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 109 Average value of CA-N-C-CB angle is 34.27 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 = 1699 old number = 0 * PHE A 18 Total number of residues that need to be changed and total number of residues: ALA 0 8 ASP 0 4 GLU 0 11 PHE 1 4 GLY 0 8 HIS 0 3 ILE 0 5 LYS 0 10 LEU 0 8 MET 0 4 ASN 0 5 PRO 0 6 GLN 0 3 ARG 0 2 SER 0 8 THR 0 5 VAL 0 10 TRP 0 2 TYR 0 3 Processing NMR model 2 ** Unrecognized atom type [ O2 ] in residue HIS A 109 Average value of CA-N-C-CB angle is 34.18 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 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 1699 old number = 0 * TYR A 93 PHE A 94 Total number of residues that need to be changed and total number of residues: ALA 0 8 ASP 0 4 GLU 0 11 PHE 1 4 GLY 0 8 HIS 0 3 ILE 0 5 LYS 0 10 LEU 0 8 MET 0 4 ASN 0 5 PRO 0 6 GLN 0 3 ARG 0 2 SER 0 8 THR 0 5 VAL 0 10 TRP 0 2 TYR 1 3 Processing NMR model 3 ** Unrecognized atom type [ O2 ] in residue HIS A 109 Average value of CA-N-C-CB angle is 34.26 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 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 1699 old number = 0 * PHE A 3 TYR A 93 Total number of residues that need to be changed and total number of residues: ALA 0 8 ASP 0 4 GLU 0 11 PHE 1 4 GLY 0 8 HIS 0 3 ILE 0 5 LYS 0 10 LEU 0 8 MET 0 4 ASN 0 5 PRO 0 6 GLN 0 3 ARG 0 2 SER 0 8 THR 0 5 VAL 0 10 TRP 0 2 TYR 1 3 Processing NMR model 4 ** Unrecognized atom type [ O2 ] in residue HIS A 109 Average value of CA-N-C-CB angle is 34.22 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 = 1699 old number = 0 * PHE A 18 Total number of residues that need to be changed and total number of residues: ALA 0 8 ASP 0 4 GLU 0 11 PHE 1 4 GLY 0 8 HIS 0 3 ILE 0 5 LYS 0 10 LEU 0 8 MET 0 4 ASN 0 5 PRO 0 6 GLN 0 3 ARG 0 2 SER 0 8 THR 0 5 VAL 0 10 TRP 0 2 TYR 0 3 Processing NMR model 5 ** Unrecognized atom type [ O2 ] in residue HIS A 109 Average value of CA-N-C-CB angle is 34.19 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 = 1699 old number = 0 * PHE A 18 TYR A 93 Total number of residues that need to be changed and total number of residues: ALA 0 8 ASP 0 4 GLU 0 11 PHE 1 4 GLY 0 8 HIS 0 3 ILE 0 5 LYS 0 10 LEU 0 8 MET 0 4 ASN 0 5 PRO 0 6 GLN 0 3 ARG 0 2 SER 0 8 THR 0 5 VAL 0 10 TRP 0 2 TYR 1 3 Processing NMR model 6 ** Unrecognized atom type [ O2 ] in residue HIS A 109 Average value of CA-N-C-CB angle is 34.21 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 = 1699 old number = 0 * PHE A 3 TYR A 93 Total number of residues that need to be changed and total number of residues: ALA 0 8 ASP 0 4 GLU 0 11 PHE 1 4 GLY 0 8 HIS 0 3 ILE 0 5 LYS 0 10 LEU 0 8 MET 0 4 ASN 0 5 PRO 0 6 GLN 0 3 ARG 0 2 SER 0 8 THR 0 5 VAL 0 10 TRP 0 2 TYR 1 3 Processing NMR model 7 ** Unrecognized atom type [ O2 ] in residue HIS A 109 Average value of CA-N-C-CB angle is 34.24 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 = 1699 old number = 0 * PHE A 3 Total number of residues that need to be changed and total number of residues: ALA 0 8 ASP 0 4 GLU 0 11 PHE 1 4 GLY 0 8 HIS 0 3 ILE 0 5 LYS 0 10 LEU 0 8 MET 0 4 ASN 0 5 PRO 0 6 GLN 0 3 ARG 0 2 SER 0 8 THR 0 5 VAL 0 10 TRP 0 2 TYR 0 3 Processing NMR model 8 ** Unrecognized atom type [ O2 ] in residue HIS A 109 Average value of CA-N-C-CB angle is 34.21 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 = 1699 old number = 0 * PHE A 18 TYR A 93 PHE A 94 Total number of residues that need to be changed and total number of residues: ALA 0 8 ASP 0 4 GLU 0 11 PHE 2 4 GLY 0 8 HIS 0 3 ILE 0 5 LYS 0 10 LEU 0 8 MET 0 4 ASN 0 5 PRO 0 6 GLN 0 3 ARG 0 2 SER 0 8 THR 0 5 VAL 0 10 TRP 0 2 TYR 1 3 Processing NMR model 9 ** Unrecognized atom type [ O2 ] in residue HIS A 109 Average value of CA-N-C-CB angle is 34.22 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 = 1699 old number = 0 * TYR A 93 PHE A 94 Total number of residues that need to be changed and total number of residues: ALA 0 8 ASP 0 4 GLU 0 11 PHE 1 4 GLY 0 8 HIS 0 3 ILE 0 5 LYS 0 10 LEU 0 8 MET 0 4 ASN 0 5 PRO 0 6 GLN 0 3 ARG 0 2 SER 0 8 THR 0 5 