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 82 ** Unrecognized atom type [ O2 ] in residue HIS M 174 Chain break between 82 (M 82 ) and 83 (M 93 ) Average value of CA-N-C-CB angle is 34.01 Standard deviation is 0.68 * 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 = 2630 old number = 0 * PHE M 9 PHE M 41 PHE M 101 PHE M 133 Total number of residues that need to be changed and total number of residues: ALA 0 10 ASP 0 6 GLU 0 20 PHE 4 12 GLY 0 10 HIS 0 16 ILE 0 8 LYS 0 16 LEU 0 10 MET 0 8 ASN 0 10 PRO 0 4 GLN 0 2 ARG 0 4 SER 0 8 THR 0 12 VAL 0 4 TRP 0 4 Processing NMR model 2 ** Unrecognized atom type [ O2 ] in residue HIS M 82 ** Unrecognized atom type [ O2 ] in residue HIS M 174 Chain break between 82 (M 82 ) and 83 (M 93 ) Average value of CA-N-C-CB angle is 33.99 Standard deviation is 0.69 * Side chain atoms should be swapped for the following residues: * As this is an NMR ensemble the swap has not been made * PHE M 7 PHE M 34 PHE M 41 PHE M 71 PHE M 99 PHE M 126 PHE M 133 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2630 old number = 0 * PHE M 163 Total number of residues that need to be changed and total number of residues: ALA 0 10 ASP 0 6 GLU 0 20 PHE 8 12 GLY 0 10 HIS 0 16 ILE 0 8 LYS 0 16 LEU 0 10 MET 0 8 ASN 0 10 PRO 0 4 GLN 0 2 ARG 0 4 SER 0 8 THR 0 12 VAL 0 4 TRP 0 4 Processing NMR model 3 ** Unrecognized atom type [ O2 ] in residue HIS M 82 ** Unrecognized atom type [ O2 ] in residue HIS M 174 Chain break between 82 (M 82 ) and 83 (M 93 ) Average value of CA-N-C-CB angle is 34.10 Standard deviation is 0.74 * Side chain atoms should be swapped for the following residues: * As this is an NMR ensemble the swap has not been made * PHE M 7 PHE M 34 PHE M 41 PHE M 71 PHE M 99 PHE M 126 PHE M 133 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2630 old number = 0 * PHE M 163 Total number of residues that need to be changed and total number of residues: ALA 0 10 ASP 0 6 GLU 0 20 PHE 8 12 GLY 0 10 HIS 0 16 ILE 0 8 LYS 0 16 LEU 0 10 MET 0 8 ASN 0 10 PRO 0 4 GLN 0 2 ARG 0 4 SER 0 8 THR 0 12 VAL 0 4 TRP 0 4 Processing NMR model 4 ** Unrecognized atom type [ O2 ] in residue HIS M 82 ** Unrecognized atom type [ O2 ] in residue HIS M 174 Chain break between 82 (M 82 ) and 83 (M 93 ) Average value of CA-N-C-CB angle is 34.07 Standard deviation is 0.71 * 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 = 2630 old number = 0 * PHE M 7 PHE M 41 PHE M 99 PHE M 133 Total number of residues that need to be changed and total number of residues: ALA 0 10 ASP 0 6 GLU 0 20 PHE 4 12 GLY 0 10 HIS 0 16 ILE 0 8 LYS 0 16 LEU 0 10 MET 0 8 ASN 0 10 PRO 0 4 GLN 0 2 ARG 0 4 SER 0 8 THR 0 12 VAL 0 4 TRP 0 4 Processing NMR model 5 ** Unrecognized atom type [ O2 ] in residue HIS M 82 ** Unrecognized atom type [ O2 ] in residue HIS M 174 Chain break between 82 (M 82 ) and 83 (M 93 ) Average value of CA-N-C-CB angle is 34.00 Standard deviation is 0.79 * 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 = 2630 old number = 0 * PHE M 7 PHE M 99 Total number of residues that need to be changed and total number of residues: ALA 0 10 ASP 0 6 GLU 0 20 PHE 2 12 GLY 0 10 HIS 0 16 ILE 0 8 LYS 0 16 LEU 0 10 MET 0 8 ASN 0 10 PRO 0 4 GLN 0 2 