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 108 Average value of CA-N-C-CB angle is 34.16 Standard deviation is 0.94 * 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 = 1688 old number = 0 * PHE A 3 PHE A 67 Total number of residues that need to be changed and total number of residues: ALA 0 3 ASP 0 4 GLU 0 12 PHE 2 3 GLY 0 8 HIS 0 1 ILE 0 4 LYS 0 7 LEU 0 8 MET 0 2 ASN 0 10 PRO 0 5 GLN 0 1 ARG 0 2 SER 0 4 THR 0 10 VAL 0 18 TRP 0 2 TYR 0 4 Processing NMR model 2 ** Unrecognized atom type [ O2 ] in residue GLU A 108 Average value of CA-N-C-CB angle is 34.16 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 = 1688 old number = 0 * PHE A 3 TYR A 24 PHE A 67 Total number of residues that need to be changed and total number of residues: ALA 0 3 ASP 0 4 GLU 0 12 PHE 2 3 GLY 0 8 HIS 0 1 ILE 0 4 LYS 0 7 LEU 0 8 MET 0 2 ASN 0 10 PRO 0 5 GLN 0 1 ARG 0 2 SER 0 4 THR 0 10 VAL 0 18 TRP 0 2 TYR 1 4 Processing NMR model 3 ** Unrecognized atom type [ O2 ] in residue GLU A 108 Average value of CA-N-C-CB angle is 34.18 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 = 1688 old number = 0 * PHE A 3 PHE A 67 PHE A 101 Total number of residues that need to be changed and total number of residues: ALA 0 3 ASP 0 4 GLU 0 12 PHE 3 3 GLY 0 8 HIS 0 1 ILE 0 4 LYS 0 7 LEU 0 8 MET 0 2 ASN 0 10 PRO 0 5 GLN 0 1 ARG 0 2 SER 0 4 THR 0 10 VAL 0 18 TRP 0 2 TYR 0 4 Processing NMR model 4 ** Unrecognized atom type [ O2 ] in residue GLU A 108 Average value of CA-N-C-CB angle is 34.17 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 = 1688 old number = 0 * TYR A 24 PHE A 67 Total number of residues that need to be changed and total number of residues: ALA 0 3 ASP 0 4 GLU 0 12 PHE 1 3 GLY 0 8 HIS 0 1 ILE 0 4 LYS 0 7 LEU 0 8 MET 0 2 ASN 0 10 PRO 0 5 GLN 0 1 ARG 0 2 SER 0 4 THR 0 10 VAL 0 18 TRP 0 2 TYR 1 4 Processing NMR model 5 ** Unrecognized atom type [ O2 ] in residue GLU A 108 Average value of CA-N-C-CB angle is 34.19 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 = 1688 old number = 0 * PHE A 3 PHE A 67 Total number of residues that need to be changed and total number of residues: ALA 0 3 ASP 0 4 GLU 0 12 PHE 2 3 GLY 0 8 HIS 0 1 ILE 0 4 LYS 0 7 LEU 0 8 MET 0 2 ASN 0 10 PRO 0 5 GLN 0 1 ARG 0 2 SER 0 4 THR 0 10 VAL 0 18 TRP 0 2 TYR 0 4 Processing NMR model 6 ** Unrecognized atom type [ O2 ] in residue GLU A 108 Average value of CA-N-C-CB angle is 34.16 Standard deviation is 0.99 * 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 = 1688 old number = 0 * PHE A 3 PHE A 67 Total number of residues that need to be changed and total number of residues: ALA 0 3 ASP 0 4 GLU 0 12 PHE 2 3 GLY 0 8 HIS 0 1 ILE 0 4 LYS 0 7 LEU 0 8 MET 0 2 ASN 0 10 PRO 0 5 GLN 0 1 ARG 0 2 SER 0 4 THR 0 10 VAL 0 18 TRP 0 2 TYR 0 4 Processing NMR model 7 ** Unrecognized atom type [ O2 ] in residue GLU A 108 Average value of CA-N-C-CB angle is 34.15 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 = 1688 old number = 0 * PHE A 3 TYR A 24 TYR A 44 PHE A 67 Total number of residues that need to be changed and total number of residues: ALA 0 3 ASP 0 4 GLU 0 12 PHE 2 3 GLY 0 8 HIS 0 1 ILE 0 4 LYS 0 7 