) cc_final: 0.8562 (tt) REVERT: D 1300 ARG cc_start: 0.8531 (ttp80) cc_final: 0.7942 (ttp80) REVERT: D 1343 LYS cc_start: 0.8519 (pptt) cc_final: 0.8288 (ptpt) REVERT: D 1419 GLN cc_start: 0.7934 (OUTLIER) cc_final: 0.7653 (pt0) REVERT: D 1437 TRP cc_start: 0.8457 (t-100) cc_final: 0.8203 (t-100) REVERT: D 2022 MET cc_start: 0.8667 (tpp) cc_final: 0.8372 (mmt) REVERT: D 2311 MET cc_start: 0.8770 (tpp) cc_final: 0.8375 (mmt) REVERT: E 51 ASP cc_start: 0.7946 (m-30) cc_final: 0.7561 (m-30) REVERT: E 56 GLN cc_start: 0.8087 (tm-30) cc_final: 0.7778 (tt0) REVERT: E 94 ASN cc_start: 0.7934 (m-40) cc_final: 0.7714 (m-40) REVERT: E 186 MET cc_start: 0.8940 (mmt) cc_final: 0.8717 (mmp) REVERT: E 231 MET cc_start: 0.7313 (mtm) cc_final: 0.7059 (mtm) REVERT: E 299 LYS cc_start: 0.8519 (mmtm) cc_final: 0.8201 (mttm) REVERT: E 462 ARG cc_start: 0.8214 (ttm170) cc_final: 0.7809 (mmt90) REVERT: E 1003 ASN cc_start: 0.8147 (t0) cc_final: 0.7921 (t0) REVERT: E 1020 ASP cc_start: 0.7753 (m-30) cc_final: 0.7449 (m-30) REVERT: E 1115 GLU cc_start: 0.7572 (mm-30) cc_final: 0.7105 (mt-10) REVERT: E 1321 ASP cc_start: 0.6987 (t70) cc_final: 0.6782 (t0) REVERT: E 1423 LEU cc_start: 0.9313 (OUTLIER) cc_final: 0.9094 (mt) REVERT: E 1463 LYS cc_start: 0.8492 (mttt) cc_final: 0.7986 (mmtt) REVERT: E 2042 ASN cc_start: 0.8127 (t0) cc_final: 0.7372 (m-40) REVERT: E 2232 GLU cc_start: 0.8101 (OUTLIER) cc_final: 0.7494 (mp0) REVERT: E 2505 ASN cc_start: 0.8476 (t0) cc_final: 0.7846 (t0) outliers start: 197 outliers final: 141 residues processed: 1209 average time/residue: 0.8819 time to fit residues: 1841.3052 Evaluate side-chains 1161 residues out of total 10500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 1004 time to evaluate : 8.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 ASN Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 533 ASP Chi-restraints excluded: chain A residue 558 ASP Chi-restraints excluded: chain A residue 572 ASP Chi-restraints excluded: chain A residue 713 LEU Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 800 SER Chi-restraints excluded: chain A residue 816 GLU Chi-restraints excluded: chain A residue 869 SER Chi-restraints excluded: chain A residue 983 THR Chi-restraints excluded: chain A residue 1087 GLN Chi-restraints excluded: chain A residue 1101 ILE Chi-restraints excluded: chain A residue 1139 ASN Chi-restraints excluded: chain A residue 1242 GLU Chi-restraints excluded: chain A residue 1423 LEU Chi-restraints excluded: chain A residue 1444 SER Chi-restraints excluded: chain A residue 1446 THR Chi-restraints excluded: chain A residue 1461 LEU Chi-restraints excluded: chain A residue 1465 ASP Chi-restraints excluded: chain A residue 1683 ASP Chi-restraints excluded: chain A residue 1898 LEU Chi-restraints excluded: chain A residue 1927 ARG Chi-restraints excluded: chain A residue 1945 THR Chi-restraints excluded: chain A residue 1956 MET Chi-restraints excluded: chain A residue 2228 LYS Chi-restraints excluded: chain A residue 2330 GLU Chi-restraints excluded: chain A residue 2367 SER Chi-restraints excluded: chain A residue 2381 THR Chi-restraints excluded: chain A residue 2422 LEU Chi-restraints excluded: chain A residue 2483 THR Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 240 ASN Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 352 ASN Chi-restraints excluded: chain B residue 455 THR Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 511 GLN Chi-restraints excluded: chain B residue 558 ASP Chi-restraints excluded: chain B residue 601 THR Chi-restraints excluded: chain B residue 603 ASP Chi-restraints excluded: chain B residue 625 LYS Chi-restraints excluded: chain B residue 1103 ASN Chi-restraints excluded: chain B residue 1139 ASN Chi-restraints excluded: chain B residue 1156 SER Chi-restraints excluded: chain B residue 1192 THR Chi-restraints excluded: chain B residue 1255 THR Chi-restraints excluded: chain B residue 1364 TYR Chi-restraints excluded: chain B residue 1365 GLU Chi-restraints excluded: chain B residue 1423 LEU Chi-restraints excluded: chain B residue 1459 ASP Chi-restraints excluded: chain B residue 1461 LEU Chi-restraints excluded: chain B residue 1499 GLN Chi-restraints excluded: chain B residue 1528 MET Chi-restraints excluded: chain B residue 1684 THR Chi-restraints excluded: chain B residue 1719 THR Chi-restraints excluded: chain B residue 1811 ILE Chi-restraints excluded: chain B residue 1870 GLN Chi-restraints excluded: chain B residue 1872 GLU Chi-restraints excluded: chain B residue 1898 LEU Chi-restraints excluded: chain B residue 1957 MET Chi-restraints excluded: chain B residue 1977 ASP Chi-restraints excluded: chain B residue 2182 SER Chi-restraints excluded: chain B residue 2287 ASP Chi-restraints excluded: chain B residue 2325 ASP Chi-restraints excluded: chain B residue 2352 SER Chi-restraints excluded: chain B residue 2428 ASP Chi-restraints excluded: chain C residue 291 GLU Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 458 GLU Chi-restraints excluded: chain C residue 504 SER Chi-restraints excluded: chain C residue 534 GLU Chi-restraints excluded: chain C residue 648 VAL Chi-restraints excluded: chain C residue 1014 SER Chi-restraints excluded: chain C residue 1101 ILE Chi-restraints excluded: chain C residue 1139 ASN Chi-restraints excluded: chain C residue 1156 SER Chi-restraints excluded: chain C residue 1191 GLU Chi-restraints excluded: chain C residue 1243 ASP Chi-restraints excluded: chain C residue 1252 GLN Chi-restraints excluded: chain C residue 1461 LEU Chi-restraints excluded: chain C residue 1518 SER Chi-restraints excluded: chain C residue 1830 ASP Chi-restraints excluded: chain C residue 1946 ASP Chi-restraints excluded: chain C residue 1977 ASP Chi-restraints excluded: chain C residue 1991 ASP Chi-restraints excluded: chain C residue 2330 GLU Chi-restraints excluded: chain C residue 2331 VAL Chi-restraints excluded: chain C residue 2357 ILE Chi-restraints excluded: chain C residue 2360 LEU Chi-restraints excluded: chain C residue 2434 SER Chi-restraints excluded: chain C residue 2477 ILE Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 195 SER Chi-restraints excluded: chain D residue 275 SER Chi-restraints excluded: chain D residue 299 LYS Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 496 LEU Chi-restraints excluded: chain D residue 601 THR Chi-restraints excluded: chain D residue 603 ASP Chi-restraints excluded: chain D residue 748 THR Chi-restraints excluded: chain D residue 1056 MET Chi-restraints excluded: chain D residue 1139 ASN Chi-restraints excluded: chain D residue 1165 SER Chi-restraints excluded: chain D residue 1317 SER Chi-restraints excluded: chain D residue 1318 SER Chi-restraints excluded: chain D residue 1419 GLN Chi-restraints excluded: chain D residue 1423 LEU Chi-restraints excluded: chain D residue 1461 LEU Chi-restraints excluded: chain D residue 1524 SER Chi-restraints excluded: chain D residue 1652 LEU Chi-restraints excluded: chain D residue 1657 ASP Chi-restraints excluded: chain D residue 1811 ILE Chi-restraints excluded: chain D residue 2002 THR Chi-restraints excluded: chain D residue 2225 THR Chi-restraints excluded: chain D residue 2323 LYS Chi-restraints excluded: chain D residue 2340 VAL Chi-restraints excluded: chain D residue 2390 SER Chi-restraints excluded: chain D residue 2416 SER Chi-restraints excluded: chain E residue 88 GLU Chi-restraints excluded: chain E residue 325 VAL Chi-restraints excluded: chain E residue 331 THR Chi-restraints excluded: chain E residue 381 THR Chi-restraints excluded: chain E residue 468 LEU Chi-restraints excluded: chain E residue 603 ASP Chi-restraints excluded: chain E residue 666 GLU Chi-restraints excluded: chain E residue 763 GLU Chi-restraints excluded: chain E residue 790 THR Chi-restraints excluded: chain E residue 799 LEU Chi-restraints excluded: chain E residue 805 THR Chi-restraints excluded: chain E residue 881 VAL Chi-restraints excluded: chain E residue 909 THR Chi-restraints excluded: chain E residue 1139 ASN Chi-restraints excluded: chain E residue 1296 THR Chi-restraints excluded: chain E residue 1309 ASP Chi-restraints excluded: chain E residue 1396 ASN Chi-restraints excluded: chain E residue 1423 LEU Chi-restraints excluded: chain E residue 1429 THR Chi-restraints excluded: chain E residue 1461 LEU Chi-restraints excluded: chain E residue 1465 ASP Chi-restraints excluded: chain E residue 1578 VAL Chi-restraints excluded: chain E residue 1652 LEU Chi-restraints excluded: chain E residue 1683 ASP Chi-restraints excluded: chain E residue 1695 ASP Chi-restraints excluded: chain E residue 1730 LYS Chi-restraints excluded: chain E residue 1734 THR Chi-restraints excluded: chain E residue 1790 ASP Chi-restraints excluded: chain E residue 1913 ILE Chi-restraints excluded: chain E residue 2125 THR Chi-restraints excluded: chain E residue 2232 GLU Chi-restraints excluded: chain E residue 2236 SER Chi-restraints excluded: chain E residue 2330 GLU Chi-restraints excluded: chain E residue 2337 LEU Chi-restraints excluded: chain E residue 2409 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1225 random chunks: chunk 398 optimal weight: 1.9990 chunk 1066 optimal weight: 0.2980 chunk 234 optimal weight: 0.0170 chunk 695 optimal weight: 1.9990 chunk 292 optimal weight: 3.9990 chunk 1185 optimal weight: 0.8980 chunk 983 optimal weight: 4.9990 chunk 548 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 392 optimal weight: 0.8980 chunk 622 optimal weight: 2.9990 overall best weight: 0.8220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 305 GLN A1180 GLN A1674 HIS ** A2047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 102 GLN B 214 GLN ** B1547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 302 ASN C1003 ASN ** C1293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1373 ASN ** C2047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2459 GLN ** C2497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 709 HIS D 749 GLN D 834 GLN ** D2047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E2041 GLN ** E2497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.3722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 99495 Z= 0.170 Angle : 0.461 10.129 135140 Z= 0.241 Chirality : 0.040 0.299 14960 Planarity : 0.003 0.071 17580 Dihedral : 4.076 34.517 13370 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.84 % Allowed : 8.51 % Favored : 89.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.00 % 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: 0.82 (0.08), residues: 12240 helix: 1.87 (0.07), residues: 5540 sheet: 0.02 (0.11), residues: 2135 loop : -0.84 (0.09), residues: 4565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C1171 HIS 0.006 0.001 HIS D1888 PHE 0.020 0.001 PHE B 937 TYR 0.016 0.001 TYR A1868 ARG 0.007 0.000 ARG A2153 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 24480 Ramachandran restraints generated. 