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 GLU A 116 Average value of CA-N-C-CB angle is 34.06 Standard deviation is 0.87 * 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 = 1771 old number = 0 * PHE A 22 PHE A 50 TYR A 85 Total number of residues that need to be changed and total number of residues: ALA 0 18 ASP 0 9 GLU 0 11 PHE 2 4 GLY 0 10 HIS 0 3 ILE 0 3 LYS 0 4 LEU 0 17 MET 0 1 ASN 0 1 PRO 0 4 GLN 0 5 ARG 0 7 SER 0 5 THR 0 3 VAL 0 6 TRP 0 3 TYR 1 2 Processing NMR model 2 ** Unrecognized atom type [ O2 ] in residue GLU A 116 Average value of CA-N-C-CB angle is 34.05 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 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 1771 old number = 0 * PHE A 50 TYR A 85 Total number of residues that need to be changed and total number of residues: ALA 0 18 ASP 0 9 GLU 0 11 PHE 1 4 GLY 0 10 HIS 0 3 ILE 0 3 LYS 0 4 LEU 0 17 MET 0 1 ASN 0 1 PRO 0 4 GLN 0 5 ARG 0 7 SER 0 5 THR 0 3 VAL 0 6 TRP 0 3 TYR 1 2 Processing NMR model 3 ** Unrecognized atom type [ O2 ] in residue GLU A 116 Average value of CA-N-C-CB angle is 34.04 Standard deviation is 0.92 * 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 = 1771 old number = 0 * PHE A 50 Total number of residues that need to be changed and total number of residues: ALA 0 18 ASP 0 9 GLU 0 11 PHE 1 4 GLY 0 10 HIS 0 3 ILE 0 3 LYS 0 4 LEU 0 17 MET 0 1 ASN 0 1 PRO 0 4 GLN 0 5 ARG 0 7 SER 0 5 THR 0 3 VAL 0 6 TRP 0 3 TYR 0 2 Processing NMR model 4 ** Unrecognized atom type [ O2 ] in residue GLU A 116 Average value of CA-N-C-CB angle is 34.07 Standard deviation is 0.93 * 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 = 1771 old number = 0 * PHE A 50 TYR A 85 Total number of residues that need to be changed and total number of residues: ALA 0 18 ASP 0 9 GLU 0 11 PHE 1 4 GLY 0 10 HIS 0 3 ILE 0 3 LYS 0 4 LEU 0 17 MET 0 1 ASN 0 1 PRO 0 4 GLN 0 5 ARG 0 7 SER 0 5 THR 0 3 VAL 0 6 TRP 0 3 TYR 1 2 Processing NMR model 5 ** Unrecognized atom type [ O2 ] in residue GLU A 116 Average value of CA-N-C-CB angle is 34.05 Standard deviation is 0.96 * 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 = 1771 old number = 0 * PHE A 50 PHE A 81 Total number of residues that need to be changed and total number of residues: ALA 0 18 ASP 0 9 GLU 0 11 PHE 2 4 GLY 0 10 HIS 0 3 ILE 0 3 LYS 0 4 LEU 0 17 MET 0 1 ASN 0 1 PRO 0 4 GLN 0 5 ARG 0 7 SER 0 5 THR 0 3 VAL 0 6 TRP 0 3 TYR 0 2 Processing NMR model 6 ** Unrecognized atom type [ O2 ] in residue GLU A 116 Average value of CA-N-C-CB angle is 34.03 Standard deviation is 0.92 * 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 = 1771 old number = 0 * TYR A 85 Total number of residues that need to be changed and total number of residues: ALA 0 18 ASP 0 9 GLU 0 11 PHE 0 4 GLY 0 10 HIS 0 3 ILE 0 3 LYS 0 4 LEU 0 17 MET 0 1 ASN 0 1 PRO 0 4 GLN 0 5 ARG 0 7 SER 0 5 THR 0 3 VAL 0 6 TRP 0 3 TYR 1 2 Processing NMR model 7 ** Unrecognized atom type [ O2 ] in residue GLU A 116 Average value of CA-N-C-CB angle is 34.08 Standard deviation is 0.92 * 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 = 1771 old number = 0 * ASP A 28 PHE A 33 PHE A 50 TYR A 85 Total number of residues that need to be changed and total number of residues: ALA 0 18 ASP 1 9 GLU 0 11 