ARG 0 4 SER 0 8 THR 0 12 VAL 0 4 TRP 0 4 Processing NMR model 6 ** Unrecognized atom type [ O2 ] in residue HIS M 82 ** Unrecognized atom type [ O2 ] in residue HIS M 174 Chain break between 82 (M 82 ) and 83 (M 93 ) Average value of CA-N-C-CB angle is 33.99 Standard deviation is 0.73 * 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 = 2630 old number = 0 * PHE M 7 PHE M 41 ASP M 42 PHE M 99 PHE M 133 ASP M 134 Total number of residues that need to be changed and total number of residues: ALA 0 10 ASP 2 6 GLU 0 20 PHE 4 12 GLY 0 10 HIS 0 16 ILE 0 8 LYS 0 16 LEU 0 10 MET 0 8 ASN 0 10 PRO 0 4 GLN 0 2 ARG 0 4 SER 0 8 THR 0 12 VAL 0 4 TRP 0 4 Processing NMR model 7 ** Unrecognized atom type [ O2 ] in residue HIS M 82 ** Unrecognized atom type [ O2 ] in residue HIS M 174 Chain break between 82 (M 82 ) and 83 (M 93 ) Average value of CA-N-C-CB angle is 34.02 Standard deviation is 0.79 * 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 = 2630 old number = 0 * PHE M 41 PHE M 133 Total number of residues that need to be changed and total number of residues: ALA 0 10 ASP 0 6 GLU 0 20 PHE 2 12 GLY 0 10 HIS 0 16 ILE 0 8 LYS 0 16 LEU 0 10 MET 0 8 ASN 0 10 PRO 0 4 GLN 0 2 ARG 0 4 SER 0 8 THR 0 12 VAL 0 4 TRP 0 4 Processing NMR model 8 ** Unrecognized atom type [ O2 ] in residue HIS M 82 ** Unrecognized atom type [ O2 ] in residue HIS M 174 Chain break between 82 (M 82 ) and 83 (M 93 ) Average value of CA-N-C-CB angle is 34.03 Standard deviation is 0.70 * 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 = 2630 old number = 0 * PHE M 9 PHE M 34 PHE M 41 PHE M 101 PHE M 126 PHE M 133 Total number of residues that need to be changed and total number of residues: ALA 0 10 ASP 0 6 GLU 0 20 PHE 6 12 GLY 0 10 HIS 0 16 ILE 0 8 LYS 0 16 LEU 0 10 MET 0 8 ASN 0 10 PRO 0 4 GLN 0 2 ARG 0 4 SER 0 8 THR 0 12 VAL 0 4 TRP 0 4 Processing NMR model 9 ** Unrecognized atom type [ O2 ] in residue HIS M 82 ** Unrecognized atom type [ O2 ] in residue HIS M 174 Chain break between 82 (M 82 ) and 83 (M 93 ) Average value of CA-N-C-CB angle is 33.98 Standard deviation is 0.82 * 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 = 2630 old number = 0 * PHE M 7 PHE M 34 PHE M 41 PHE M 99 PHE M 126 PHE M 133 Total number of residues that need to be changed and total number of residues: ALA 0 10 ASP 0 6 GLU 0 20 PHE 6 12 GLY 0 10 HIS 0 16 ILE 0 8 LYS 0 16 LEU 0 10 MET 0 8 ASN 0 10 PRO 0 4 GLN 0 2 ARG 0 4 SER 0 8 THR 0 12 VAL 0 4 TRP 0 4 Processing NMR model 10 ** Unrecognized atom type [ O2 ] in residue HIS M 82 ** Unrecognized atom type [ O2 ] in residue HIS M 174 Chain break between 82 (M 82 ) and 83 (M 93 ) Average value of CA-N-C-CB angle is 34.02 Standard deviation is 0.82 * 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 = 2630 old number = 0 * PHE M 7 PHE M 9 PHE M 34 PHE M 99 PHE M 101 PHE M 126 Total number of residues that need to be changed and total number of residues: ALA 0 10 ASP 0 6 GLU 0 20 PHE 6 12 GLY 0 10 HIS 0 16 ILE 0 8 LYS 0 16 LEU 0 10 MET 0 8 ASN 0 10 PRO 0 4 GLN 0 2 ARG 0 4 SER 0 8 THR 0 12 VAL 0 4 TRP 0 4 Processing NMR model 11 ** Unrecognized atom type [ O2 ] in residue HIS M 82 ** Unrecognized atom type [ O2 ] in residue HIS M 174 