12240 Oldfield, 0 Emsley, 12240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 24480 Ramachandran restraints generated. 12240 Oldfield, 0 Emsley, 12240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1255 residues out of total 10500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 193 poor density : 1062 time to evaluate : 8.897 Fit side-chains REVERT: A 231 MET cc_start: 0.8501 (mtp) cc_final: 0.8217 (mtm) REVERT: A 262 GLU cc_start: 0.8059 (tm-30) cc_final: 0.7722 (tp30) REVERT: A 287 ASN cc_start: 0.8803 (t0) cc_final: 0.8421 (t0) REVERT: A 374 ASP cc_start: 0.7679 (t0) cc_final: 0.7155 (t0) REVERT: A 764 MET cc_start: 0.8186 (ttm) cc_final: 0.7922 (ttt) REVERT: A 803 MET cc_start: 0.8603 (tmm) cc_final: 0.8048 (tmm) REVERT: A 839 MET cc_start: 0.9155 (mtp) cc_final: 0.8790 (mtt) REVERT: A 902 TYR cc_start: 0.8662 (m-10) cc_final: 0.8406 (m-10) REVERT: A 1101 ILE cc_start: 0.8728 (OUTLIER) cc_final: 0.8410 (tt) REVERT: A 1746 SER cc_start: 0.8080 (t) cc_final: 0.7785 (m) REVERT: A 1898 LEU cc_start: 0.7955 (OUTLIER) cc_final: 0.7724 (pp) REVERT: A 1927 ARG cc_start: 0.9032 (OUTLIER) cc_final: 0.8730 (ttp-110) REVERT: A 2076 GLU cc_start: 0.8294 (mt-10) cc_final: 0.8003 (mt-10) REVERT: A 2422 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8458 (mm) REVERT: A 2427 GLN cc_start: 0.7235 (mm110) cc_final: 0.6995 (mm-40) REVERT: B 136 TYR cc_start: 0.9190 (m-80) cc_final: 0.8888 (m-80) REVERT: B 309 SER cc_start: 0.8666 (t) cc_final: 0.8326 (p) REVERT: B 448 ARG cc_start: 0.8163 (mtm110) cc_final: 0.7908 (mtm-85) REVERT: B 462 ARG cc_start: 0.8737 (mmt-90) cc_final: 0.8533 (mmt-90) REVERT: B 570 ASP cc_start: 0.8320 (t0) cc_final: 0.8093 (t0) REVERT: B 574 LYS cc_start: 0.8137 (mmtt) cc_final: 0.7907 (mmtt) REVERT: B 601 THR cc_start: 0.8764 (OUTLIER) cc_final: 0.8450 (p) REVERT: B 1015 ARG cc_start: 0.8252 (mtt180) cc_final: 0.7652 (mmp-170) REVERT: B 1051 ILE cc_start: 0.9289 (mp) cc_final: 0.8999 (mt) REVERT: B 1388 TYR cc_start: 0.9122 (m-80) cc_final: 0.8717 (m-80) REVERT: B 1461 LEU cc_start: 0.6259 (OUTLIER) cc_final: 0.6054 (pp) REVERT: B 1499 GLN cc_start: 0.8498 (OUTLIER) cc_final: 0.8269 (pm20) REVERT: B 1824 ASP cc_start: 0.6975 (t0) cc_final: 0.6546 (t70) REVERT: B 1870 GLN cc_start: 0.8861 (OUTLIER) cc_final: 0.7583 (mp10) REVERT: B 1872 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.6811 (mp0) REVERT: B 2022 MET cc_start: 0.8656 (tpp) cc_final: 0.8300 (tpp) REVERT: B 2165 MET cc_start: 0.8832 (mtp) cc_final: 0.8598 (mtp) REVERT: B 2242 GLN cc_start: 0.8707 (mt0) cc_final: 0.8319 (mt0) REVERT: B 2351 PHE cc_start: 0.7799 (p90) cc_final: 0.7501 (p90) REVERT: C 148 MET cc_start: 0.8770 (ptm) cc_final: 0.8080 (ptm) REVERT: C 162 LEU cc_start: 0.9052 (tp) cc_final: 0.8800 (tp) REVERT: C 291 GLU cc_start: 0.7524 (OUTLIER) cc_final: 0.7312 (mt-10) REVERT: C 904 GLN cc_start: 0.6370 (mp10) cc_final: 0.6012 (mp10) REVERT: C 916 GLU cc_start: 0.8230 (tt0) cc_final: 0.7897 (tt0) REVERT: C 1015 ARG cc_start: 0.7730 (mtt180) cc_final: 0.6929 (mmp-170) REVERT: C 1252 GLN cc_start: 0.9347 (OUTLIER) cc_final: 0.9001 (mt0) REVERT: C 1334 ASN cc_start: 0.8648 (m-40) cc_final: 0.8145 (m110) REVERT: C 1461 LEU cc_start: 0.7953 (OUTLIER) cc_final: 0.7408 (pp) REVERT: C 1596 MET cc_start: 0.8886 (ttp) cc_final: 0.8547 (ttp) REVERT: C 1913 ILE cc_start: 0.8729 (pt) cc_final: 0.8492 (mt) REVERT: C 1961 GLN cc_start: 0.8426 (mt0) cc_final: 0.8155 (mt0) REVERT: C 2263 PHE cc_start: 0.8597 (t80) cc_final: 0.8189 (t80) REVERT: C 2386 SER cc_start: 0.9208 (m) cc_final: 0.8856 (p) REVERT: C 2494 LYS cc_start: 0.8402 (mttt) cc_final: 0.8117 (ttpp) REVERT: D 299 LYS cc_start: 0.8605 (OUTLIER) cc_final: 0.8193 (mmtp) REVERT: D 462 ARG cc_start: 0.8252 (mtt-85) cc_final: 0.8000 (mtt-85) REVERT: D 683 LYS cc_start: 0.7645 (ttpp) cc_final: 0.7187 (tptt) REVERT: D 1300 ARG cc_start: 0.8453 (ttp80) cc_final: 0.7786 (ttp80) REVERT: D 1343 LYS cc_start: 0.8467 (pptt) cc_final: 0.8232 (ptpt) REVERT: D 1364 TYR cc_start: 0.6284 (OUTLIER) cc_final: 0.5186 (m-10) REVERT: D 1419 GLN cc_start: 0.7962 (OUTLIER) cc_final: 0.7608 (pt0) REVERT: D 1437 TRP cc_start: 0.8458 (t-100) cc_final: 0.8218 (t-100) REVERT: D 2022 MET cc_start: 0.8737 (tpp) cc_final: 0.8407 (mmt) REVERT: D 2491 MET cc_start: 0.7899 (mtp) cc_final: 0.7662 (mtp) REVERT: E 51 ASP cc_start: 0.7935 (m-30) cc_final: 0.7585 (m-30) REVERT: E 56 GLN cc_start: 0.8078 (tm-30) cc_final: 0.7759 (tt0) REVERT: E 94 ASN cc_start: 0.7923 (m-40) cc_final: 0.7722 (m-40) REVERT: E 155 MET cc_start: 0.9160 (ttp) cc_final: 0.8950 (ttt) REVERT: E 186 MET cc_start: 0.8936 (mmt) cc_final: 0.8711 (mmp) REVERT: E 299 LYS cc_start: 0.8430 (mmtm) cc_final: 0.8180 (mttm) REVERT: E 462 ARG cc_start: 0.8270 (ttm170) cc_final: 0.7851 (mmt90) REVERT: E 1020 ASP cc_start: 0.7743 (m-30) cc_final: 0.7458 (m-30) REVERT: E 1115 GLU cc_start: 0.7537 (mm-30) cc_final: 0.6959 (mt-10) REVERT: E 1321 ASP cc_start: 0.7092 (t70) cc_final: 0.6851 (t0) REVERT: E 1343 LYS cc_start: 0.8259 (ptpt) cc_final: 0.7882 (pttt) REVERT: E 1423 LEU cc_start: 0.9306 (OUTLIER) cc_final: 0.9092 (mt) REVERT: E 1920 ASP cc_start: 0.8072 (m-30) cc_final: 0.7811 (m-30) REVERT: E 2042 ASN cc_start: 0.8119 (t0) cc_final: 0.7377 (m-40) REVERT: E 2232 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7502 (mp0) REVERT: E 2257 ARG cc_start: 0.8714 (mmm-85) cc_final: 0.8407 (mmm160) REVERT: E 2505 ASN cc_start: 0.8424 (t0) cc_final: 0.7745 (t0) outliers start: 193 outliers final: 146 residues processed: 1193 average time/residue: 0.8854 time to fit residues: 1827.0309 Evaluate side-chains 1169 residues out of total 10500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 1006 time to evaluate : 8.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 ASN Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 558 ASP Chi-restraints excluded: chain A residue 572 ASP Chi-restraints excluded: chain A residue 713 LEU Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 800 SER Chi-restraints excluded: chain A residue 816 GLU Chi-restraints excluded: chain A residue 869 SER Chi-restraints excluded: chain A residue 983 THR Chi-restraints excluded: chain A residue 1087 GLN Chi-restraints excluded: chain A residue 1101 ILE Chi-restraints excluded: chain A residue 1120 GLU Chi-restraints excluded: chain A residue 1139 ASN Chi-restraints excluded: chain A residue 1423 LEU Chi-restraints excluded: chain A residue 1444 SER Chi-restraints excluded: chain A residue 1446 THR Chi-restraints excluded: chain A residue 1461 LEU Chi-restraints excluded: chain A residue 1465 ASP Chi-restraints excluded: chain A residue 1683 ASP Chi-restraints excluded: chain A residue 1898 LEU Chi-restraints excluded: chain A residue 1927 ARG Chi-restraints excluded: chain A residue 1945 THR Chi-restraints excluded: chain A residue 1956 MET Chi-restraints excluded: chain A residue 2228 LYS Chi-restraints excluded: chain A residue 2330 GLU Chi-restraints excluded: chain A residue 2367 SER Chi-restraints excluded: chain A residue 2381 THR Chi-restraints excluded: chain A residue 2422 LEU Chi-restraints excluded: chain A residue 2483 THR Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 240 ASN Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 352 ASN Chi-restraints excluded: chain B residue 455 THR Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 511 GLN Chi-restraints excluded: chain B residue 601 THR Chi-restraints excluded: chain B residue 603 ASP Chi-restraints excluded: chain B residue 625 LYS Chi-restraints excluded: chain B residue 1103 ASN Chi-restraints excluded: chain B residue 1115 GLU Chi-restraints excluded: chain B residue 1139 ASN Chi-restraints excluded: chain B residue 1156 SER Chi-restraints excluded: chain B residue 1165 SER Chi-restraints excluded: chain B residue 1192 THR Chi-restraints excluded: chain B residue 1364 TYR Chi-restraints excluded: chain B residue 1365 GLU Chi-restraints excluded: chain B residue 1423 LEU Chi-restraints excluded: chain B residue 1459 ASP Chi-restraints excluded: chain B residue 1461 LEU Chi-restraints excluded: chain B residue 1477 LYS Chi-restraints excluded: chain B residue 1499 GLN Chi-restraints excluded: chain B residue 1528 MET Chi-restraints excluded: chain B residue 1684 THR Chi-restraints excluded: chain B residue 1709 MET Chi-restraints excluded: chain B residue 1719 THR Chi-restraints excluded: chain B residue 1811 ILE Chi-restraints excluded: chain B residue 1870 GLN Chi-restraints excluded: chain B residue 1872 GLU Chi-restraints excluded: chain B residue 1874 ASP Chi-restraints excluded: chain B residue 1957 MET Chi-restraints excluded: chain B residue 1977 ASP Chi-restraints excluded: chain B residue 2128 VAL Chi-restraints excluded: chain B residue 2182 SER Chi-restraints excluded: chain B residue 2287 ASP Chi-restraints excluded: chain B residue 2325 ASP Chi-restraints excluded: chain B residue 2352 SER Chi-restraints excluded: chain B residue 2428 ASP Chi-restraints excluded: chain C residue 90 ILE Chi-restraints excluded: chain C residue 291 GLU Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 458 GLU Chi-restraints excluded: chain C residue 504 SER Chi-restraints excluded: chain C residue 534 GLU Chi-restraints excluded: chain C residue 648 VAL Chi-restraints excluded: chain C residue 1014 SER Chi-restraints excluded: chain C residue 1101 ILE Chi-restraints excluded: chain C residue 1139 ASN Chi-restraints excluded: chain C residue 1156 SER Chi-restraints excluded: chain C residue 1243 ASP Chi-restraints excluded: chain C residue 1252 GLN Chi-restraints excluded: chain C residue 1461 LEU Chi-restraints excluded: chain C residue 1518 SER Chi-restraints excluded: chain C residue 1830 ASP Chi-restraints excluded: chain C residue 1946 ASP Chi-restraints excluded: chain C residue 2330 GLU Chi-restraints excluded: chain C residue 2331 VAL Chi-restraints excluded: chain C residue 2360 LEU Chi-restraints excluded: chain C residue 2381 THR Chi-restraints excluded: chain C residue 2434 SER Chi-restraints excluded: chain C residue 2477 ILE Chi-restraints excluded: chain C residue 2493 GLU Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 195 SER Chi-restraints excluded: chain D residue 275 SER Chi-restraints excluded: chain D residue 299 LYS Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 496 LEU Chi-restraints excluded: chain D residue 601 THR Chi-restraints excluded: chain D residue 748 THR Chi-restraints excluded: chain D residue 1056 MET Chi-restraints excluded: chain D residue 1139 ASN Chi-restraints excluded: chain D residue 1165 SER Chi-restraints excluded: chain D residue 1285 VAL Chi-restraints excluded: chain D residue 1317 SER Chi-restraints excluded: chain D residue 1318 SER Chi-restraints excluded: chain D residue 1364 TYR Chi-restraints excluded: chain D residue 1419 