VAL 0 10 TRP 0 2 TYR 1 3 Processing NMR model 10 ** Unrecognized atom type [ O2 ] in residue HIS A 109 Average value of CA-N-C-CB angle is 34.22 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 = 1699 old number = 0 * PHE A 3 PHE A 18 Total number of residues that need to be changed and total number of residues: ALA 0 8 ASP 0 4 GLU 0 11 PHE 2 4 GLY 0 8 HIS 0 3 ILE 0 5 LYS 0 10 LEU 0 8 MET 0 4 ASN 0 5 PRO 0 6 GLN 0 3 ARG 0 2 SER 0 8 THR 0 5 VAL 0 10 TRP 0 2 TYR 0 3 Processing NMR model 11 ** Unrecognized atom type [ O2 ] in residue HIS A 109 Average value of CA-N-C-CB angle is 34.19 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 = 1699 old number = 0 * PHE A 18 TYR A 93 PHE A 94 Total number of residues that need to be changed and total number of residues: ALA 0 8 ASP 0 4 GLU 0 11 PHE 2 4 GLY 0 8 HIS 0 3 ILE 0 5 LYS 0 10 LEU 0 8 MET 0 4 ASN 0 5 PRO 0 6 GLN 0 3 ARG 0 2 SER 0 8 THR 0 5 VAL 0 10 TRP 0 2 TYR 1 3 Processing NMR model 12 ** Unrecognized atom type [ O2 ] in residue HIS A 109 Average value of CA-N-C-CB angle is 34.24 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 = 1699 old number = 0 * TYR A 93 PHE A 94 Total number of residues that need to be changed and total number of residues: ALA 0 8 ASP 0 4 GLU 0 11 PHE 1 4 GLY 0 8 HIS 0 3 ILE 0 5 LYS 0 10 LEU 0 8 MET 0 4 ASN 0 5 PRO 0 6 GLN 0 3 ARG 0 2 SER 0 8 THR 0 5 VAL 0 10 TRP 0 2 TYR 1 3 Processing NMR model 13 ** Unrecognized atom type [ O2 ] in residue HIS A 109 Average value of CA-N-C-CB angle is 34.19 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 = 1699 old number = 0 * PHE A 18 Total number of residues that need to be changed and total number of residues: ALA 0 8 ASP 0 4 GLU 0 11 PHE 1 4 GLY 0 8 HIS 0 3 ILE 0 5 LYS 0 10 LEU 0 8 MET 0 4 ASN 0 5 PRO 0 6 GLN 0 3 ARG 0 2 SER 0 8 THR 0 5 VAL 0 10 TRP 0 2 TYR 0 3 Processing NMR model 14 ** Unrecognized atom type [ O2 ] in residue HIS A 109 Average value of CA-N-C-CB angle is 34.18 Standard deviation is 0.98 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 1699 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 8 ASP 0 4 GLU 0 11 PHE 0 4 GLY 0 8 HIS 0 3 ILE 0 5 LYS 0 10 LEU 0 8 MET 0 4 ASN 0 5 PRO 0 6 GLN 0 3 ARG 0 2 SER 0 8 THR 0 5 VAL 0 10 TRP 0 2 TYR 0 3 Processing NMR model 15 ** Unrecognized atom type [ O2 ] in residue HIS A 109 Average value of CA-N-C-CB angle is 34.24 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 = 1699 old number = 0 * TYR A 93 Total number of residues that need to be changed and total number of residues: ALA 0 8 ASP 0 4 GLU 0 11 PHE 0 4 GLY 0 8 HIS 0 3 ILE 0 5 LYS 0 10 LEU 0 8 MET 0 4 ASN 0 5 PRO 0 6 GLN 0 3 ARG 0 2 SER 0 8 THR 0 5 VAL 0 10 TRP 0 2 TYR 1 3 Processing NMR model 16 ** Unrecognized atom type [ O2 ] in residue HIS A 109 Average value of CA-N-C-CB angle is 34.19 Standard deviation is 1.00 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 1699 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 8 ASP 0 4 GLU 0 11 PHE 0 4 GLY 0 8 HIS 0 3 ILE 0 5 LYS 0 10 LEU 0 8 MET 0 4 ASN 0 5 PRO 0 6 GLN 0 3 ARG 0 2 SER 0 8 THR 0 5 VAL 0 10 TRP 0 2 TYR 0 3 Processing NMR model 17 ** Unrecognized atom type [ O2 ] in residue HIS A 109 Average value of CA-N-C-CB angle is 34.15 Standard deviation is 1.10 * 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 = 1699 old number = 0 * PHE A 18 TYR A 93 Total number of residues that need to be changed and total number of residues: ALA 0 8 ASP 0 4 GLU 0 11 PHE 1 4 GLY 0 8 HIS 0 3 ILE 0 5 LYS 0 10 LEU 0 8 MET 0 4 ASN 0 5 PRO 0 6 GLN 0 3 ARG 0 2 SER 0 8 THR 0 5 VAL 0 10 TRP 0 2 TYR 1 3 Processing NMR model 18 ** Unrecognized atom type [ O2 ] in residue HIS A 109 Average value of CA-N-C-CB angle is 34.25 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 = 1699 old number = 0 * PHE A 3 PHE A 18 TYR A 93 Total number of residues that need to be changed and total number of residues: ALA 0 8 ASP 0 4 GLU 0 11 PHE 2 4 GLY 0 8 HIS 0 3 ILE 0 5 LYS 0 10 LEU 0 8 MET 0 4 ASN 0 5 PRO 0 6 GLN 0 3 ARG 0 2 SER 0 8 THR 0 5 VAL 0 10 TRP 0 2 TYR 1 3 * NMR ensemble comprises 18 model structures * Program completed