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 M 108 ** Unrecognized atom type [ O2 ] in residue HIS M 226 Chain break between 108 (M 108 ) and 109 (M 119 ) Average value of CA-N-C-CB angle is 34.12 Standard deviation is 0.46 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 3326 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 38 ASP 0 10 GLU 0 14 PHE 0 2 GLY 0 18 HIS 0 14 ILE 0 6 LYS 0 6 LEU 0 28 MET 0 4 ASN 0 6 GLN 0 14 ARG 0 20 SER 0 6 THR 0 10 VAL 0 16 TYR 0 4 Processing NMR model 2 ** Unrecognized atom type [ O2 ] in residue HIS M 108 ** Unrecognized atom type [ O2 ] in residue HIS M 226 Chain break between 108 (M 108 ) and 109 (M 119 ) Average value of CA-N-C-CB angle is 34.13 Standard deviation is 0.52 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 3326 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 38 ASP 0 10 GLU 0 14 PHE 0 2 GLY 0 18 HIS 0 14 ILE 0 6 LYS 0 6 LEU 0 28 MET 0 4 ASN 0 6 GLN 0 14 ARG 0 20 SER 0 6 THR 0 10 VAL 0 16 TYR 0 4 Processing NMR model 3 ** Unrecognized atom type [ O2 ] in residue HIS M 108 ** Unrecognized atom type [ O2 ] in residue HIS M 226 Chain break between 108 (M 108 ) and 109 (M 119 ) Average value of CA-N-C-CB angle is 34.12 Standard deviation is 0.50 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 3326 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 38 ASP 0 10 GLU 0 14 PHE 0 2 GLY 0 18 HIS 0 14 ILE 0 6 LYS 0 6 LEU 0 28 MET 0 4 ASN 0 6 GLN 0 14 ARG 0 20 SER 0 6 THR 0 10 VAL 0 16 TYR 0 4 Processing NMR model 4 ** Unrecognized atom type [ O2 ] in residue HIS M 108 ** Unrecognized atom type [ O2 ] in residue HIS M 226 Chain break between 108 (M 108 ) and 109 (M 119 ) Average value of CA-N-C-CB angle is 34.13 Standard deviation is 0.49 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 3326 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 38 ASP 0 10 GLU 0 14 PHE 0 2 GLY 0 18 HIS 0 14 ILE 0 6 LYS 0 6 LEU 0 28 MET 0 4 ASN 0 6 GLN 0 14 ARG 0 20 SER 0 6 THR 0 10 VAL 0 16 TYR 0 4 Processing NMR model 5 ** Unrecognized atom type [ O2 ] in residue HIS M 108 ** Unrecognized atom type [ O2 ] in residue HIS M 226 Chain break between 108 (M 108 ) and 109 (M 119 ) Average value of CA-N-C-CB angle is 34.09 Standard deviation is 0.54 * 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 = 3326 old number = 0 * ASP M 131 Total number of residues that need to be changed and total number of residues: ALA 0 38 ASP 1 10 GLU 0 14 PHE 0 2 GLY 0 18 HIS 0 14 ILE 0 6 LYS 0 6 LEU 0 28 MET 0 4 ASN 0 6 GLN 0 14 ARG 0 20 SER 0 6 THR 0 10 VAL 0 16 TYR 0 4 Processing NMR model 6 ** Unrecognized atom type [ O2 ] in residue HIS M 108 ** Unrecognized atom type [ O2 ] in residue HIS M 226 Chain break between 108 (M 108 ) and 109 (M 119 ) Average value of CA-N-C-CB angle is 34.13 Standard deviation is 0.45 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 3326 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 38 ASP 0 10 GLU 0 14 PHE 0 2 GLY 0 18 HIS 0 14 ILE 0 6 LYS 0 6 LEU 0 28 MET 0 4 ASN 0 6 GLN 0 14 ARG 0 20 SER 0 6 THR 0 10 VAL 0 16 TYR 0 4 Processing NMR model 7 ** Unrecognized atom type [ O2 ] in residue HIS M 108 ** Unrecognized atom type [ O2 ] in residue HIS M 226 Chain break between 108 (M 108 ) and 109 (M 119 ) Average value of CA-N-C-CB angle is 34.07 Standard deviation is 0.47 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 3326 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 