GLN Chi-restraints excluded: chain D residue 1423 LEU Chi-restraints excluded: chain D residue 1461 LEU Chi-restraints excluded: chain D residue 1524 SER Chi-restraints excluded: chain D residue 1652 LEU Chi-restraints excluded: chain D residue 1657 ASP Chi-restraints excluded: chain D residue 1811 ILE Chi-restraints excluded: chain D residue 1921 SER Chi-restraints excluded: chain D residue 2002 THR Chi-restraints excluded: chain D residue 2225 THR Chi-restraints excluded: chain D residue 2340 VAL Chi-restraints excluded: chain D residue 2347 ASP Chi-restraints excluded: chain D residue 2390 SER Chi-restraints excluded: chain D residue 2416 SER Chi-restraints excluded: chain E residue 88 GLU Chi-restraints excluded: chain E residue 325 VAL Chi-restraints excluded: chain E residue 331 THR Chi-restraints excluded: chain E residue 381 THR Chi-restraints excluded: chain E residue 410 LEU Chi-restraints excluded: chain E residue 468 LEU Chi-restraints excluded: chain E residue 603 ASP Chi-restraints excluded: chain E residue 666 GLU Chi-restraints excluded: chain E residue 763 GLU Chi-restraints excluded: chain E residue 790 THR Chi-restraints excluded: chain E residue 805 THR Chi-restraints excluded: chain E residue 881 VAL Chi-restraints excluded: chain E residue 909 THR Chi-restraints excluded: chain E residue 1139 ASN Chi-restraints excluded: chain E residue 1148 ASP Chi-restraints excluded: chain E residue 1177 ILE Chi-restraints excluded: chain E residue 1296 THR Chi-restraints excluded: chain E residue 1396 ASN Chi-restraints excluded: chain E residue 1423 LEU Chi-restraints excluded: chain E residue 1429 THR Chi-restraints excluded: chain E residue 1461 LEU Chi-restraints excluded: chain E residue 1578 VAL Chi-restraints excluded: chain E residue 1652 LEU Chi-restraints excluded: chain E residue 1683 ASP Chi-restraints excluded: chain E residue 1730 LYS Chi-restraints excluded: chain E residue 1734 THR Chi-restraints excluded: chain E residue 1790 ASP Chi-restraints excluded: chain E residue 1913 ILE Chi-restraints excluded: chain E residue 1977 ASP Chi-restraints excluded: chain E residue 2125 THR Chi-restraints excluded: chain E residue 2232 GLU Chi-restraints excluded: chain E residue 2236 SER Chi-restraints excluded: chain E residue 2330 GLU Chi-restraints excluded: chain E residue 2337 LEU Chi-restraints excluded: chain E residue 2347 ASP Chi-restraints excluded: chain E residue 2385 THR Chi-restraints excluded: chain E residue 2409 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1225 random chunks: chunk 1142 optimal weight: 4.9990 chunk 133 optimal weight: 2.9990 chunk 675 optimal weight: 0.8980 chunk 865 optimal weight: 0.9980 chunk 670 optimal weight: 0.6980 chunk 997 optimal weight: 1.9990 chunk 661 optimal weight: 2.9990 chunk 1180 optimal weight: 0.8980 chunk 738 optimal weight: 0.7980 chunk 719 optimal weight: 5.9990 chunk 545 optimal weight: 5.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 305 GLN A1007 ASN A1394 ASN ** A1419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2298 GLN ** B 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 302 ASN C1003 ASN ** C1293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2427 GLN ** C2497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 834 GLN D1520 GLN ** D2047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 53 GLN ** E 581 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 772 ASN ** E1394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E2497 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.3815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 99495 Z= 0.175 Angle : 0.461 9.749 135140 Z= 0.242 Chirality : 0.040 0.339 14960 Planarity : 0.003 0.071 17580 Dihedral : 4.059 35.618 13370 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.92 % Allowed : 8.72 % Favored : 89.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.00 % 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: 0.97 (0.08), residues: 12240 helix: 1.97 (0.07), residues: 5560 sheet: 0.11 (0.11), residues: 2135 loop : -0.74 (0.09), residues: 4545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C1171 HIS 0.007 0.001 HIS E1888 PHE 0.018 0.001 PHE B 937 TYR 0.015 0.001 TYR B 968 ARG 0.007 0.000 ARG D1659 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 24480 Ramachandran restraints generated. 12240 Oldfield, 0 Emsley, 12240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 24480 Ramachandran restraints generated. 12240 Oldfield, 0 Emsley, 12240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1249 residues out of total 10500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 202 poor density : 1047 time to evaluate : 8.791 Fit side-chains REVERT: A 231 MET cc_start: 0.8514 (mtp) cc_final: 0.8252 (mtm) REVERT: A 262 GLU cc_start: 0.8068 (tm-30) cc_final: 0.7718 (tp30) REVERT: A 287 ASN cc_start: 0.8809 (t0) cc_final: 0.8446 (t0) REVERT: A 374 ASP cc_start: 0.7841 (t0) cc_final: 0.7336 (t0) REVERT: A 402 ILE cc_start: 0.8770 (mm) cc_final: 0.8407 (mt) REVERT: A 645 LYS cc_start: 0.8745 (mttt) cc_final: 0.8401 (mtmt) REVERT: A 666 GLU cc_start: 0.8373 (mp0) cc_final: 0.8160 (pm20) REVERT: A 764 MET cc_start: 0.8204 (ttm) cc_final: 0.7926 (ttt) REVERT: A 803 MET cc_start: 0.8602 (tmm) cc_final: 0.8048 (tmm) REVERT: A 806 ARG cc_start: 0.8031 (mmt90) cc_final: 0.7603 (mtp85) REVERT: A 839 MET cc_start: 0.9160 (mtp) cc_final: 0.8804 (mtt) REVERT: A 1101 ILE cc_start: 0.8758 (OUTLIER) cc_final: 0.8452 (tt) REVERT: A 1236 CYS cc_start: 0.8654 (t) cc_final: 0.8449 (t) REVERT: A 1394 ASN cc_start: 0.8848 (OUTLIER) cc_final: 0.8179 (m-40) REVERT: A 1746 SER cc_start: 0.8106 (t) cc_final: 0.7797 (m) REVERT: A 1898 LEU cc_start: 0.8023 (OUTLIER) cc_final: 0.7795 (pp) REVERT: A 1927 ARG cc_start: 0.9027 (OUTLIER) cc_final: 0.8734 (ttp-110) REVERT: A 2076 GLU cc_start: 0.8297 (mt-10) cc_final: 0.8031 (mt-10) REVERT: A 2081 GLU cc_start: 0.8166 (mm-30) cc_final: 0.7907 (mm-30) REVERT: A 2422 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8468 (mm) REVERT: B 136 TYR cc_start: 0.9220 (m-80) cc_final: 0.8915 (m-80) REVERT: B 309 SER cc_start: 0.8678 (t) cc_final: 0.8332 (p) REVERT: B 448 ARG cc_start: 0.8160 (mtm110) cc_final: 0.7895 (mtm-85) REVERT: B 462 ARG cc_start: 0.8793 (mmt-90) cc_final: 0.8569 (mmt-90) REVERT: B 574 LYS cc_start: 0.8142 (mmtt) cc_final: 0.7771 (mmmt) REVERT: B 601 THR cc_start: 0.8762 (OUTLIER) cc_final: 0.8443 (p) REVERT: B 1015 ARG cc_start: 0.8259 (mtt180) cc_final: 0.7650 (mmp-170) REVERT: B 1051 ILE cc_start: 0.9303 (mp) cc_final: 0.9028 (mt) REVERT: B 1388 TYR cc_start: 0.9119 (m-80) cc_final: 0.8686 (m-80) REVERT: B 1423 LEU cc_start: 0.9082 (OUTLIER) cc_final: 0.8830 (mt) REVERT: B 1461 LEU cc_start: 0.6274 (OUTLIER) cc_final: 0.6061 (pp) REVERT: B 1499 GLN cc_start: 0.8516 (OUTLIER) cc_final: 0.8285 (pm20) REVERT: B 1824 ASP cc_start: 0.6815 (t0) cc_final: 0.6549 (t70) REVERT: B 1870 GLN cc_start: 0.8849 (OUTLIER) cc_final: 0.8147 (mp10) REVERT: B 1872 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7875 (mt-10) REVERT: B 2022 MET cc_start: 0.8657 (tpp) cc_final: 0.8243 (tpp) REVERT: B 2242 GLN cc_start: 0.8704 (mt0) cc_final: 0.8311 (mt0) REVERT: B 2351 PHE cc_start: 0.7856 (p90) cc_final: 0.7578 (p90) REVERT: C 148 MET cc_start: 0.8769 (ptm) cc_final: 0.8066 (ptm) REVERT: C 162 LEU cc_start: 0.9047 (tp) cc_final: 0.8803 (tp) REVERT: C 351 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.7994 (tt0) REVERT: C 904 GLN cc_start: 0.6395 (mp10) cc_final: 0.6113 (mp10) REVERT: C 1015 ARG cc_start: 0.7740 (mtt180) cc_final: 0.6930 (mmp-170) REVERT: C 1334 ASN cc_start: 0.8656 (m-40) cc_final: 0.8206 (m110) REVERT: C 1461 LEU cc_start: 0.7959 (OUTLIER) cc_final: 0.6942 (pp) REVERT: C 1596 MET cc_start: 0.8874 (ttp) cc_final: 0.8590 (ttp) REVERT: C 1913 ILE cc_start: 0.8724 (pt) cc_final: 0.8491 (mt) REVERT: C 1961 GLN cc_start: 0.8432 (mt0) cc_final: 0.8142 (mt0) REVERT: C 2263 PHE cc_start: 0.8559 (t80) cc_final: 0.8138 (t80) REVERT: C 2386 SER cc_start: 0.9204 (m) cc_final: 0.8830 (p) REVERT: C 2494 LYS cc_start: 0.8405 (mttt) cc_final: 0.8115 (ttpp) REVERT: D 299 LYS cc_start: 0.8606 (OUTLIER) cc_final: 0.8195 (mmtp) REVERT: D 683 LYS cc_start: 0.7573 (ttpp) cc_final: 0.7194 (tptt) REVERT: D 822 LEU cc_start: 0.9243 (mt) cc_final: 0.9014 (mt) REVERT: D 1300 ARG cc_start: 0.8451 (ttp80) cc_final: 0.7824 (ttp80) REVERT: D 1343 LYS cc_start: 0.8476 (pptt) cc_final: 0.8214 (ptpt) REVERT: D 1364 TYR cc_start: 0.6173 (OUTLIER) cc_final: 0.5464 (m-10) REVERT: D 1437 TRP cc_start: 0.8447 (t-100) cc_final: 0.8200 (t-100) REVERT: D 1702 ASP cc_start: 0.7991 (m-30) cc_final: 0.7702 (t0) REVERT: D 2022 MET cc_start: 0.8752 (tpp) cc_final: 0.8393 (mmt) REVERT: E 51 ASP cc_start: 0.8016 (m-30) cc_final: 0.7703 (m-30) REVERT: E 56 GLN cc_start: 0.8073 (tm-30) cc_final: 0.7752 (tt0) REVERT: E 155 MET cc_start: 0.9160 (ttp) cc_final: 0.8940 (ttt) REVERT: E 186 MET cc_start: 0.8933 (mmt) cc_final: 0.8724 (mmp) REVERT: E 299 LYS cc_start: 0.8422 (mmtm) cc_final: 0.8192 (mttp) REVERT: E 462 ARG cc_start: 0.8273 (ttm170) cc_final: 0.7842 (mmt90) REVERT: E 1020 ASP cc_start: 0.7740 (m-30) cc_final: 0.7430 (m-30) REVERT: E 1115 GLU cc_start: 0.7499 (mm-30) cc_final: 0.6900 (mt-10) REVERT: E 1321 ASP cc_start: 0.7125 (t70) cc_final: 0.6899 (t0) REVERT: E 1343 LYS cc_start: 0.8248 (ptpt) cc_final: 0.7890 (pttt) REVERT: E 1423 LEU cc_start: 0.9306 (OUTLIER) cc_final: 0.9097 (mt) REVERT: E 1463 LYS cc_start: 0.8393 (mtpt) cc_final: 0.7966 (mmtt) REVERT: E 1753 ILE cc_start: 0.8547 (tp) cc_final: 0.8299 (mt) REVERT: E 1920 ASP cc_start: 0.8076 (m-30) cc_final: 0.7819 (m-30) REVERT: E 2042 ASN cc_start: 0.8119 (t0) cc_final: 0.7381 (m-40) REVERT: E 2232 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.7474 (mp0) REVERT: E 2257 ARG cc_start: 0.8704 (mmm-85) cc_final: 0.8410 (mmm160) REVERT: E 2505 ASN cc_start: 0.8420 (t0) cc_final: 0.7746 (t0) outliers start: 202 outliers final: 153 residues processed: 1188 average time/residue: 0.9070 time to fit residues: 1866.2190 Evaluate side-chains 1174 residues out of total 10500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 1004 time to evaluate : 8.