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 155 Average value of CA-N-C-CB angle is 34.03 Standard deviation is 1.06 * Side chain atoms should be swapped for the following residues: * As this is an NMR ensemble the swap has not been made * PHE A 5 PHE A 37 PHE A 80 PHE A 84 PHE A 94 TYR A 111 TYR A 144 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2509 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 15 ASP 0 5 GLU 0 12 PHE 5 9 GLY 0 8 HIS 0 7 ILE 0 8 LYS 0 10 LEU 0 13 MET 0 2 ASN 0 4 PRO 0 7 GLN 0 8 ARG 0 12 SER 0 15 THR 0 2 VAL 0 8 TYR 2 10 Processing NMR model 2 ** Unrecognized atom type [ O2 ] in residue HIS A 155 Average value of CA-N-C-CB angle is 34.02 Standard deviation is 1.07 * 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 = 2509 old number = 0 * TYR A 4 PHE A 37 TYR A 76 PHE A 80 PHE A 84 TYR A 144 Total number of residues that need to be changed and total number of residues: ALA 0 15 ASP 0 5 GLU 0 12 PHE 3 9 GLY 0 8 HIS 0 7 ILE 0 8 LYS 0 10 LEU 0 13 MET 0 2 ASN 0 4 PRO 0 7 GLN 0 8 ARG 0 12 SER 0 15 THR 0 2 VAL 0 8 TYR 3 10 Processing NMR model 3 ** Unrecognized atom type [ O2 ] in residue HIS A 155 Average value of CA-N-C-CB angle is 34.03 Standard deviation is 1.03 * Side chain atoms should be swapped for the following residues: * As this is an NMR ensemble the swap has not been made * PHE A 5 TYR A 14 TYR A 33 PHE A 37 PHE A 80 PHE A 84 TYR A 111 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2509 old number = 0 * TYR A 136 PHE A 137 TYR A 144 Total number of residues that need to be changed and total number of residues: ALA 0 15 ASP 0 5 GLU 0 12 PHE 5 9 GLY 0 8 HIS 0 7 ILE 0 8 LYS 0 10 LEU 0 13 MET 0 2 ASN 0 4 PRO 0 7 GLN 0 8 ARG 0 12 SER 0 15 THR 0 2 VAL 0 8 TYR 5 10 Processing NMR model 4 ** Unrecognized atom type [ O2 ] in residue HIS A 155 Average value of CA-N-C-CB angle is 34.05 Standard deviation is 1.06 * Side chain atoms should be swapped for the following residues: * As this is an NMR ensemble the swap has not been made * PHE A 5 TYR A 14 TYR A 33 PHE A 37 PHE A 80 PHE A 84 TYR A 111 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2509 old number = 0 * PHE A 137 TYR A 144 Total number of residues that need to be changed and total number of residues: ALA 0 15 ASP 0 5 GLU 0 12 PHE 5 9 GLY 0 8 HIS 0 7 ILE 0 8 LYS 0 10 LEU 0 13 MET 0 2 ASN 0 4 PRO 0 7 GLN 0 8 ARG 0 12 SER 0 15 THR 0 2 VAL 0 8 TYR 4 10 Processing NMR model 5 ** Unrecognized atom type [ O2 ] in residue HIS A 155 Average value of CA-N-C-CB angle is 34.03 Standard deviation is 1.03 * Side chain atoms should be swapped for the following residues: * As this is an NMR ensemble the swap has not been made * PHE A 5 TYR A 33 PHE A 37 PHE A 80 PHE A 84 PHE A 94 TYR A 111 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2509 old number = 0 * TYR A 133 PHE A 137 Total number of residues that need to be changed and total number of residues: ALA 0 15 ASP 0 5 GLU 0 12 PHE 6 9 GLY 0 8 HIS 0 7 ILE 0 8 LYS 0 10 LEU 0 13 MET 0 2 ASN 0 4 PRO 0 7 GLN 0 8 ARG 0 12 SER 0 15 THR 0 2 