38 ASP 0 10 GLU 0 14 PHE 0 2 GLY 0 18 HIS 0 14 ILE 0 6 LYS 0 6 LEU 0 28 MET 0 4 ASN 0 6 GLN 0 14 ARG 0 20 SER 0 6 THR 0 10 VAL 0 16 TYR 0 4 Processing NMR model 8 ** Unrecognized atom type [ O2 ] in residue HIS M 108 ** Unrecognized atom type [ O2 ] in residue HIS M 226 Chain break between 108 (M 108 ) and 109 (M 119 ) Average value of CA-N-C-CB angle is 34.09 Standard deviation is 0.54 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 3326 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 38 ASP 0 10 GLU 0 14 PHE 0 2 GLY 0 18 HIS 0 14 ILE 0 6 LYS 0 6 LEU 0 28 MET 0 4 ASN 0 6 GLN 0 14 ARG 0 20 SER 0 6 THR 0 10 VAL 0 16 TYR 0 4 Processing NMR model 9 ** Unrecognized atom type [ O2 ] in residue HIS M 108 ** Unrecognized atom type [ O2 ] in residue HIS M 226 Chain break between 108 (M 108 ) and 109 (M 119 ) Average value of CA-N-C-CB angle is 34.14 Standard deviation is 0.49 * 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 = 3326 old number = 0 * ASP M 85 Total number of residues that need to be changed and total number of residues: ALA 0 38 ASP 1 10 GLU 0 14 PHE 0 2 GLY 0 18 HIS 0 14 ILE 0 6 LYS 0 6 LEU 0 28 MET 0 4 ASN 0 6 GLN 0 14 ARG 0 20 SER 0 6 THR 0 10 VAL 0 16 TYR 0 4 Processing NMR model 10 ** Unrecognized atom type [ O2 ] in residue HIS M 108 ** Unrecognized atom type [ O2 ] in residue HIS M 226 Chain break between 108 (M 108 ) and 109 (M 119 ) Average value of CA-N-C-CB angle is 34.16 Standard deviation is 0.44 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 3326 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 38 ASP 0 10 GLU 0 14 PHE 0 2 GLY 0 18 HIS 0 14 ILE 0 6 LYS 0 6 LEU 0 28 MET 0 4 ASN 0 6 GLN 0 14 ARG 0 20 SER 0 6 THR 0 10 VAL 0 16 TYR 0 4 Processing NMR model 11 ** Unrecognized atom type [ O2 ] in residue HIS M 108 ** Unrecognized atom type [ O2 ] in residue HIS M 226 Chain break between 108 (M 108 ) and 109 (M 119 ) Average value of CA-N-C-CB angle is 34.13 Standard deviation is 0.51 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 3326 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 38 ASP 0 10 GLU 0 14 PHE 0 2 GLY 0 18 HIS 0 14 ILE 0 6 LYS 0 6 LEU 0 28 MET 0 4 ASN 0 6 GLN 0 14 ARG 0 20 SER 0 6 THR 0 10 VAL 0 16 TYR 0 4 Processing NMR model 12 ** Unrecognized atom type [ O2 ] in residue HIS M 108 ** Unrecognized atom type [ O2 ] in residue HIS M 226 Chain break between 108 (M 108 ) and 109 (M 119 ) Average value of CA-N-C-CB angle is 34.07 Standard deviation is 0.54 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 3326 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 38 ASP 0 10 GLU 0 14 PHE 0 2 GLY 0 18 HIS 0 14 ILE 0 6 LYS 0 6 LEU 0 28 MET 0 4 ASN 0 6 GLN 0 14 ARG 0 20 SER 0 6 THR 0 10 VAL 0 16 TYR 0 4 Processing NMR model 13 ** Unrecognized atom type [ O2 ] in residue HIS M 108 ** Unrecognized atom type [ O2 ] in residue HIS M 226 Chain break between 108 (M 108 ) and 109 (M 119 ) Average value of CA-N-C-CB angle is 34.08 Standard deviation is 0.49 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 3326 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 38 ASP 0 10 GLU 0 14 PHE 0 2 GLY 0 18 HIS 0 14 ILE 0 6 LYS 0 6 LEU 0 28 MET 0 4 ASN 0 6 GLN 0 14 ARG 0 20 SER 0 6 THR 0 10 VAL 0 16 TYR 0 4 Processing NMR model 14 ** Unrecognized atom type [ O2 ] in residue HIS M 108 ** Unrecognized atom type [ O2 ] in residue HIS M 226 Chain break between 108 (M 108 ) and 109 (M 119 ) Average value of CA-N-C-CB angle is 34.07 Standard deviation is 0.54 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 3326 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 38 ASP 0 10 GLU 0 14 PHE 0 2 GLY 0 18 HIS 0 14 ILE 0 6 LYS 0 6 LEU 0 28 MET 0 4 ASN 0 6 GLN 0 14 ARG 0 20 SER 0 6 THR 0 10 VAL 0 16 TYR 0 4 Processing NMR model 15 ** Unrecognized atom type [ O2 ] in residue HIS M 108 ** Unrecognized atom type [ O2 ] in residue HIS M 226 Chain break between 108 (M 108 ) and 109 (M 119 ) Average value of CA-N-C-CB angle is 34.11 Standard deviation is 0.54 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 3326 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 38 ASP 0 10 GLU 0 14 PHE 0 2 GLY 0 18 HIS 0 14 ILE 0 6 LYS 0 6 LEU 0 28 MET 0 4 ASN 0 6 GLN 0 14 ARG 0 20 SER 0 6 THR 0 10 VAL 0 16 TYR 0 4 Processing NMR model 16 ** Unrecognized atom type [ O2 ] in residue HIS M 108 ** Unrecognized atom type [ O2 ] in residue HIS M 226 Chain break between 108 (M 108 ) and 109 (M 119 ) Average value of CA-N-C-CB angle is 34.13 Standard deviation is 0.57 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 3326 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 38 ASP 0 10 GLU 0 14 PHE 0 2 GLY 0 18 HIS 0 14 ILE 0 6 LYS 0 6 LEU 0 28 MET 0 4 ASN 0 6 GLN 0 14 ARG 0 20 SER 0 6 THR 0 10 VAL 0 16 TYR 0 4 Processing NMR model 17 ** Unrecognized atom type [ O2 ] in residue HIS M 108 ** Unrecognized atom type [ O2 ] in residue HIS M 226 Chain break between 108 (M 108 ) and 109 (M 119 ) Average value of CA-N-C-CB angle is 34.13 Standard deviation is 0.46 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 3326 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 38 ASP 0 10 GLU 0 14 PHE 0 2 GLY 0 18 HIS 0 14 ILE 0 6 LYS 0 6 LEU 0 28 MET 0 4 ASN 0 6 GLN 0 14 ARG 0 20 SER 0 6 THR 0 10 VAL 0 16 TYR 0 4 Processing NMR model 18 ** Unrecognized atom type [ O2 ] in residue HIS M 108 ** Unrecognized atom type [ O2 ] in residue HIS M 226 Chain break between 108 (M 108 ) and 109 (M 119 ) Average value of CA-N-C-CB angle is 34.10 Standard deviation is 0.51 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 3326 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 38 ASP 0 10 GLU 0 14 PHE 0 2 GLY 0 18 HIS 0 14 ILE 0 6 LYS 0 6 LEU 0 28 MET 0 4 ASN 0 6 GLN 0 14 ARG 0 20 SER 0 6 THR 0 10 VAL 0 16 TYR 0 4 Processing NMR model 19 ** Unrecognized atom type [ O2 ] in residue HIS M 108 ** Unrecognized atom type [ O2 ] in residue HIS M 226 Chain break between 108 (M 108 ) and 109 (M 119 ) Average value of CA-N-C-CB angle is 34.13 Standard deviation is 0.56 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 3326 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 38 ASP 0 10 GLU 0 14 PHE 0 2 GLY 0 18 HIS 0 14 ILE 0 6 LYS 0 6 LEU 0 28 MET 0 4 ASN 0 6 GLN 0 14 ARG 0 20 SER 0 6 THR 0 10 VAL 0 16 TYR 0 4 Processing NMR model 20 ** Unrecognized atom type [ O2 ] in residue HIS M 108 ** Unrecognized atom type [ O2 ] in residue HIS M 226 Chain break between 108 (M 108 ) and 109 (M 119 ) Average value of CA-N-C-CB angle is 34.12 Standard deviation is 0.53 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 3326 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 38 ASP 0 10 GLU 0 14 PHE 0 2 GLY 0 18 HIS 0 14 ILE 0 6 LYS 0 6 LEU 0 28 MET 0 4 ASN 0 6 GLN 0 14 ARG 0 20 SER 0 6 THR 0 10 VAL 0 16 TYR 0 4 * NMR ensemble comprises 20 model structures * Program completed