PHE 2 4 GLY 0 10 HIS 0 3 ILE 0 3 LYS 0 4 LEU 0 17 MET 0 1 ASN 0 1 PRO 0 4 GLN 0 5 ARG 0 7 SER 0 5 THR 0 3 VAL 0 6 TRP 0 3 TYR 1 2 Processing NMR model 8 ** Unrecognized atom type [ O2 ] in residue GLU A 116 Average value of CA-N-C-CB angle is 34.07 Standard deviation is 0.97 * 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 = 1771 old number = 0 * PHE A 33 PHE A 50 Total number of residues that need to be changed and total number of residues: ALA 0 18 ASP 0 9 GLU 0 11 PHE 2 4 GLY 0 10 HIS 0 3 ILE 0 3 LYS 0 4 LEU 0 17 MET 0 1 ASN 0 1 PRO 0 4 GLN 0 5 ARG 0 7 SER 0 5 THR 0 3 VAL 0 6 TRP 0 3 TYR 0 2 Processing NMR model 9 ** Unrecognized atom type [ O2 ] in residue GLU A 116 Average value of CA-N-C-CB angle is 34.04 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 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 1771 old number = 0 * PHE A 33 PHE A 50 Total number of residues that need to be changed and total number of residues: ALA 0 18 ASP 0 9 GLU 0 11 PHE 2 4 GLY 0 10 HIS 0 3 ILE 0 3 LYS 0 4 LEU 0 17 MET 0 1 ASN 0 1 PRO 0 4 GLN 0 5 ARG 0 7 SER 0 5 THR 0 3 VAL 0 6 TRP 0 3 TYR 0 2 Processing NMR model 10 ** Unrecognized atom type [ O2 ] in residue GLU A 116 Average value of CA-N-C-CB angle is 34.08 Standard deviation is 0.97 * 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 = 1771 old number = 0 * TYR A 5 PHE A 50 Total number of residues that need to be changed and total number of residues: ALA 0 18 ASP 0 9 GLU 0 11 PHE 1 4 GLY 0 10 HIS 0 3 ILE 0 3 LYS 0 4 LEU 0 17 MET 0 1 ASN 0 1 PRO 0 4 GLN 0 5 ARG 0 7 SER 0 5 THR 0 3 VAL 0 6 TRP 0 3 TYR 1 2 Processing NMR model 11 ** Unrecognized atom type [ O2 ] in residue GLU A 116 Average value of CA-N-C-CB angle is 34.07 Standard deviation is 0.95 * 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 = 1771 old number = 0 * PHE A 50 TYR A 85 Total number of residues that need to be changed and total number of residues: ALA 0 18 ASP 0 9 GLU 0 11 PHE 1 4 GLY 0 10 HIS 0 3 ILE 0 3 LYS 0 4 LEU 0 17 MET 0 1 ASN 0 1 PRO 0 4 GLN 0 5 ARG 0 7 SER 0 5 THR 0 3 VAL 0 6 TRP 0 3 TYR 1 2 Processing NMR model 12 ** Unrecognized atom type [ O2 ] in residue GLU A 116 Average value of CA-N-C-CB angle is 34.04 Standard deviation is 0.91 * 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 = 1771 old number = 0 * PHE A 50 TYR A 85 Total number of residues that need to be changed and total number of residues: ALA 0 18 ASP 0 9 GLU 0 11 PHE 1 4 GLY 0 10 HIS 0 3 ILE 0 3 LYS 0 4 LEU 0 17 MET 0 1 ASN 0 1 PRO 0 4 GLN 0 5 ARG 0 7 SER 0 5 THR 0 3 VAL 0 6 TRP 0 3 TYR 1 2 Processing NMR model 13 ** Unrecognized atom type [ O2 ] in residue GLU A 116 Average value of CA-N-C-CB angle is 34.04 Standard deviation is 0.90 * 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 = 1771 old number = 0 * PHE A 33 TYR A 85 Total number of residues that need to be changed and total number of residues: ALA 0 18 ASP 0 9 GLU 0 11 PHE 1 4 GLY 0 10 HIS 0 3 ILE 0 3 LYS 0 4 LEU 0 17 MET 0 1 ASN 0 1 PRO 0 4 GLN 0 5 ARG 0 7 SER 0 5 THR 0 3 VAL 0 6 TRP 0 3 TYR 1 2 Processing NMR model 14 ** Unrecognized atom type [ O2 ] in residue GLU A 116 Average value of CA-N-C-CB angle is 34.06 Standard deviation is 0.97 * 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 = 1771 old