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 142 Average value of CA-N-C-CB angle is 34.38 Standard deviation is 1.23 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2255 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 12 ASP 0 11 GLU 0 9 PHE 0 6 GLY 0 7 HIS 0 7 ILE 0 6 LYS 0 2 LEU 0 15 MET 0 3 ASN 0 3 PRO 0 9 GLN 0 7 ARG 0 11 SER 0 8 THR 0 9 VAL 0 12 TRP 0 5 Processing NMR model 2 ** Unrecognized atom type [ O2 ] in residue HIS A 142 Average value of CA-N-C-CB angle is 34.48 Standard deviation is 1.23 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2255 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 12 ASP 0 11 GLU 0 9 PHE 0 6 GLY 0 7 HIS 0 7 ILE 0 6 LYS 0 2 LEU 0 15 MET 0 3 ASN 0 3 PRO 0 9 GLN 0 7 ARG 0 11 SER 0 8 THR 0 9 VAL 0 12 TRP 0 5 Processing NMR model 3 ** Unrecognized atom type [ O2 ] in residue HIS A 142 Average value of CA-N-C-CB angle is 34.48 Standard deviation is 1.28 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2255 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 12 ASP 0 11 GLU 0 9 PHE 0 6 GLY 0 7 HIS 0 7 ILE 0 6 LYS 0 2 LEU 0 15 MET 0 3 ASN 0 3 PRO 0 9 GLN 0 7 ARG 0 11 SER 0 8 THR 0 9 VAL 0 12 TRP 0 5 Processing NMR model 4 ** Unrecognized atom type [ O2 ] in residue HIS A 142 Average value of CA-N-C-CB angle is 34.40 Standard deviation is 1.28 * 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 = 2255 old number = 0 * GLU A 131 Total number of residues that need to be changed and total number of residues: ALA 0 12 ASP 0 11 GLU 1 9 PHE 0 6 GLY 0 7 HIS 0 7 ILE 0 6 LYS 0 2 LEU 0 15 MET 0 3 ASN 0 3 PRO 0 9 GLN 0 7 ARG 0 11 SER 0 8 THR 0 9 VAL 0 12 TRP 0 5 Processing NMR model 5 ** Unrecognized atom type [ O2 ] in residue HIS A 142 Average value of CA-N-C-CB angle is 34.41 Standard deviation is 1.25 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2255 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 12 ASP 0 11 GLU 0 9 PHE 0 6 GLY 0 7 HIS 0 7 ILE 0 6 LYS 0 2 LEU 0 15 MET 0 3 ASN 0 3 PRO 0 9 GLN 0 7 ARG 0 11 SER 0 8 THR 0 9 VAL 0 12 TRP 0 5 Processing NMR model 6 ** Unrecognized atom type [ O2 ] in residue HIS A 142 Average value of CA-N-C-CB angle is 34.37 Standard deviation is 1.30 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2255 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 12 ASP 0 11 GLU 0 9 PHE 0 6 GLY 0 7 HIS 0 7 ILE 0 6 LYS 0 2 LEU 0 15 MET 0 3 ASN 0 3 PRO 0 9 GLN 0 7 ARG 0 11 SER 0 8 THR 0 9 VAL 0 12 TRP 0 5 Processing NMR model 7 ** Unrecognized atom type [ O2 ] in residue HIS A 142 Average value of CA-N-C-CB angle is 34.47 Standard deviation is 1.24 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2255 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 12 ASP 0 11 GLU 0 9 PHE 0 6 GLY 0 7 HIS 0 7 ILE 0 6 LYS 0 2 LEU 0 15 MET 0 3 ASN 0 3 PRO 0 9 GLN 0 7 ARG 0 11 SER 0 8 THR 0 9 VAL 0 12 TRP 0 5 Processing NMR model 8 ** Unrecognized atom type [ O2 ] in residue HIS A 142 Average value of CA-N-C-CB angle is 34.41 Standard deviation is 1.27 * 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 = 2255 old number = 0 * GLU A 78 Total number of residues that need to be changed and total number of residues: ALA 0 12 ASP 0 11 GLU 1 9 PHE 0 6 GLY 0 7 HIS 0 7 ILE 0 6 LYS 0 2 LEU 0 15 MET 0 3 ASN 0 3 PRO 0 9 GLN 0 7 ARG 0 11 SER 0 8 THR 0 9 VAL 0 12 TRP 0 5 Processing NMR model 9 ** Unrecognized atom type [ O2 ] in residue HIS A 142 Average value of CA-N-C-CB angle is 34.46 Standard deviation is 1.20 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2255 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 12 ASP 0 11 GLU 0 9 PHE 0 6 GLY 0 7 HIS 0 7 ILE 0 6 LYS 0 2 LEU 0 15 MET 0 3 ASN 0 3 PRO 0 9 GLN 0 7 ARG 0 11 SER 0 8 THR 0 9 VAL 0 12 TRP 0 5 Processing NMR model 10 ** Unrecognized atom type [ O2 ] in residue HIS A 142 Average value of CA-N-C-CB angle is 34.50 Standard deviation is 1.19 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2255 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 12 ASP 0 11 GLU 0 9 PHE 0 6 GLY 0 7 HIS 0 7 ILE 0 6 LYS 0 2 LEU 0 15 MET 0 3 ASN 0 3 PRO 0 9 GLN 0 7 ARG 0 11 SER 0 8 THR 0 9 