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 SER A 121 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 = 1902 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 10 ASP 0 6 GLU 0 3 PHE 0 8 GLY 0 8 HIS 0 9 ILE 0 7 LYS 0 6 LEU 0 10 MET 0 6 ASN 0 3 PRO 0 9 GLN 0 12 ARG 0 3 SER 0 9 THR 0 4 VAL 0 5 TRP 0 2 TYR 0 1 Processing NMR model 2 ** Unrecognized atom type [ O2 ] in residue SER A 121 Average value of CA-N-C-CB angle is 34.42 Standard deviation is 1.39 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 1902 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 10 ASP 0 6 GLU 0 3 PHE 0 8 GLY 0 8 HIS 0 9 ILE 0 7 LYS 0 6 LEU 0 10 MET 0 6 ASN 0 3 PRO 0 9 GLN 0 12 ARG 0 3 SER 0 9 THR 0 4 VAL 0 5 TRP 0 2 TYR 0 1 Processing NMR model 3 ** Unrecognized atom type [ O2 ] in residue SER A 121 Average value of CA-N-C-CB angle is 34.47 Standard deviation is 1.36 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 1902 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 10 ASP 0 6 GLU 0 3 PHE 0 8 GLY 0 8 HIS 0 9 ILE 0 7 LYS 0 6 LEU 0 10 MET 0 6 ASN 0 3 PRO 0 9 GLN 0 12 ARG 0 3 SER 0 9 THR 0 4 VAL 0 5 TRP 0 2 TYR 0 1 Processing NMR model 4 ** Unrecognized atom type [ O2 ] in residue SER A 121 Average value of CA-N-C-CB angle is 34.44 Standard deviation is 1.37 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 1902 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 10 ASP 0 6 GLU 0 3 PHE 0 8 GLY 0 8 HIS 0 9 ILE 0 7 LYS 0 6 LEU 0 10 MET 0 6 ASN 0 3 PRO 0 9 GLN 0 12 ARG 0 3 SER 0 9 THR 0 4 VAL 0 5 TRP 0 2 TYR 0 1 Processing NMR model 5 ** Unrecognized atom type [ O2 ] in residue SER A 121 Average value of CA-N-C-CB angle is 34.49 Standard deviation is 1.34 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 1902 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 10 ASP 0 6 GLU 0 3 PHE 0 8 GLY 0 8 HIS 0 9 ILE 0 7 LYS 0 6 LEU 0 10 MET 0 6 ASN 0 3 PRO 0 9 GLN 0 12 ARG 0 3 SER 0 9 THR 0 4 VAL 0 5 TRP 0 2 TYR 0 1 Processing NMR model 6 ** Unrecognized atom type [ O2 ] in residue SER A 121 Average value of CA-N-C-CB angle is 34.47 Standard deviation is 1.33 * 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 = 1902 old number = 0 * PHE A 57 Total number of residues that need to be changed and total number of residues: ALA 0 10 ASP 0 6 GLU 0 3 PHE 1 8 GLY 0 8 HIS 0 9 ILE 0 7 LYS 0 6 LEU 0 10 MET 0 6 ASN 0 3 PRO 0 9 GLN 0 12 ARG 0 3 SER 0 9 THR 0 4 VAL 0 5 TRP 0 2 TYR 0 1 Processing NMR model 7 ** Unrecognized atom type [ O2 ] in residue SER A 121 Average value of CA-N-C-CB angle is 34.45 Standard deviation is 1.35 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 1902 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 10 ASP 0 6 GLU 0 3 PHE 0 8 GLY 0 8 HIS 0 9 ILE 0 7 LYS 0 6 LEU 0 10 MET 0 6 ASN 0 3 PRO 0 9 GLN 0 12 ARG 0 3 SER 0 9 THR 0 4 VAL 0 5 TRP 0 2 TYR 0 1 Processing NMR model 8 ** Unrecognized atom type [ O2 ] in residue SER A 121 Average value of CA-N-C-CB angle is 34.41 Standard deviation is 1.34 * 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 = 1902 old number = 0 * GLU A 31 PHE A 57 Total number of residues that need to be changed and total number of residues: ALA 0 10 ASP 0 6 GLU 1 3 PHE 1 8 GLY 0 8 HIS 0 9 ILE 0 7 LYS 0 6 LEU 0 10 MET 0 6 ASN 0 3 PRO 0 9 GLN 0 12 ARG 0 3 SER 0 9 THR 0 4 VAL 0 5 TRP 0 2 TYR 0 1 Processing NMR model 9 ** Unrecognized atom type [ O2 ] in residue SER A 121 Average value of CA-N-C-CB angle is 34.45 Standard deviation is 1.38 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 1902 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 10 ASP 0 6 GLU 0 3 PHE 0 8 GLY 0 8 HIS 0 9 ILE 0 7 LYS 0 6 LEU 0 10 MET 0 6 ASN 0 3 PRO 0 9 GLN 0 12 ARG 0 3 SER 0 9 THR 0 4 VAL 0 5 TRP 0 2 TYR 0 1 Processing NMR model 10 ** Unrecognized atom type [ O2 ] in residue SER A 121 Average value of CA-N-C-CB angle is 34.46 Standard deviation is 1.37 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 1902 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 10 ASP 0 6 GLU 0 3 PHE 0 8 GLY 0 8 HIS 0 9 ILE 0 7 LYS 0 6 LEU 0 10 MET 0 6 ASN 0 3 PRO 0 9 GLN 0 12 ARG 0 3 SER 0 9 THR 0 4 VAL 0 5 TRP 0 2 TYR 0 1 Processing