Starting phenix.real_space_refine (version: 1.21rc1) on Mon Apr 24 10:34:43 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pgs_13394/04_2023/7pgs_13394.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pgs_13394/04_2023/7pgs_13394.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pgs_13394/04_2023/7pgs_13394.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pgs_13394/04_2023/7pgs_13394.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pgs_13394/04_2023/7pgs_13394.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pgs_13394/04_2023/7pgs_13394.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 S 223 5.16 5 C 21340 2.51 5 N 5661 2.21 5 O 6170 1.98 5 H 33807 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 67202 Number of models: 1 Model: "" Number of chains: 2 Chain: "N" Number of atoms: 28493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1787, 28493 Classifications: {'peptide': 1787} Link IDs: {'PTRANS': 65, 'TRANS': 1721} Chain breaks: 7 Chain: "F" Number of atoms: 38709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2424, 38709 Unusual residues: {' ZN': 1} Classifications: {'peptide': 2423, 'undetermined': 1} Link IDs: {'PTRANS': 94, 'TRANS': 2328, None: 1} Not linked: pdbres="GLY F2745 " pdbres=" ZN F2901 " Chain breaks: 7 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 42600 SG CYS F1032 33.635 82.067 114.515 1.00135.43 S Time building chain proxies: 20.80, per 1000 atoms: 0.31 Number of scatterers: 67202 At special positions: 0 Unit cell: (136.133, 139.061, 327.891, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 223 16.00 O 6170 8.00 N 5661 7.00 C 21340 6.00 H 33807 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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: 40.96 Conformation dependent library (CDL) restraints added in 4.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN F2901 " pdb="ZN ZN F2901 " - pdb=" SG CYS F1032 " pdb="ZN ZN F2901 " - pdb=" NE2 HIS F1558 " pdb="ZN ZN F2901 " - pdb=" NE2 HIS F1576 " 8356 Ramachandran restraints generated. 4178 Oldfield, 0 Emsley, 4178 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8108 Finding SS restraints... Secondary structure from input PDB file: 237 helices and 4 sheets defined 76.1% alpha, 1.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.28 Creating SS restraints... Processing helix chain 'N' and resid 4 through 19 removed outlier: 3.823A pdb=" N GLU N 8 " --> pdb=" O HIS N 4 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLN N 11 " --> pdb=" O VAL N 7 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA N 12 " --> pdb=" O GLU N 8 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASP N 18 " --> pdb=" O VAL N 14 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLU N 19 " --> pdb=" O SER N 15 " (cutoff:3.500A) Processing helix chain 'N' and resid 33 through 48 removed outlier: 3.521A pdb=" N LYS N 40 " --> pdb=" O THR N 36 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N LYS N 48 " --> pdb=" O ILE N 44 " (cutoff:3.500A) Processing helix chain 'N' and resid 50 through 67 Processing helix chain 'N' and resid 72 through 97 removed outlier: 3.586A pdb=" N ILE N 86 " --> pdb=" O SER N 82 " (cutoff:3.500A) Processing helix chain 'N' and resid 105 through 112 removed outlier: 3.744A pdb=" N LYS N 111 " --> pdb=" O THR N 107 " (cutoff:3.500A) Processing helix chain 'N' and resid 113 through 122 removed outlier: 4.021A pdb=" N PHE N 120 " --> pdb=" O GLU N 116 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU N 121 " --> pdb=" O ILE N 117 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N HIS N 122 " --> pdb=" O CYS N 118 " (cutoff:3.500A) Processing helix chain 'N' and resid 129 through 147 removed outlier: 3.775A pdb=" N GLU N 133 " --> pdb=" O GLN N 129 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASN N 136 " --> pdb=" O ALA N 132 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N CYS N 147 " --> pdb=" O PHE N 143 " (cutoff:3.500A) Processing helix chain 'N' and resid 149 through 167 removed outlier: 3.556A pdb=" N VAL N 153 " --> pdb=" O ASN N 149 " (cutoff:3.500A) Processing helix chain 'N' and resid 173 through 182 removed outlier: 4.203A pdb=" N ASP N 176 " --> pdb=" O ASP N 173 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU N 180 " --> pdb=" O ILE N 177 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLN N 181 " --> pdb=" O GLU N 178 " (cutoff:3.500A) Processing helix chain 'N' and resid 186 through 202 removed outlier: 3.624A pdb=" N ARG N 192 " --> pdb=" O ALA N 188 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS N 200 " --> pdb=" O GLU N 196 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N LYS N 202 " --> pdb=" O ALA N 198 " (cutoff:3.500A) Processing helix chain 'N' and resid 205 through 227 removed outlier: 3.895A pdb=" N TRP N 221 " --> pdb=" O GLU N 217 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASN N 222 " --> pdb=" O LYS N 218 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TRP N 223 " --> pdb=" O ALA N 219 " (cutoff:3.500A) Processing helix chain 'N' and resid 227 through 237 removed outlier: 3.634A pdb=" N PHE N 231 " --> pdb=" O TYR N 227 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N TYR N 235 " --> pdb=" O PHE N 231 " (cutoff:3.500A) Processing helix chain 'N' and resid 239 through 257 Processing helix chain 'N' and resid 259 through 277 removed outlier: 3.607A pdb=" N ALA N 265 " --> pdb=" O LYS N 261 " (cutoff:3.500A) Proline residue: N 268 - end of helix removed outlier: 3.735A pdb=" N ILE N 272 " --> pdb=" O PRO N 268 " (cutoff:3.500A) Processing helix chain 'N' and resid 277 through 286 removed outlier: 4.003A pdb=" N ILE N 281 " --> pdb=" O CYS N 277 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLN N 282 " --> pdb=" O PRO N 278 " (cutoff:3.500A) Processing helix chain 'N' and resid 293 through 308 removed outlier: 3.541A pdb=" N LYS N 297 " --> pdb=" O ASN N 293 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ARG N 304 " --> pdb=" O LEU N 300 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA N 306 " --> pdb=" O SER N 302 " (cutoff:3.500A) Processing helix chain 'N' and resid 313 through 334 removed outlier: 4.236A pdb=" N TYR N 333 " --> pdb=" O LYS N 329 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ILE N 334 " --> pdb=" O ALA N 330 " (cutoff:3.500A) Processing helix chain 'N' and resid 340 through 358 removed outlier: 3.895A pdb=" N LEU N 344 " --> pdb=" O SER N 340 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N MET N 349 " --> pdb=" O LEU N 345 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N VAL N 351 " --> pdb=" O GLN N 347 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N ASP N 352 " --> pdb=" O SER N 348 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASN N 355 " --> pdb=" O VAL N 351 " (cutoff:3.500A) Processing helix chain 'N' and resid 372 through 387 Processing helix chain 'N' and resid 393 through 399 Processing helix chain 'N' and resid 403 through 420 removed outlier: 3.609A pdb=" N HIS N 407 " --> pdb=" O PRO N 403 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE N 418 " --> pdb=" O LEU N 414 " (cutoff:3.500A) Processing helix chain 'N' and resid 428 through 434 removed outlier: 4.185A pdb=" N CYS N 434 " --> pdb=" O ALA N 431 " (cutoff:3.500A) Processing helix chain 'N' and resid 435 through 455 removed outlier: 3.618A pdb=" N ASN N 441 " --> pdb=" O VAL N 437 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N CYS N 454 " --> pdb=" O ALA N 450 " (cutoff:3.500A) Processing helix chain 'N' and resid 483 through 503 Processing helix chain 'N' and resid 504 through 509 removed outlier: 3.538A pdb=" N CYS N 509 " --> pdb=" O LYS N 505 " (cutoff:3.500A) Processing helix chain 'N' and resid 521 through 531 Processing helix chain 'N' and resid 538 through 552 removed outlier: 3.502A pdb=" N GLU N 544 " --> pdb=" O GLU N 540 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU N 552 " --> pdb=" O ALA N 548 " (cutoff:3.500A) Processing helix chain 'N' and resid 554 through 559 removed outlier: 4.089A pdb=" N ASP N 559 " --> pdb=" O LEU N 555 " (cutoff:3.500A) Processing helix chain 'N' and resid 560 through 562 No H-bonds generated for 'chain 'N' and resid 560 through 562' Processing helix chain 'N' and resid 568 through 588 removed outlier: 3.837A pdb=" N GLN N 576 " --> pdb=" O GLU N 572 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N HIS N 588 " --> pdb=" O LYS N 584 " (cutoff:3.500A) Processing helix chain 'N' and resid 592 through 618 removed outlier: 4.236A pdb=" N LYS N 598 " --> pdb=" O THR N 594 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLU N 602 " --> pdb=" O LYS N 598 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS N 609 " --> pdb=" O ILE N 605 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N PHE N 610 " --> pdb=" O CYS N 606 " (cutoff:3.500A) Processing helix chain 'N' and resid 677 through 693 removed outlier: 4.156A pdb=" N LYS N 686 " --> pdb=" O GLN N 682 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU N 688 " --> pdb=" O GLN N 684 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N MET N 693 " --> pdb=" O VAL N 689 " (cutoff:3.500A) Processing helix chain 'N' and resid 699 through 709 Processing helix chain 'N' and resid 709 through 721 removed outlier: 3.606A pdb=" N LEU N 713 " --> pdb=" O CYS N 709 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLU N 716 " --> pdb=" O HIS N 712 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ALA N 717 " --> pdb=" O LEU N 713 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASP N 718 " --> pdb=" O CYS N 714 " (cutoff:3.500A) Processing helix chain 'N' and resid 723 through 728 removed outlier: 3.816A pdb=" N SER N 727 " --> pdb=" O VAL N 723 " (cutoff:3.500A) Processing helix chain 'N' and resid 734 through 746 removed outlier: 3.630A pdb=" N PHE N 738 " --> pdb=" O ASN N 734 