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 ASN Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 558 ASP Chi-restraints excluded: chain A residue 572 ASP Chi-restraints excluded: chain A residue 713 LEU Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 800 SER Chi-restraints excluded: chain A residue 816 GLU Chi-restraints excluded: chain A residue 869 SER Chi-restraints excluded: chain A residue 983 THR Chi-restraints excluded: chain A residue 1087 GLN Chi-restraints excluded: chain A residue 1092 LYS Chi-restraints excluded: chain A residue 1101 ILE Chi-restraints excluded: chain A residue 1120 GLU Chi-restraints excluded: chain A residue 1139 ASN Chi-restraints excluded: chain A residue 1394 ASN Chi-restraints excluded: chain A residue 1423 LEU Chi-restraints excluded: chain A residue 1444 SER Chi-restraints excluded: chain A residue 1446 THR Chi-restraints excluded: chain A residue 1461 LEU Chi-restraints excluded: chain A residue 1465 ASP Chi-restraints excluded: chain A residue 1484 SER Chi-restraints excluded: chain A residue 1576 LEU Chi-restraints excluded: chain A residue 1683 ASP Chi-restraints excluded: chain A residue 1898 LEU Chi-restraints excluded: chain A residue 1927 ARG Chi-restraints excluded: chain A residue 1945 THR Chi-restraints excluded: chain A residue 1956 MET Chi-restraints excluded: chain A residue 2107 ILE Chi-restraints excluded: chain A residue 2228 LYS Chi-restraints excluded: chain A residue 2330 GLU Chi-restraints excluded: chain A residue 2367 SER Chi-restraints excluded: chain A residue 2381 THR Chi-restraints excluded: chain A residue 2422 LEU Chi-restraints excluded: chain A residue 2483 THR Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 240 ASN Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 352 ASN Chi-restraints excluded: chain B residue 455 THR Chi-restraints excluded: chain B residue 511 GLN Chi-restraints excluded: chain B residue 601 THR Chi-restraints excluded: chain B residue 603 ASP Chi-restraints excluded: chain B residue 625 LYS Chi-restraints excluded: chain B residue 1103 ASN Chi-restraints excluded: chain B residue 1139 ASN Chi-restraints excluded: chain B residue 1156 SER Chi-restraints excluded: chain B residue 1165 SER Chi-restraints excluded: chain B residue 1169 LEU Chi-restraints excluded: chain B residue 1192 THR Chi-restraints excluded: chain B residue 1364 TYR Chi-restraints excluded: chain B residue 1365 GLU Chi-restraints excluded: chain B residue 1423 LEU Chi-restraints excluded: chain B residue 1458 THR Chi-restraints excluded: chain B residue 1459 ASP Chi-restraints excluded: chain B residue 1461 LEU Chi-restraints excluded: chain B residue 1477 LYS Chi-restraints excluded: chain B residue 1499 GLN Chi-restraints excluded: chain B residue 1528 MET Chi-restraints excluded: chain B residue 1684 THR Chi-restraints excluded: chain B residue 1709 MET Chi-restraints excluded: chain B residue 1719 THR Chi-restraints excluded: chain B residue 1870 GLN Chi-restraints excluded: chain B residue 1872 GLU Chi-restraints excluded: chain B residue 1874 ASP Chi-restraints excluded: chain B residue 1957 MET Chi-restraints excluded: chain B residue 1977 ASP Chi-restraints excluded: chain B residue 2128 VAL Chi-restraints excluded: chain B residue 2182 SER Chi-restraints excluded: chain B residue 2287 ASP Chi-restraints excluded: chain B residue 2325 ASP Chi-restraints excluded: chain B residue 2352 SER Chi-restraints excluded: chain B residue 2428 ASP Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 351 GLU Chi-restraints excluded: chain C residue 458 GLU Chi-restraints excluded: chain C residue 504 SER Chi-restraints excluded: chain C residue 534 GLU Chi-restraints excluded: chain C residue 648 VAL Chi-restraints excluded: chain C residue 1014 SER Chi-restraints excluded: chain C residue 1101 ILE Chi-restraints excluded: chain C residue 1139 ASN Chi-restraints excluded: chain C residue 1191 GLU Chi-restraints excluded: chain C residue 1243 ASP Chi-restraints excluded: chain C residue 1461 LEU Chi-restraints excluded: chain C residue 1518 SER Chi-restraints excluded: chain C residue 1830 ASP Chi-restraints excluded: chain C residue 1946 ASP Chi-restraints excluded: chain C residue 1977 ASP Chi-restraints excluded: chain C residue 1991 ASP Chi-restraints excluded: chain C residue 2330 GLU Chi-restraints excluded: chain C residue 2331 VAL Chi-restraints excluded: chain C residue 2360 LEU Chi-restraints excluded: chain C residue 2381 THR Chi-restraints excluded: chain C residue 2434 SER Chi-restraints excluded: chain C residue 2477 ILE Chi-restraints excluded: chain C residue 2493 GLU Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 195 SER Chi-restraints excluded: chain D residue 275 SER Chi-restraints excluded: chain D residue 299 LYS Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 496 LEU Chi-restraints excluded: chain D residue 557 ILE Chi-restraints excluded: chain D residue 601 THR Chi-restraints excluded: chain D residue 603 ASP Chi-restraints excluded: chain D residue 664 THR Chi-restraints excluded: chain D residue 748 THR Chi-restraints excluded: chain D residue 1056 MET Chi-restraints excluded: chain D residue 1139 ASN Chi-restraints excluded: chain D residue 1165 SER Chi-restraints excluded: chain D residue 1192 THR Chi-restraints excluded: chain D residue 1285 VAL Chi-restraints excluded: chain D residue 1317 SER Chi-restraints excluded: chain D residue 1318 SER Chi-restraints excluded: chain D residue 1364 TYR Chi-restraints excluded: chain D residue 1403 MET Chi-restraints excluded: chain D residue 1423 LEU Chi-restraints excluded: chain D residue 1461 LEU Chi-restraints excluded: chain D residue 1652 LEU Chi-restraints excluded: chain D residue 1657 ASP Chi-restraints excluded: chain D residue 1811 ILE Chi-restraints excluded: chain D residue 2002 THR Chi-restraints excluded: chain D residue 2225 THR Chi-restraints excluded: chain D residue 2340 VAL Chi-restraints excluded: chain D residue 2347 ASP Chi-restraints excluded: chain D residue 2390 SER Chi-restraints excluded: chain D residue 2416 SER Chi-restraints excluded: chain E residue 88 GLU Chi-restraints excluded: chain E residue 101 SER Chi-restraints excluded: chain E residue 325 VAL Chi-restraints excluded: chain E residue 331 THR Chi-restraints excluded: chain E residue 381 THR Chi-restraints excluded: chain E residue 411 THR Chi-restraints excluded: chain E residue 468 LEU Chi-restraints excluded: chain E residue 603 ASP Chi-restraints excluded: chain E residue 666 GLU Chi-restraints excluded: chain E residue 763 GLU Chi-restraints excluded: chain E residue 790 THR Chi-restraints excluded: chain E residue 799 LEU Chi-restraints excluded: chain E residue 805 THR Chi-restraints excluded: chain E residue 881 VAL Chi-restraints excluded: chain E residue 909 THR Chi-restraints excluded: chain E residue 1139 ASN Chi-restraints excluded: chain E residue 1148 ASP Chi-restraints excluded: chain E residue 1177 ILE Chi-restraints excluded: chain E residue 1296 THR Chi-restraints excluded: chain E residue 1381 LEU Chi-restraints excluded: chain E residue 1396 ASN Chi-restraints excluded: chain E residue 1423 LEU Chi-restraints excluded: chain E residue 1461 LEU Chi-restraints excluded: chain E residue 1465 ASP Chi-restraints excluded: chain E residue 1578 VAL Chi-restraints excluded: chain E residue 1683 ASP Chi-restraints excluded: chain E residue 1695 ASP Chi-restraints excluded: chain E residue 1730 LYS Chi-restraints excluded: chain E residue 1734 THR Chi-restraints excluded: chain E residue 1790 ASP Chi-restraints excluded: chain E residue 1913 ILE Chi-restraints excluded: chain E residue 1977 ASP Chi-restraints excluded: chain E residue 2125 THR Chi-restraints excluded: chain E residue 2232 GLU Chi-restraints excluded: chain E residue 2236 SER Chi-restraints excluded: chain E residue 2330 GLU Chi-restraints excluded: chain E residue 2337 LEU Chi-restraints excluded: chain E residue 2347 ASP Chi-restraints excluded: chain E residue 2385 THR Chi-restraints excluded: chain E residue 2409 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1225 random chunks: chunk 730 optimal weight: 2.9990 chunk 471 optimal weight: 4.9990 chunk 705 optimal weight: 0.6980 chunk 355 optimal weight: 1.9990 chunk 232 optimal weight: 6.9990 chunk 228 optimal weight: 3.9990 chunk 750 optimal weight: 2.9990 chunk 804 optimal weight: 0.9980 chunk 583 optimal weight: 4.9990 chunk 110 optimal weight: 3.9990 chunk 928 optimal weight: 6.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 GLN ** A 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1007 ASN A1180 GLN A1394 ASN ** A1419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1425 HIS ** B 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 102 GLN ** B1547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 302 ASN C1003 ASN C1293 GLN C1413 ASN ** C2047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2427 GLN ** C2497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 573 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 834 GLN D1007 ASN D1373 ASN D1413 ASN D1785 HIS ** D2047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2093 GLN E 311 ASN E 514 GLN ** E 581 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 772 ASN ** E1394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E2223 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.3931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 99495 Z= 0.337 Angle : 0.560 10.149 135140 Z= 0.290 Chirality : 0.044 0.318 14960 Planarity : 0.004 0.074 17580 Dihedral : 4.457 36.123 13370 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.91 % Allowed : 9.04 % Favored : 89.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.00 % 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: 0.67 (0.08), residues: 12240 helix: 1.64 (0.07), residues: 5570 sheet: 0.03 (0.11), residues: 2125 loop : -0.81 (0.09), residues: 4545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B1324 HIS 0.010 0.001 HIS A1888 PHE 0.019 0.002 PHE B 937 TYR 0.025 0.002 TYR D 968 ARG 0.008 0.001 ARG D2290 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 24480 Ramachandran restraints generated. 12240 Oldfield, 0 Emsley, 12240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 24480 Ramachandran restraints generated. 