CLEAN - Clean-up program ------------------------ Clean-up program CLEAN - Written by David Keith Smith, 1989. Amended by Roman Laskowski, 1992. Enter filename containing coordinates of structure (for file containing ensemble of NMR structures enter @filename; for set of separate PDB files to be processed, enter %filelist, where filelist contains a list of PDB files to be cleaned up) ** Unrecognized atom type [HE21] in residue GLN 16 ** Unrecognized atom type [HE22] in residue GLN 16 ** Unrecognized atom type [HG11] in residue VAL 20 ** Unrecognized atom type [HG12] in residue VAL 20 ** Unrecognized atom type [HG13] in residue VAL 20 ** Unrecognized atom type [HG21] in residue VAL 20 ** Unrecognized atom type [HG22] in residue VAL 20 ** Unrecognized atom type [HG23] in residue VAL 20 ** Unrecognized atom type [HG11] in residue VAL 22 ** Unrecognized atom type [HG12] in residue VAL 22 ** Unrecognized atom type [HG13] in residue VAL 22 ** Unrecognized atom type [HG21] in residue VAL 22 ** Unrecognized atom type [HG22] in residue VAL 22 ** Unrecognized atom type [HG23] in residue VAL 22 ** Unrecognized atom type [HE21] in residue GLN 27 ** Unrecognized atom type [HE22] in residue GLN 27 ** Unrecognized atom type [HG11] in residue VAL 31 ** Unrecognized atom type [HG12] in residue VAL 31 ** Unrecognized atom type [HG13] in residue VAL 31 ** Unrecognized atom type [HG21] in residue VAL 31 ** Unrecognized atom type [HG22] in residue VAL 31 ** Unrecognized atom type [HG23] in residue VAL 31 ** Unrecognized atom type [HG11] in residue ILE 32 ** Unrecognized atom type [HG12] in residue ILE 32 ** Unrecognized atom type [HG21] in residue ILE 32 ** Unrecognized atom type [HG22] in residue ILE 32 ** Unrecognized atom type [HG23] in residue ILE 32 ** Unrecognized atom type [HG11] in residue VAL 34 ** Unrecognized atom type [HG12] in residue VAL 34 ** Unrecognized atom type [HG13] in residue VAL 34 ** Unrecognized atom type [HG21] in residue VAL 34 ** Unrecognized atom type [HG22] in residue VAL 34 ** Unrecognized atom type [HG23] in residue VAL 34 ** Unrecognized atom type [HG21] in residue THR 39 ** Unrecognized atom type [HG22] in residue THR 39 ** Unrecognized atom type [HG23] in residue THR 39 ** Unrecognized atom type [HG11] in residue ILE 42 ** Unrecognized atom type [HG12] in residue ILE 42 ** Unrecognized atom type [HG21] in residue ILE 42 ** Unrecognized atom type [HG22] in residue ILE 42 ** Unrecognized atom type [HG23] in residue ILE 42 ** Unrecognized atom type [HG11] in residue VAL 43 ** Unrecognized atom type [HG12] in residue VAL 43 ** Unrecognized atom type [HG13] in residue VAL 43 ** Unrecognized atom type [HG21] in residue VAL 43 ** Unrecognized atom type [HG22] in residue VAL 43 ** Unrecognized atom type [HG23] in residue VAL 43 ** Unrecognized atom type [HG21] in residue THR 46 ** Unrecognized atom type [HG22] in residue THR 46 ** Unrecognized atom type [HG23] in residue THR 46 ** Unrecognized atom type [HE21] in residue GLN 51 ** Unrecognized atom type [HE22] in residue GLN 51 ** Unrecognized atom type [HG11] in residue ILE 63 ** Unrecognized atom type [HG12] in residue ILE 63 ** Unrecognized atom type [HG21] in residue ILE 63 ** Unrecognized atom type [HG22] in residue ILE 63 ** Unrecognized atom type [HG23] in residue ILE 63 ** Unrecognized atom type [HG11] in residue VAL 64 ** Unrecognized atom type [HG12] in residue VAL 64 ** Unrecognized atom type [HG13] in residue VAL 64 ** Unrecognized atom type [HG21] in residue VAL 64 ** Unrecognized atom type [HG22] in residue VAL 64 ** Unrecognized atom type [HG23] in residue VAL 64 ** Unrecognized atom type [HG11] in residue VAL 71 ** Unrecognized atom type [HG12] in residue VAL 71 ** Unrecognized atom type [HG13] in residue VAL 71 ** Unrecognized atom type [HG21] in residue VAL 71 ** Unrecognized atom type [HG22] in residue VAL 71 ** Unrecognized atom type [HG23] in residue VAL 71 ** Unrecognized atom type [HG11] in residue VAL 75 ** Unrecognized atom type [HG12] in residue VAL 75 ** Unrecognized atom type [HG13] in residue VAL 75 ** Unrecognized atom type [HG21] in residue VAL 75 ** Unrecognized atom type [HG22] in residue VAL 75 ** Unrecognized atom type [HG23] in residue VAL 75 ** Unrecognized atom type [HG11] in residue VAL 79 ** Unrecognized atom type [HG12] in residue VAL 79 ** Unrecognized atom type [HG13] in residue VAL 79 ** Unrecognized atom type [HG21] in residue VAL 79 ** Unrecognized atom type [HG22] in residue VAL 79 ** Unrecognized atom type [HG23] in residue VAL 79 ** Unrecognized atom type [HG21] in residue THR 80 ** Unrecognized atom type [HG22] in residue THR 80 ** Unrecognized atom type [HG23] in