number = 0 * PHE A 33 PHE A 50 PHE A 81 Total number of residues that need to be changed and total number of residues: ALA 0 18 ASP 0 9 GLU 0 11 PHE 3 4 GLY 0 10 HIS 0 3 ILE 0 3 LYS 0 4 LEU 0 17 MET 0 1 ASN 0 1 PRO 0 4 GLN 0 5 ARG 0 7 SER 0 5 THR 0 3 VAL 0 6 TRP 0 3 TYR 0 2 Processing NMR model 15 ** Unrecognized atom type [ O2 ] in residue GLU A 116 Average value of CA-N-C-CB angle is 34.05 Standard deviation is 0.87 * 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 = 1771 old number = 0 * PHE A 50 TYR A 85 Total number of residues that need to be changed and total number of residues: ALA 0 18 ASP 0 9 GLU 0 11 PHE 1 4 GLY 0 10 HIS 0 3 ILE 0 3 LYS 0 4 LEU 0 17 MET 0 1 ASN 0 1 PRO 0 4 GLN 0 5 ARG 0 7 SER 0 5 THR 0 3 VAL 0 6 TRP 0 3 TYR 1 2 Processing NMR model 16 ** Unrecognized atom type [ O2 ] in residue GLU A 116 Average value of CA-N-C-CB angle is 34.02 Standard deviation is 0.88 * 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 = 1771 old number = 0 * PHE A 50 TYR A 85 Total number of residues that need to be changed and total number of residues: ALA 0 18 ASP 0 9 GLU 0 11 PHE 1 4 GLY 0 10 HIS 0 3 ILE 0 3 LYS 0 4 LEU 0 17 MET 0 1 ASN 0 1 PRO 0 4 GLN 0 5 ARG 0 7 SER 0 5 THR 0 3 VAL 0 6 TRP 0 3 TYR 1 2 Processing NMR model 17 ** Unrecognized atom type [ O2 ] in residue GLU A 116 Average value of CA-N-C-CB angle is 34.07 Standard deviation is 0.96 * 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 = 1771 old number = 0 * PHE A 33 PHE A 50 Total number of residues that need to be changed and total number of residues: ALA 0 18 ASP 0 9 GLU 0 11 PHE 2 4 GLY 0 10 HIS 0 3 ILE 0 3 LYS 0 4 LEU 0 17 MET 0 1 ASN 0 1 PRO 0 4 GLN 0 5 ARG 0 7 SER 0 5 THR 0 3 VAL 0 6 TRP 0 3 TYR 0 2 Processing NMR model 18 ** Unrecognized atom type [ O2 ] in residue GLU A 116 Average value of CA-N-C-CB angle is 34.05 Standard deviation is 0.88 * 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 = 1771 old number = 0 * PHE A 33 PHE A 81 TYR A 85 Total number of residues that need to be changed and total number of residues: ALA 0 18 ASP 0 9 GLU 0 11 PHE 2 4 GLY 0 10 HIS 0 3 ILE 0 3 LYS 0 4 LEU 0 17 MET 0 1 ASN 0 1 PRO 0 4 GLN 0 5 ARG 0 7 SER 0 5 THR 0 3 VAL 0 6 TRP 0 3 TYR 1 2 Processing NMR model 19 ** Unrecognized atom type [ O2 ] in residue GLU A 116 Average value of CA-N-C-CB angle is 34.04 Standard deviation is 1.01 * 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 = 1771 old number = 0 * PHE A 33 PHE A 50 PHE A 81 Total number of residues that need to be changed and total number of residues: ALA 0 18 ASP 0 9 GLU 0 11 PHE 3 4 GLY 0 10 HIS 0 3 ILE 0 3 LYS 0 4 LEU 0 17 MET 0 1 ASN 0 1 PRO 0 4 GLN 0 5 ARG 0 7 SER 0 5 THR 0 3 VAL 0 6 TRP 0 3 TYR 0 2 Processing NMR model 20 ** Unrecognized atom type [ O2 ] in residue GLU A 116 Average value of CA-N-C-CB angle is 34.03 Standard deviation is 0.90 * 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 = 1771 old number = 0 * PHE A 33 PHE A 50 PHE A 81 Total number of residues that need to be changed and total number of residues: ALA 0 18 ASP 0 9 GLU 0 11 PHE 3 4 GLY 0 10 HIS 0 3 ILE 0 3 LYS 0 4 LEU 0 17 MET 0 1 ASN 0 1 PRO 0 4 GLN 0 5 ARG 0 7 SER 0 5 THR 0 3 VAL 0 6 TRP 0 3 TYR 0 2 * NMR ensemble comprises 20 model structures * Program completed