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 125 Average value of CA-N-C-CB angle is 34.07 Standard deviation is 1.19 * 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 = 2070 old number = 0 * PHE A 6 PHE A 25 Total number of residues that need to be changed and total number of residues: ALA 0 6 ASP 0 11 GLU 0 7 PHE 2 4 GLY 0 6 HIS 0 11 ILE 0 9 LYS 0 12 LEU 0 11 MET 0 3 ASN 0 5 PRO 0 8 GLN 0 5 ARG 0 5 SER 0 4 THR 0 3 VAL 0 6 TRP 0 3 TYR 0 6 Processing NMR model 2 ** Unrecognized atom type [ O2 ] in residue HIS A 125 Average value of CA-N-C-CB angle is 34.23 Standard deviation is 1.25 * 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 = 2070 old number = 0 * PHE A 25 PHE A 31 TYR A 40 TYR A 81 TYR A 84 Total number of residues that need to be changed and total number of residues: ALA 0 6 ASP 0 11 GLU 0 7 PHE 2 4 GLY 0 6 HIS 0 11 ILE 0 9 LYS 0 12 LEU 0 11 MET 0 3 ASN 0 5 PRO 0 8 GLN 0 5 ARG 0 5 SER 0 4 THR 0 3 VAL 0 6 TRP 0 3 TYR 3 6 Processing NMR model 3 ** Unrecognized atom type [ O2 ] in residue HIS A 125 Average value of CA-N-C-CB angle is 34.16 Standard deviation is 1.24 * 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 = 2070 old number = 0 * PHE A 6 TYR A 14 PHE A 25 PHE A 31 Total number of residues that need to be changed and total number of residues: ALA 0 6 ASP 0 11 GLU 0 7 PHE 3 4 GLY 0 6 HIS 0 11 ILE 0 9 LYS 0 12 LEU 0 11 MET 0 3 ASN 0 5 PRO 0 8 GLN 0 5 ARG 0 5 SER 0 4 THR 0 3 VAL 0 6 TRP 0 3 TYR 1 6 Processing NMR model 4 ** Unrecognized atom type [ O2 ] in residue HIS A 125 Average value of CA-N-C-CB angle is 34.12 Standard deviation is 1.22 * 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 = 2070 old number = 0 * TYR A 14 PHE A 25 TYR A 81 Total number of residues that need to be changed and total number of residues: ALA 0 6 ASP 0 11 GLU 0 7 PHE 1 4 GLY 0 6 HIS 0 11 ILE 0 9 LYS 0 12 LEU 0 11 MET 0 3 ASN 0 5 PRO 0 8 GLN 0 5 ARG 0 5 SER 0 4 THR 0 3 VAL 0 6 TRP 0 3 TYR 2 6 Processing NMR model 5 ** Unrecognized atom type [ O2 ] in residue HIS A 125 Average value of CA-N-C-CB angle is 34.11 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 = 2070 old number = 0 * TYR A 14 PHE A 25 TYR A 84 Total number of residues that need to be changed and total number of residues: ALA 0 6 ASP 0 11 GLU 0 7 PHE 1 4 GLY 0 6 HIS 0 11 ILE 0 9 LYS 0 12 LEU 0 11 MET 0 3 ASN 0 5 PRO 0 8 GLN 0 5 ARG 0 5 SER 0 4 THR 0 3 VAL 0 6 TRP 0 3 TYR 2 6 Processing NMR model 6 ** Unrecognized atom type [ O2 ] in residue HIS A 125 Average value of CA-N-C-CB angle is 34.12 Standard deviation is 1.19 * 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 = 2070 old number = 0 * PHE A 6 PHE A 25 PHE A 31 Total number of residues that need to be changed and total number of residues: ALA 0 6 ASP 0 11 GLU 0 7 PHE 3 4 GLY 0 6 HIS 0 11 ILE 0 9 LYS 0 12 LEU 0 11 MET 0 3 ASN 0 5 PRO 0 8 GLN 0 5 ARG 0 5 SER 0 4 THR 0 3 VAL 0 6 TRP 0 3 TYR 0 6 Processing NMR model 7 ** Unrecognized atom type [ O2 ] in residue HIS A 125 Average value of CA-N-C-CB angle is 34.29 Standard deviation is 1.28 * 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 = 2070 old number = 0 * TYR A 14 PHE A 25 TYR A 84 Total number of residues that need to be changed and total number of residues: ALA 0 6 ASP 0 11 GLU 0 7 PHE 1 4 