LEU 0 8 MET 0 2 ASN 0 10 PRO 0 5 GLN 0 1 ARG 0 2 SER 0 4 THR 0 10 VAL 0 18 TRP 0 2 TYR 2 4 Processing NMR model 8 ** Unrecognized atom type [ O2 ] in residue GLU A 108 Average value of CA-N-C-CB angle is 34.20 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 = 1688 old number = 0 * PHE A 3 PHE A 67 Total number of residues that need to be changed and total number of residues: ALA 0 3 ASP 0 4 GLU 0 12 PHE 2 3 GLY 0 8 HIS 0 1 ILE 0 4 LYS 0 7 LEU 0 8 MET 0 2 ASN 0 10 PRO 0 5 GLN 0 1 ARG 0 2 SER 0 4 THR 0 10 VAL 0 18 TRP 0 2 TYR 0 4 Processing NMR model 9 ** Unrecognized atom type [ O2 ] in residue GLU A 108 Average value of CA-N-C-CB angle is 34.13 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 = 1688 old number = 0 * PHE A 3 TYR A 24 PHE A 67 Total number of residues that need to be changed and total number of residues: ALA 0 3 ASP 0 4 GLU 0 12 PHE 2 3 GLY 0 8 HIS 0 1 ILE 0 4 LYS 0 7 LEU 0 8 MET 0 2 ASN 0 10 PRO 0 5 GLN 0 1 ARG 0 2 SER 0 4 THR 0 10 VAL 0 18 TRP 0 2 TYR 1 4 Processing NMR model 10 ** Unrecognized atom type [ O2 ] in residue GLU A 108 Average value of CA-N-C-CB angle is 34.16 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 = 1688 old number = 0 * PHE A 3 TYR A 24 PHE A 67 Total number of residues that need to be changed and total number of residues: ALA 0 3 ASP 0 4 GLU 0 12 PHE 2 3 GLY 0 8 HIS 0 1 ILE 0 4 LYS 0 7 LEU 0 8 MET 0 2 ASN 0 10 PRO 0 5 GLN 0 1 ARG 0 2 SER 0 4 THR 0 10 VAL 0 18 TRP 0 2 TYR 1 4 Processing NMR model 11 ** Unrecognized atom type [ O2 ] in residue GLU A 108 Average value of CA-N-C-CB angle is 34.16 Standard deviation is 0.99 * 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 = 1688 old number = 0 * PHE A 3 PHE A 67 Total number of residues that need to be changed and total number of residues: ALA 0 3 ASP 0 4 GLU 0 12 PHE 2 3 GLY 0 8 HIS 0 1 ILE 0 4 LYS 0 7 LEU 0 8 MET 0 2 ASN 0 10 PRO 0 5 GLN 0 1 ARG 0 2 SER 0 4 THR 0 10 VAL 0 18 TRP 0 2 TYR 0 4 Processing NMR model 12 ** Unrecognized atom type [ O2 ] in residue GLU A 108 Average value of CA-N-C-CB angle is 34.12 Standard deviation is 0.89 * 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 = 1688 old number = 0 * PHE A 3 TYR A 24 PHE A 67 Total number of residues that need to be changed and total number of residues: ALA 0 3 ASP 0 4 GLU 0 12 PHE 2 3 GLY 0 8 HIS 0 1 ILE 0 4 LYS 0 7 LEU 0 8 MET 0 2 ASN 0 10 PRO 0 5 GLN 0 1 ARG 0 2 SER 0 4 THR 0 10 VAL 0 18 TRP 0 2 TYR 1 4 Processing NMR model 13 ** Unrecognized atom type [ O2 ] in residue GLU A 108 Average value of CA-N-C-CB angle is 34.13 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 = 1688 old number = 0 * PHE A 3 PHE A 67 Total number of residues that need to be changed and total number of residues: ALA 0 3 ASP 0 4 GLU 0 12 PHE 2 3 GLY 0 8 HIS 0 1 ILE 0 4 LYS 0 7 LEU 0 8 MET 0 2 ASN 0 10 PRO 0 5 GLN 0 1 ARG 0 2 SER 0 4 THR 0 10 VAL 0 18 TRP 0 2 TYR 0 4 Processing NMR model 14 ** Unrecognized atom type [ O2 ] in residue GLU A 108 Average value of CA-N-C-CB angle is 34.14 Standard deviation is 0.94 * 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 = 1688 old number = 0 * PHE A 3 TYR A 24 PHE A 67 Total