12240 Oldfield, 0 Emsley, 12240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1210 residues out of total 10500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 201 poor density : 1009 time to evaluate : 8.822 Fit side-chains REVERT: A 262 GLU cc_start: 0.8086 (tm-30) cc_final: 0.7790 (tp30) REVERT: A 287 ASN cc_start: 0.8842 (t0) cc_final: 0.8487 (t0) REVERT: A 374 ASP cc_start: 0.8028 (t0) cc_final: 0.7559 (t0) REVERT: A 402 ILE cc_start: 0.8919 (mm) cc_final: 0.8672 (mt) REVERT: A 425 LYS cc_start: 0.8743 (ttpt) cc_final: 0.8383 (ttmt) REVERT: A 508 TYR cc_start: 0.6735 (m-80) cc_final: 0.6112 (m-80) REVERT: A 803 MET cc_start: 0.8628 (tmm) cc_final: 0.8095 (tmm) REVERT: A 839 MET cc_start: 0.9204 (mtp) cc_final: 0.8702 (mtp) REVERT: A 1170 LEU cc_start: 0.8996 (OUTLIER) cc_final: 0.8446 (mp) REVERT: A 1236 CYS cc_start: 0.8630 (t) cc_final: 0.8277 (t) REVERT: A 1394 ASN cc_start: 0.8900 (OUTLIER) cc_final: 0.8631 (m-40) REVERT: A 1685 ASN cc_start: 0.7880 (OUTLIER) cc_final: 0.7240 (m-40) REVERT: A 1898 LEU cc_start: 0.7949 (OUTLIER) cc_final: 0.7706 (pp) REVERT: A 1927 ARG cc_start: 0.9090 (OUTLIER) cc_final: 0.8414 (ttp-110) REVERT: A 2076 GLU cc_start: 0.8350 (mt-10) cc_final: 0.8093 (mt-10) REVERT: B 136 TYR cc_start: 0.9218 (m-80) cc_final: 0.8895 (m-80) REVERT: B 309 SER cc_start: 0.8762 (t) cc_final: 0.8405 (p) REVERT: B 448 ARG cc_start: 0.8179 (mtm110) cc_final: 0.7962 (mtm-85) REVERT: B 601 THR cc_start: 0.8827 (OUTLIER) cc_final: 0.8545 (p) REVERT: B 1015 ARG cc_start: 0.8285 (mtt180) cc_final: 0.7650 (mmp-170) REVERT: B 1295 ASP cc_start: 0.8133 (m-30) cc_final: 0.7880 (m-30) REVERT: B 1388 TYR cc_start: 0.9158 (m-80) cc_final: 0.8695 (m-80) REVERT: B 1461 LEU cc_start: 0.6678 (OUTLIER) cc_final: 0.6409 (pp) REVERT: B 1870 GLN cc_start: 0.8777 (OUTLIER) cc_final: 0.8217 (mm-40) REVERT: B 1872 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.6862 (mp0) REVERT: B 2022 MET cc_start: 0.8702 (tpp) cc_final: 0.8377 (tpp) REVERT: B 2242 GLN cc_start: 0.8798 (mt0) cc_final: 0.8437 (mt0) REVERT: C 148 MET cc_start: 0.8849 (ptm) cc_final: 0.8143 (ptm) REVERT: C 292 GLU cc_start: 0.7667 (mt-10) cc_final: 0.7346 (mt-10) REVERT: C 351 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.8074 (tt0) REVERT: C 904 GLN cc_start: 0.6505 (mp10) cc_final: 0.6229 (mp10) REVERT: C 1015 ARG cc_start: 0.7783 (mtt180) cc_final: 0.6820 (mmp-170) REVERT: C 1461 LEU cc_start: 0.8057 (OUTLIER) cc_final: 0.7509 (pp) REVERT: C 1596 MET cc_start: 0.8882 (ttp) cc_final: 0.8637 (ttp) REVERT: C 1913 ILE cc_start: 0.8813 (pt) cc_final: 0.8484 (mt) REVERT: C 2029 MET cc_start: 0.8997 (tpp) cc_final: 0.8592 (tpp) REVERT: C 2177 ASP cc_start: 0.7898 (m-30) cc_final: 0.7540 (m-30) REVERT: C 2263 PHE cc_start: 0.8649 (t80) cc_final: 0.8235 (t80) REVERT: C 2386 SER cc_start: 0.9229 (m) cc_final: 0.8817 (p) REVERT: C 2494 LYS cc_start: 0.8401 (mttt) cc_final: 0.8084 (ttpp) REVERT: C 2505 ASN cc_start: 0.8560 (t0) cc_final: 0.8051 (t0) REVERT: D 88 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.7662 (pm20) REVERT: D 299 LYS cc_start: 0.8642 (OUTLIER) cc_final: 0.8277 (mmtp) REVERT: D 683 LYS cc_start: 0.7710 (ttpp) cc_final: 0.7259 (tptt) REVERT: D 799 LEU cc_start: 0.8951 (mt) cc_final: 0.8623 (mt) REVERT: D 1343 LYS cc_start: 0.8545 (pptt) cc_final: 0.8336 (ptpt) REVERT: D 1364 TYR cc_start: 0.6405 (OUTLIER) cc_final: 0.5501 (m-10) REVERT: D 1830 ASP cc_start: 0.7822 (t70) cc_final: 0.7353 (t70) REVERT: D 2022 MET cc_start: 0.8754 (tpp) cc_final: 0.8412 (mmt) REVERT: D 2311 MET cc_start: 0.8760 (tpp) cc_final: 0.8357 (mmt) REVERT: D 2463 ASP cc_start: 0.8078 (t0) cc_final: 0.7817 (m-30) REVERT: E 51 ASP cc_start: 0.8007 (m-30) cc_final: 0.7644 (m-30) REVERT: E 56 GLN cc_start: 0.8103 (tm-30) cc_final: 0.7804 (tt0) REVERT: E 94 ASN cc_start: 0.7660 (m-40) cc_final: 0.7442 (m-40) REVERT: E 186 MET cc_start: 0.8984 (mmt) cc_final: 0.8771 (mmp) REVERT: E 299 LYS cc_start: 0.8687 (mmtm) cc_final: 0.8302 (mttp) REVERT: E 410 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8291 (mt) REVERT: E 462 ARG cc_start: 0.8304 (ttm170) cc_final: 0.7722 (mmt90) REVERT: E 1020 ASP cc_start: 0.7866 (m-30) cc_final: 0.7553 (m-30) REVERT: E 1115 GLU cc_start: 0.7580 (mm-30) cc_final: 0.7089 (mt-10) REVERT: E 1264 MET cc_start: 0.9122 (mmp) cc_final: 0.8261 (mmp) REVERT: E 1321 ASP cc_start: 0.7395 (t70) cc_final: 0.7185 (t0) REVERT: E 1343 LYS cc_start: 0.8284 (ptpt) cc_final: 0.7923 (pttt) REVERT: E 1423 LEU cc_start: 0.9333 (OUTLIER) cc_final: 0.9099 (mt) REVERT: E 1463 LYS cc_start: 0.8547 (mtpt) cc_final: 0.8118 (mmtt) REVERT: E 1920 ASP cc_start: 0.8092 (m-30) cc_final: 0.7828 (m-30) REVERT: E 2042 ASN cc_start: 0.8167 (t0) cc_final: 0.7404 (m-40) REVERT: E 2228 LYS cc_start: 0.8450 (mtmt) cc_final: 0.8132 (mtmm) REVERT: E 2232 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7467 (mp0) REVERT: E 2257 ARG cc_start: 0.8832 (mmm-85) cc_final: 0.8579 (mmm160) REVERT: E 2491 MET cc_start: 0.8021 (tpp) cc_final: 0.7560 (tpt) REVERT: E 2505 ASN cc_start: 0.8451 (t0) cc_final: 0.7781 (t0) outliers start: 201 outliers final: 152 residues processed: 1150 average time/residue: 0.9174 time to fit residues: 1830.8857 Evaluate side-chains 1127 residues out of total 10500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 958 time to evaluate : 8.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 ASN Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 396 THR Chi-restraints excluded: chain A residue 558 ASP Chi-restraints excluded: chain A residue 572 ASP Chi-restraints excluded: chain A residue 705 GLU Chi-restraints excluded: chain A residue 713 LEU Chi-restraints excluded: chain A residue 800 SER Chi-restraints excluded: chain A residue 869 SER Chi-restraints excluded: chain A residue 983 THR Chi-restraints excluded: chain A residue 1087 GLN Chi-restraints excluded: chain A residue 1092 LYS Chi-restraints excluded: chain A residue 1101 ILE Chi-restraints excluded: chain A residue 1120 GLU Chi-restraints excluded: chain A residue 1139 ASN Chi-restraints excluded: chain A residue 1170 LEU Chi-restraints excluded: chain A residue 1394 ASN Chi-restraints excluded: chain A residue 1423 LEU Chi-restraints excluded: chain A residue 1444 SER Chi-restraints excluded: chain A residue 1446 THR Chi-restraints excluded: chain A residue 1461 LEU Chi-restraints excluded: chain A residue 1465 ASP Chi-restraints excluded: chain A residue 1484 SER Chi-restraints excluded: chain A residue 1683 ASP Chi-restraints excluded: chain A residue 1685 ASN Chi-restraints excluded: chain A residue 1898 LEU Chi-restraints excluded: chain A residue 1927 ARG Chi-restraints excluded: chain A residue 1945 THR Chi-restraints excluded: chain A residue 2228 LYS Chi-restraints excluded: chain A residue 2330 GLU Chi-restraints excluded: chain A residue 2367 SER Chi-restraints excluded: chain A residue 2381 THR Chi-restraints excluded: chain A residue 2483 THR Chi-restraints excluded: chain B residue 240 ASN Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 352 ASN Chi-restraints excluded: chain B residue 455 THR Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 511 GLN Chi-restraints excluded: chain B residue 601 THR Chi-restraints excluded: chain B residue 603 ASP Chi-restraints excluded: chain B residue 906 MET Chi-restraints excluded: chain B residue 1103 ASN Chi-restraints excluded: chain B residue 1139 ASN Chi-restraints excluded: chain B residue 1156 SER Chi-restraints excluded: chain B residue 1165 SER Chi-restraints excluded: chain B residue 1192 THR Chi-restraints excluded: chain B residue 1321 ASP Chi-restraints excluded: chain B residue 1330 SER Chi-restraints excluded: chain B residue 1364 TYR Chi-restraints excluded: chain B residue 1365 GLU Chi-restraints excluded: chain B residue 1423 LEU Chi-restraints excluded: chain B residue 1458 THR Chi-restraints excluded: chain B residue 1459 ASP Chi-restraints excluded: chain B residue 1461 LEU Chi-restraints excluded: chain B residue 1477 LYS Chi-restraints excluded: chain B residue 1528 MET Chi-restraints excluded: chain B residue 1684 THR Chi-restraints excluded: chain B residue 1709 MET Chi-restraints excluded: chain B residue 1719 THR Chi-restraints excluded: chain B residue 1870 GLN Chi-restraints excluded: chain B residue 1872 GLU Chi-restraints excluded: chain B residue 1874 ASP Chi-restraints excluded: chain B residue 1957 MET Chi-restraints excluded: chain B residue 1977 ASP Chi-restraints excluded: chain B residue 2128 VAL Chi-restraints excluded: chain B residue 2182 SER Chi-restraints excluded: chain B residue 2322 LEU Chi-restraints excluded: chain B residue 2325 ASP Chi-restraints excluded: chain B residue 2352 SER Chi-restraints excluded: chain B residue 2428 ASP Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 351 GLU Chi-restraints excluded: chain C residue 504 SER Chi-restraints excluded: chain C residue 534 GLU Chi-restraints excluded: chain C residue 648 VAL Chi-restraints excluded: chain C residue 705 GLU Chi-restraints excluded: chain C residue 764 MET Chi-restraints excluded: chain C residue 1014 SER Chi-restraints excluded: chain C residue 1101 ILE Chi-restraints excluded: chain C residue 1139 ASN Chi-restraints excluded: chain C residue 1243 ASP Chi-restraints excluded: chain C residue 1461 LEU Chi-restraints excluded: chain C residue 1518 SER Chi-restraints excluded: chain C residue 1657 ASP Chi-restraints excluded: chain C residue 1830 ASP Chi-restraints excluded: chain C residue 1946 ASP Chi-restraints excluded: chain C residue 1991 ASP Chi-restraints excluded: chain C residue 2331 VAL Chi-restraints excluded: chain C residue 2360 LEU Chi-restraints excluded: chain C residue 2381 THR Chi-restraints excluded: chain C residue 2434 SER Chi-restraints excluded: chain C residue 2477 ILE Chi-restraints excluded: chain C residue 2493 GLU Chi-restraints excluded: chain D residue 88 GLU Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 195 SER Chi-restraints excluded: chain D residue 275 SER Chi-restraints excluded: chain D residue 299 LYS Chi-restraints excluded: chain D residue 496 LEU Chi-restraints excluded: chain D residue 557 ILE Chi-restraints excluded: chain D residue 601 THR Chi-restraints excluded: chain D residue 603 ASP Chi-restraints excluded: chain D residue 664 THR Chi-restraints excluded: chain D residue 748 THR Chi-restraints excluded: chain D residue 1056 MET Chi-restraints excluded: chain D residue 1139 ASN Chi-restraints excluded: chain D residue 1165 SER Chi-restraints excluded: chain D residue 1192 THR Chi-restraints excluded: chain D residue 1285 VAL Chi-restraints excluded: chain D residue 1317 SER Chi-restraints excluded: chain D residue 1318 SER Chi-restraints excluded: chain D residue 1364 TYR Chi-restraints excluded: chain D residue 1403 MET Chi-restraints excluded: chain D residue 1423 LEU Chi-restraints excluded: chain D residue 1461 LEU Chi-restraints excluded: chain D residue 1652 LEU Chi-restraints excluded: chain D residue 1657 ASP Chi-restraints excluded: chain D residue 1811 ILE Chi-restraints excluded: chain D residue 1921 SER Chi-restraints excluded: chain D residue 2002 THR Chi-restraints excluded: chain D residue 2107 ILE Chi-restraints excluded: chain D residue 2225 THR Chi-restraints excluded: chain D residue 2340 VAL Chi-restraints excluded: chain D residue 2347 ASP Chi-restraints excluded: chain D residue 2390 SER Chi-restraints excluded: chain D residue 2416 SER Chi-restraints excluded: chain E residue 88 GLU Chi-restraints excluded: chain E residue 101 SER Chi-restraints excluded: chain E residue 325 VAL Chi-restraints excluded: chain E residue 331 THR Chi-restraints excluded: chain E residue 381 THR Chi-restraints excluded: chain E residue 410 LEU Chi-restraints excluded: chain E residue 468 LEU Chi-restraints excluded: chain E residue 581 ASN Chi-restraints excluded: chain E residue 603 ASP Chi-restraints excluded: chain E residue 666 GLU Chi-restraints excluded: chain E residue 763 GLU Chi-restraints excluded: chain E residue 790 THR Chi-restraints excluded: chain E residue 799 LEU Chi-restraints excluded: chain E residue 