VAL 0 8 TYR 3 10 Processing NMR model 6 ** Unrecognized atom type [ O2 ] in residue HIS A 155 Average value of CA-N-C-CB angle is 34.05 Standard deviation is 1.07 * 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 = 2509 old number = 0 * TYR A 4 TYR A 14 PHE A 37 PHE A 84 TYR A 111 Total number of residues that need to be changed and total number of residues: ALA 0 15 ASP 0 5 GLU 0 12 PHE 2 9 GLY 0 8 HIS 0 7 ILE 0 8 LYS 0 10 LEU 0 13 MET 0 2 ASN 0 4 PRO 0 7 GLN 0 8 ARG 0 12 SER 0 15 THR 0 2 VAL 0 8 TYR 3 10 Processing NMR model 7 ** Unrecognized atom type [ O2 ] in residue HIS A 155 Average value of CA-N-C-CB angle is 34.02 Standard deviation is 1.05 * Side chain atoms should be swapped for the following residues: * As this is an NMR ensemble the swap has not been made * TYR A 4 PHE A 5 TYR A 14 TYR A 33 PHE A 37 TYR A 76 PHE A 80 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2509 old number = 0 * PHE A 84 TYR A 111 PHE A 137 TYR A 144 Total number of residues that need to be changed and total number of residues: ALA 0 15 ASP 0 5 GLU 0 12 PHE 5 9 GLY 0 8 HIS 0 7 ILE 0 8 LYS 0 10 LEU 0 13 MET 0 2 ASN 0 4 PRO 0 7 GLN 0 8 ARG 0 12 SER 0 15 THR 0 2 VAL 0 8 TYR 6 10 Processing NMR model 8 ** Unrecognized atom type [ O2 ] in residue HIS A 155 Average value of CA-N-C-CB angle is 34.05 Standard deviation is 1.07 * 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 = 2509 old number = 0 * TYR A 14 PHE A 80 PHE A 84 TYR A 111 PHE A 137 TYR A 144 Total number of residues that need to be changed and total number of residues: ALA 0 15 ASP 0 5 GLU 0 12 PHE 3 9 GLY 0 8 HIS 0 7 ILE 0 8 LYS 0 10 LEU 0 13 MET 0 2 ASN 0 4 PRO 0 7 GLN 0 8 ARG 0 12 SER 0 15 THR 0 2 VAL 0 8 TYR 3 10 Processing NMR model 9 ** Unrecognized atom type [ O2 ] in residue HIS A 155 Average value of CA-N-C-CB angle is 34.04 Standard deviation is 1.05 * Side chain atoms should be swapped for the following residues: * As this is an NMR ensemble the swap has not been made * TYR A 4 TYR A 14 TYR A 33 PHE A 37 PHE A 80 PHE A 84 PHE A 137 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2509 old number = 0 * TYR A 144 Total number of residues that need to be changed and total number of residues: ALA 0 15 ASP 0 5 GLU 0 12 PHE 4 9 GLY 0 8 HIS 0 7 ILE 0 8 LYS 0 10 LEU 0 13 MET 0 2 ASN 0 4 PRO 0 7 GLN 0 8 ARG 0 12 SER 0 15 THR 0 2 VAL 0 8 TYR 4 10 Processing NMR model 10 ** Unrecognized atom type [ O2 ] in residue HIS A 155 Average value of CA-N-C-CB angle is 34.04 Standard deviation is 1.06 * Side chain atoms should be swapped for the following residues: * As this is an NMR ensemble the swap has not been made * TYR A 4 PHE A 5 TYR A 14 TYR A 33 PHE A 37 PHE A 80 PHE A 84 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2509 old number = 0 * TYR A 111 PHE A 137 Total number of residues that need to be changed and total number of residues: ALA 0 15 ASP 0 5 GLU 0 12 PHE 5 9 GLY 0 8 HIS 0 7 ILE 0 8 LYS 0 10 LEU 0 13 MET 0 2 ASN 0 4 PRO 0 7 GLN 0 8 ARG 0 12 SER 0 15 THR 0 2 VAL 0 8 TYR 4 10 Processing NMR model 11 ** Unrecognized