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 MET A 83 Average value of CA-N-C-CB angle is 34.26 Standard deviation is 1.08 * 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 = 1331 old number = 0 * TYR A 57 TYR A 58 Total number of residues that need to be changed and total number of residues: ALA 0 5 CYS 0 2 ASP 0 3 GLU 0 3 PHE 0 2 GLY 0 2 HIS 0 9 ILE 0 2 LYS 0 8 LEU 0 6 MET 0 6 ASN 0 4 PRO 0 3 GLN 0 4 ARG 0 2 SER 0 10 THR 0 4 VAL 0 3 TRP 0 2 TYR 2 3 Processing NMR model 2 ** Unrecognized atom type [ O2 ] in residue MET A 83 Average value of CA-N-C-CB angle is 34.25 Standard deviation is 1.13 * 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 = 1331 old number = 0 * TYR A 57 Total number of residues that need to be changed and total number of residues: ALA 0 5 CYS 0 2 ASP 0 3 GLU 0 3 PHE 0 2 GLY 0 2 HIS 0 9 ILE 0 2 LYS 0 8 LEU 0 6 MET 0 6 ASN 0 4 PRO 0 3 GLN 0 4 ARG 0 2 SER 0 10 THR 0 4 VAL 0 3 TRP 0 2 TYR 1 3 Processing NMR model 3 ** Unrecognized atom type [ O2 ] in residue MET A 83 Average value of CA-N-C-CB angle is 34.25 Standard deviation is 1.08 * 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 = 1331 old number = 0 * TYR A 57 TYR A 58 Total number of residues that need to be changed and total number of residues: ALA 0 5 CYS 0 2 ASP 0 3 GLU 0 3 PHE 0 2 GLY 0 2 HIS 0 9 ILE 0 2 LYS 0 8 LEU 0 6 MET 0 6 ASN 0 4 PRO 0 3 GLN 0 4 ARG 0 2 SER 0 10 THR 0 4 VAL 0 3 TRP 0 2 TYR 2 3 Processing NMR model 4 ** Unrecognized atom type [ O2 ] in residue MET A 83 Average value of CA-N-C-CB angle is 34.26 Standard deviation is 1.16 * 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 = 1331 old number = 0 * TYR A 57 Total number of residues that need to be changed and total number of residues: ALA 0 5 CYS 0 2 ASP 0 3 GLU 0 3 PHE 0 2 GLY 0 2 HIS 0 9 ILE 0 2 LYS 0 8 LEU 0 6 MET 0 6 ASN 0 4 PRO 0 3 GLN 0 4 ARG 0 2 SER 0 10 THR 0 4 VAL 0 3 TRP 0 2 TYR 1 3 Processing NMR model 5 ** Unrecognized atom type [ O2 ] in residue MET A 83 Average value of CA-N-C-CB angle is 34.28 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 = 1331 old number = 0 * TYR A 57 TYR A 58 Total number of residues that need to be changed and total number of residues: ALA 0 5 CYS 0 2 ASP 0 3 GLU 0 3 PHE 0 2 GLY 0 2 HIS 0 9 ILE 0 2 LYS 0 8 LEU 0 6 MET 0 6 ASN 0 4 PRO 0 3 GLN 0 4 ARG 0 2 SER 0 10 THR 0 4 VAL 0 3 TRP 0 2 TYR 2 3 Processing NMR model 6 ** Unrecognized atom type [ O2 ] in residue MET A 83 Average value of CA-N-C-CB angle is 34.27 Standard deviation is 1.13 * 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 = 1331 old number = 0 * TYR A 57 Total number of residues that need to be changed and total number of residues: ALA 0 5 CYS 0 2 ASP 0 3 GLU 0 3 PHE 0 2 GLY 0 2 HIS 0 9 ILE 0 2 LYS 0 8 LEU 0 6 MET 0 6 ASN 0 4 PRO 0 3 GLN 0 4 ARG 0 2 SER 0 10 THR 0 4 VAL 0 3 TRP 0 2 TYR 1 3 Processing NMR model 7 ** Unrecognized atom type [ O2 ] in residue MET A 83 Average value of CA-N-C-CB angle is 34.24 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 = 1331 old number = 0 * TYR A 57 Total number of residues that need to be changed and total number of residues: ALA 0 5 CYS 0 2 ASP 0 3 GLU 0 3 PHE 0 2 GLY 0 2 HIS 0 9 ILE 