VAL 0 12 TRP 0 5 Processing NMR model 11 ** Unrecognized atom type [ O2 ] in residue HIS A 142 Average value of CA-N-C-CB angle is 34.45 Standard deviation is 1.29 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2255 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 12 ASP 0 11 GLU 0 9 PHE 0 6 GLY 0 7 HIS 0 7 ILE 0 6 LYS 0 2 LEU 0 15 MET 0 3 ASN 0 3 PRO 0 9 GLN 0 7 ARG 0 11 SER 0 8 THR 0 9 VAL 0 12 TRP 0 5 Processing NMR model 12 ** Unrecognized atom type [ O2 ] in residue HIS A 142 Average value of CA-N-C-CB angle is 34.40 Standard deviation is 1.25 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2255 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 12 ASP 0 11 GLU 0 9 PHE 0 6 GLY 0 7 HIS 0 7 ILE 0 6 LYS 0 2 LEU 0 15 MET 0 3 ASN 0 3 PRO 0 9 GLN 0 7 ARG 0 11 SER 0 8 THR 0 9 VAL 0 12 TRP 0 5 Processing NMR model 13 ** Unrecognized atom type [ O2 ] in residue HIS A 142 Average value of CA-N-C-CB angle is 34.40 Standard deviation is 1.32 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2255 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 12 ASP 0 11 GLU 0 9 PHE 0 6 GLY 0 7 HIS 0 7 ILE 0 6 LYS 0 2 LEU 0 15 MET 0 3 ASN 0 3 PRO 0 9 GLN 0 7 ARG 0 11 SER 0 8 THR 0 9 VAL 0 12 TRP 0 5 Processing NMR model 14 ** Unrecognized atom type [ O2 ] in residue HIS A 142 Average value of CA-N-C-CB angle is 34.36 Standard deviation is 1.25 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2255 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 12 ASP 0 11 GLU 0 9 PHE 0 6 GLY 0 7 HIS 0 7 ILE 0 6 LYS 0 2 LEU 0 15 MET 0 3 ASN 0 3 PRO 0 9 GLN 0 7 ARG 0 11 SER 0 8 THR 0 9 VAL 0 12 TRP 0 5 Processing NMR model 15 ** Unrecognized atom type [ O2 ] in residue HIS A 142 Average value of CA-N-C-CB angle is 34.42 Standard deviation is 1.25 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2255 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 12 ASP 0 11 GLU 0 9 PHE 0 6 GLY 0 7 HIS 0 7 ILE 0 6 LYS 0 2 LEU 0 15 MET 0 3 ASN 0 3 PRO 0 9 GLN 0 7 ARG 0 11 SER 0 8 THR 0 9 VAL 0 12 TRP 0 5 Processing NMR model 16 ** Unrecognized atom type [ O2 ] in residue HIS A 142 Average value of CA-N-C-CB angle is 34.51 Standard deviation is 1.23 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2255 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 12 ASP 0 11 GLU 0 9 PHE 0 6 GLY 0 7 HIS 0 7 ILE 0 6 LYS 0 2 LEU 0 15 MET 0 3 ASN 0 3 PRO 0 9 GLN 0 7 ARG 0 11 SER 0 8 THR 0 9 VAL 0 12 TRP 0 5 Processing NMR model 17 ** Unrecognized atom type [ O2 ] in residue HIS A 142 Average value of CA-N-C-CB angle is 34.45 Standard deviation is 1.24 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2255 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 12 ASP 0 11 GLU 0 9 PHE 0 6 GLY 0 7 HIS 0 7 ILE 0 6 LYS 0 2 LEU 0 15 MET 0 3 ASN 0 3 PRO 0 9 GLN 0 7 ARG 0 11 SER 0 8 THR 0 9 VAL 0 12 TRP 0 5 Processing NMR model 18 ** Unrecognized atom type [ O2 ] in residue HIS A 142 Average value of CA-N-C-CB angle is 34.45 Standard deviation is 1.25 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2255 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 12 ASP 0 11 GLU 0 9 PHE 0 6 GLY 0 7 HIS 0 7 ILE 0 6 LYS 0 2 LEU 0 15 MET 0 3 ASN 0 3 PRO 0 9 GLN 0 7 ARG 0 11 SER 0 8 THR 0 9 VAL 0 12 TRP 0 5 Processing NMR model 19 ** Unrecognized atom type [ O2 ] in residue HIS A 142 Average value of CA-N-C-CB angle is 34.41 Standard deviation is 1.33 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2255 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 12 ASP 0 11 GLU 0 9 PHE 0 6 GLY 0 7 HIS 0 7 ILE 0 6 LYS 0 2 LEU 0 15 MET 0 3 ASN 0 3 PRO 0 9 GLN 0 7 ARG 0 11 SER 0 8 THR 0 9 VAL 0 12 TRP 0 5 Processing NMR model 20 ** Unrecognized atom type [ O2 ] in residue HIS A 142 Average value of CA-N-C-CB angle is 34.38 Standard deviation is 1.31 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2255 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 12 ASP 0 11 GLU 0 9 PHE 0 6 GLY 0 7 HIS 0 7 ILE 0 6 LYS 0 2 LEU 0 15 MET 0 3 ASN 0 3 PRO 0 9 GLN 0 7 ARG 0 11 SER 0 8 THR 0 9 VAL 0 12 TRP 0 5 * NMR ensemble comprises 20 model structures * Program completed