805 THR Chi-restraints excluded: chain E residue 881 VAL Chi-restraints excluded: chain E residue 909 THR Chi-restraints excluded: chain E residue 1013 ILE Chi-restraints excluded: chain E residue 1139 ASN Chi-restraints excluded: chain E residue 1148 ASP Chi-restraints excluded: chain E residue 1177 ILE Chi-restraints excluded: chain E residue 1296 THR Chi-restraints excluded: chain E residue 1381 LEU Chi-restraints excluded: chain E residue 1396 ASN Chi-restraints excluded: chain E residue 1423 LEU Chi-restraints excluded: chain E residue 1460 SER Chi-restraints excluded: chain E residue 1578 VAL Chi-restraints excluded: chain E residue 1683 ASP Chi-restraints excluded: chain E residue 1695 ASP Chi-restraints excluded: chain E residue 1734 THR Chi-restraints excluded: chain E residue 1790 ASP Chi-restraints excluded: chain E residue 1913 ILE Chi-restraints excluded: chain E residue 1977 ASP Chi-restraints excluded: chain E residue 2125 THR Chi-restraints excluded: chain E residue 2232 GLU Chi-restraints excluded: chain E residue 2236 SER Chi-restraints excluded: chain E residue 2330 GLU Chi-restraints excluded: chain E residue 2337 LEU Chi-restraints excluded: chain E residue 2347 ASP Chi-restraints excluded: chain E residue 2385 THR Chi-restraints excluded: chain E residue 2409 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1225 random chunks: chunk 1074 optimal weight: 0.5980 chunk 1131 optimal weight: 1.9990 chunk 1032 optimal weight: 0.6980 chunk 1100 optimal weight: 1.9990 chunk 1130 optimal weight: 4.9990 chunk 662 optimal weight: 0.5980 chunk 479 optimal weight: 2.9990 chunk 863 optimal weight: 2.9990 chunk 337 optimal weight: 0.8980 chunk 994 optimal weight: 0.6980 chunk 1040 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1180 GLN ** A1419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1582 ASN ** B2248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 302 ASN C 848 GLN C1003 ASN C1334 ASN ** C2047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2242 GLN ** C2497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 573 ASN D1007 ASN D1413 ASN D2032 GLN ** D2047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 311 ASN E 514 GLN ** E 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.3961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 99495 Z= 0.155 Angle : 0.468 9.851 135140 Z= 0.246 Chirality : 0.040 0.341 14960 Planarity : 0.003 0.071 17580 Dihedral : 4.163 35.017 13370 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.52 % Allowed : 9.77 % Favored : 88.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.00 % 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: 0.99 (0.08), residues: 12240 helix: 1.97 (0.07), residues: 5580 sheet: 0.11 (0.11), residues: 2135 loop : -0.72 (0.09), residues: 4525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP D1437 HIS 0.005 0.001 HIS E1888 PHE 0.016 0.001 PHE B 937 TYR 0.017 0.001 TYR B 264 ARG 0.008 0.000 ARG D2290 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 24480 Ramachandran restraints generated. 12240 Oldfield, 0 Emsley, 12240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 24480 Ramachandran restraints generated. 12240 Oldfield, 0 Emsley, 12240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1198 residues out of total 10500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 1038 time to evaluate : 8.628 Fit side-chains REVERT: A 231 MET cc_start: 0.8529 (mtp) cc_final: 0.8273 (mtm) REVERT: A 262 GLU cc_start: 0.8078 (tm-30) cc_final: 0.7735 (tp30) REVERT: A 287 ASN cc_start: 0.8821 (t0) cc_final: 0.8502 (t0) REVERT: A 374 ASP cc_start: 0.7893 (t0) cc_final: 0.7467 (t0) REVERT: A 402 ILE cc_start: 0.8886 (mm) cc_final: 0.8602 (mt) REVERT: A 508 TYR cc_start: 0.6842 (m-80) cc_final: 0.6325 (m-80) REVERT: A 803 MET cc_start: 0.8599 (tmm) cc_final: 0.8070 (tmm) REVERT: A 839 MET cc_start: 0.9161 (mtp) cc_final: 0.8801 (mtt) REVERT: A 1101 ILE cc_start: 0.8820 (OUTLIER) cc_final: 0.8565 (tt) REVERT: A 1170 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8407 (mp) REVERT: A 1236 CYS cc_start: 0.8601 (t) cc_final: 0.8260 (t) REVERT: A 1685 ASN cc_start: 0.7695 (OUTLIER) cc_final: 0.7312 (m-40) REVERT: A 1701 GLN cc_start: 0.7953 (mm-40) cc_final: 0.7747 (tp40) REVERT: A 1898 LEU cc_start: 0.7878 (OUTLIER) cc_final: 0.7626 (pp) REVERT: A 1927 ARG cc_start: 0.9057 (OUTLIER) cc_final: 0.8750 (ttp-110) REVERT: A 2076 GLU cc_start: 0.8279 (mt-10) cc_final: 0.8018 (mt-10) REVERT: B 136 TYR cc_start: 0.9205 (m-80) cc_final: 0.8887 (m-80) REVERT: B 309 SER cc_start: 0.8680 (t) cc_final: 0.8336 (p) REVERT: B 448 ARG cc_start: 0.8156 (mtm110) cc_final: 0.7898 (mtm-85) REVERT: B 462 ARG cc_start: 0.8881 (mmt-90) cc_final: 0.8642 (mmt-90) REVERT: B 574 LYS cc_start: 0.8335 (mmtt) cc_final: 0.7968 (tptm) REVERT: B 601 THR cc_start: 0.8820 (OUTLIER) cc_final: 0.8524 (p) REVERT: B 1015 ARG cc_start: 0.8294 (mtt180) cc_final: 0.7667 (mmp-170) REVERT: B 1051 ILE cc_start: 0.9283 (mp) cc_final: 0.9017 (mt) REVERT: B 1388 TYR cc_start: 0.9129 (m-80) cc_final: 0.8686 (m-80) REVERT: B 1423 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8839 (mt) REVERT: B 1461 LEU cc_start: 0.6577 (OUTLIER) cc_final: 0.6326 (pp) REVERT: B 1870 GLN cc_start: 0.8778 (OUTLIER) cc_final: 0.7959 (mp10) REVERT: B 1872 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7683 (mt-10) REVERT: B 2022 MET cc_start: 0.8683 (tpp) cc_final: 0.8216 (tpp) REVERT: B 2029 MET cc_start: 0.7567 (mtp) cc_final: 0.6772 (ttt) REVERT: B 2165 MET cc_start: 0.8775 (mtp) cc_final: 0.8529 (mtp) REVERT: B 2242 GLN cc_start: 0.8761 (mt0) cc_final: 0.8377 (mt0) REVERT: B 2272 ARG cc_start: 0.7431 (mtt90) cc_final: 0.7001 (mtt90) REVERT: B 2330 GLU cc_start: 0.6830 (pt0) cc_final: 0.6583 (pt0) REVERT: C 148 MET cc_start: 0.8813 (ptm) cc_final: 0.8152 (ptm) REVERT: C 292 GLU cc_start: 0.7650 (mt-10) cc_final: 0.7422 (mt-10) REVERT: C 351 GLU cc_start: 0.8221 (OUTLIER) cc_final: 0.7995 (tt0) REVERT: C 614 GLU cc_start: 0.7539 (mm-30) cc_final: 0.7225 (mm-30) REVERT: C 904 GLN cc_start: 0.6267 (mp10) cc_final: 0.6036 (mp10) REVERT: C 1015 ARG cc_start: 0.7762 (mtt180) cc_final: 0.6828 (mmp-170) REVERT: C 1264 MET cc_start: 0.8618 (OUTLIER) cc_final: 0.7922 (mmt) REVERT: C 1334 ASN cc_start: 0.8641 (m-40) cc_final: 0.8188 (m110) REVERT: C 1461 LEU cc_start: 0.7999 (OUTLIER) cc_final: 0.7069 (pp) REVERT: C 1596 MET cc_start: 0.8856 (ttp) cc_final: 0.8598 (ttp) REVERT: C 1961 GLN cc_start: 0.8410 (mt0) cc_final: 0.8128 (mt0) REVERT: C 2263 PHE cc_start: 0.8629 (t80) cc_final: 0.8247 (t80) REVERT: C 2357 ILE cc_start: 0.8813 (mm) cc_final: 0.8372 (tt) REVERT: C 2386 SER cc_start: 0.9227 (m) cc_final: 0.8827 (p) REVERT: C 2494 LYS cc_start: 0.8392 (mttt) cc_final: 0.8079 (ttpp) REVERT: C 2505 ASN cc_start: 0.8463 (t0) cc_final: 0.7953 (t0) REVERT: D 88 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.7538 (pm20) REVERT: D 299 LYS cc_start: 0.8627 (OUTLIER) cc_final: 0.8179 (mmtp) REVERT: D 683 LYS cc_start: 0.7639 (ttpp) cc_final: 0.7192 (tptt) REVERT: D 1300 ARG cc_start: 0.8460 (ttp80) cc_final: 0.7760 (ttp80) REVERT: D 1364 TYR cc_start: 0.6228 (OUTLIER) cc_final: 0.5520 (m-10) REVERT: D 1702 ASP cc_start: 0.7984 (m-30) cc_final: 0.7703 (t0) REVERT: D 2022 MET cc_start: 0.8798 (tpp) cc_final: 0.8400 (mmt) REVERT: D 2311 MET cc_start: 0.8766 (tpp) cc_final: 0.8418 (mmm) REVERT: D 2463 ASP cc_start: 0.8051 (t0) cc_final: 0.7757 (m-30) REVERT: E 51 ASP cc_start: 0.8033 (m-30) cc_final: 0.7752 (m-30) REVERT: E 56 GLN cc_start: 0.8111 (tm-30) cc_final: 0.7812 (tt0) REVERT: E 94 ASN cc_start: 0.7530 (m-40) cc_final: 0.7297 (m-40) REVERT: E 155 MET cc_start: 0.9133 (ttp) cc_final: 0.8904 (ttt) REVERT: E 299 LYS cc_start: 0.8498 (mmtm) cc_final: 0.8258 (mttm) REVERT: E 374 ASP cc_start: 0.8122 (t70) cc_final: 0.7845 (t0) REVERT: E 462 ARG cc_start: 0.8252 (ttm170) cc_final: 0.7776 (mmt90) REVERT: E 1020 ASP cc_start: 0.8004 (m-30) cc_final: 0.7677 (m-30) REVERT: E 1079 MET cc_start: 0.9134 (mmm) cc_final: 0.8603 (mmp) REVERT: E 1115 GLU cc_start: 0.7549 (mm-30) cc_final: 0.7044 (mt-10) REVERT: E 1264 MET cc_start: 0.9156 (mmp) cc_final: 0.8240 (mmp) REVERT: E 1343 LYS cc_start: 0.8318 (ptpt) cc_final: 0.7965 (pttt) REVERT: E 1463 LYS cc_start: 0.8262 (mtpt) cc_final: 0.7897 (mmtt) REVERT: E 1920 ASP cc_start: 0.8074 (m-30) cc_final: 0.7820 (m-30) REVERT: E 2042 ASN cc_start: 0.8091 (t0) cc_final: 0.7385 (m-40) REVERT: E 2232 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7458 (mp0) REVERT: E 2257 ARG cc_start: 0.8769 (mmm-85) cc_final: 0.8492 (mmm160) REVERT: E 2491 MET cc_start: 0.8035 (tpp) cc_final: 0.7587 (tpt) REVERT: E 2505 ASN cc_start: 0.8435 (t0) cc_final: 0.7803 (t0) outliers start: 160 outliers final: 132 residues processed: 1146 average time/residue: 0.8898 time to fit residues: 1766.9715 Evaluate side-chains 1143 residues out of total 10500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 994 time to evaluate : 8.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 ASN Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 550 ILE Chi-restraints excluded: chain A residue 558 ASP Chi-restraints excluded: chain A residue 713 LEU Chi-restraints excluded: chain A residue 800 SER Chi-restraints excluded: chain A residue 869 SER Chi-restraints excluded: chain A residue 983 THR Chi-restraints excluded: chain A residue 1087 GLN Chi-restraints excluded: chain A residue 1101 ILE Chi-restraints excluded: chain A residue 1120 GLU Chi-restraints excluded: chain A residue 1139 ASN Chi-restraints excluded: chain A residue 1170 LEU Chi-restraints excluded: chain A residue 1364 TYR Chi-restraints excluded: chain A residue 1423 LEU Chi-restraints excluded: chain A residue 1444 SER Chi-restraints excluded: chain A residue 1446 THR Chi-restraints excluded: chain A residue 1461 LEU Chi-restraints excluded: chain A residue 1465 ASP Chi-restraints excluded: chain A residue 1576 LEU Chi-restraints excluded: chain A residue 1683 ASP Chi-restraints excluded: chain A residue 1685 ASN Chi-restraints excluded: chain A residue 1898 LEU Chi-restraints excluded: chain A residue 1927 ARG Chi-restraints excluded: chain A residue 1945 THR Chi-restraints excluded: chain A residue 1956 MET Chi-restraints excluded: chain A residue 2228 LYS Chi-restraints excluded: chain A residue 2330 GLU Chi-restraints excluded: chain A residue 2381 THR Chi-restraints excluded: chain A residue 2483 THR Chi-restraints excluded: chain B residue 240 ASN Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 511 GLN Chi-restraints excluded: chain B residue 601 THR Chi-restraints excluded: chain B residue 603 ASP Chi-restraints excluded: chain B residue 906 MET Chi-restraints excluded: chain B residue 1103 ASN Chi-restraints excluded: chain B residue 1139 ASN Chi-restraints excluded: chain B residue 1156 SER Chi-restraints excluded: chain B residue 1169 LEU Chi-restraints