0 2 LYS 0 8 LEU 0 6 MET 0 6 ASN 0 4 PRO 0 3 GLN 0 4 ARG 0 2 SER 0 10 THR 0 4 VAL 0 3 TRP 0 2 TYR 1 3 Processing NMR model 8 ** Unrecognized atom type [ O2 ] in residue MET A 83 Average value of CA-N-C-CB angle is 34.25 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 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 1331 old number = 0 * TYR A 57 TYR A 58 PHE A 69 Total number of residues that need to be changed and total number of residues: ALA 0 5 CYS 0 2 ASP 0 3 GLU 0 3 PHE 1 2 GLY 0 2 HIS 0 9 ILE 0 2 LYS 0 8 LEU 0 6 MET 0 6 ASN 0 4 PRO 0 3 GLN 0 4 ARG 0 2 SER 0 10 THR 0 4 VAL 0 3 TRP 0 2 TYR 2 3 Processing NMR model 9 ** Unrecognized atom type [ O2 ] in residue MET A 83 Average value of CA-N-C-CB angle is 34.24 Standard deviation is 1.07 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 1331 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 5 CYS 0 2 ASP 0 3 GLU 0 3 PHE 0 2 GLY 0 2 HIS 0 9 ILE 0 2 LYS 0 8 LEU 0 6 MET 0 6 ASN 0 4 PRO 0 3 GLN 0 4 ARG 0 2 SER 0 10 THR 0 4 VAL 0 3 TRP 0 2 TYR 0 3 Processing NMR model 10 ** Unrecognized atom type [ O2 ] in residue MET A 83 Average value of CA-N-C-CB angle is 34.27 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 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 1331 old number = 0 * TYR A 57 TYR A 58 TYR A 73 Total number of residues that need to be changed and total number of residues: ALA 0 5 CYS 0 2 ASP 0 3 GLU 0 3 PHE 0 2 GLY 0 2 HIS 0 9 ILE 0 2 LYS 0 8 LEU 0 6 MET 0 6 ASN 0 4 PRO 0 3 GLN 0 4 ARG 0 2 SER 0 10 THR 0 4 VAL 0 3 TRP 0 2 TYR 3 3 Processing NMR model 11 ** Unrecognized atom type [ O2 ] in residue MET A 83 Average value of CA-N-C-CB angle is 34.26 Standard deviation is 1.18 * 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 = 1331 old number = 0 * TYR A 57 Total number of residues that need to be changed and total number of residues: ALA 0 5 CYS 0 2 ASP 0 3 GLU 0 3 PHE 0 2 GLY 0 2 HIS 0 9 ILE 0 2 LYS 0 8 LEU 0 6 MET 0 6 ASN 0 4 PRO 0 3 GLN 0 4 ARG 0 2 SER 0 10 THR 0 4 VAL 0 3 TRP 0 2 TYR 1 3 Processing NMR model 12 ** Unrecognized atom type [ O2 ] in residue MET A 83 Average value of CA-N-C-CB angle is 34.22 Standard deviation is 1.09 * 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 = 1331 old number = 0 * TYR A 57 Total number of residues that need to be changed and total number of residues: ALA 0 5 CYS 0 2 ASP 0 3 GLU 0 3 PHE 0 2 GLY 0 2 HIS 0 9 ILE 0 2 LYS 0 8 LEU 0 6 MET 0 6 ASN 0 4 PRO 0 3 GLN 0 4 ARG 0 2 SER 0 10 THR 0 4 VAL 0 3 TRP 0 2 TYR 1 3 Processing NMR model 13 ** Unrecognized atom type [ O2 ] in residue MET A 83 Average value of CA-N-C-CB angle is 34.32 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 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 1331 old number = 0 * TYR A 57 Total number of residues that need to be changed and total number of residues: ALA 0 5 CYS 0 2 ASP 0 3 GLU 0 3 PHE 0 2 GLY 0 2 HIS 0 9 ILE 0 2 LYS 0 8 LEU 0 6 MET 0 6 ASN 0 4 PRO 0 3 GLN 0 4 ARG 0 2 SER 0 10 THR 0 4 VAL 0 3 TRP 0 2 TYR 1 3 Processing NMR model 14 ** Unrecognized atom type [ O2 ] in residue MET A 83 Average value of CA-N-C-CB angle is 34.26 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 = 