GLY 0 6 HIS 0 11 ILE 0 9 LYS 0 12 LEU 0 11 MET 0 3 ASN 0 5 PRO 0 8 GLN 0 5 ARG 0 5 SER 0 4 THR 0 3 VAL 0 6 TRP 0 3 TYR 2 6 Processing NMR model 8 ** Unrecognized atom type [ O2 ] in residue HIS A 125 Average value of CA-N-C-CB angle is 34.14 Standard deviation is 1.21 * 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 = 2070 old number = 0 * PHE A 25 PHE A 31 TYR A 84 Total number of residues that need to be changed and total number of residues: ALA 0 6 ASP 0 11 GLU 0 7 PHE 2 4 GLY 0 6 HIS 0 11 ILE 0 9 LYS 0 12 LEU 0 11 MET 0 3 ASN 0 5 PRO 0 8 GLN 0 5 ARG 0 5 SER 0 4 THR 0 3 VAL 0 6 TRP 0 3 TYR 1 6 Processing NMR model 9 ** Unrecognized atom type [ O2 ] in residue HIS A 125 Average value of CA-N-C-CB angle is 34.16 Standard deviation is 1.22 * 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 = 2070 old number = 0 * TYR A 14 PHE A 25 PHE A 31 TYR A 84 Total number of residues that need to be changed and total number of residues: ALA 0 6 ASP 0 11 GLU 0 7 PHE 2 4 GLY 0 6 HIS 0 11 ILE 0 9 LYS 0 12 LEU 0 11 MET 0 3 ASN 0 5 PRO 0 8 GLN 0 5 ARG 0 5 SER 0 4 THR 0 3 VAL 0 6 TRP 0 3 TYR 2 6 Processing NMR model 10 ** Unrecognized atom type [ O2 ] in residue HIS A 125 Average value of CA-N-C-CB angle is 34.16 Standard deviation is 1.29 * 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 = 2070 old number = 0 * TYR A 14 PHE A 25 TYR A 81 Total number of residues that need to be changed and total number of residues: ALA 0 6 ASP 0 11 GLU 0 7 PHE 1 4 GLY 0 6 HIS 0 11 ILE 0 9 LYS 0 12 LEU 0 11 MET 0 3 ASN 0 5 PRO 0 8 GLN 0 5 ARG 0 5 SER 0 4 THR 0 3 VAL 0 6 TRP 0 3 TYR 2 6 Processing NMR model 11 ** Unrecognized atom type [ O2 ] in residue HIS A 125 Average value of CA-N-C-CB angle is 34.19 Standard deviation is 1.20 * 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 = 2070 old number = 0 * PHE A 25 TYR A 81 TYR A 84 Total number of residues that need to be changed and total number of residues: ALA 0 6 ASP 0 11 GLU 0 7 PHE 1 4 GLY 0 6 HIS 0 11 ILE 0 9 LYS 0 12 LEU 0 11 MET 0 3 ASN 0 5 PRO 0 8 GLN 0 5 ARG 0 5 SER 0 4 THR 0 3 VAL 0 6 TRP 0 3 TYR 2 6 Processing NMR model 12 ** Unrecognized atom type [ O2 ] in residue HIS A 125 Average value of CA-N-C-CB angle is 34.16 Standard deviation is 1.20 * 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 = 2070 old number = 0 * TYR A 14 PHE A 25 TYR A 40 TYR A 81 Total number of residues that need to be changed and total number of residues: ALA 0 6 ASP 0 11 GLU 0 7 PHE 1 4 GLY 0 6 HIS 0 11 ILE 0 9 LYS 0 12 LEU 0 11 MET 0 3 ASN 0 5 PRO 0 8 GLN 0 5 ARG 0 5 SER 0 4 THR 0 3 VAL 0 6 TRP 0 3 TYR 3 6 Processing NMR model 13 ** Unrecognized atom type [ O2 ] in residue HIS A 125 Average value of CA-N-C-CB angle is 34.11 Standard deviation is 1.19 * 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 = 2070 old number = 0 * TYR A 14 PHE A 25 TYR A 81 Total number of residues that need to be changed and total number of residues: ALA 0 6 ASP 0 11 GLU 0 7 PHE 1 4 GLY 0 6 HIS 0 11 ILE 0 9 LYS 0 12 LEU 0 11 MET 0 3 ASN 0 5 PRO 0 8 GLN 0 5 ARG 0 5 SER 0 4 THR 0 3 VAL 0 6 TRP 0 3 TYR 2 6 Processing NMR model 14 ** Unrecognized atom type [ O2 ] in residue HIS A 125 Average value of CA-N-C-CB angle is 34.29 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 = 2070 old number = 0 * PHE A 25 TYR A 81 TYR A 84 Total number of residues that need to be changed and total number of residues: ALA 0 6 ASP 0 11 GLU 0 7 PHE 1 4 GLY 0 6 HIS 0 11 ILE 0 9 LYS 0 12 LEU 0 11 MET 0 3 ASN 0 5 PRO 0 8 GLN 0 5 ARG 0 5 SER 0 4 THR 0 3 VAL 0 6 TRP 0 3 TYR 2 6 Processing NMR model 15 ** Unrecognized atom type [ O2 ] in residue HIS A 125 Average value of CA-N-C-CB angle is 34.22 Standard deviation is 1.25 * 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 = 2070 old number = 0 * TYR A 14 PHE A 25 TYR A 84 Total number of residues that need to be changed and total number of residues: ALA 0 6 ASP 0 11 GLU 0 7 PHE 1 4 GLY 0 6 HIS 0 11 ILE 0 9 LYS 0 12 LEU 0 11 MET 0 3 ASN 0 5 PRO 0 8 GLN 0 5 ARG 0 5 SER 0 4 THR 0 3 VAL 0 6 TRP 0 3 TYR 2 6 Processing NMR model 16 ** Unrecognized atom type [ O2 ] in residue HIS A 125 Average value of CA-N-C-CB angle is 34.11 Standard deviation is 1.19 * 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 = 2070 old number = 0 * PHE A 6 TYR A 14 PHE A 25 PHE A 31 TYR A 84 Total number of residues that need to be changed and total number of residues: ALA 0 6 ASP 0 11 GLU 0 7 PHE 3 4 GLY 0 6 HIS 0 11 ILE 0 9 LYS 0 12 LEU 0 11 MET 0 3 ASN 0 5 PRO 0 8 GLN 0 5 ARG 0 5 SER 0 4 THR 0 3 VAL 0 6 TRP 0 3 TYR 2 6 Processing NMR model 17 ** Unrecognized atom type [ O2 ] in residue HIS A 125 Average value of CA-N-C-CB angle is 34.14 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 = 2070 old number = 0 * PHE A 6 TYR A 14 PHE A 25 PHE A 31 Total number of residues that need to be changed and total number of residues: ALA 0 6 ASP 0 11 GLU 0 7 PHE 3 4 GLY 0 6 HIS 0 11 ILE 0 9 LYS 0 12 LEU 0 11 MET 0 3 ASN 0 5 PRO 0 8 GLN 0 5 ARG 0 5 SER 0 4 THR 0 3 VAL 0 6 TRP 0 3 TYR 1 6 Processing NMR model 18 ** Unrecognized atom type [ O2 ] in residue HIS A 125 Average value of CA-N-C-CB angle is 34.15 Standard deviation is 1.25 * 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 = 2070 old number = 0 * PHE A 25 TYR A 40 Total number of residues that need to be changed and total number of residues: ALA 0 6 ASP 0 11 GLU 0 7 PHE 1 4 GLY 0 6 HIS 0 11 ILE 0 9 LYS 0 12 LEU 0 11 MET 0 3 ASN 0 5 PRO 0 8 GLN 0 5 ARG 0 5 SER 0 4 THR 0 3 VAL 0 6 TRP 0 3 TYR 1 6 Processing NMR model 19 ** Unrecognized atom type [ O2 ] in residue HIS A 125 Average value of CA-N-C-CB angle is 34.21 Standard deviation is 1.24 * 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 = 2070 old number = 0 * PHE A 25 TYR A 81 Total number of residues that need to be changed and total number of residues: ALA 0 6 ASP 0 11 GLU 0 7 PHE 1 4 GLY 0 6 HIS 0 11 ILE 0 9 LYS 0 12 LEU 0 11 MET 0 3 ASN 0 5 PRO 0 8 GLN 0 5 ARG 0 5 SER 0 4 THR 0 3 VAL 0 6 TRP 0 3 TYR 1 6 Processing NMR model 20 ** Unrecognized atom type [ O2 ] in residue HIS A 125 Average value of CA-N-C-CB angle is 34.20 Standard deviation is 1.22 * 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 = 2070 old number = 0 * PHE A 6 TYR A 14 PHE A 25 PHE A 31 TYR A 81 Total number of residues that need to be changed and total number of residues: ALA 0 6 ASP 0 11 GLU 0 7 PHE 3 4 GLY 0 6 HIS 0 11 ILE 0 9 LYS 0 12 LEU 0 11 MET 0 3 ASN 0 5 PRO 0 8 GLN 0 5 ARG 0 5 SER 0 4 THR 0 3 VAL 0 6 TRP 0 3 TYR 2 6 * NMR ensemble comprises 20 model structures * Program completed