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 LEU A 86 Average value of CA-N-C-CB angle is 34.49 Standard deviation is 1.62 * 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 = 1397 old number = 0 * TYR A 52 Total number of residues that need to be changed and total number of residues: ALA 0 3 CYS 0 3 ASP 0 4 GLU 0 6 PHE 0 1 GLY 0 5 HIS 0 2 ILE 0 5 LYS 0 7 LEU 0 8 MET 0 3 ASN 0 2 PRO 0 8 GLN 0 3 ARG 0 6 SER 0 3 THR 0 4 VAL 0 10 TRP 0 2 TYR 1 1 Processing NMR model 2 ** Unrecognized atom type [ O2 ] in residue LEU A 86 Average value of CA-N-C-CB angle is 34.47 Standard deviation is 1.62 * 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 = 1397 old number = 0 * PHE A 14 TYR A 52 Total number of residues that need to be changed and total number of residues: ALA 0 3 CYS 0 3 ASP 0 4 GLU 0 6 PHE 1 1 GLY 0 5 HIS 0 2 ILE 0 5 LYS 0 7 LEU 0 8 MET 0 3 ASN 0 2 PRO 0 8 GLN 0 3 ARG 0 6 SER 0 3 THR 0 4 VAL 0 10 TRP 0 2 TYR 1 1 Processing NMR model 3 ** Unrecognized atom type [ O2 ] in residue LEU A 86 Average value of CA-N-C-CB angle is 34.53 Standard deviation is 1.62 * 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 = 1397 old number = 0 * PHE A 14 TYR A 52 Total number of residues that need to be changed and total number of residues: ALA 0 3 CYS 0 3 ASP 0 4 GLU 0 6 PHE 1 1 GLY 0 5 HIS 0 2 ILE 0 5 LYS 0 7 LEU 0 8 MET 0 3 ASN 0 2 PRO 0 8 GLN 0 3 ARG 0 6 SER 0 3 THR 0 4 VAL 0 10 TRP 0 2 TYR 1 1 Processing NMR model 4 ** Unrecognized atom type [ O2 ] in residue LEU A 86 Average value of CA-N-C-CB angle is 34.44 Standard deviation is 1.58 * 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 = 1397 old number = 0 * TYR A 52 Total number of residues that need to be changed and total number of residues: ALA 0 3 CYS 0 3 ASP 0 4 GLU 0 6 PHE 0 1 GLY 0 5 HIS 0 2 ILE 0 5 LYS 0 7 LEU 0 8 MET 0 3 ASN 0 2 PRO 0 8 GLN 0 3 ARG 0 6 SER 0 3 THR 0 4 VAL 0 10 TRP 0 2 TYR 1 1 Processing NMR model 5 ** Unrecognized atom type [ O2 ] in residue LEU A 86 Average value of CA-N-C-CB angle is 34.43 Standard deviation is 1.53 * 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 = 1397 old number = 0 * PHE A 14 TYR A 52 Total number of residues that need to be changed and total number of residues: ALA 0 3 CYS 0 3 ASP 0 4 GLU 0 6 PHE 1 1 GLY 0 5 HIS 0 2 ILE 0 5 LYS 0 7 LEU 0 8 MET 0 3 ASN 0 2 PRO 0 8 GLN 0 3 ARG 0 6 SER 0 3 THR 0 4 VAL 0 10 TRP 0 2 TYR 1 1 Processing NMR model 6 ** Unrecognized atom type [ O2 ] in residue LEU A 86 Average value of CA-N-C-CB angle is 34.45 Standard deviation is 1.53 * 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 = 1397 old number = 0 * PHE A 14 Total number of residues that need to be changed and total number of residues: ALA 0 3 CYS 0 3 ASP 0 4 GLU 0 6 PHE 1 1 GLY 0 5 HIS 0 2 ILE 0 5 LYS 0 7 LEU 0 8 MET 0 3 ASN 0 2 PRO 0 8 GLN 0 3 ARG 0 6 SER 0 3 THR 0 4 VAL 0 10 TRP 0 2 TYR 0 1 Processing NMR model 7 ** Unrecognized atom type [ O2 ] in residue LEU A 86 Average value of CA-N-C-CB angle is 34.45 Standard deviation is 1.56 * 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 = 1397 old number = 0 * TYR A 52 Total number of residues that need to be