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N MET N 739 " --> pdb=" O TYR N 735 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLU N 740 " --> pdb=" O ASN N 736 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N PHE N 741 " --> pdb=" O THR N 737 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ALA N 742 " --> pdb=" O PHE N 738 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N SER N 743 " --> pdb=" O MET N 739 " (cutoff:3.500A) Processing helix chain 'N' and resid 751 through 764 removed outlier: 3.621A pdb=" N ARG N 758 " --> pdb=" O ALA N 754 " (cutoff:3.500A) Processing helix chain 'N' and resid 770 through 794 removed outlier: 4.081A pdb=" N GLU N 778 " --> pdb=" O THR N 774 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU N 790 " --> pdb=" O GLN N 786 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE N 791 " --> pdb=" O ALA N 787 " (cutoff:3.500A) Processing helix chain 'N' and resid 832 through 847 Processing helix chain 'N' and resid 848 through 852 Processing helix chain 'N' and resid 889 through 903 removed outlier: 3.649A pdb=" N MET N 902 " --> pdb=" O LEU N 898 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N VAL N 903 " --> pdb=" O LEU N 899 " (cutoff:3.500A) Processing helix chain 'N' and resid 909 through 924 removed outlier: 3.675A pdb=" N ASP N 919 " --> pdb=" O THR N 915 " (cutoff:3.500A) Processing helix chain 'N' and resid 926 through 928 No H-bonds generated for 'chain 'N' and resid 926 through 928' Processing helix chain 'N' and resid 929 through 943 removed outlier: 4.013A pdb=" N ASN N 935 " --> pdb=" O PRO N 931 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE N 941 " --> pdb=" O LEU N 937 " (cutoff:3.500A) Processing helix chain 'N' and resid 954 through 974 removed outlier: 3.564A pdb=" N GLU N 962 " --> pdb=" O THR N 958 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA N 966 " --> pdb=" O GLU N 962 " (cutoff:3.500A) Processing helix chain 'N' and resid 978 through 984 removed outlier: 3.646A pdb=" N HIS N 982 " --> pdb=" O GLY N 978 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLY N 984 " --> pdb=" O SER N 980 " (cutoff:3.500A) Processing helix chain 'N' and resid 988 through 1001 removed outlier: 3.543A pdb=" N ARG N 997 " --> pdb=" O LEU N 993 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N TYR N 998 " --> pdb=" O ASN N 994 " (cutoff:3.500A) Processing helix chain 'N' and resid 1005 through 1023 removed outlier: 3.800A pdb=" N GLN N1010 " --> pdb=" O VAL N1006 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE N1011 " --> pdb=" O HIS N1007 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N MET N1023 " --> pdb=" O VAL N1019 " (cutoff:3.500A) Processing helix chain 'N' and resid 1033 through 1047 removed outlier: 4.035A pdb=" N LYS N1040 " --> pdb=" O LYS N1036 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ASP N1047 " --> pdb=" O GLU N1043 " (cutoff:3.500A) Processing helix chain 'N' and resid 1052 through 1057 removed outlier: 3.858A pdb=" N ALA N1056 " --> pdb=" O THR N1052 " (cutoff:3.500A) Processing helix chain 'N' and resid 1059 through 1062 Processing helix chain 'N' and resid 1063 through 1081 removed outlier: 3.669A pdb=" N ASP N1067 " --> pdb=" O CYS N1063 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLU N1074 " --> pdb=" O GLN N1070 " (cutoff:3.500A) Processing helix chain 'N' and resid 1094 through 1117 removed outlier: 3.734A pdb=" N LEU N1109 " --> pdb=" O LYS N1105 " (cutoff:3.500A) Processing helix chain 'N' and resid 1135 through 1156 removed outlier: 3.554A pdb=" N MET N1149 " --> pdb=" O THR N1145 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ALA N1155 " --> pdb=" O ASN N1151 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASN N1156 " --> pdb=" O LEU N1152 " (cutoff:3.500A) Processing helix chain 'N' and resid 1156 through 1165 removed outlier: 5.635A pdb=" N MET N1162 " --> pdb=" O ASP N1158 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N HIS N1163 " --> pdb=" O SER N1159 " (cutoff:3.500A) Processing helix chain 'N' and resid 1166 through 1170 removed outlier: 3.629A pdb=" N TYR N1169 " --> pdb=" O GLY N1166 " (cutoff:3.500A) Processing helix chain 'N' and resid 1172 through 1189 removed outlier: 3.896A pdb=" N THR N1178 " --> pdb=" O GLN N1174 " (cutoff:3.500A) Processing helix chain 'N' and resid 1846 through 1849 Processing helix chain 'N' and resid 1850 through 1862 removed outlier: 3.576A pdb=" N LEU N1854 " --> pdb=" O VAL N1850 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASN N1856 " --> pdb=" O GLY N1852 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ILE N1857 " --> pdb=" O THR N1853 " (cutoff:3.500A) Processing helix chain 'N' and resid 1866 through 1885 removed outlier: 3.922A pdb=" N SER N1871 " --> pdb=" O PRO N1867 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ALA N1872 " --> pdb=" O SER N1868 " (cutoff:3.500A) Processing helix chain 'N' and resid 1905 through 1918 Processing helix chain 'N' and resid 1919 through 1921 No H-bonds generated for 'chain 'N' and resid 1919 through 1921' Processing helix chain 'N' and resid 1922 through 1937 removed outlier: 3.553A pdb=" N GLU N1929 " --> pdb=" O GLU N1925 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N SER N1935 " --> pdb=" O ILE N1931 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LYS N1936 " --> pdb=" O SER N1932 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER N1937 " --> pdb=" O GLY N1933 " (cutoff:3.500A) Processing helix chain 'N' and resid 1938 through 1954 removed outlier: 3.659A pdb=" N LEU N1944 " --> pdb=" O GLU N1940 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLU N1947 " --> pdb=" O HIS N1943 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR N1950 " --> pdb=" O LEU N1946 " (cutoff:3.500A) Proline residue: N1951 - end of helix removed outlier: 4.119A pdb=" N SER N1954 " --> pdb=" O THR N1950 " (cutoff:3.500A) Processing helix chain 'N' and resid 1955 through 1961 removed outlier: 4.614A pdb=" N PHE N1959 " --> pdb=" O ASN N1955 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N LYS N1961 " --> pdb=" O VAL N1957 " (cutoff:3.500A) Processing helix chain 'N' and resid 1966 through 1985 removed outlier: 3.517A pdb=" N ARG N1970 " --> pdb=" O ALA N1966 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N THR N1972 " --> pdb=" O ARG N1968 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE N1983 " --> pdb=" O ILE N1979 " (cutoff:3.500A) Processing helix chain 'N' and resid 1988 through 2001 removed outlier: 3.969A pdb=" N ALA N1994 " --> pdb=" O PRO N1990 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N TRP N1997 " --> pdb=" O GLN N1993 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N GLY N1998 " --> pdb=" O ALA N1994 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER N1999 " --> pdb=" O LYS N1995 " (cutoff:3.500A) Processing helix chain 'N' and resid 2002 through 2005 removed outlier: 6.503A pdb=" N ASP N2005 " --> pdb=" O GLN N2002 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 2002 through 2005' Processing helix chain 'N' and resid 2006 through 2022 removed outlier: 3.543A pdb=" N ILE N2015 " --> pdb=" O LEU N2011 " (cutoff:3.500A) Processing helix chain 'N' and resid 2025 through 2042 removed outlier: 3.520A pdb=" N ASP N2033 " --> pdb=" O GLU N2029 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N VAL N2036 " --> pdb=" O ALA N2032 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ALA N2037 " --> pdb=" O ASP N2033 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N GLY N2041 " --> pdb=" O ALA N2037 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ASN N2042 " --> pdb=" O LEU N2038 " (cutoff:3.500A) Processing helix chain 'N' and resid 2042 through 2060 removed outlier: 3.870A pdb=" N SER N2048 " --> pdb=" O LYS N2044 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N GLY N2052 " --> pdb=" O SER N2048 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ARG N2053 " --> pdb=" O LYS N2049 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LYS N2056 " --> pdb=" O GLY N2052 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASP N2059 " --> pdb=" O CYS N2055 " (cutoff:3.500A) Processing helix chain 'N' and resid 2068 through 2073 removed outlier: 6.139A pdb=" N LEU N2073 " --> pdb=" O GLU N2070 " (cutoff:3.500A) Processing helix chain 'N' and resid 2074 through 2090 removed outlier: 3.561A pdb=" N ARG N2083 " --> pdb=" O ALA N2079 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N PHE N2090 " --> pdb=" O LEU N2086 " (cutoff:3.500A) Processing helix chain 'N' and resid 2091 through 2093 No H-bonds generated for 'chain 'N' and resid 2091 through 2093' Processing helix chain 'N' and resid 2095 through 2108 Proline residue: N2101 - end of helix removed outlier: 3.659A pdb=" N VAL N2106 " --> pdb=" O TYR N2102 " (cutoff:3.500A) Processing helix chain 'N' and resid 2115 through 2135 Processing helix chain 'N' and resid 2142 through 2156 removed outlier: 3.717A pdb=" N GLN N2147 " --> pdb=" O GLU N2143 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL N2148 " --> pdb=" O GLU N2144 " (cutoff:3.500A) Processing helix chain 'N' and resid 2158 through 2166 removed outlier: 3.554A pdb=" N LEU N2163 " --> pdb=" O PRO N2159 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU N2164 " --> pdb=" O LYS N2160 " (cutoff:3.500A) Processing helix chain 'N' and resid 2172 through 2178 removed outlier: 4.073A pdb=" N ILE N2176 " --> pdb=" O SER N2172 " (cutoff:3.500A) Processing helix chain 'N' and resid 2198 through 2220 removed outlier: 3.549A pdb=" N GLU N2203 " --> pdb=" O LEU N2199 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR N2204 " --> pdb=" O THR N2200 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ASP N2219 " --> pdb=" O ALA N2215 " (cutoff:3.500A) Processing helix chain 'N' and resid 2224 through 2238 removed outlier: 3.760A pdb=" N PHE N2236 " --> pdb=" O LEU N2232 