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) Processing NMR model 1 ** Unrecognized atom type [ O2 ] in residue HIS A 158 Average value of CA-N-C-CB angle is 34.56 Standard deviation is 1.32 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2366 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 25 ASP 0 8 GLU 0 10 PHE 0 3 GLY 0 13 HIS 0 9 ILE 0 4 LYS 0 1 LEU 0 17 MET 0 4 ASN 0 4 PRO 0 12 GLN 0 7 ARG 0 10 SER 0 4 THR 0 8 VAL 0 15 TRP 0 1 TYR 0 3 Processing NMR model 2 ** Unrecognized atom type [ O2 ] in residue HIS A 158 Average value of CA-N-C-CB angle is 34.60 Standard deviation is 1.27 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2366 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 25 ASP 0 8 GLU 0 10 PHE 0 3 GLY 0 13 HIS 0 9 ILE 0 4 LYS 0 1 LEU 0 17 MET 0 4 ASN 0 4 PRO 0 12 GLN 0 7 ARG 0 10 SER 0 4 THR 0 8 VAL 0 15 TRP 0 1 TYR 0 3 Processing NMR model 3 ** Unrecognized atom type [ O2 ] in residue HIS A 158 Average value of CA-N-C-CB angle is 34.56 Standard deviation is 1.32 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2366 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 25 ASP 0 8 GLU 0 10 PHE 0 3 GLY 0 13 HIS 0 9 ILE 0 4 LYS 0 1 LEU 0 17 MET 0 4 ASN 0 4 PRO 0 12 GLN 0 7 ARG 0 10 SER 0 4 THR 0 8 VAL 0 15 TRP 0 1 TYR 0 3 Processing NMR model 4 ** Unrecognized atom type [ O2 ] in residue HIS A 158 Average value of CA-N-C-CB angle is 34.55 Standard deviation is 1.27 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2366 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 25 ASP 0 8 GLU 0 10 PHE 0 3 GLY 0 13 HIS 0 9 ILE 0 4 LYS 0 1 LEU 0 17 MET 0 4 ASN 0 4 PRO 0 12 GLN 0 7 ARG 0 10 SER 0 4 THR 0 8 VAL 0 15 TRP 0 1 TYR 0 3 Processing NMR model 5 ** Unrecognized atom type [ O2 ] in residue HIS A 158 Average value of CA-N-C-CB angle is 34.55 Standard deviation is 1.33 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2366 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 25 ASP 0 8 GLU 0 10 PHE 0 3 GLY 0 13 HIS 0 9 ILE 0 4 LYS 0 1 LEU 0 17 MET 0 4 ASN 0 4 PRO 0 12 GLN 0 7 ARG 0 10 SER 0 4 THR 0 8 VAL 0 15 TRP 0 1 TYR 0 3 Processing NMR model 6 ** Unrecognized atom type [ O2 ] in residue HIS A 158 Average value of CA-N-C-CB angle is 34.61 Standard deviation is 1.29 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2366 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 25 ASP 0 8 GLU 0 10 PHE 0 3 GLY 0 13 HIS 0 9 ILE 0 4 LYS 0 1 LEU 0 17 MET 0 4 ASN 0 4 PRO 0 12 GLN 0 7 ARG 0 10 SER 0 4 THR 0 8 VAL 0 15 TRP 0 1 TYR 0 3 Processing NMR model 7 ** Unrecognized atom type [ O2 ] in residue HIS A 158 Average value of CA-N-C-CB angle is 34.57 Standard deviation is 1.30 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2366 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 25 ASP 0 8 GLU 0 10 PHE 0 3 GLY 0 13 HIS 0 9 ILE 0 4 LYS 0 1 LEU 0 17 MET 0 4 ASN 0 4 PRO 0 12 GLN 0 7 ARG 0 10 SER 0 4 THR 0 8 VAL 0 15 TRP 0 1 TYR 0 3 Processing NMR model 8 ** Unrecognized atom type [ O2 ] in residue HIS A 158 Average value of CA-N-C-CB angle is 34.57 Standard deviation is 1.29 * Side chain atoms should be swapped for the following residues: * As this is an NMR ensemble the swap has not been made WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2366 old number = 0 * ASP A 122 Total number of residues that need to be changed and total number of residues: ALA 0 25 ASP 1 8 GLU 0 10 PHE 0 3 GLY 0 13 HIS 0 9 ILE 0 4 LYS 0 1 LEU 0 17 MET 0 4 ASN 0 4 PRO 0 12 GLN 0 7 ARG 0 10 SER 0 4 THR 0 8 VAL 0 15 TRP 0 1 TYR 0 3 Processing NMR model 9 ** Unrecognized atom type [ O2 ] in residue HIS A 158 Average value of CA-N-C-CB angle is 34.54 Standard deviation is 1.28 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2366 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 25 ASP 0 8 GLU 0 10 PHE 0 3 GLY 0 13 HIS 0 9 ILE 0 4 LYS 0 1 LEU 0 17 MET 0 4 ASN 0 4 PRO 0 12 GLN 0 7 ARG 0 10 SER 0 4 THR 0 8 VAL 0 15 TRP 0 1 TYR 0 3 Processing NMR model 10 ** Unrecognized atom type [ O2 ] in residue HIS A 158 Average value of CA-N-C-CB angle is 34.51 Standard deviation is 1.34 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2366 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 25 ASP 0 8 GLU 0 10 PHE 0 3 GLY 0 13 HIS 0 9 ILE 0 4 LYS 0 1 LEU 0 17 