NMR model 11 ** Unrecognized atom type [ O2 ] in residue SER A 121 Average value of CA-N-C-CB angle is 34.45 Standard deviation is 1.33 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 1902 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 10 ASP 0 6 GLU 0 3 PHE 0 8 GLY 0 8 HIS 0 9 ILE 0 7 LYS 0 6 LEU 0 10 MET 0 6 ASN 0 3 PRO 0 9 GLN 0 12 ARG 0 3 SER 0 9 THR 0 4 VAL 0 5 TRP 0 2 TYR 0 1 Processing NMR model 12 ** Unrecognized atom type [ O2 ] in residue SER A 121 Average value of CA-N-C-CB angle is 34.55 Standard deviation is 1.22 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 1902 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 10 ASP 0 6 GLU 0 3 PHE 0 8 GLY 0 8 HIS 0 9 ILE 0 7 LYS 0 6 LEU 0 10 MET 0 6 ASN 0 3 PRO 0 9 GLN 0 12 ARG 0 3 SER 0 9 THR 0 4 VAL 0 5 TRP 0 2 TYR 0 1 Processing NMR model 13 ** Unrecognized atom type [ O2 ] in residue SER A 121 Average value of CA-N-C-CB angle is 34.53 Standard deviation is 1.38 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 1902 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 10 ASP 0 6 GLU 0 3 PHE 0 8 GLY 0 8 HIS 0 9 ILE 0 7 LYS 0 6 LEU 0 10 MET 0 6 ASN 0 3 PRO 0 9 GLN 0 12 ARG 0 3 SER 0 9 THR 0 4 VAL 0 5 TRP 0 2 TYR 0 1 Processing NMR model 14 ** Unrecognized atom type [ O2 ] in residue SER A 121 Average value of CA-N-C-CB angle is 34.47 Standard deviation is 1.32 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 1902 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 10 ASP 0 6 GLU 0 3 PHE 0 8 GLY 0 8 HIS 0 9 ILE 0 7 LYS 0 6 LEU 0 10 MET 0 6 ASN 0 3 PRO 0 9 GLN 0 12 ARG 0 3 SER 0 9 THR 0 4 VAL 0 5 TRP 0 2 TYR 0 1 Processing NMR model 15 ** Unrecognized atom type [ O2 ] in residue SER A 121 Average value of CA-N-C-CB angle is 34.41 Standard deviation is 1.34 * 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 = 1902 old number = 0 * PHE A 57 Total number of residues that need to be changed and total number of residues: ALA 0 10 ASP 0 6 GLU 0 3 PHE 1 8 GLY 0 8 HIS 0 9 ILE 0 7 LYS 0 6 LEU 0 10 MET 0 6 ASN 0 3 PRO 0 9 GLN 0 12 ARG 0 3 SER 0 9 THR 0 4 VAL 0 5 TRP 0 2 TYR 0 1 Processing NMR model 16 ** Unrecognized atom type [ O2 ] in residue SER A 121 Average value of CA-N-C-CB angle is 34.42 Standard deviation is 1.38 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 1902 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 10 ASP 0 6 GLU 0 3 PHE 0 8 GLY 0 8 HIS 0 9 ILE 0 7 LYS 0 6 LEU 0 10 MET 0 6 ASN 0 3 PRO 0 9 GLN 0 12 ARG 0 3 SER 0 9 THR 0 4 VAL 0 5 TRP 0 2 TYR 0 1 Processing NMR model 17 ** Unrecognized atom type [ O2 ] in residue SER A 121 Average value of CA-N-C-CB angle is 34.43 Standard deviation is 1.35 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 1902 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 10 ASP 0 6 GLU 0 3 PHE 0 8 GLY 0 8 HIS 0 9 ILE 0 7 LYS 0 6 LEU 0 10 MET 0 6 ASN 0 3 PRO 0 9 GLN 0 12 ARG 0 3 SER 0 9 THR 0 4 VAL 0 5 TRP 0 2 TYR 0 1 Processing NMR model 18 ** Unrecognized atom type [ O2 ] in residue SER A 121 Average value of CA-N-C-CB angle is 34.47 Standard deviation is 1.41 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 1902 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 10 ASP 0 6 GLU 0 3 PHE 0 8 GLY 0 8 HIS 0 9 ILE 0 7 LYS 0 6 LEU 0 10 MET 0 6 ASN 0 3 PRO 0 9 GLN 0 12 ARG 0 3 SER 0 9 THR 0 4 VAL 0 5 TRP 0 2 TYR 0 1 Processing NMR model 19 ** Unrecognized atom type [ O2 ] in residue SER A 121 Average value of CA-N-C-CB angle is 34.52 Standard deviation is 1.30 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 1902 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 10 ASP 0 6 GLU 0 3 PHE 0 8 GLY 0 8 HIS 0 9 ILE 0 7 LYS 0 6 LEU 0 10 MET 0 6 ASN 0 3 PRO 0 9 GLN 0 12 ARG 0 3 SER 0 9 THR 0 4 VAL 0 5 TRP 0 2 TYR 0 1 Processing NMR model 20 ** Unrecognized atom type [ O2 ] in residue SER A 121 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 = 1902 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 10 ASP 0 6 GLU 0 3 PHE 0 8 GLY 0 8 HIS 0 9 ILE 0 7 LYS 0 6 LEU 0 10 MET 0 6 ASN 0 3 PRO 0 9 GLN 0 12 ARG 0 3 SER 0 9 THR 0 4 VAL 0 5 TRP 0 2 TYR 0 1 * NMR ensemble comprises 20 model structures * Program completed