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N PHE N2238 " --> pdb=" O GLN N2234 " (cutoff:3.500A) Processing helix chain 'N' and resid 2244 through 2256 removed outlier: 3.500A pdb=" N VAL N2251 " --> pdb=" O ARG N2247 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE N2252 " --> pdb=" O ALA N2248 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N CYS N2254 " --> pdb=" O VAL N2250 " (cutoff:3.500A) Processing helix chain 'N' and resid 2260 through 2281 removed outlier: 3.590A pdb=" N GLN N2266 " --> pdb=" O GLY N2262 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LYS N2273 " --> pdb=" O ARG N2269 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU N2276 " --> pdb=" O SER N2272 " (cutoff:3.500A) Processing helix chain 'N' and resid 2289 through 2302 removed outlier: 3.581A pdb=" N THR N2294 " --> pdb=" O LEU N2290 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS N2300 " --> pdb=" O ILE N2296 " (cutoff:3.500A) Processing helix chain 'N' and resid 2303 through 2305 No H-bonds generated for 'chain 'N' and resid 2303 through 2305' Processing helix chain 'N' and resid 2310 through 2324 removed outlier: 5.223A pdb=" N PHE N2316 " --> pdb=" O HIS N2312 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N TRP N2317 " --> pdb=" O LYS N2313 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N VAL N2318 " --> pdb=" O ALA N2314 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ALA N2319 " --> pdb=" O LEU N2315 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLN N2324 " --> pdb=" O VAL N2320 " (cutoff:3.500A) Processing helix chain 'N' and resid 2327 through 2348 removed outlier: 3.714A pdb=" N ALA N2336 " --> pdb=" O SER N2332 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER N2347 " --> pdb=" O HIS N2343 " (cutoff:3.500A) Processing helix chain 'N' and resid 2355 through 2364 Processing helix chain 'N' and resid 2367 through 2379 removed outlier: 3.541A pdb=" N CYS N2371 " --> pdb=" O LEU N2367 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLN N2373 " --> pdb=" O TRP N2369 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N MET N2374 " --> pdb=" O HIS N2370 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N PHE N2377 " --> pdb=" O GLN N2373 " (cutoff:3.500A) Processing helix chain 'N' and resid 2385 through 2393 removed outlier: 4.060A pdb=" N VAL N2391 " --> pdb=" O ASN N2387 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N HIS N2393 " --> pdb=" O ALA N2389 " (cutoff:3.500A) Processing helix chain 'N' and resid 2395 through 2400 Processing helix chain 'N' and resid 2402 through 2425 removed outlier: 3.578A pdb=" N VAL N2406 " --> pdb=" O SER N2402 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ALA N2407 " --> pdb=" O PRO N2403 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU N2419 " --> pdb=" O THR N2415 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ARG N2424 " --> pdb=" O VAL N2420 " (cutoff:3.500A) Processing helix chain 'N' and resid 2436 through 2442 removed outlier: 3.538A pdb=" N ALA N2441 " --> pdb=" O ALA N2437 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU N2442 " --> pdb=" O TYR N2438 " (cutoff:3.500A) Processing helix chain 'N' and resid 2443 through 2445 No H-bonds generated for 'chain 'N' and resid 2443 through 2445' Processing helix chain 'N' and resid 2446 through 2453 Processing helix chain 'N' and resid 2612 through 2630 removed outlier: 3.841A pdb=" N LEU N2619 " --> pdb=" O ILE N2615 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LEU N2620 " --> pdb=" O GLN N2616 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR N2621 " --> pdb=" O ALA N2617 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU N2623 " --> pdb=" O LEU N2619 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL N2627 " --> pdb=" O LEU N2623 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N TYR N2629 " --> pdb=" O THR N2625 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N THR N2630 " --> pdb=" O LEU N2626 " (cutoff:3.500A) Processing helix chain 'N' and resid 2632 through 2650 removed outlier: 3.518A pdb=" N ILE N2638 " --> pdb=" O PHE N2634 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N TYR N2642 " --> pdb=" O ILE N2638 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU N2645 " --> pdb=" O GLU N2641 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA N2646 " --> pdb=" O TYR N2642 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N VAL N2648 " --> pdb=" O ALA N2644 " (cutoff:3.500A) Processing helix chain 'N' and resid 2653 through 2656 Processing helix chain 'N' and resid 2657 through 2672 removed outlier: 3.548A pdb=" N LEU N2661 " --> pdb=" O VAL N2657 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N SER N2663 " --> pdb=" O ASN N2659 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N LYS N2664 " --> pdb=" O LEU N2660 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER N2670 " --> pdb=" O ASN N2666 " (cutoff:3.500A) Processing helix chain 'N' and resid 2674 through 2691 Proline residue: N2680 - end of helix Processing helix chain 'N' and resid 2699 through 2707 removed outlier: 4.405A pdb=" N LEU N2703 " --> pdb=" O THR N2700 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N SER N2705 " --> pdb=" O TYR N2702 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLY N2707 " --> pdb=" O GLN N2704 " (cutoff:3.500A) Processing helix chain 'N' and resid 2727 through 2743 removed outlier: 3.967A pdb=" N ILE N2731 " --> pdb=" O TYR N2727 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LYS N2733 " --> pdb=" O GLU N2729 " (cutoff:3.500A) Processing helix chain 'F' and resid 5 through 19 removed outlier: 3.570A pdb=" N GLN F 11 " --> pdb=" O VAL F 7 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA F 12 " --> pdb=" O GLU F 8 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL F 13 " --> pdb=" O TRP F 9 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLU F 19 " --> pdb=" O SER F 15 " (cutoff:3.500A) Processing helix chain 'F' and resid 33 through 47 removed outlier: 3.522A pdb=" N ASN F 39 " --> pdb=" O SER F 35 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LYS F 40 " --> pdb=" O THR F 36 " (cutoff:3.500A) Processing helix chain 'F' and resid 50 through 67 Processing helix chain 'F' and resid 72 through 97 removed outlier: 3.520A pdb=" N ILE F 86 " --> pdb=" O SER F 82 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU F 94 " --> pdb=" O LEU F 90 " (cutoff:3.500A) Processing helix chain 'F' and resid 105 through 112 removed outlier: 3.694A pdb=" N LYS F 111 " --> pdb=" O THR F 107 " (cutoff:3.500A) Processing helix chain 'F' and resid 113 through 122 removed outlier: 3.535A pdb=" N HIS F 119 " --> pdb=" O PRO F 115 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N PHE F 120 " --> pdb=" O GLU F 116 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LEU F 121 " --> pdb=" O ILE F 117 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N HIS F 122 " --> pdb=" O CYS F 118 " (cutoff:3.500A) Processing helix chain 'F' and resid 129 through 147 removed outlier: 3.605A pdb=" N GLU F 133 " --> pdb=" O GLN F 129 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASN F 136 " --> pdb=" O ALA F 132 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N CYS F 147 " --> pdb=" O PHE F 143 " (cutoff:3.500A) Processing helix chain 'F' and resid 149 through 167 removed outlier: 3.702A pdb=" N VAL F 153 " --> pdb=" O ASN F 149 " (cutoff:3.500A) Processing helix chain 'F' and resid 173 through 182 removed outlier: 4.210A pdb=" N ASP F 176 " --> pdb=" O ASP F 173 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU F 179 " --> pdb=" O ASP F 176 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU F 180 " --> pdb=" O ILE F 177 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLN F 181 " --> pdb=" O GLU F 178 " (cutoff:3.500A) Processing helix chain 'F' and resid 186 through 202 removed outlier: 3.712A pdb=" N ARG F 192 " --> pdb=" O ALA F 188 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS F 200 " --> pdb=" O GLU F 196 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N LYS F 202 " --> pdb=" O ALA F 198 " (cutoff:3.500A) Processing helix chain 'F' and resid 205 through 227 removed outlier: 3.548A pdb=" N PHE F 220 " --> pdb=" O LEU F 216 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N TRP F 221 " --> pdb=" O GLU F 217 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASN F 222 " --> pdb=" O LYS F 218 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TRP F 223 " --> pdb=" O ALA F 219 " (cutoff:3.500A) Processing helix chain 'F' and resid 227 through 237 removed outlier: 3.641A pdb=" N PHE F 231 " --> pdb=" O TYR F 227 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N TYR F 235 " --> pdb=" O PHE F 231 " (cutoff:3.500A) Processing helix chain 'F' and resid 239 through 257 removed outlier: 3.554A pdb=" N ALA F 246 " --> pdb=" O MET F 242 " (cutoff:3.500A) Processing helix chain 'F' and resid 259 through 277 Proline residue: F 268 - end of helix removed outlier: 3.502A pdb=" N ILE F 271 " --> pdb=" O TRP F 267 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ILE F 272 " --> pdb=" O PRO F 268 " (cutoff:3.500A) Processing helix chain 'F' and resid 277 through 286 removed outlier: 4.271A pdb=" N ILE F 281 " --> pdb=" O CYS F 277 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLN F 282 " --> pdb=" O PRO F 278 " (cutoff:3.500A) Processing helix chain 'F' and resid 293 through 308 removed outlier: 3.588A pdb=" N ARG F 304 " --> pdb=" O LEU F 300 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA F 306 " --> pdb=" O SER F 302 " (cutoff:3.500A) Processing helix chain 'F' and resid 313 through 332 Processing helix chain 'F' and resid 340 through 358 removed outlier: 3.787A pdb=" N LEU F 344 " --> pdb=" O SER F 340 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N MET F 349 " --> pdb=" O LEU F 345 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N VAL F 351 " --> pdb=" O GLN F 347 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N ASP F 352 " --> pdb=" O SER F 348 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASN F 355 " --> pdb=" O VAL F 351 " (cutoff:3.500A) Processing helix chain 'F' and resid 372 through 387 Processing helix chain 'F' and resid 393 through 399 Processing helix chain 'F' and resid 403 through 420 removed outlier: 3.569A pdb=" N HIS F 407 " --> pdb=" O PRO F 403 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE F 418 " --> pdb=" O LEU F 414 " (cutoff:3.500A) Processing helix chain 'F' and resid 428 through 434 removed outlier: 4.239A pdb=" N CYS F 434 " --> pdb=" O ALA F 431 " (cutoff:3.500A) Processing helix chain 'F' and resid 435 through 455 removed outlier: 3.622A pdb=" N ASN F 441 " --> pdb=" O VAL F 437 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N CYS F 454 " --> pdb=" O ALA F 450 " (cutoff:3.500A) Processing helix chain 'F' and resid 483 through 503 Processing helix chain 'F' and resid 504 through 509 removed outlier: 3.512A pdb=" N LEU F 508 " --> pdb=" O PRO F 504 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N CYS F 509 " --> pdb=" O LYS F 505 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 504 through 509' Processing helix chain 'F' and resid 521 through 531 Processing helix chain 'F' and resid 538 through 552 removed outlier: 3.643A pdb=" N GLU F 547 " --> pdb=" O GLN F 543 " (cutoff:3.500A) Processing helix chain 'F' and resid 554 through 559 removed outlier: 4.335A pdb=" N ASP F 559 " --> pdb=" O LEU F 555 " (cutoff:3.500A) Processing helix chain 'F' and resid 560 through 562 No H-bonds generated for 'chain 'F' and resid 560 through 562' Processing helix chain 'F' and resid 568 through 588 removed outlier: 3.774A pdb=" N GLN F 576 " --> pdb=" O GLU F 572 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N HIS F 588 " --> pdb=" O LYS F 584 " (cutoff:3.500A) Processing helix chain 'F' and resid 592 through 618 removed outlier: 4.183A pdb=" N LYS F 598 " --> pdb=" O THR F 594 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLU F 602 " --> pdb=" O LYS F 598 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS F 609 " --> pdb=" O ILE F 605 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N PHE F 610 " --> pdb=" O CYS F 606 " (cutoff:3.500A) Processing helix chain 'F' and resid 677 through 692 removed outlier: 4.054A pdb=" N LYS F 686 " --> pdb=" O GLN F 682 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU F 687 " --> pdb=" O ALA F 683 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU F 688 " --> pdb=" O GLN F 684 " (cutoff:3.500A) Processing helix chain 'F' and resid 699 through 709 Processing helix chain 'F' and resid 709 through 721 removed outlier: 3.825A pdb=" N LEU F 713 " --> pdb=" O CYS F 709 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLU F 716 " --> pdb=" O HIS F 712 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ALA F 717 " --> pdb=" O LEU F 713 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASP F 718 " --> pdb=" O CYS F 714 " (cutoff:3.500A) Processing helix chain 'F' and resid 723 through 728 removed outlier: 3.835A pdb=" N SER F 727 " --> pdb=" O VAL F 723 " (cutoff:3.500A) Processing helix chain 'F' and resid 734 through 746 removed outlier: 3.551A pdb=" N PHE F 738 " --> pdb=" O ASN F 734 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N MET F 739 " --> pdb=" O TYR F 735 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLU F 740 " --> pdb=" O ASN F 736 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N PHE F 741 " --> pdb=" O THR F 737 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ALA F 742 " --> pdb=" O PHE F 738 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N SER F 743 " --> pdb=" O MET F 739 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL F 744 " --> pdb=" O GLU F 740 " (cutoff:3.500A) Processing helix chain 'F' and resid 751 through 764 removed outlier: 3.778A pdb=" N ARG F 758 " --> pdb=" O ALA F 754 " (cutoff:3.500A) Processing helix chain 'F' and resid 770 through 794 removed outlier: 3.965A pdb=" N GLU F 778 " --> pdb=" O THR F 774 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LYS F 783 " --> pdb=" O ASP F 779 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU F 790 " --> pdb=" O GLN F 786 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE F 791 " --> pdb=" O ALA F 787 " (cutoff:3.500A) Processing helix chain 'F' and resid 832 through 847 Processing helix chain 'F' and resid 848 through 852 Processing helix chain 'F' and resid 889 through 903 removed outlier: 3.603A pdb=" N MET F 902 " --> pdb=" O LEU F 898 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N VAL F 903 " --> pdb=" O LEU F 899 " (cutoff:3.500A) Processing helix chain 'F' and resid 909 through 924 removed outlier: 3.736A pdb=" N ASP F 919 " --> pdb=" O THR F 915 " (cutoff:3.500A) Processing helix chain 'F' and resid 929 through 943 removed outlier: 3.942A pdb=" N ASN F 935 " --> pdb=" O PRO F 931 " (cutoff:3.500A) Processing helix chain 'F' and resid 954 through 974 removed outlier: 3.817A pdb=" N ALA F 966 " --> pdb=" O GLU F 962 " (cutoff:3.500A) Processing helix chain 'F' and resid 978 through 984 removed outlier: 3.801A pdb=" N HIS F 982 " --> pdb=" O GLY F 978 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLY F 984 " --> pdb=" O SER F 980 " (cutoff:3.500A) Processing helix chain 'F' and resid 988 through 1001 removed outlier: 3.592A pdb=" N ARG F 997 " --> pdb=" O LEU F 993 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TYR F 998 " --> pdb=" O ASN F 994 " (cutoff:3.500A) Processing helix chain 'F' and resid 1005 through 1023 removed outlier: 3.719A pdb=" N GLN F1010 " --> pdb=" O VAL F1006 " (cutoff:3.500A) Processing helix chain 'F' and resid 1033 through 1047 removed outlier: 3.990A pdb=" N LYS F1040 " --> pdb=" O LYS F1036 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ASP F1047 " --> pdb=" O GLU F1043 " (cutoff:3.500A) Processing helix chain 'F' and resid 1052 through 1057 removed outlier: 3.750A pdb=" N ALA F1056 " --> pdb=" O THR F1052 " (cutoff:3.500A) Processing helix chain 'F' and resid 1059 through 1062 Processing helix chain 'F' and resid 1063 through 1081 removed outlier: 3.792A pdb=" N ASP F1067 " --> pdb=" O CYS F1063 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU F1074 " --> pdb=" O GLN F1070 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA F1081 " --> pdb=" O VAL F1077 " (cutoff:3.500A) Processing helix chain 'F' and resid 1094 through 1117 removed outlier: 3.504A pdb=" N SER F1100 " --> pdb=" O MET F1096 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TYR F1106 " --> pdb=" O LEU F1102 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU F1109 " --> pdb=" O LYS F1105 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N CYS F1117 " --> pdb=" O LEU F1113 " (cutoff:3.500A) Processing helix chain 'F' and resid 1135 through 1156 removed outlier: 3.545A pdb=" N MET F1149 " --> pdb=" O THR F1145 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASN F1156 " --> pdb=" O LEU F1152 " (cutoff:3.500A) Processing helix chain 'F' and resid 1160 through 1165 removed outlier: 3.561A pdb=" N SER F1164 " --> pdb=" O GLY F1160 " (cutoff:3.500A) Processing helix chain 'F' and resid 1166 through 1170 removed outlier: 3.744A pdb=" N TYR F1169 " --> pdb=" O GLY F1166 " (cutoff:3.500A) Processing helix chain 'F' and resid 1172 through 1189 removed outlier: 3.594A pdb=" N LEU F1187 " --> pdb=" O LEU F1183 " (cutoff:3.500A) Processing helix chain 'F' and resid 1199 through 1205 Processing helix chain 'F' and resid 1205 through 1213 removed outlier: 3.988A pdb=" N VAL F1209 " --> pdb=" O PHE F1205 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLU F1210 " --> pdb=" O GLU F1206 " (cutoff:3.500A) Processing helix chain 'F' and resid 1221 through 1231 removed outlier: 3.680A pdb=" N ASN F1229 " --> pdb=" O MET F1225 " (cutoff:3.500A) Processing helix chain 'F' and resid 1232 through 1234 No H-bonds generated for 'chain 'F' and resid 1232 through 1234' Processing helix chain 'F' and resid 1235 through 1250 Processing helix chain 'F' and resid 1252 through 1268 removed outlier: 3.585A pdb=" N LEU F1256 " --> pdb=" O LEU F1252 " (cutoff:3.500A) Processing helix chain 'F' and resid 1270 through 1277 removed outlier: 3.524A pdb=" N PHE F1275 " --> pdb=" O MET F1271 " (cutoff:3.500A) Processing helix chain 'F' and resid 1279 through 1311 removed outlier: 3.554A pdb=" N MET F1285 " --> pdb=" O ALA F1281 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA F1294 " --> pdb=" O LYS F1290 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N THR F1295 " --> pdb=" O VAL F1291 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N TYR F1296 " --> pdb=" O TYR F1292 " (cutoff:3.500A) Proline residue: F1303 - end of helix removed outlier: 3.610A pdb=" N ILE F1307 " --> pdb=" O PRO F1303 " (cutoff:3.500A) Processing helix chain 'F' and resid 1331 through 1353 Processing helix chain 'F' and resid 1358 through 1379 Processing helix chain 'F' and resid 1400 through 1413 Processing helix chain 'F' and resid 1413 through 1420 removed outlier: 4.429A pdb=" N ALA F1417 " --> pdb=" O PHE F1413 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE F1418 " --> pdb=" O ILE F1414 " (cutoff:3.500A) Processing helix chain 'F' and resid 1420 through 1425 removed outlier: 3.502A pdb=" N ALA F1424 " --> pdb=" O SER F1420 " (cutoff:3.500A) Processing helix chain 'F' and resid 1432 through 1452 removed outlier: 3.707A pdb=" N GLY F1438 " --> pdb=" O ARG F1434 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA F1450 " --> pdb=" O LEU F1446 " (cutoff:3.500A) Processing helix chain 'F' and resid 1461 through 1463 No H-bonds generated for 'chain 'F' and resid 1461 through 1463' Processing helix chain 'F' and resid 1464 through 1484 removed outlier: 3.766A pdb=" N VAL F1468 " --> pdb=" O PHE F1464 