atom type [ O2 ] in residue HIS A 155 Average value of CA-N-C-CB angle is 34.02 Standard deviation is 1.07 * Side chain atoms should be swapped for the following residues: * As this is an NMR ensemble the swap has not been made * TYR A 14 TYR A 33 PHE A 37 PHE A 80 PHE A 84 PHE A 94 PHE A 137 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2509 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 15 ASP 0 5 GLU 0 12 PHE 5 9 GLY 0 8 HIS 0 7 ILE 0 8 LYS 0 10 LEU 0 13 MET 0 2 ASN 0 4 PRO 0 7 GLN 0 8 ARG 0 12 SER 0 15 THR 0 2 VAL 0 8 TYR 2 10 Processing NMR model 12 ** Unrecognized atom type [ O2 ] in residue HIS A 155 Average value of CA-N-C-CB angle is 34.03 Standard deviation is 1.05 * Side chain atoms should be swapped for the following residues: * As this is an NMR ensemble the swap has not been made * TYR A 14 PHE A 37 PHE A 80 PHE A 84 PHE A 94 TYR A 111 PHE A 137 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2509 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 15 ASP 0 5 GLU 0 12 PHE 5 9 GLY 0 8 HIS 0 7 ILE 0 8 LYS 0 10 LEU 0 13 MET 0 2 ASN 0 4 PRO 0 7 GLN 0 8 ARG 0 12 SER 0 15 THR 0 2 VAL 0 8 TYR 2 10 Processing NMR model 13 ** Unrecognized atom type [ O2 ] in residue HIS A 155 Average value of CA-N-C-CB angle is 34.03 Standard deviation is 1.07 * Side chain atoms should be swapped for the following residues: * As this is an NMR ensemble the swap has not been made * TYR A 14 TYR A 33 PHE A 37 PHE A 84 PHE A 94 TYR A 136 PHE A 137 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2509 old number = 0 * TYR A 144 Total number of residues that need to be changed and total number of residues: ALA 0 15 ASP 0 5 GLU 0 12 PHE 4 9 GLY 0 8 HIS 0 7 ILE 0 8 LYS 0 10 LEU 0 13 MET 0 2 ASN 0 4 PRO 0 7 GLN 0 8 ARG 0 12 SER 0 15 THR 0 2 VAL 0 8 TYR 4 10 Processing NMR model 14 ** Unrecognized atom type [ O2 ] in residue HIS A 155 Average value of CA-N-C-CB angle is 34.03 Standard deviation is 1.02 * 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 = 2509 old number = 0 * PHE A 5 TYR A 14 PHE A 37 TYR A 111 Total number of residues that need to be changed and total number of residues: ALA 0 15 ASP 0 5 GLU 0 12 PHE 2 9 GLY 0 8 HIS 0 7 ILE 0 8 LYS 0 10 LEU 0 13 MET 0 2 ASN 0 4 PRO 0 7 GLN 0 8 ARG 0 12 SER 0 15 THR 0 2 VAL 0 8 TYR 2 10 Processing NMR model 15 ** Unrecognized atom type [ O2 ] in residue HIS A 155 Average value of CA-N-C-CB angle is 34.02 Standard deviation is 1.02 * Side chain atoms should be swapped for the following residues: * As this is an NMR ensemble the swap has not been made * TYR A 4 PHE A 5 TYR A 33 PHE A 37 TYR A 45 PHE A 80 TYR A 111 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2509 old number = 0 * TYR A 136 PHE A 137 Total number of residues that need to be changed and total number of residues: ALA 0 15 ASP 0 5 GLU 0 12 PHE 4 9 GLY 0 8 HIS 0 7 ILE 0 8 LYS 0 10 LEU 0 13 MET 0 2 ASN 0 4 PRO 0 7 GLN 0 8 ARG 0 12 SER 0 15 THR 0 2 VAL 0 8 TYR 5 10 Processing NMR model 16 ** Unrecognized atom type [ O2 ] in residue HIS A 155 Average value of CA-N-C-CB