excluded: chain B residue 1192 THR Chi-restraints excluded: chain B residue 1364 TYR Chi-restraints excluded: chain B residue 1365 GLU Chi-restraints excluded: chain B residue 1423 LEU Chi-restraints excluded: chain B residue 1458 THR Chi-restraints excluded: chain B residue 1459 ASP Chi-restraints excluded: chain B residue 1461 LEU Chi-restraints excluded: chain B residue 1528 MET Chi-restraints excluded: chain B residue 1684 THR Chi-restraints excluded: chain B residue 1709 MET Chi-restraints excluded: chain B residue 1719 THR Chi-restraints excluded: chain B residue 1870 GLN Chi-restraints excluded: chain B residue 1872 GLU Chi-restraints excluded: chain B residue 1874 ASP Chi-restraints excluded: chain B residue 1957 MET Chi-restraints excluded: chain B residue 1977 ASP Chi-restraints excluded: chain B residue 2128 VAL Chi-restraints excluded: chain B residue 2182 SER Chi-restraints excluded: chain B residue 2325 ASP Chi-restraints excluded: chain B residue 2352 SER Chi-restraints excluded: chain B residue 2428 ASP Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 351 GLU Chi-restraints excluded: chain C residue 458 GLU Chi-restraints excluded: chain C residue 504 SER Chi-restraints excluded: chain C residue 534 GLU Chi-restraints excluded: chain C residue 648 VAL Chi-restraints excluded: chain C residue 764 MET Chi-restraints excluded: chain C residue 1014 SER Chi-restraints excluded: chain C residue 1101 ILE Chi-restraints excluded: chain C residue 1139 ASN Chi-restraints excluded: chain C residue 1264 MET Chi-restraints excluded: chain C residue 1461 LEU Chi-restraints excluded: chain C residue 1518 SER Chi-restraints excluded: chain C residue 1830 ASP Chi-restraints excluded: chain C residue 1946 ASP Chi-restraints excluded: chain C residue 1991 ASP Chi-restraints excluded: chain C residue 2330 GLU Chi-restraints excluded: chain C residue 2331 VAL Chi-restraints excluded: chain C residue 2360 LEU Chi-restraints excluded: chain C residue 2434 SER Chi-restraints excluded: chain C residue 2477 ILE Chi-restraints excluded: chain C residue 2493 GLU Chi-restraints excluded: chain D residue 88 GLU Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 275 SER Chi-restraints excluded: chain D residue 299 LYS Chi-restraints excluded: chain D residue 496 LEU Chi-restraints excluded: chain D residue 557 ILE Chi-restraints excluded: chain D residue 601 THR Chi-restraints excluded: chain D residue 603 ASP Chi-restraints excluded: chain D residue 664 THR Chi-restraints excluded: chain D residue 748 THR Chi-restraints excluded: chain D residue 1056 MET Chi-restraints excluded: chain D residue 1073 THR Chi-restraints excluded: chain D residue 1139 ASN Chi-restraints excluded: chain D residue 1165 SER Chi-restraints excluded: chain D residue 1192 THR Chi-restraints excluded: chain D residue 1317 SER Chi-restraints excluded: chain D residue 1318 SER Chi-restraints excluded: chain D residue 1364 TYR Chi-restraints excluded: chain D residue 1403 MET Chi-restraints excluded: chain D residue 1423 LEU Chi-restraints excluded: chain D residue 1461 LEU Chi-restraints excluded: chain D residue 1652 LEU Chi-restraints excluded: chain D residue 1657 ASP Chi-restraints excluded: chain D residue 1811 ILE Chi-restraints excluded: chain D residue 2002 THR Chi-restraints excluded: chain D residue 2031 SER Chi-restraints excluded: chain D residue 2347 ASP Chi-restraints excluded: chain D residue 2390 SER Chi-restraints excluded: chain D residue 2416 SER Chi-restraints excluded: chain E residue 88 GLU Chi-restraints excluded: chain E residue 325 VAL Chi-restraints excluded: chain E residue 331 THR Chi-restraints excluded: chain E residue 381 THR Chi-restraints excluded: chain E residue 411 THR Chi-restraints excluded: chain E residue 468 LEU Chi-restraints excluded: chain E residue 581 ASN Chi-restraints excluded: chain E residue 603 ASP Chi-restraints excluded: chain E residue 666 GLU Chi-restraints excluded: chain E residue 763 GLU Chi-restraints excluded: chain E residue 790 THR Chi-restraints excluded: chain E residue 805 THR Chi-restraints excluded: chain E residue 909 THR Chi-restraints excluded: chain E residue 1139 ASN Chi-restraints excluded: chain E residue 1148 ASP Chi-restraints excluded: chain E residue 1177 ILE Chi-restraints excluded: chain E residue 1296 THR Chi-restraints excluded: chain E residue 1396 ASN Chi-restraints excluded: chain E residue 1578 VAL Chi-restraints excluded: chain E residue 1652 LEU Chi-restraints excluded: chain E residue 1683 ASP Chi-restraints excluded: chain E residue 1695 ASP Chi-restraints excluded: chain E residue 1730 LYS Chi-restraints excluded: chain E residue 1734 THR Chi-restraints excluded: chain E residue 1790 ASP Chi-restraints excluded: chain E residue 1913 ILE Chi-restraints excluded: chain E residue 1977 ASP Chi-restraints excluded: chain E residue 2125 THR Chi-restraints excluded: chain E residue 2232 GLU Chi-restraints excluded: chain E residue 2236 SER Chi-restraints excluded: chain E residue 2330 GLU Chi-restraints excluded: chain E residue 2337 LEU Chi-restraints excluded: chain E residue 2347 ASP Chi-restraints excluded: chain E residue 2409 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1225 random chunks: chunk 1096 optimal weight: 2.9990 chunk 722 optimal weight: 8.9990 chunk 1163 optimal weight: 0.8980 chunk 710 optimal weight: 2.9990 chunk 551 optimal weight: 1.9990 chunk 808 optimal weight: 0.8980 chunk 1220 optimal weight: 0.6980 chunk 1123 optimal weight: 9.9990 chunk 971 optimal weight: 2.9990 chunk 100 optimal weight: 0.9990 chunk 750 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 GLN ** A 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1007 ASN ** A1419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 302 ASN C1003 ASN ** C2047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 295 GLN D1087 GLN D1180 GLN D1785 HIS ** D2047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 311 ASN ** E 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 772 ASN ** E1394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.3994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 99495 Z= 0.212 Angle : 0.488 9.915 135140 Z= 0.255 Chirality : 0.041 0.394 14960 Planarity : 0.003 0.074 17580 Dihedral : 4.182 36.307 13370 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.52 % Allowed : 9.85 % Favored : 88.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.08), residues: 12240 helix: 1.97 (0.07), residues: 5585 sheet: 0.12 (0.11), residues: 2135 loop : -0.70 (0.09), residues: 4520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D1437 HIS 0.007 0.001 HIS A1888 PHE 0.016 0.001 PHE B 937 TYR 0.019 0.001 TYR A2163 ARG 0.009 0.000 ARG D2290 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 24480 Ramachandran restraints generated. 12240 Oldfield, 0 Emsley, 12240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 24480 Ramachandran restraints generated. 12240 Oldfield, 0 Emsley, 12240 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1156 residues out of total 10500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 996 time to evaluate : 8.660 Fit side-chains REVERT: A 231 MET cc_start: 0.8533 (mtp) cc_final: 0.8276 (mtm) REVERT: A 262 GLU cc_start: 0.8045 (tm-30) cc_final: 0.7737 (tp30) REVERT: A 287 ASN cc_start: 0.8834 (t0) cc_final: 0.8524 (t0) REVERT: A 374 ASP cc_start: 0.7950 (t0) cc_final: 0.7526 (t0) REVERT: A 402 ILE cc_start: 0.8888 (mm) cc_final: 0.8624 (mt) REVERT: A 508 TYR cc_start: 0.6718 (m-80) cc_final: 0.6161 (m-80) REVERT: A 713 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8503 (tt) REVERT: A 803 MET cc_start: 0.8606 (tmm) cc_final: 0.8078 (tmm) REVERT: A 839 MET cc_start: 0.9180 (mtp) cc_final: 0.8827 (mtt) REVERT: A 1101 ILE cc_start: 0.8815 (OUTLIER) cc_final: 0.8573 (tt) REVERT: A 1170 LEU cc_start: 0.8981 (OUTLIER) cc_final: 0.8415 (mp) REVERT: A 1236 CYS cc_start: 0.8601 (t) cc_final: 0.8240 (t) REVERT: A 1685 ASN cc_start: 0.7635 (OUTLIER) cc_final: 0.7251 (m-40) REVERT: A 1898 LEU cc_start: 0.7899 (OUTLIER) cc_final: 0.7644 (pp) REVERT: A 1927 ARG cc_start: 0.9068 (OUTLIER) cc_final: 0.8644 (ttp-110) REVERT: A 2076 GLU cc_start: 0.8319 (mt-10) cc_final: 0.8068 (mt-10) REVERT: B 136 TYR cc_start: 0.9220 (m-80) cc_final: 0.8894 (m-80) REVERT: B 309 SER cc_start: 0.8695 (t) cc_final: 0.8349 (p) REVERT: B 448 ARG cc_start: 0.8161 (mtm110) cc_final: 0.7900 (mtm-85) REVERT: B 462 ARG cc_start: 0.8900 (mmt-90) cc_final: 0.8666 (mmt-90) REVERT: B 574 LYS cc_start: 0.8350 (mmtt) cc_final: 0.7967 (tptm) REVERT: B 601 THR cc_start: 0.8828 (OUTLIER) cc_final: 0.8533 (p) REVERT: B 1015 ARG cc_start: 0.8261 (mtt180) cc_final: 0.7646 (mmp-170) REVERT: B 1051 ILE cc_start: 0.9259 (mp) cc_final: 0.8988 (mt) REVERT: B 1388 TYR cc_start: 0.9129 (m-80) cc_final: 0.8683 (m-80) REVERT: B 1423 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8842 (mt) REVERT: B 1461 LEU cc_start: 0.6641 (OUTLIER) cc_final: 0.6385 (pp) REVERT: B 1870 GLN cc_start: 0.8772 (OUTLIER) cc_final: 0.8074 (mp10) REVERT: B 1872 GLU cc_start: 0.8152 (OUTLIER) cc_final: 0.7851 (mt-10) REVERT: B 2022 MET cc_start: 0.8697 (tpp) cc_final: 0.8238 (tpp) REVERT: B 2242 GLN cc_start: 0.8765 (mt0) cc_final: 0.8399 (mt0) REVERT: B 2272 ARG cc_start: 0.7496 (mtt90) cc_final: 0.7185 (mtt90) REVERT: B 2330 GLU cc_start: 0.6878 (pt0) cc_final: 0.6613 (pt0) REVERT: C 148 MET cc_start: 0.8842 (ptm) cc_final: 0.8191 (ptm) REVERT: C 292 GLU cc_start: 0.7652 (mt-10) cc_final: 0.7414 (mt-10) REVERT: C 351 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.8029 (tt0) REVERT: C 574 LYS cc_start: 0.8614 (mmtt) cc_final: 0.8297 (mmtt) REVERT: C 904 GLN cc_start: 0.6282 (mp10) cc_final: 0.6058 (mp10) REVERT: C 1015 ARG cc_start: 0.7746 (mtt180) cc_final: 0.6791 (mmp-170) REVERT: C 1264 MET cc_start: 0.8624 (OUTLIER) cc_final: 0.7910 (mmt) REVERT: C 1461 LEU cc_start: 0.8047 (OUTLIER) cc_final: 0.7091 (pp) REVERT: C 1596 MET cc_start: 0.8854 (ttp) cc_final: 0.8596 (ttp) REVERT: C 1961 GLN cc_start: 0.8431 (mt0) cc_final: 0.8173 (mt0) REVERT: C 2263 PHE cc_start: 0.8579 (t80) cc_final: 0.8159 (t80) REVERT: C 2357 ILE cc_start: 0.8828 (mm) cc_final: 0.8394 (tt) REVERT: C 2386 SER cc_start: 0.9230 (m) cc_final: 0.8825 (p) REVERT: C 2494 LYS cc_start: 0.8396 (mttt) cc_final: 0.8074 (ttpp) REVERT: C 2505 ASN cc_start: 0.8543 (t0) cc_final: 0.8032 (t0) REVERT: D 88 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.7644 (pm20) REVERT: D 299 LYS cc_start: 0.8611 (OUTLIER) cc_final: 0.8215 (mmtm) REVERT: D 683 LYS cc_start: 0.7667 (ttpp) cc_final: 0.7212 (tptt) REVERT: D 1300 ARG cc_start: 0.8465 (ttp80) cc_final: 0.7784 (ttp80) REVERT: D 1364 TYR cc_start: 0.6233 (OUTLIER) cc_final: 0.5479 (m-10) REVERT: D 1702 ASP cc_start: 0.7974 (m-30) cc_final: 0.7745 (t0) REVERT: D 1823 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7760 (pt0) REVERT: D 2022 MET cc_start: 0.8782 (tpp) cc_final: 0.8404 (mmt) REVERT: D 2311 MET cc_start: 0.8750 (tpp) cc_final: 0.8351 (mmt) REVERT: E 56 GLN cc_start: 0.8104 (tm-30) cc_final: 0.7788 (tt0) REVERT: E 94 ASN cc_start: 0.7627 (m-40) cc_final: 0.7417 (m-40) REVERT: E 155 MET cc_start: 0.9130 (ttp) cc_final: 0.8891 (ttt) REVERT: E 299 LYS cc_start: 0.8512 (mmtm) cc_final: 0.8197 (mttm) REVERT: E 374 ASP cc_start: 0.8195 (t70) cc_final: 0.7931 (t0) REVERT: E 462 ARG cc_start: 0.8238 (ttm170) cc_final: 0.7756 (mmt90) REVERT: E 1020 ASP cc_start: 0.8014 (m-30) cc_final: 0.7698 (m-30) REVERT: E 1058 ASP cc_start: 0.7994 (m-30) cc_final: 0.7729 (m-30) REVERT: E 1115 GLU cc_start: 0.7494 (mm-30) cc_final: 0.7050 (mt-10) REVERT: E 1264 MET cc_start: 0.9145 (mmp) cc_final: 0.8331 (mmp) REVERT: E 1343 LYS cc_start: 0.8339 (ptpt) cc_final: 0.7917 (pttt) REVERT: E 1463 LYS cc_start: 0.8422 (mtpt) cc_final: 0.8047 (mmtt) REVERT: E 1920 ASP cc_start: 0.8087 (m-30) cc_final: 0.7831 (m-30) REVERT: E 2042 ASN cc_start: 0.8105 (t0) cc_final: 0.7381 (m-40) REVERT: E 2228 LYS cc_start: 0.8397 (mtmt) cc_final: 0.8070 (mtmm) REVERT: E 2232 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7470 (mp0) REVERT: E 2257 ARG cc_start: 0.8781 (mmm-85) cc_final: 0.8503 (mmm160) REVERT: E 2491 MET cc_start: 0.7993 (tpp) cc_final: 0.7520 (tpt) REVERT: E 2505 ASN cc_start: 0.8447 (t0) cc_final: 0.7815 (t0) outliers start: 160 outliers final: 130 residues processed: 1105 average time/residue: 0.9459 time to fit residues: 1819.9896 Evaluate side-chains 1136 residues out of total 10500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 987 time to evaluate : 8.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 ASN Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 550 ILE Chi-restraints excluded: chain A residue 558 ASP Chi-restraints excluded: chain A residue 713 LEU Chi-restraints excluded: chain A residue 800 SER Chi-restraints excluded: chain A residue 869 SER Chi-restraints excluded: chain A residue 983 THR Chi-restraints excluded: chain A residue 1087 GLN Chi-restraints excluded: chain A residue 1101 ILE Chi-restraints excluded: chain A residue 1120 GLU Chi-restraints excluded: chain A residue 1139 ASN Chi-restraints excluded: chain A residue 1170 LEU Chi-restraints excluded: chain A residue 1423 LEU Chi-restraints excluded: chain A residue 1444 SER Chi-restraints excluded: chain A residue 1446 THR Chi-restraints excluded: chain A residue 1461 LEU Chi-restraints excluded: chain A residue 1465 ASP Chi-restraints excluded: chain A residue 1685 ASN Chi-restraints excluded: chain A residue 1898 LEU Chi-restraints excluded: chain A residue 1927 ARG Chi-restraints excluded: chain A residue 1945 THR Chi-restraints excluded: chain A residue 1956 MET Chi-restraints excluded: chain A residue 2228 LYS Chi-restraints excluded: chain A residue 2330 GLU Chi-restraints excluded: chain A residue 2381 THR Chi-restraints excluded: chain A residue 2483 THR Chi-restraints excluded: chain B residue 240 ASN Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 331 THR Chi-restraints excluded: chain B residue 352 ASN Chi-restraints excluded: chain B residue 496 LEU Chi-restraints excluded: chain B residue 511 GLN Chi-restraints excluded: chain B residue 601 THR Chi-restraints excluded: chain B residue 603 ASP Chi-restraints excluded: chain B residue 906 MET Chi-restraints excluded: chain B residue 1103 ASN Chi-restraints excluded: chain B residue 1139 ASN Chi-restraints excluded: chain B residue 1156 SER Chi-restraints excluded: chain B residue 1169 LEU Chi-restraints excluded: chain B residue 1192 THR Chi-restraints excluded: chain B residue 1364 TYR Chi-restraints excluded: chain B residue 1365 GLU Chi-restraints excluded: chain B residue 1423 LEU Chi-restraints excluded: chain B residue 1458 THR Chi-restraints excluded: chain B residue 1459 ASP Chi-restraints excluded: chain B residue 1461 LEU Chi-restraints excluded: chain B residue 1528 MET Chi-restraints excluded: chain B residue 1684 THR Chi-restraints excluded: chain B residue 1709 MET Chi-restraints excluded: chain B residue 1719 THR Chi-restraints excluded: chain B residue 1870 GLN Chi-restraints excluded: chain B residue 1872 GLU Chi-restraints excluded: chain B residue 1874 ASP Chi-restraints excluded: chain B residue 1957 MET Chi-restraints excluded: chain B residue 1977 ASP Chi-restraints excluded: chain B residue 2128 VAL Chi-restraints excluded: chain B residue 2182 SER Chi-restraints excluded: chain B residue 2325 ASP Chi-restraints excluded: chain B residue 2352 SER Chi-restraints excluded: chain B residue 2428 ASP Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 351 GLU Chi-restraints excluded: chain C residue 458 GLU Chi-restraints excluded: chain C residue 504 SER Chi-restraints excluded: chain C residue 534 GLU Chi-restraints excluded: chain C residue 648 VAL Chi-restraints excluded: chain C residue 764 MET Chi-restraints excluded: chain C residue 1014 SER Chi-restraints excluded: chain C residue 1101 ILE Chi-restraints excluded: chain C residue 1139 ASN Chi-restraints excluded: chain C residue 1264 MET Chi-restraints excluded: chain C residue 1461 LEU Chi-restraints excluded: chain C residue 1518 SER Chi-restraints excluded: chain C residue 1830 ASP Chi-restraints excluded: chain C residue 1913 ILE Chi-restraints excluded: chain C residue 1946 ASP Chi-restraints excluded: chain C residue 1991 ASP Chi-restraints excluded: chain C residue 2330 GLU Chi-restraints excluded: chain C residue 2331 VAL Chi-restraints excluded: chain C residue 2360 LEU Chi-restraints excluded: chain C residue 2434 SER Chi-restraints excluded: chain C residue 2477 ILE Chi-restraints excluded: chain C residue 2493 GLU Chi-restraints excluded: chain D residue 88 GLU Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 275 SER Chi-restraints excluded: chain D residue 299 LYS Chi-restraints excluded: chain D residue 496 LEU Chi-restraints excluded: chain D residue 557 ILE Chi-restraints excluded: chain D residue 601 THR Chi-restraints excluded: chain D residue 603 ASP Chi-restraints excluded: chain D residue 664 THR Chi-restraints excluded: chain D residue 748 THR Chi-restraints excluded: chain D residue 1056 MET Chi-restraints excluded: chain D residue 1073 THR Chi-restraints excluded: chain D residue 1139 ASN Chi-restraints excluded: chain D residue 1165 SER Chi-restraints excluded: chain D residue 1180 GLN Chi-restraints excluded: chain D residue 1192 THR Chi-restraints excluded: chain D residue 1317 SER Chi-restraints excluded: chain D residue 1318 SER Chi-restraints excluded: chain D residue 1364 TYR Chi-restraints excluded: chain D residue 1403 MET Chi-restraints excluded: chain D residue 1423 LEU Chi-restraints excluded: chain D residue 1461 LEU Chi-restraints excluded: chain D residue 1652 LEU Chi-restraints excluded: chain D residue 1657 ASP Chi-restraints excluded: chain D residue 1811 ILE Chi-restraints excluded: chain D residue 1823 GLU Chi-restraints excluded: chain D residue 1921 SER Chi-restraints excluded: chain D residue 2002 THR Chi-restraints excluded: chain D residue 2031 SER Chi-restraints excluded: chain D residue 2347 ASP Chi-restraints excluded: chain D residue 2390 SER Chi-restraints excluded: chain D residue 2416 SER Chi-restraints excluded: chain E residue 88 GLU Chi-restraints excluded: chain E residue 325 VAL Chi-restraints excluded: chain E residue 331 THR Chi-restraints excluded: chain E residue 381 THR Chi-restraints excluded: chain E residue 411 THR Chi-restraints excluded: chain E residue 468 LEU Chi-restraints excluded: chain E residue 581 ASN Chi-restraints excluded: chain E residue 603 ASP Chi-restraints excluded: chain E residue 666 GLU Chi-restraints excluded: chain E residue 763 GLU Chi-restraints excluded: chain E residue 790 THR Chi-restraints excluded: chain E residue 805 THR Chi-restraints excluded: chain E residue 909 THR Chi-restraints excluded: chain E residue 1139 ASN Chi-restraints excluded: chain E residue 1148 ASP Chi-restraints excluded: chain E residue 1177 ILE Chi-restraints excluded: chain E residue 1296 THR Chi-restraints excluded: chain E residue 1396 ASN Chi-restraints excluded: chain E residue 1460 SER Chi-restraints excluded: chain E residue 1578 VAL Chi-restraints excluded: chain E residue 1683 ASP Chi-restraints excluded: chain E residue 1695 ASP Chi-restraints excluded: chain E residue 1734 THR Chi-restraints excluded: chain E residue 1913 ILE Chi-restraints excluded: chain E residue 1977 ASP Chi-restraints excluded: chain E residue 2125 THR Chi-restraints excluded: chain E residue 2232 GLU Chi-restraints excluded: chain E residue 2236 SER Chi-restraints excluded: chain E residue 2330 GLU Chi-restraints excluded: chain E residue 2337 LEU Chi-restraints excluded: chain E residue 2347 ASP Chi-restraints excluded: chain E residue 2409 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1225 random chunks: chunk 595 optimal weight: 2.9990 chunk 771 optimal weight: 0.0970 chunk 1035 optimal weight: 0.7980 chunk 297 optimal weight: 1.9990 chunk 896 optimal weight: 0.9980 chunk 143 optimal weight: 4.9990 chunk 270 optimal weight: 5.9990 chunk 973 optimal weight: 2.9990 chunk 407 optimal weight: 4.9990 chunk 999 optimal weight: 0.9980 chunk 123 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1007 ASN ** A1419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 302 ASN C1003 ASN ** C2047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 848 GLN D1180 GLN D1785 HIS ** D2047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 311 ASN ** E 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 772 ASN ** E1394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.103616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.088174 restraints weight = 144093.461| |-----------------------------------------------------------------------------| r_work (start): 0.2847 rms_B_bonded: 1.54 r_work: 0.2755 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2640 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.4013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 99495 Z= 0.168 Angle : 0.469 9.763 135140 Z= 0.246 Chirality : 0.041 0.377 14960 Planarity : 0.003 0.072 17580 Dihedral : 4.123 36.401 13370 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.53 % Allowed : 9.90 % Favored : 88.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.00 % 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: 1.10 (0.08), residues: 12240 helix: 2.07 (0.07), residues: 5580 sheet: 0.16 (0.11), residues: 2135 loop : -0.66 (0.09), residues: 4525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D1437 HIS 0.005 0.001 HIS E1888 PHE 0.016 0.001 PHE B 937 TYR 0.017 0.001 TYR B1024 ARG 0.009 0.000 ARG D2290 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 30129.51 seconds wall clock time: 526 minutes 20.73 seconds (31580.73 seconds total)