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LYS F1469 " --> pdb=" O ASN F1465 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N SER F1470 " --> pdb=" O ASP F1466 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASN F1471 " --> pdb=" O PHE F1467 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N ASP F1473 " --> pdb=" O LYS F1469 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ALA F1474 " --> pdb=" O SER F1470 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE F1482 " --> pdb=" O PHE F1478 " (cutoff:3.500A) Processing helix chain 'F' and resid 1500 through 1514 removed outlier: 3.524A pdb=" N LEU F1505 " --> pdb=" O ASP F1501 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ALA F1506 " --> pdb=" O GLY F1502 " (cutoff:3.500A) Processing helix chain 'F' and resid 1514 through 1525 removed outlier: 3.516A pdb=" N LEU F1522 " --> pdb=" O ILE F1518 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ASN F1525 " --> pdb=" O TYR F1521 " (cutoff:3.500A) Processing helix chain 'F' and resid 1530 through 1533 removed outlier: 4.016A pdb=" N ARG F1533 " --> pdb=" O ALA F1530 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 1530 through 1533' Processing helix chain 'F' and resid 1534 through 1547 Processing helix chain 'F' and resid 1565 through 1576 Processing helix chain 'F' and resid 1583 through 1591 removed outlier: 3.552A pdb=" N LEU F1587 " --> pdb=" O GLU F1583 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LYS F1588 " --> pdb=" O PHE F1584 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR F1589 " --> pdb=" O LYS F1585 " (cutoff:3.500A) Processing helix chain 'F' and resid 1619 through 1632 removed outlier: 4.065A pdb=" N LEU F1623 " --> pdb=" O ASN F1619 " (cutoff:3.500A) Processing helix chain 'F' and resid 1655 through 1666 removed outlier: 3.552A pdb=" N LYS F1661 " --> pdb=" O ASP F1657 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N TRP F1662 " --> pdb=" O PHE F1658 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N PHE F1663 " --> pdb=" O LEU F1659 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N VAL F1664 " --> pdb=" O SER F1660 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N PHE F1666 " --> pdb=" O TRP F1662 " (cutoff:3.500A) Processing helix chain 'F' and resid 1668 through 1673 removed outlier: 4.142A pdb=" N ASP F1672 " --> pdb=" O GLY F1668 " (cutoff:3.500A) Processing helix chain 'F' and resid 1683 through 1693 removed outlier: 3.609A pdb=" N ARG F1687 " --> pdb=" O ASN F1683 " (cutoff:3.500A) Processing helix chain 'F' and resid 1693 through 1698 Processing helix chain 'F' and resid 1699 through 1701 No H-bonds generated for 'chain 'F' and resid 1699 through 1701' Processing helix chain 'F' and resid 1711 through 1719 removed outlier: 4.168A pdb=" N LEU F1715 " --> pdb=" O CYS F1711 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ALA F1716 " --> pdb=" O PRO F1712 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N GLU F1717 " --> pdb=" O GLY F1713 " (cutoff:3.500A) Processing helix chain 'F' and resid 1727 through 1734 removed outlier: 3.786A pdb=" N GLU F1734 " --> pdb=" O THR F1730 " (cutoff:3.500A) Processing helix chain 'F' and resid 1786 through 1788 No H-bonds generated for 'chain 'F' and resid 1786 through 1788' Processing helix chain 'F' and resid 1816 through 1835 Processing helix chain 'F' and resid 1846 through 1849 Processing helix chain 'F' and resid 1850 through 1862 removed outlier: 3.718A pdb=" N LEU F1854 " --> pdb=" O VAL F1850 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASN F1856 " --> pdb=" O GLY F1852 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ILE F1857 " --> pdb=" O THR F1853 " (cutoff:3.500A) Processing helix chain 'F' and resid 1866 through 1885 removed outlier: 4.058A pdb=" N SER F1871 " --> pdb=" O PRO F1867 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ALA F1872 " --> pdb=" O SER F1868 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N CYS F1882 " --> pdb=" O CYS F1878 " (cutoff:3.500A) Processing helix chain 'F' and resid 1905 through 1918 Processing helix chain 'F' and resid 1919 through 1921 No H-bonds generated for 'chain 'F' and resid 1919 through 1921' Processing helix chain 'F' and resid 1922 through 1937 removed outlier: 3.688A pdb=" N GLU F1929 " --> pdb=" O GLU F1925 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N SER F1935 " --> pdb=" O ILE F1931 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N LYS F1936 " --> pdb=" O SER F1932 " (cutoff:3.500A) Processing helix chain 'F' and resid 1938 through 1950 removed outlier: 3.524A pdb=" N HIS F1943 " --> pdb=" O ILE F1939 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LEU F1944 " --> pdb=" O GLU F1940 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLU F1947 " --> pdb=" O HIS F1943 " (cutoff:3.500A) Processing helix chain 'F' and resid 1951 through 1954 removed outlier: 3.562A pdb=" N SER F1954 " --> pdb=" O PRO F1951 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 1951 through 1954' Processing helix chain 'F' and resid 1955 through 1960 removed outlier: 4.435A pdb=" N PHE F1959 " --> pdb=" O ASN F1955 " (cutoff:3.500A) Processing helix chain 'F' and resid 1967 through 1985 removed outlier: 3.504A pdb=" N THR F1972 " --> pdb=" O ARG F1968 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASN F1984 " --> pdb=" O THR F1980 " (cutoff:3.500A) Processing helix chain 'F' and resid 1988 through 2001 removed outlier: 4.012A pdb=" N ALA F1994 " --> pdb=" O PRO F1990 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N TRP F1997 " --> pdb=" O GLN F1993 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N GLY F1998 " --> pdb=" O ALA F1994 " (cutoff:3.500A) Processing helix chain 'F' and resid 2002 through 2005 removed outlier: 6.559A pdb=" N ASP F2005 " --> pdb=" O GLN F2002 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 2002 through 2005' Processing helix chain 'F' and resid 2006 through 2022 removed outlier: 3.531A pdb=" N ILE F2015 " --> pdb=" O LEU F2011 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLY F2021 " --> pdb=" O THR F2017 " (cutoff:3.500A) Processing helix chain 'F' and resid 2025 through 2042 removed outlier: 3.584A pdb=" N ASP F2033 " --> pdb=" O GLU F2029 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N VAL F2036 " --> pdb=" O ALA F2032 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ALA F2037 " --> pdb=" O ASP F2033 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N GLY F2041 " --> pdb=" O ALA F2037 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ASN F2042 " --> pdb=" O LEU F2038 " (cutoff:3.500A) Processing helix chain 'F' and resid 2042 through 2060 removed outlier: 4.125A pdb=" N SER F2048 " --> pdb=" O LYS F2044 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N GLY F2052 " --> pdb=" O SER F2048 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ARG F2053 " --> pdb=" O LYS F2049 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LYS F2056 " --> pdb=" O GLY F2052 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASP F2059 " --> pdb=" O CYS F2055 " (cutoff:3.500A) Processing helix chain 'F' and resid 2068 through 2073 removed outlier: 6.127A pdb=" N LEU F2073 " --> pdb=" O GLU F2070 " (cutoff:3.500A) Processing helix chain 'F' and resid 2074 through 2090 removed outlier: 3.564A pdb=" N MET F2085 " --> pdb=" O LEU F2081 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N PHE F2090 " --> pdb=" O LEU F2086 " (cutoff:3.500A) Processing helix chain 'F' and resid 2091 through 2093 No H-bonds generated for 'chain 'F' and resid 2091 through 2093' Processing helix chain 'F' and resid 2095 through 2108 Proline residue: F2101 - end of helix removed outlier: 3.824A pdb=" N VAL F2106 " --> pdb=" O TYR F2102 " (cutoff:3.500A) Processing helix chain 'F' and resid 2115 through 2135 Processing helix chain 'F' and resid 2142 through 2156 removed outlier: 3.704A pdb=" N GLN F2147 " --> pdb=" O GLU F2143 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL F2148 " --> pdb=" O GLU F2144 " (cutoff:3.500A) Processing helix chain 'F' and resid 2158 through 2166 removed outlier: 3.558A pdb=" N LEU F2163 " --> pdb=" O PRO F2159 " (cutoff:3.500A) Processing helix chain 'F' and resid 2172 through 2178 removed outlier: 3.960A pdb=" N ILE F2176 " --> pdb=" O SER F2172 " (cutoff:3.500A) Processing helix chain 'F' and resid 2198 through 2220 removed outlier: 3.579A pdb=" N LEU F2202 " --> pdb=" O ALA F2198 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU F2203 " --> pdb=" O LEU F2199 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THR F2204 " --> pdb=" O THR F2200 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ASP F2219 " --> pdb=" O ALA F2215 " (cutoff:3.500A) Processing helix chain 'F' and resid 2224 through 2238 removed outlier: 3.604A pdb=" N GLU F2231 " --> pdb=" O ASP F2227 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N PHE F2236 " --> pdb=" O LEU F2232 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N PHE F2238 " --> pdb=" O GLN F2234 " (cutoff:3.500A) Processing helix chain 'F' and resid 2244 through 2256 removed outlier: 3.528A pdb=" N VAL F2250 " --> pdb=" O PRO F2246 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL F2251 " --> pdb=" O ARG F2247 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N CYS F2254 " --> pdb=" O VAL F2250 " (cutoff:3.500A) Processing helix chain 'F' and resid 2260 through 2281 removed outlier: 3.745A pdb=" N GLN F2266 " --> pdb=" O GLY F2262 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER F2272 " --> pdb=" O ILE F2268 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU F2276 " --> pdb=" O SER F2272 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU F2279 " --> pdb=" O LEU F2275 " (cutoff:3.500A) Processing helix chain 'F' and resid 2288 through 2302 removed outlier: 3.972A pdb=" N GLU F2292 " --> pdb=" O GLN F2288 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS F2300 " --> pdb=" O ILE F2296 " (cutoff:3.500A) Processing helix chain 'F' and resid 2303 through 2305 No H-bonds generated for 'chain 'F' and resid 2303 through 2305' Processing helix chain 'F' and resid 2310 through 2315 Processing helix chain 'F' and resid 2315 through 2324 removed outlier: 3.901A pdb=" N ALA F2319 " --> pdb=" O LEU F2315 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLN F2324 " --> pdb=" O VAL F2320 " (cutoff:3.500A) Processing helix chain 'F' and resid 2327 through 2348 removed outlier: 3.580A pdb=" N ALA F2336 " --> pdb=" O SER F2332 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLN F2340 " --> pdb=" O ALA F2336 " (cutoff:3.500A) Processing helix chain 'F' and resid 2355 through 2364 Processing helix chain 'F' and resid 2367 through 2379 removed outlier: 3.795A pdb=" N GLN F2373 " --> pdb=" O TRP F2369 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N MET F2374 " --> pdb=" O HIS F2370 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N PHE F2377 " --> pdb=" O GLN F2373 " (cutoff:3.500A) Processing helix chain 'F' and resid 2385 through 2395 removed outlier: 3.644A pdb=" N HIS F2393 " --> pdb=" O ALA F2389 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU F2394 " --> pdb=" O LEU F2390 " (cutoff:3.500A) Processing helix chain 'F' and resid 2396 through 2400 Processing helix chain 'F' and resid 2402 through 2425 removed outlier: 3.697A pdb=" N VAL F2406 " --> pdb=" O SER F2402 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ALA F2407 " --> pdb=" O PRO F2403 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARG F2408 " --> pdb=" O ALA F2404 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU F2419 " --> pdb=" O THR F2415 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS F2422 " --> pdb=" O THR F2418 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ARG F2424 " --> pdb=" O VAL F2420 " (cutoff:3.500A) Processing helix chain 'F' and resid 2433 through 2435 No H-bonds generated for 'chain 'F' and resid 2433 through 2435' Processing helix chain 'F' and resid 2436 through 2442 removed outlier: 3.593A pdb=" N ALA F2441 " --> pdb=" O ALA F2437 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU F2442 " --> pdb=" O TYR F2438 " (cutoff:3.500A) Processing helix chain 'F' and resid 2446 through 2453 Processing helix chain 'F' and resid 2612 through 2630 removed outlier: 4.000A pdb=" N LEU F2619 " --> pdb=" O ILE F2615 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU F2620 " --> pdb=" O GLN F2616 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU F2623 " --> pdb=" O LEU F2619 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N TYR F2629 " --> pdb=" O THR F2625 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR F2630 " --> pdb=" O LEU F2626 " (cutoff:3.500A) Processing helix chain 'F' and resid 2632 through 2650 removed outlier: 3.642A pdb=" N ILE F2638 " --> pdb=" O PHE F2634 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TYR F2642 " --> pdb=" O ILE F2638 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL F2648 " --> pdb=" O ALA F2644 " (cutoff:3.500A) Processing helix chain 'F' and resid 2653 through 2656 Processing helix chain 'F' and resid 2657 through 2672 removed outlier: 3.523A pdb=" N LEU F2661 " --> pdb=" O VAL F2657 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N SER F2663 " --> pdb=" O ASN F2659 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N LYS F2664 " --> pdb=" O LEU F2660 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER F2670 " --> pdb=" O ASN F2666 " (cutoff:3.500A) Processing helix chain 'F' and resid 2674 through 2691 Proline residue: F2680 - end of helix Processing helix chain 'F' and resid 2699 through 2707 removed outlier: 4.341A pdb=" N LEU F2703 " --> pdb=" O THR F2700 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N SER F2705 " --> pdb=" O TYR F2702 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLY F2707 " --> pdb=" O GLN F2704 " (cutoff:3.500A) Processing helix chain 'F' and resid 2728 through 2743 removed outlier: 3.930A pdb=" N LYS F2733 " --> pdb=" O GLU F2729 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'F' and resid 1594 through 1595 removed outlier: 5.685A pdb=" N PHE F1606 " --> pdb=" O VAL F1642 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ASP F1644 " --> pdb=" O PHE F1606 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N TYR F1608 " --> pdb=" O ASP F1644 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N TYR F1639 " --> pdb=" O SER F1675 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N VAL F1677 " --> pdb=" O TYR F1639 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N ILE F1641 " --> pdb=" O VAL F1677 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N ILE F1679 " --> pdb=" O ILE F1641 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N VAL F1643 " --> pdb=" O ILE F1679 " (cutoff:3.500A) removed outlier: 8.382A pdb=" N VAL F1707 " --> pdb=" O SER F1675 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N VAL F1677 " --> pdb=" O VAL F1707 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 1743 through 1745 removed outlier: 3.866A pdb=" N THR F1751 " --> pdb=" O LYS F1745 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'F' and resid 1770 through 1772 Processing sheet with id=AA4, first strand: chain 'F' and resid 1790 through 1792 removed outlier: 3.646A pdb=" N GLU F1790 " --> pdb=" O THR F1802 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N PHE F1812 " --> pdb=" O PHE F1799 " (cutoff:3.500A) 1862 hydrogen bonds defined for protein. 5451 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: 24.98 Time building geometry restraints manager: 43.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 33700 1.03 - 1.23: 112 1.23 - 1.42: 13852 1.42 - 1.62: 19864 1.62 - 1.81: 338 Bond restraints: 67866 Sorted by residual: bond pdb=" C GLN N 97 " pdb=" N PRO N 98 " ideal model delta sigma weight residual 1.331 1.341 -0.009 1.21e-02 6.83e+03 5.82e-01 bond pdb=" CG PRO N1901 " pdb=" CD PRO N1901 " ideal model delta sigma weight residual 1.503 1.480 0.023 3.40e-02 8.65e+02 4.51e-01 bond pdb=" CB PRO N2101 " pdb=" CG PRO N2101 " ideal model delta sigma weight residual 1.492 1.460 0.032 5.00e-02 4.00e+02 4.10e-01 bond pdb=" CB GLU N2203 " pdb=" CG GLU N2203 " ideal model delta sigma weight residual 1.520 1.502 0.018 3.00e-02 1.11e+03 3.67e-01 bond pdb=" C ILE F1845 " pdb=" N ARG F1846 " ideal model delta sigma weight residual 1.340 1.305 0.036 5.87e-02 2.90e+02 3.67e-01 ... (remaining 67861 not shown) Histogram of bond angle deviations from ideal: 99.43 - 106.34: 912 106.34 - 113.25: 81464 113.25 - 120.16: 20882 120.16 - 127.07: 19343 127.07 - 133.98: 406 Bond angle restraints: 123007 Sorted by residual: angle pdb=" N VAL F2436 " pdb=" CA VAL F2436 " pdb=" C VAL F2436 " ideal model delta sigma weight residual 112.96 109.70 3.26 1.00e+00 1.00e+00 1.06e+01 angle pdb=" N VAL F2251 " pdb=" CA VAL F2251 " pdb=" C VAL F2251 " ideal model delta sigma weight residual 111.81 109.84 1.97 8.60e-01 1.35e+00 5.24e+00 angle pdb=" N GLY N2707 " pdb=" CA GLY N2707 " pdb=" C GLY N2707 " ideal model delta sigma weight residual 113.18 117.60 -4.42 2.37e+00 1.78e-01 3.48e+00 angle pdb=" N GLY F2707 " pdb=" CA GLY F2707 " pdb=" C GLY F2707 " ideal model delta sigma weight residual 113.18 117.24 -4.06 2.37e+00 1.78e-01 2.94e+00 angle pdb=" N PRO F1535 " pdb=" CA PRO F1535 " pdb=" C PRO F1535 " ideal model delta sigma weight residual 112.47 115.95 -3.48 2.06e+00 2.36e-01 2.85e+00 ... (remaining 123002 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.55: 25905 17.55 - 35.11: 1188 35.11 - 52.66: 164 52.66 - 70.22: 53 70.22 - 87.77: 14 Dihedral angle restraints: 27324 sinusoidal: 12883 harmonic: 14441 Sorted by residual: dihedral pdb=" CA SER N2093 " pdb=" C SER N2093 " pdb=" N LEU N2094 " pdb=" CA LEU N2094 " ideal model delta harmonic sigma weight residual 180.00 158.38 21.62 0 5.00e+00 4.00e-02 1.87e+01 dihedral pdb=" CA PHE F2706 " pdb=" C PHE F2706 " pdb=" N GLY F2707 " pdb=" CA GLY F2707 " ideal model delta harmonic sigma weight residual 180.00 159.76 20.24 0 5.00e+00 4.00e-02 1.64e+01 dihedral pdb=" CA PHE N2706 " pdb=" C PHE N2706 " pdb=" N GLY N2707 " pdb=" CA GLY N2707 " ideal model delta harmonic sigma weight residual 180.00 159.83 20.17 0 5.00e+00 4.00e-02 1.63e+01 ... (remaining 27321 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 3854 0.030 - 0.061: 1085 0.061 - 0.091: 338 0.091 - 0.122: 122 0.122 - 0.152: 5 Chirality restraints: 5404 Sorted by residual: chirality pdb=" CA ILE F2724 " pdb=" N ILE F2724 " pdb=" C ILE F2724 " pdb=" CB ILE F2724 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.80e-01 chirality pdb=" CA ILE N2724 " pdb=" N ILE N2724 " pdb=" C ILE N2724 " pdb=" CB ILE N2724 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.66e-01 chirality pdb=" CA PRO F1535 " pdb=" N PRO F1535 " pdb=" C PRO F1535 " pdb=" CB PRO F1535 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.40e-01 ... (remaining 5401 not shown) Planarity restraints: 9867 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR N2066 " 0.028 5.00e-02 4.00e+02 4.26e-02 2.90e+00 pdb=" N PRO N2067 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO N2067 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO N2067 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR F2066 " -0.027 5.00e-02 4.00e+02 4.14e-02 2.74e+00 pdb=" N PRO F2067 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO F2067 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO F2067 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE N2654 " -0.027 5.00e-02 4.00e+02 4.11e-02 2.71e+00 pdb=" N PRO N2655 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO N2655 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO N2655 " -0.023 5.00e-02 4.00e+02 ... (remaining 9864 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.17: 1923 2.17 - 2.78: 133041 2.78 - 3.39: 178079 3.39 - 3.99: 219643 3.99 - 4.60: 356921 Nonbonded interactions: 889607 Sorted by model distance: nonbonded pdb=" O THR N1980 " pdb="HD22 ASN N1984 " model vdw 1.566 1.850 nonbonded pdb=" O ILE N1857 " pdb="HD22 ASN N1861 " model vdw 1.571 1.850 nonbonded pdb=" O ILE F 44 " pdb=" HG SER F 47 " model vdw 1.589 1.850 nonbonded pdb=" O PRO N1920 " pdb=" HG1 THR N1923 " model vdw 1.594 1.850 nonbonded pdb=" OE1 GLN N2302 " pdb="HE21 GLN N2340 " model vdw 1.606 1.850 ... (remaining 889602 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 4.