1331 old number = 0 * TYR A 57 PHE A 76 Total number of residues that need to be changed and total number of residues: ALA 0 5 CYS 0 2 ASP 0 3 GLU 0 3 PHE 1 2 GLY 0 2 HIS 0 9 ILE 0 2 LYS 0 8 LEU 0 6 MET 0 6 ASN 0 4 PRO 0 3 GLN 0 4 ARG 0 2 SER 0 10 THR 0 4 VAL 0 3 TRP 0 2 TYR 1 3 Processing NMR model 15 ** Unrecognized atom type [ O2 ] in residue MET A 83 Average value of CA-N-C-CB angle is 34.24 Standard deviation is 1.13 * 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 = 1331 old number = 0 * TYR A 57 Total number of residues that need to be changed and total number of residues: ALA 0 5 CYS 0 2 ASP 0 3 GLU 0 3 PHE 0 2 GLY 0 2 HIS 0 9 ILE 0 2 LYS 0 8 LEU 0 6 MET 0 6 ASN 0 4 PRO 0 3 GLN 0 4 ARG 0 2 SER 0 10 THR 0 4 VAL 0 3 TRP 0 2 TYR 1 3 Processing NMR model 16 ** Unrecognized atom type [ O2 ] in residue MET A 83 Average value of CA-N-C-CB angle is 34.24 Standard deviation is 1.15 * 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 = 1331 old number = 0 * TYR A 57 Total number of residues that need to be changed and total number of residues: ALA 0 5 CYS 0 2 ASP 0 3 GLU 0 3 PHE 0 2 GLY 0 2 HIS 0 9 ILE 0 2 LYS 0 8 LEU 0 6 MET 0 6 ASN 0 4 PRO 0 3 GLN 0 4 ARG 0 2 SER 0 10 THR 0 4 VAL 0 3 TRP 0 2 TYR 1 3 Processing NMR model 17 ** Unrecognized atom type [ O2 ] in residue MET A 83 Average value of CA-N-C-CB angle is 34.24 Standard deviation is 1.13 * 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 = 1331 old number = 0 * TYR A 57 Total number of residues that need to be changed and total number of residues: ALA 0 5 CYS 0 2 ASP 0 3 GLU 0 3 PHE 0 2 GLY 0 2 HIS 0 9 ILE 0 2 LYS 0 8 LEU 0 6 MET 0 6 ASN 0 4 PRO 0 3 GLN 0 4 ARG 0 2 SER 0 10 THR 0 4 VAL 0 3 TRP 0 2 TYR 1 3 Processing NMR model 18 ** Unrecognized atom type [ O2 ] in residue MET A 83 Average value of CA-N-C-CB angle is 34.27 Standard deviation is 1.13 * 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 = 1331 old number = 0 * TYR A 57 Total number of residues that need to be changed and total number of residues: ALA 0 5 CYS 0 2 ASP 0 3 GLU 0 3 PHE 0 2 GLY 0 2 HIS 0 9 ILE 0 2 LYS 0 8 LEU 0 6 MET 0 6 ASN 0 4 PRO 0 3 GLN 0 4 ARG 0 2 SER 0 10 THR 0 4 VAL 0 3 TRP 0 2 TYR 1 3 Processing NMR model 19 ** Unrecognized atom type [ O2 ] in residue MET A 83 Average value of CA-N-C-CB angle is 34.28 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 = 1331 old number = 0 * TYR A 57 PHE A 69 Total number of residues that need to be changed and total number of residues: ALA 0 5 CYS 0 2 ASP 0 3 GLU 0 3 PHE 1 2 GLY 0 2 HIS 0 9 ILE 0 2 LYS 0 8 LEU 0 6 MET 0 6 ASN 0 4 PRO 0 3 GLN 0 4 ARG 0 2 SER 0 10 THR 0 4 VAL 0 3 TRP 0 2 TYR 1 3 Processing NMR model 20 ** Unrecognized atom type [ O2 ] in residue MET A 83 Average value of CA-N-C-CB angle is 34.26 Standard deviation is 1.17 * 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 = 1331 old number = 0 * TYR A 57 Total number of residues that need to be changed and total number of residues: ALA 0 5 CYS 0 2 ASP 0 3 GLU 0 3 PHE 0 2 GLY 0 2 HIS 0 9 ILE 0 2 LYS 0 8 LEU 0 6 MET 0 6 ASN 0 4 PRO 0 3 GLN 0 4 ARG 0 2 SER 0 10 THR 0 4 VAL 0 3 TRP 0 2 TYR 1 3 * NMR ensemble comprises 20 model structures * Program completed