changed and total number of residues: ALA 0 3 CYS 0 3 ASP 0 4 GLU 0 6 PHE 0 1 GLY 0 5 HIS 0 2 ILE 0 5 LYS 0 7 LEU 0 8 MET 0 3 ASN 0 2 PRO 0 8 GLN 0 3 ARG 0 6 SER 0 3 THR 0 4 VAL 0 10 TRP 0 2 TYR 1 1 Processing NMR model 8 ** Unrecognized atom type [ O2 ] in residue LEU A 86 Average value of CA-N-C-CB angle is 34.47 Standard deviation is 1.64 * 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 = 1397 old number = 0 * TYR A 52 Total number of residues that need to be changed and total number of residues: ALA 0 3 CYS 0 3 ASP 0 4 GLU 0 6 PHE 0 1 GLY 0 5 HIS 0 2 ILE 0 5 LYS 0 7 LEU 0 8 MET 0 3 ASN 0 2 PRO 0 8 GLN 0 3 ARG 0 6 SER 0 3 THR 0 4 VAL 0 10 TRP 0 2 TYR 1 1 Processing NMR model 9 ** Unrecognized atom type [ O2 ] in residue LEU A 86 Average value of CA-N-C-CB angle is 34.46 Standard deviation is 1.59 * 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 = 1397 old number = 0 * TYR A 52 Total number of residues that need to be changed and total number of residues: ALA 0 3 CYS 0 3 ASP 0 4 GLU 0 6 PHE 0 1 GLY 0 5 HIS 0 2 ILE 0 5 LYS 0 7 LEU 0 8 MET 0 3 ASN 0 2 PRO 0 8 GLN 0 3 ARG 0 6 SER 0 3 THR 0 4 VAL 0 10 TRP 0 2 TYR 1 1 Processing NMR model 10 ** Unrecognized atom type [ O2 ] in residue LEU A 86 Average value of CA-N-C-CB angle is 34.46 Standard deviation is 1.55 * 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 = 1397 old number = 0 * PHE A 14 Total number of residues that need to be changed and total number of residues: ALA 0 3 CYS 0 3 ASP 0 4 GLU 0 6 PHE 1 1 GLY 0 5 HIS 0 2 ILE 0 5 LYS 0 7 LEU 0 8 MET 0 3 ASN 0 2 PRO 0 8 GLN 0 3 ARG 0 6 SER 0 3 THR 0 4 VAL 0 10 TRP 0 2 TYR 0 1 Processing NMR model 11 ** Unrecognized atom type [ O2 ] in residue LEU A 86 Average value of CA-N-C-CB angle is 34.48 Standard deviation is 1.60 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 1397 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 3 CYS 0 3 ASP 0 4 GLU 0 6 PHE 0 1 GLY 0 5 HIS 0 2 ILE 0 5 LYS 0 7 LEU 0 8 MET 0 3 ASN 0 2 PRO 0 8 GLN 0 3 ARG 0 6 SER 0 3 THR 0 4 VAL 0 10 TRP 0 2 TYR 0 1 Processing NMR model 12 ** Unrecognized atom type [ O2 ] in residue LEU A 86 Average value of CA-N-C-CB angle is 34.44 Standard deviation is 1.56 * 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 = 1397 old number = 0 * TYR A 52 Total number of residues that need to be changed and total number of residues: ALA 0 3 CYS 0 3 ASP 0 4 GLU 0 6 PHE 0 1 GLY 0 5 HIS 0 2 ILE 0 5 LYS 0 7 LEU 0 8 MET 0 3 ASN 0 2 PRO 0 8 GLN 0 3 ARG 0 6 SER 0 3 THR 0 4 VAL 0 10 TRP 0 2 TYR 1 1 Processing NMR model 13 ** Unrecognized atom type [ O2 ] in residue LEU A 86 Average value of CA-N-C-CB angle is 34.46 Standard deviation is 1.56 * 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 = 1397 old number = 0 * PHE A 14 TYR A 52 Total number of residues that need to be changed and total number of residues: ALA 0 3 CYS 0 3 ASP 0 4 GLU 0 6 PHE 1 1 GLY 0 5 HIS 0 2 ILE 0 5 LYS 0 7 LEU 0 8 MET 0 3 ASN 0 2 PRO 0 8 GLN 0 3 ARG 0 6 SER 0 3 THR 0 4 VAL 0 10 TRP 0 2 TYR 1 1 Processing NMR model 14 ** Unrecognized atom type [ O2 ] in residue LEU A 86 Average value of CA-N-C-CB angle is 34.46 Standard deviation is 