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.710 Extract box with map and model: 22.810 Check model and map are aligned: 0.730 Set scattering table: 0.430 Process input model: 170.880 Find NCS groups from input model: 1.030 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 204.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 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 : 0.002 0.036 34059 Z= 0.160 Angle : 0.401 4.799 46171 Z= 0.210 Chirality : 0.034 0.152 5404 Planarity : 0.003 0.043 5834 Dihedral : 10.769 87.741 12581 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer Outliers : 0.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.33 (0.13), residues: 4178 helix: 0.22 (0.10), residues: 2688 sheet: 0.47 (0.71), residues: 63 loop : -0.91 (0.16), residues: 1427 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8356 Ramachandran restraints generated. 4178 Oldfield, 0 Emsley, 4178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8356 Ramachandran restraints generated. 4178 Oldfield, 0 Emsley, 4178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 3771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 444 time to evaluate : 4.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 13 residues processed: 469 average time/residue: 0.9980 time to fit residues: 744.5389 Evaluate side-chains 262 residues out of total 3771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 249 time to evaluate : 4.037 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.7654 time to fit residues: 22.5900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 354 optimal weight: 0.9980 chunk 318 optimal weight: 2.9990 chunk 176 optimal weight: 0.9980 chunk 108 optimal weight: 0.2980 chunk 214 optimal weight: 0.6980 chunk 170 optimal weight: 0.9980 chunk 329 optimal weight: 10.0000 chunk 127 optimal weight: 0.7980 chunk 200 optimal weight: 1.9990 chunk 245 optimal weight: 0.7980 chunk 381 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 435 HIS N 554 GLN N 697 ASN N1054 ASN N1055 GLN N1856 ASN N2425 ASN ** F 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 435 HIS ** F 746 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F1055 GLN F1683 ASN F2425 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.077 34059 Z= 0.274 Angle : 0.606 7.107 46171 Z= 0.340 Chirality : 0.038 0.163 5404 Planarity : 0.004 0.045 5834 Dihedral : 3.943 19.502 4462 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer Outliers : 0.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.32 (0.13), residues: 4178 helix: 0.76 (0.10), residues: 2835 sheet: 0.43 (0.68), residues: 70 loop : -0.91 (0.17), residues: 1273 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8356 Ramachandran restraints generated. 4178 Oldfield, 0 Emsley, 4178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8356 Ramachandran restraints generated. 4178 Oldfield, 0 Emsley, 4178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 3771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 264 time to evaluate : 3.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 15 residues processed: 279 average time/residue: 0.8823 time to fit residues: 401.9063 Evaluate side-chains 256 residues out of total 3771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 241 time to evaluate : 4.000 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.6892 time to fit residues: 23.7973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 211 optimal weight: 2.9990 chunk 118 optimal weight: 0.9980 chunk 317 optimal weight: 5.9990 chunk 259 optimal weight: 0.2980 chunk 105 optimal weight: 0.2980 chunk 382 optimal weight: 0.9990 chunk 412 optimal weight: 0.8980 chunk 340 optimal weight: 0.5980 chunk 378 optimal weight: 0.9980 chunk 130 optimal weight: 0.3980 chunk 306 optimal weight: 10.0000 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 746 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.089 34059 Z= 0.198 Angle : 0.516 7.151 46171 Z= 0.278 Chirality : 0.035 0.150 5404 Planarity : 0.003 0.045 5834 Dihedral : 3.886 21.223 4462 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer Outliers : 0.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.73 (0.13), residues: 4178 helix: 1.14 (0.10), residues: 2836 sheet: 0.17 (0.67), residues: 72 loop : -0.92 (0.17), residues: 1270 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8356 Ramachandran restraints generated. 4178 Oldfield, 0 Emsley, 4178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8356 Ramachandran restraints generated. 4178 Oldfield, 0 Emsley, 4178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 3771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 261 time to evaluate : 4.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 8 residues processed: 271 average time/residue: 0.8971 time to fit residues: 395.5902 Evaluate side-chains 245 residues out of total 3771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 237 time to evaluate : 3.991 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.6180 time to fit residues: 14.3370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 377 optimal weight: 0.9980 chunk 287 optimal weight: 6.9990 chunk 198 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 182 optimal weight: 0.9990 chunk 256 optimal weight: 0.9990 chunk 383 optimal weight: 0.9980 chunk 405 optimal weight: 2.9990 chunk 200 optimal weight: 1.9990 chunk 363 optimal weight: 0.9990 chunk 109 optimal weight: 0.6980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 554 GLN F 746 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.2911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.076 34059 Z= 0.302 Angle : 0.543 8.997 46171 Z= 0.291 Chirality : 0.037 0.157 5404 Planarity : 0.003 0.049 5834 Dihedral : 3.997 18.870 4462 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.30 % Favored : 96.67 % Rotamer Outliers : 0.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.69 (0.13), residues: 4178 helix: 1.13 (0.10), residues: 2841 sheet: 0.06 (0.66), residues: 72 loop : -0.98 (0.17), residues: 1265 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8356 Ramachandran restraints generated. 4178 Oldfield, 0 Emsley, 4178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8356 Ramachandran restraints generated. 4178 Oldfield, 0 Emsley, 4178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 3771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 245 time to evaluate : 4.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 8 residues processed: 263 average time/residue: 0.9029 time to fit residues: 390.1155 Evaluate side-chains 238 residues out of total 3771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 230 time to evaluate : 3.957 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.7108 time to fit residues: 15.1394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 338 optimal weight: 3.9990 chunk 230 optimal weight: 0.5980 chunk 5 optimal weight: 0.9990 chunk 302 optimal weight: 0.9990 chunk 167 optimal weight: 0.8980 chunk 346 optimal weight: 0.8980 chunk 280 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 207 optimal weight: 1.9990 chunk 364 optimal weight: 0.2980 chunk 102 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N2673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 31 HIS ** F 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 746 ASN F1374 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.3136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.069 34059 Z= 0.214 Angle : 0.497 7.115 46171 Z= 0.265 Chirality : 0.035 0.149 5404 Planarity : 0.003 0.047 5834 Dihedral : 3.914 22.202 4462 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.94 % Favored : 97.03 % Rotamer Outliers : 0.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 0.94 (0.13), residues: 4178 helix: 1.34 (0.10), residues: 2850 sheet: 0.11 (0.66), residues: 72 loop : -0.97 (0.17), residues: 1256 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8356 Ramachandran restraints generated. 4178 Oldfield, 0 Emsley, 4178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8356 Ramachandran restraints generated. 4178 Oldfield, 0 Emsley, 4178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 3771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 244 time to evaluate : 4.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 13 residues processed: 259 average time/residue: 0.9034 time to fit residues: 377.3360 Evaluate side-chains 243 residues out of total 3771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 230 time to evaluate : 3.989 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.6964 time to fit residues: 21.5131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 136 optimal weight: 0.8980 chunk 365 optimal weight: 0.8980 chunk 80 optimal weight: 2.9990 chunk 238 optimal weight: 0.1980 chunk 100 optimal weight: 0.9990 chunk 406 optimal weight: 0.8980 chunk 337 optimal weight: 4.9990 chunk 188 optimal weight: 0.6980 chunk 33 optimal weight: 0.2980 chunk 134 optimal weight: 0.7980 chunk 213 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N2673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 149 ASN F 746 ASN F1673 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.3326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.063 34059 Z= 0.202 Angle : 0.491 8.729 46171 Z= 0.258 Chirality : 0.035 0.148 5404 Planarity : 0.003 0.045 5834 Dihedral : 3.832 18.536 4462 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.35 % Favored : 96.63 % Rotamer Outliers : 0.