angle is 34.06 Standard deviation is 1.00 * Side chain atoms should be swapped for the following residues: * As this is an NMR ensemble the swap has not been made * TYR A 33 PHE A 37 PHE A 80 PHE A 84 TYR A 111 PHE A 137 TYR A 144 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2509 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 15 ASP 0 5 GLU 0 12 PHE 4 9 GLY 0 8 HIS 0 7 ILE 0 8 LYS 0 10 LEU 0 13 MET 0 2 ASN 0 4 PRO 0 7 GLN 0 8 ARG 0 12 SER 0 15 THR 0 2 VAL 0 8 TYR 3 10 Processing NMR model 17 ** Unrecognized atom type [ O2 ] in residue HIS A 155 Average value of CA-N-C-CB angle is 34.06 Standard deviation is 1.04 * Side chain atoms should be swapped for the following residues: * As this is an NMR ensemble the swap has not been made * TYR A 14 TYR A 33 PHE A 37 PHE A 80 PHE A 84 TYR A 111 TYR A 144 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2509 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 15 ASP 0 5 GLU 0 12 PHE 3 9 GLY 0 8 HIS 0 7 ILE 0 8 LYS 0 10 LEU 0 13 MET 0 2 ASN 0 4 PRO 0 7 GLN 0 8 ARG 0 12 SER 0 15 THR 0 2 VAL 0 8 TYR 4 10 Processing NMR model 18 ** Unrecognized atom type [ O2 ] in residue HIS A 155 Average value of CA-N-C-CB angle is 34.04 Standard deviation is 1.12 * Side chain atoms should be swapped for the following residues: * As this is an NMR ensemble the swap has not been made * TYR A 14 TYR A 33 PHE A 37 PHE A 80 PHE A 84 PHE A 94 TYR A 111 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2509 old number = 0 * TYR A 136 TYR A 144 Total number of residues that need to be changed and total number of residues: ALA 0 15 ASP 0 5 GLU 0 12 PHE 4 9 GLY 0 8 HIS 0 7 ILE 0 8 LYS 0 10 LEU 0 13 MET 0 2 ASN 0 4 PRO 0 7 GLN 0 8 ARG 0 12 SER 0 15 THR 0 2 VAL 0 8 TYR 5 10 Processing NMR model 19 ** Unrecognized atom type [ O2 ] in residue HIS A 155 Average value of CA-N-C-CB angle is 34.03 Standard deviation is 1.03 * Side chain atoms should be swapped for the following residues: * As this is an NMR ensemble the swap has not been made * TYR A 4 TYR A 33 PHE A 37 PHE A 80 PHE A 84 TYR A 111 TYR A 144 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2509 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 15 ASP 0 5 GLU 0 12 PHE 3 9 GLY 0 8 HIS 0 7 ILE 0 8 LYS 0 10 LEU 0 13 MET 0 2 ASN 0 4 PRO 0 7 GLN 0 8 ARG 0 12 SER 0 15 THR 0 2 VAL 0 8 TYR 4 10 Processing NMR model 20 ** Unrecognized atom type [ O2 ] in residue HIS A 155 Average value of CA-N-C-CB angle is 34.02 Standard deviation is 1.00 * Side chain atoms should be swapped for the following residues: * As this is an NMR ensemble the swap has not been made * TYR A 14 PHE A 37 TYR A 45 PHE A 80 PHE A 84 PHE A 94 TYR A 111 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2509 old number = 0 * TYR A 144 Total number of residues that need to be changed and total number of residues: ALA 0 15 ASP 0 5 GLU 0 12 PHE 4 9 GLY 0 8 HIS 0 7 ILE 0 8 LYS 0 10 LEU 0 13 MET 0 2 ASN 0 4 PRO 0 7 GLN 0 8 ARG 0 12 SER 0 15 THR 0 2 VAL 0 8 TYR 4 10 * NMR ensemble comprises 20 model structures * Program completed