MET 0 4 ASN 0 4 PRO 0 12 GLN 0 7 ARG 0 10 SER 0 4 THR 0 8 VAL 0 15 TRP 0 1 TYR 0 3 Processing NMR model 11 ** Unrecognized atom type [ O2 ] in residue HIS A 158 Average value of CA-N-C-CB angle is 34.54 Standard deviation is 1.31 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2366 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 25 ASP 0 8 GLU 0 10 PHE 0 3 GLY 0 13 HIS 0 9 ILE 0 4 LYS 0 1 LEU 0 17 MET 0 4 ASN 0 4 PRO 0 12 GLN 0 7 ARG 0 10 SER 0 4 THR 0 8 VAL 0 15 TRP 0 1 TYR 0 3 Processing NMR model 12 ** Unrecognized atom type [ O2 ] in residue HIS A 158 Average value of CA-N-C-CB angle is 34.57 Standard deviation is 1.28 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2366 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 25 ASP 0 8 GLU 0 10 PHE 0 3 GLY 0 13 HIS 0 9 ILE 0 4 LYS 0 1 LEU 0 17 MET 0 4 ASN 0 4 PRO 0 12 GLN 0 7 ARG 0 10 SER 0 4 THR 0 8 VAL 0 15 TRP 0 1 TYR 0 3 Processing NMR model 13 ** Unrecognized atom type [ O2 ] in residue HIS A 158 Average value of CA-N-C-CB angle is 34.59 Standard deviation is 1.30 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2366 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 25 ASP 0 8 GLU 0 10 PHE 0 3 GLY 0 13 HIS 0 9 ILE 0 4 LYS 0 1 LEU 0 17 MET 0 4 ASN 0 4 PRO 0 12 GLN 0 7 ARG 0 10 SER 0 4 THR 0 8 VAL 0 15 TRP 0 1 TYR 0 3 Processing NMR model 14 ** Unrecognized atom type [ O2 ] in residue HIS A 158 Average value of CA-N-C-CB angle is 34.56 Standard deviation is 1.29 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2366 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 25 ASP 0 8 GLU 0 10 PHE 0 3 GLY 0 13 HIS 0 9 ILE 0 4 LYS 0 1 LEU 0 17 MET 0 4 ASN 0 4 PRO 0 12 GLN 0 7 ARG 0 10 SER 0 4 THR 0 8 VAL 0 15 TRP 0 1 TYR 0 3 Processing NMR model 15 ** Unrecognized atom type [ O2 ] in residue HIS A 158 Average value of CA-N-C-CB angle is 34.58 Standard deviation is 1.27 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2366 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 25 ASP 0 8 GLU 0 10 PHE 0 3 GLY 0 13 HIS 0 9 ILE 0 4 LYS 0 1 LEU 0 17 MET 0 4 ASN 0 4 PRO 0 12 GLN 0 7 ARG 0 10 SER 0 4 THR 0 8 VAL 0 15 TRP 0 1 TYR 0 3 Processing NMR model 16 ** Unrecognized atom type [ O2 ] in residue HIS A 158 Average value of CA-N-C-CB angle is 34.53 Standard deviation is 1.32 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2366 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 25 ASP 0 8 GLU 0 10 PHE 0 3 GLY 0 13 HIS 0 9 ILE 0 4 LYS 0 1 LEU 0 17 MET 0 4 ASN 0 4 PRO 0 12 GLN 0 7 ARG 0 10 SER 0 4 THR 0 8 VAL 0 15 TRP 0 1 TYR 0 3 Processing NMR model 17 ** Unrecognized atom type [ O2 ] in residue HIS A 158 Average value of CA-N-C-CB angle is 34.56 Standard deviation is 1.32 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2366 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 25 ASP 0 8 GLU 0 10 PHE 0 3 GLY 0 13 HIS 0 9 ILE 0 4 LYS 0 1 LEU 0 17 MET 0 4 ASN 0 4 PRO 0 12 GLN 0 7 ARG 0 10 SER 0 4 THR 0 8 VAL 0 15 TRP 0 1 TYR 0 3 Processing NMR model 18 ** Unrecognized atom type [ O2 ] in residue HIS A 158 Average value of CA-N-C-CB angle is 34.58 Standard deviation is 1.33 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2366 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 25 ASP 0 8 GLU 0 10 PHE 0 3 GLY 0 13 HIS 0 9 ILE 0 4 LYS 0 1 LEU 0 17 MET 0 4 ASN 0 4 PRO 0 12 GLN 0 7 ARG 0 10 SER 0 4 THR 0 8 VAL 0 15 TRP 0 1 TYR 0 3 Processing NMR model 19 ** Unrecognized atom type [ O2 ] in residue HIS A 158 Average value of CA-N-C-CB angle is 34.63 Standard deviation is 1.34 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2366 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 25 ASP 0 8 GLU 0 10 PHE 0 3 GLY 0 13 HIS 0 9 ILE 0 4 LYS 0 1 LEU 0 17 MET 0 4 ASN 0 4 PRO 0 12 GLN 0 7 ARG 0 10 SER 0 4 THR 0 8 VAL 0 15 TRP 0 1 TYR 0 3 Processing NMR model 20 ** Unrecognized atom type [ O2 ] in residue HIS A 158 Average value of CA-N-C-CB angle is 34.56 Standard deviation is 1.30 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2366 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 25 ASP 0 8 GLU 0 10 PHE 0 3 GLY 0 13 HIS 0 9 ILE 0 4 LYS 0 1 LEU 0 17 MET 0 4 ASN 0 4 PRO 0 12 GLN 0 7 ARG 0 10 SER 0 4 THR 0 8 VAL 0 15 TRP 0 1 TYR 0 3 * NMR ensemble comprises 20 model structures * Program completed