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.19 (0.13), residues: 4178 helix: 1.56 (0.10), residues: 2849 sheet: 0.15 (0.66), residues: 72 loop : -0.93 (0.17), residues: 1257 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8356 Ramachandran restraints generated. 4178 Oldfield, 0 Emsley, 4178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8356 Ramachandran restraints generated. 4178 Oldfield, 0 Emsley, 4178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 3771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 239 time to evaluate : 4.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 7 residues processed: 245 average time/residue: 0.8974 time to fit residues: 357.2815 Evaluate side-chains 234 residues out of total 3771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 227 time to evaluate : 4.051 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.6850 time to fit residues: 13.8085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 391 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 chunk 231 optimal weight: 1.9990 chunk 296 optimal weight: 9.9990 chunk 229 optimal weight: 0.6980 chunk 342 optimal weight: 4.9990 chunk 226 optimal weight: 0.7980 chunk 404 optimal weight: 1.9990 chunk 253 optimal weight: 0.9980 chunk 246 optimal weight: 0.6980 chunk 186 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N2673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 746 ASN F1112 ASN F1856 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.3461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.075 34059 Z= 0.264 Angle : 0.511 8.372 46171 Z= 0.270 Chirality : 0.036 0.145 5404 Planarity : 0.003 0.051 5834 Dihedral : 3.885 22.252 4462 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.37 % Favored : 96.60 % Rotamer Outliers : 0.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.15 (0.13), residues: 4178 helix: 1.54 (0.10), residues: 2852 sheet: 0.10 (0.65), residues: 72 loop : -0.98 (0.17), residues: 1254 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8356 Ramachandran restraints generated. 4178 Oldfield, 0 Emsley, 4178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8356 Ramachandran restraints generated. 4178 Oldfield, 0 Emsley, 4178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 3771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 233 time to evaluate : 4.006 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 11 residues processed: 244 average time/residue: 0.8900 time to fit residues: 356.8424 Evaluate side-chains 240 residues out of total 3771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 229 time to evaluate : 4.072 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.6553 time to fit residues: 18.6524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 250 optimal weight: 0.9990 chunk 161 optimal weight: 0.7980 chunk 241 optimal weight: 1.9990 chunk 121 optimal weight: 0.4980 chunk 79 optimal weight: 2.9990 chunk 78 optimal weight: 0.9980 chunk 257 optimal weight: 1.9990 chunk 275 optimal weight: 1.9990 chunk 200 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 318 optimal weight: 3.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N2241 ASN ** N2673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 746 ASN F1471 ASN ** F2373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.3556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.055 34059 Z= 0.314 Angle : 0.529 9.195 46171 Z= 0.282 Chirality : 0.037 0.146 5404 Planarity : 0.003 0.055 5834 Dihedral : 3.971 18.147 4462 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.04 % Favored : 95.93 % Rotamer Outliers : 0.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.04 (0.13), residues: 4178 helix: 1.46 (0.10), residues: 2857 sheet: 0.04 (0.65), residues: 72 loop : -1.05 (0.17), residues: 1249 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8356 Ramachandran restraints generated. 4178 Oldfield, 0 Emsley, 4178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8356 Ramachandran restraints generated. 4178 Oldfield, 0 Emsley, 4178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 3771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 238 time to evaluate : 3.998 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 5 residues processed: 244 average time/residue: 0.9058 time to fit residues: 362.7390 Evaluate side-chains 234 residues out of total 3771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 229 time to evaluate : 3.996 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.6407 time to fit residues: 11.0222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 368 optimal weight: 0.6980 chunk 387 optimal weight: 0.9980 chunk 353 optimal weight: 0.9980 chunk 377 optimal weight: 0.7980 chunk 227 optimal weight: 0.9990 chunk 164 optimal weight: 1.9990 chunk 296 optimal weight: 8.9990 chunk 115 optimal weight: 0.0980 chunk 340 optimal weight: 0.7980 chunk 356 optimal weight: 0.9980 chunk 375 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 588 HIS ** N2673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 746 ASN F1156 ASN ** F2373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.3646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.057 34059 Z= 0.200 Angle : 0.491 8.330 46171 Z= 0.258 Chirality : 0.035 0.149 5404 Planarity : 0.003 0.049 5834 Dihedral : 3.851 21.746 4462 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.49 % Favored : 96.48 % Rotamer Outliers : 0.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.30 (0.13), residues: 4178 helix: 1.67 (0.10), residues: 2856 sheet: 0.05 (0.64), residues: 72 loop : -0.98 (0.17), residues: 1250 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8356 Ramachandran restraints generated. 4178 Oldfield, 0 Emsley, 4178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8356 Ramachandran restraints generated. 4178 Oldfield, 0 Emsley, 4178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 3771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 233 time to evaluate : 4.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 236 average time/residue: 0.8978 time to fit residues: 348.9895 Evaluate side-chains 232 residues out of total 3771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 230 time to evaluate : 4.067 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.5884 time to fit residues: 7.6926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 247 optimal weight: 0.8980 chunk 398 optimal weight: 0.8980 chunk 243 optimal weight: 0.9990 chunk 189 optimal weight: 0.4980 chunk 277 optimal weight: 0.9990 chunk 418 optimal weight: 0.9980 chunk 385 optimal weight: 0.6980 chunk 333 optimal weight: 0.7980 chunk 34 optimal weight: 0.0970 chunk 257 optimal weight: 1.9990 chunk 204 optimal weight: 0.0980 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N2673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 746 ASN F1229 ASN ** F2373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.3761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 34059 Z= 0.165 Angle : 0.473 7.205 46171 Z= 0.246 Chirality : 0.034 0.148 5404 Planarity : 0.003 0.046 5834 Dihedral : 3.719 17.990 4462 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.42 % Favored : 96.55 % Rotamer Outliers : 0.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.60 (0.13), residues: 4178 helix: 1.92 (0.10), residues: 2860 sheet: 0.07 (0.64), residues: 72 loop : -0.91 (0.17), residues: 1246 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8356 Ramachandran restraints generated. 4178 Oldfield, 0 Emsley, 4178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8356 Ramachandran restraints generated. 4178 Oldfield, 0 Emsley, 4178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 3771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 234 time to evaluate : 4.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 236 average time/residue: 0.9016 time to fit residues: 350.2595 Evaluate side-chains 230 residues out of total 3771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 229 time to evaluate : 3.974 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.5915 time to fit residues: 6.4042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 420 random chunks: chunk 264 optimal weight: 0.2980 chunk 354 optimal weight: 0.6980 chunk 102 optimal weight: 0.9980 chunk 307 optimal weight: 9.9990 chunk 49 optimal weight: 0.6980 chunk 92 optimal weight: 0.8980 chunk 333 optimal weight: 2.9990 chunk 139 optimal weight: 0.7980 chunk 342 optimal weight: 2.9990 chunk 42 optimal weight: 0.0010 chunk 61 optimal weight: 0.9980 overall best weight: 0.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N2673 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 746 ASN ** F2373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.148648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.092364 restraints weight = 191410.220| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 3.55 r_work: 0.3026 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.3812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 34059 Z= 0.178 Angle : 0.477 7.378 46171 Z= 0.248 Chirality : 0.034 0.147 5404 Planarity : 0.003 0.046 5834 Dihedral : 3.703 21.069 4462 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.26 % Favored : 96.72 % Rotamer Outliers : 0.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: 1.64 (0.13), residues: 4178 helix: 1.95 (0.10), residues: 2858 sheet: 0.06 (0.65), residues: 72 loop : -0.88 (0.17), residues: 1248 =============================================================================== Job complete usr+sys time: 10185.79 seconds wall clock time: 178 minutes 30.61 seconds (10710.61 seconds total)