1.59 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 1397 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 3 CYS 0 3 ASP 0 4 GLU 0 6 PHE 0 1 GLY 0 5 HIS 0 2 ILE 0 5 LYS 0 7 LEU 0 8 MET 0 3 ASN 0 2 PRO 0 8 GLN 0 3 ARG 0 6 SER 0 3 THR 0 4 VAL 0 10 TRP 0 2 TYR 0 1 Processing NMR model 15 ** Unrecognized atom type [ O2 ] in residue LEU A 86 Average value of CA-N-C-CB angle is 34.48 Standard deviation is 1.66 * 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 = 1397 old number = 0 * PHE A 14 TYR A 52 Total number of residues that need to be changed and total number of residues: ALA 0 3 CYS 0 3 ASP 0 4 GLU 0 6 PHE 1 1 GLY 0 5 HIS 0 2 ILE 0 5 LYS 0 7 LEU 0 8 MET 0 3 ASN 0 2 PRO 0 8 GLN 0 3 ARG 0 6 SER 0 3 THR 0 4 VAL 0 10 TRP 0 2 TYR 1 1 Processing NMR model 16 ** Unrecognized atom type [ O2 ] in residue LEU A 86 Average value of CA-N-C-CB angle is 34.43 Standard deviation is 1.61 * 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 = 1397 old number = 0 * TYR A 52 Total number of residues that need to be changed and total number of residues: ALA 0 3 CYS 0 3 ASP 0 4 GLU 0 6 PHE 0 1 GLY 0 5 HIS 0 2 ILE 0 5 LYS 0 7 LEU 0 8 MET 0 3 ASN 0 2 PRO 0 8 GLN 0 3 ARG 0 6 SER 0 3 THR 0 4 VAL 0 10 TRP 0 2 TYR 1 1 Processing NMR model 17 ** Unrecognized atom type [ O2 ] in residue LEU A 86 Average value of CA-N-C-CB angle is 34.52 Standard deviation is 1.59 * 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 = 1397 old number = 0 * TYR A 52 Total number of residues that need to be changed and total number of residues: ALA 0 3 CYS 0 3 ASP 0 4 GLU 0 6 PHE 0 1 GLY 0 5 HIS 0 2 ILE 0 5 LYS 0 7 LEU 0 8 MET 0 3 ASN 0 2 PRO 0 8 GLN 0 3 ARG 0 6 SER 0 3 THR 0 4 VAL 0 10 TRP 0 2 TYR 1 1 Processing NMR model 18 ** Unrecognized atom type [ O2 ] in residue LEU A 86 Average value of CA-N-C-CB angle is 34.44 Standard deviation is 1.55 * 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 = 1397 old number = 0 * TYR A 52 Total number of residues that need to be changed and total number of residues: ALA 0 3 CYS 0 3 ASP 0 4 GLU 0 6 PHE 0 1 GLY 0 5 HIS 0 2 ILE 0 5 LYS 0 7 LEU 0 8 MET 0 3 ASN 0 2 PRO 0 8 GLN 0 3 ARG 0 6 SER 0 3 THR 0 4 VAL 0 10 TRP 0 2 TYR 1 1 Processing NMR model 19 ** Unrecognized atom type [ O2 ] in residue LEU A 86 Average value of CA-N-C-CB angle is 34.46 Standard deviation is 1.60 * 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 = 1397 old number = 0 * TYR A 52 Total number of residues that need to be changed and total number of residues: ALA 0 3 CYS 0 3 ASP 0 4 GLU 0 6 PHE 0 1 GLY 0 5 HIS 0 2 ILE 0 5 LYS 0 7 LEU 0 8 MET 0 3 ASN 0 2 PRO 0 8 GLN 0 3 ARG 0 6 SER 0 3 THR 0 4 VAL 0 10 TRP 0 2 TYR 1 1 Processing NMR model 20 ** Unrecognized atom type [ O2 ] in residue LEU A 86 Average value of CA-N-C-CB angle is 34.47 Standard deviation is 1.58 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 1397 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 3 CYS 0 3 ASP 0 4 GLU 0 6 PHE 0 1 GLY 0 5 HIS 0 2 ILE 0 5 LYS 0 7 LEU 0 8 MET 0 3 ASN 0 2 PRO 0 8 GLN 0 3 ARG 0 6 SER 0 3 THR 0 4 VAL 0 10 TRP 0 2 TYR 0 1 * NMR ensemble comprises 20 model structures * Program completed