Chain break between 82 (M 82 ) and 83 (M 93 ) Average value of CA-N-C-CB angle is 34.02 Standard deviation is 0.79 * 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 = 2630 old number = 0 * PHE M 7 PHE M 41 PHE M 99 PHE M 133 Total number of residues that need to be changed and total number of residues: ALA 0 10 ASP 0 6 GLU 0 20 PHE 4 12 GLY 0 10 HIS 0 16 ILE 0 8 LYS 0 16 LEU 0 10 MET 0 8 ASN 0 10 PRO 0 4 GLN 0 2 ARG 0 4 SER 0 8 THR 0 12 VAL 0 4 TRP 0 4 Processing NMR model 12 ** Unrecognized atom type [ O2 ] in residue HIS M 82 ** Unrecognized atom type [ O2 ] in residue HIS M 174 Chain break between 82 (M 82 ) and 83 (M 93 ) Average value of CA-N-C-CB angle is 34.07 Standard deviation is 0.80 * 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 = 2630 old number = 0 * PHE M 7 PHE M 9 PHE M 41 PHE M 99 PHE M 101 PHE M 133 Total number of residues that need to be changed and total number of residues: ALA 0 10 ASP 0 6 GLU 0 20 PHE 6 12 GLY 0 10 HIS 0 16 ILE 0 8 LYS 0 16 LEU 0 10 MET 0 8 ASN 0 10 PRO 0 4 GLN 0 2 ARG 0 4 SER 0 8 THR 0 12 VAL 0 4 TRP 0 4 Processing NMR model 13 ** Unrecognized atom type [ O2 ] in residue HIS M 82 ** Unrecognized atom type [ O2 ] in residue HIS M 174 Chain break between 82 (M 82 ) and 83 (M 93 ) Average value of CA-N-C-CB angle is 34.05 Standard deviation is 0.79 * 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 = 2630 old number = 0 * PHE M 9 PHE M 41 PHE M 71 PHE M 101 PHE M 133 PHE M 163 Total number of residues that need to be changed and total number of residues: ALA 0 10 ASP 0 6 GLU 0 20 PHE 6 12 GLY 0 10 HIS 0 16 ILE 0 8 LYS 0 16 LEU 0 10 MET 0 8 ASN 0 10 PRO 0 4 GLN 0 2 ARG 0 4 SER 0 8 THR 0 12 VAL 0 4 TRP 0 4 Processing NMR model 14 ** Unrecognized atom type [ O2 ] in residue HIS M 82 ** Unrecognized atom type [ O2 ] in residue HIS M 174 Chain break between 82 (M 82 ) and 83 (M 93 ) Average value of CA-N-C-CB angle is 34.05 Standard deviation is 0.74 * Side chain atoms should be swapped for the following residues: * As this is an NMR ensemble the swap has not been made * PHE M 9 PHE M 34 PHE M 41 PHE M 71 PHE M 101 PHE M 126 PHE M 133 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2630 old number = 0 * PHE M 163 Total number of residues that need to be changed and total number of residues: ALA 0 10 ASP 0 6 GLU 0 20 PHE 8 12 GLY 0 10 HIS 0 16 ILE 0 8 LYS 0 16 LEU 0 10 MET 0 8 ASN 0 10 PRO 0 4 GLN 0 2 ARG 0 4 SER 0 8 THR 0 12 VAL 0 4 TRP 0 4 Processing NMR model 15 ** Unrecognized atom type [ O2 ] in residue HIS M 82 ** Unrecognized atom type [ O2 ] in residue HIS M 174 Chain break between 82 (M 82 ) and 83 (M 93 ) Average value of CA-N-C-CB angle is 34.02 Standard deviation is 0.72 * 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 = 2630 old number = 0 * PHE M 7 PHE M 41 PHE M 99 PHE M 133 Total number of residues that need to be changed and total number of residues: ALA 0 10 ASP 0 6 GLU 0 20 PHE 4 12 GLY 0 10 HIS 0 16 ILE 0 8 LYS 0 16 LEU 0 10 MET 0 8 ASN 0 10 PRO 0 4 GLN 0 2 ARG 0 4 SER 0 8 THR 0 12 VAL 0 4 TRP 0 4 Processing NMR model 16 ** Unrecognized atom type [ O2 ] in residue HIS M 82 ** Unrecognized atom type [ O2 ] in residue HIS M 174 Chain break between 82 (M 82 ) and 83 (M 93 ) Average value of CA-N-C-CB angle is 34.00 Standard deviation is 0.69 * 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 = 2630 old number = 0 * PHE M 41 PHE M 133 Total number of residues that need to be changed and total number of residues: ALA 0 10 ASP 0 6 GLU 0 20 PHE 2 12 GLY 0 10 HIS 0 16 ILE 0 8 LYS 0 16 LEU 0 10 MET 0 8 ASN 0 10 PRO 0 4 GLN 0 2 ARG 0 4 SER 0 8 THR 0 12 VAL 0 4 TRP 0 4 Processing NMR model 17 ** Unrecognized atom type [ O2 ] in residue HIS M 82 ** Unrecognized atom type [ O2 ] in residue HIS M 174 Chain break between 82 (M 82 ) and 83 (M 93 ) Average value of CA-N-C-CB angle is 34.12 Standard deviation is 0.69 * 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 = 2630 old number = 0 * PHE M 9 PHE M 34 PHE M 41 PHE M 101 PHE M 126 PHE M 133 Total number of residues that need to be changed and total number of residues: ALA 0 10 ASP 0 6 GLU 0 20 PHE 6 12 GLY 0 10 HIS 0 16 ILE 0 8 LYS 0 16 LEU 0 10 MET 0 8 ASN 0 10 PRO 0 4 GLN 0 2 ARG 0 4 SER 0 8 THR 0 12 VAL 0 4 TRP 0 4 Processing NMR model 18 ** Unrecognized atom type [ O2 ] in residue HIS M 82 ** Unrecognized atom type [ O2 ] in residue HIS M 174 Chain break between 82 (M 82 ) and 83 (M 93 ) Average value of CA-N-C-CB angle is 34.04 Standard deviation is 0.75 * Side chain atoms should be swapped for the following residues: * As this is an NMR ensemble the swap has not been made * PHE M 7 PHE M 9 PHE M 34 PHE M 41 PHE M 99 PHE M 101 PHE M 126 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2630 old number = 0 * PHE M 133 Total number of residues that need to be changed and total number of residues: ALA 0 10 ASP 0 6 GLU 0 20 PHE 8 12 GLY 0 10 HIS 0 16 ILE 0 8 LYS 0 16 LEU 0 10 MET 0 8 ASN 0 10 PRO 0 4 GLN 0 2 ARG 0 4 SER 0 8 THR 0 12 VAL 0 4 TRP 0 4 Processing NMR model 19 ** Unrecognized atom type [ O2 ] in residue HIS M 82 ** Unrecognized atom type [ O2 ] in residue HIS M 174 Chain break between 82 (M 82 ) and 83 (M 93 ) Average value of CA-N-C-CB angle is 33.97 Standard deviation is 0.77 * 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 = 2630 old number = 0 * PHE M 7 PHE M 34 PHE M 41 PHE M 99 PHE M 126 PHE M 133 Total number of residues that need to be changed and total number of residues: ALA 0 10 ASP 0 6 GLU 0 20 PHE 6 12 GLY 0 10 HIS 0 16 ILE 0 8 LYS 0 16 LEU 0 10 MET 0 8 ASN 0 10 PRO 0 4 GLN 0 2 ARG 0 4 SER 0 8 THR 0 12 VAL 0 4 TRP 0 4 Processing NMR model 20 ** Unrecognized atom type [ O2 ] in residue HIS M 82 ** Unrecognized atom type [ O2 ] in residue HIS M 174 Chain break between 82 (M 82 ) and 83 (M 93 ) Average value of CA-N-C-CB angle is 34.03 Standard deviation is 0.76 * Side chain atoms should be swapped for the following residues: * As this is an NMR ensemble the swap has not been made * PHE M 9 PHE M 34 PHE M 41 ASP M 42 PHE M 101 PHE M 126 PHE M 133 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2630 old number = 0 * ASP M 134 Total number of residues that need to be changed and total number of residues: ALA 0 10 ASP 2 6 GLU 0 20 PHE 6 12 GLY 0 10 HIS 0 16 ILE 0 8 LYS 0 16 LEU 0 10 MET 0 8 ASN 0 10 PRO 0 4 GLN 0 2 ARG 0 4 SER 0 8 THR 0 12 VAL 0 4 TRP 0 4 * NMR ensemble comprises 20 model structures * Program completed