residue THR 80 ** Unrecognized atom type [HG11] in residue VAL 90 ** Unrecognized atom type [HG12] in residue VAL 90 ** Unrecognized atom type [HG13] in residue VAL 90 ** Unrecognized atom type [HG21] in residue VAL 90 ** Unrecognized atom type [HG22] in residue VAL 90 ** Unrecognized atom type [HG23] in residue VAL 90 ** Unrecognized atom type [HG11] in residue VAL 98 ** Unrecognized atom type [HG12] in residue VAL 98 ** Unrecognized atom type [HG13] in residue VAL 98 ** Unrecognized atom type [HG21] in residue VAL 98 ** Unrecognized atom type [HG22] in residue VAL 98 ** Unrecognized atom type [HG23] in residue VAL 98 ** Unrecognized atom type [HG21] in residue THR 99 ** Unrecognized atom type [HG22] in residue THR 99 ** Unrecognized atom type [HG23] in residue THR 99 ** Unrecognized atom type [HG11] in residue VAL 100 ** Unrecognized atom type [HG12] in residue VAL 100 ** Unrecognized atom type [HG13] in residue VAL 100 ** Unrecognized atom type [HG21] in residue VAL 100 ** Unrecognized atom type [HG22] in residue VAL 100 ** Unrecognized atom type [HG23] in residue VAL 100 ** Unrecognized atom type [HG11] in residue ILE 102 ** Unrecognized atom type [HG12] in residue ILE 102 ** Unrecognized atom type [HG21] in residue ILE 102 ** Unrecognized atom type [HG22] in residue ILE 102 ** Unrecognized atom type [HG23] in residue ILE 102 ** Unrecognized atom type [HG11] in residue VAL 103 ** Unrecognized atom type [HG12] in residue VAL 103 ** Unrecognized atom type [HG13] in residue VAL 103 ** Unrecognized atom type [HG21] in residue VAL 103 ** Unrecognized atom type [HG22] in residue VAL 103 ** Unrecognized atom type [HG23] in residue VAL 103 ** Unrecognized atom type [HG11] in residue VAL 113 ** Unrecognized atom type [HG12] in residue VAL 113 ** Unrecognized atom type [HG13] in residue VAL 113 ** Unrecognized atom type [HG21] in residue VAL 113 ** Unrecognized atom type [HG22] in residue VAL 113 ** Unrecognized atom type [HG23] in residue VAL 113 ** Unrecognized atom type [HG21] in residue THR 115 ** Unrecognized atom type [HG22] in residue THR 115 ** Unrecognized atom type [HG23] in residue THR 115 ** Unrecognized atom type [HG11] in residue ILE 119 ** Unrecognized atom type [HG12] in residue ILE 119 ** Unrecognized atom type [HG21] in residue ILE 119 ** Unrecognized atom type [HG22] in residue ILE 119 ** Unrecognized atom type [HG23] in residue ILE 119 ** Unrecognized atom type [HG11] in residue ILE 144 ** Unrecognized atom type [HG12] in residue ILE 144 ** Unrecognized atom type [HG21] in residue ILE 144 ** Unrecognized atom type [HG22] in residue ILE 144 ** Unrecognized atom type [HG23] in residue ILE 144 ** Unrecognized atom type [HG21] in residue THR 146 ** Unrecognized atom type [HG22] in residue THR 146 ** Unrecognized atom type [HG23] in residue THR 146 ** Unrecognized atom type [HG11] in residue ILE 150 ** Unrecognized atom type [HG12] in residue ILE 150 ** Unrecognized atom type [HG21] in residue ILE 150 ** Unrecognized atom type [HG22] in residue ILE 150 ** Unrecognized atom type [HG23] in residue ILE 150 ** Unrecognized atom type [HE21] in residue GLN 158 ** Unrecognized atom type [HE22] in residue GLN 158 ** Unrecognized atom type [HE21] in residue GLN 160 ** Unrecognized atom type [HE22] in residue GLN 160 ** Unrecognized atom type [HG11] in residue ILE 165 ** Unrecognized atom type [HG12] in residue ILE 165 ** Unrecognized atom type [HG21] in residue ILE 165 ** Unrecognized atom type [HG22] in residue ILE 165 ** Unrecognized atom type [HG23] in residue ILE 165 ** Unrecognized atom type [HG11] in residue VAL 168 ** Unrecognized atom type [HG12] in residue VAL 168 ** Unrecognized atom type [HG13] in residue VAL 168 ** Unrecognized atom type [HG21] in residue VAL 168 ** Unrecognized atom type [HG22] in residue VAL 168 ** Unrecognized atom type [HG23] in residue VAL 168 ** Unrecognized atom type [HE21] in residue GLN 173 ** Unrecognized atom type [HE22] in residue GLN 173 ** Unrecognized atom type [ OT1] in residue GLN 173 ** Unrecognized atom type [ OT2] in residue GLN 173 Average value of CA-N-C-CB angle is 34.60 Standard deviation is .86 * Side chain atoms swapped for residues: * ASP 13 TYR 23 ASP 28 ASP 30 GLU 41 GLU 67 GLU 70 * ASP 88 GLU 94 TYR 95 GLU 105 TYR 116 ASP 125 GLU 129 * PHE 132 GLU 133 GLU 134 GLU 145 GLU 152 ASP 163 GLU 171 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2632 old number = 0 Total number of residues changed and total number of residues: ALA 0 4 CYS 0 3 ASP 6 12 GLU 11 17 PHE 1 8 GLY 0 12 HIS 0 10 ILE 0 8 LYS 0 15 LEU 0 12 MET 0 6 ASN 0 8 PRO 0 7 GLN 0 6 ARG 0 8 SER 0 9 THR 0 6 VAL 0 15 TRP 0 3 TYR 3 4 * Program completed