number of residues that need to be changed and total number of residues: ALA 0 3 ASP 0 4 GLU 0 12 PHE 2 3 GLY 0 8 HIS 0 1 ILE 0 4 LYS 0 7 LEU 0 8 MET 0 2 ASN 0 10 PRO 0 5 GLN 0 1 ARG 0 2 SER 0 4 THR 0 10 VAL 0 18 TRP 0 2 TYR 1 4 Processing NMR model 15 ** Unrecognized atom type [ O2 ] in residue GLU A 108 Average value of CA-N-C-CB angle is 34.15 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 = 1688 old number = 0 * PHE A 3 TYR A 24 PHE A 67 TYR A 77 Total number of residues that need to be changed and total number of residues: ALA 0 3 ASP 0 4 GLU 0 12 PHE 2 3 GLY 0 8 HIS 0 1 ILE 0 4 LYS 0 7 LEU 0 8 MET 0 2 ASN 0 10 PRO 0 5 GLN 0 1 ARG 0 2 SER 0 4 THR 0 10 VAL 0 18 TRP 0 2 TYR 2 4 Processing NMR model 16 ** Unrecognized atom type [ O2 ] in residue GLU A 108 Average value of CA-N-C-CB angle is 34.17 Standard deviation is 0.98 * 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 = 1688 old number = 0 * PHE A 67 Total number of residues that need to be changed and total number of residues: ALA 0 3 ASP 0 4 GLU 0 12 PHE 1 3 GLY 0 8 HIS 0 1 ILE 0 4 LYS 0 7 LEU 0 8 MET 0 2 ASN 0 10 PRO 0 5 GLN 0 1 ARG 0 2 SER 0 4 THR 0 10 VAL 0 18 TRP 0 2 TYR 0 4 Processing NMR model 17 ** Unrecognized atom type [ O2 ] in residue GLU A 108 Average value of CA-N-C-CB angle is 34.18 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 = 1688 old number = 0 * PHE A 3 PHE A 67 Total number of residues that need to be changed and total number of residues: ALA 0 3 ASP 0 4 GLU 0 12 PHE 2 3 GLY 0 8 HIS 0 1 ILE 0 4 LYS 0 7 LEU 0 8 MET 0 2 ASN 0 10 PRO 0 5 GLN 0 1 ARG 0 2 SER 0 4 THR 0 10 VAL 0 18 TRP 0 2 TYR 0 4 Processing NMR model 18 ** Unrecognized atom type [ O2 ] in residue GLU A 108 Average value of CA-N-C-CB angle is 34.15 Standard deviation is 0.94 * 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 = 1688 old number = 0 * PHE A 3 TYR A 24 PHE A 67 Total number of residues that need to be changed and total number of residues: ALA 0 3 ASP 0 4 GLU 0 12 PHE 2 3 GLY 0 8 HIS 0 1 ILE 0 4 LYS 0 7 LEU 0 8 MET 0 2 ASN 0 10 PRO 0 5 GLN 0 1 ARG 0 2 SER 0 4 THR 0 10 VAL 0 18 TRP 0 2 TYR 1 4 Processing NMR model 19 ** Unrecognized atom type [ O2 ] in residue GLU A 108 Average value of CA-N-C-CB angle is 34.16 Standard deviation is 0.99 * 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 = 1688 old number = 0 * PHE A 3 TYR A 24 TYR A 44 PHE A 67 Total number of residues that need to be changed and total number of residues: ALA 0 3 ASP 0 4 GLU 0 12 PHE 2 3 GLY 0 8 HIS 0 1 ILE 0 4 LYS 0 7 LEU 0 8 MET 0 2 ASN 0 10 PRO 0 5 GLN 0 1 ARG 0 2 SER 0 4 THR 0 10 VAL 0 18 TRP 0 2 TYR 2 4 Processing NMR model 20 ** Unrecognized atom type [ O2 ] in residue GLU A 108 Average value of CA-N-C-CB angle is 34.17 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 = 1688 old number = 0 * PHE A 3 PHE A 67 PHE A 101 Total number of residues that need to be changed and total number of residues: ALA 0 3 ASP 0 4 GLU 0 12 PHE 3 3 GLY 0 8 HIS 0 1 ILE 0 4 LYS 0 7 LEU 0 8 MET 0 2 ASN 0 10 PRO 0 5 GLN 0 1 ARG 0 2 SER 0 4 THR 0 10 VAL 0 18 TRP 0 2 TYR 0 4 * NMR ensemble comprises 20 model structures * Program completed