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 121 Average value of CA-N-C-CB angle is 34.11 Standard deviation is 0.76 * Side chain atoms should be swapped for the following residues: * As this is an NMR ensemble the swap has not been made * TYR A 34 TYR A 46 TYR A 57 PHE A 68 PHE A 75 TYR A 99 TYR A 100 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2005 old number = 0 * PHE A 108 TYR A 113 Total number of residues that need to be changed and total number of residues: ALA 0 4 ASP 0 8 GLU 0 5 PHE 3 7 GLY 0 5 HIS 0 7 ILE 0 8 LYS 0 13 LEU 0 14 MET 0 2 ASN 0 13 PRO 0 4 GLN 0 9 ARG 0 1 SER 0 6 THR 0 3 VAL 0 3 TYR 6 9 Processing NMR model 2 ** Unrecognized atom type [ O2 ] in residue HIS A 121 Average value of CA-N-C-CB angle is 34.12 Standard deviation is 0.80 * Side chain atoms should be swapped for the following residues: * As this is an NMR ensemble the swap has not been made * TYR A 47 TYR A 57 PHE A 68 PHE A 75 TYR A 100 PHE A 108 TYR A 113 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2005 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 4 ASP 0 8 GLU 0 5 PHE 3 7 GLY 0 5 HIS 0 7 ILE 0 8 LYS 0 13 LEU 0 14 MET 0 2 ASN 0 13 PRO 0 4 GLN 0 9 ARG 0 1 SER 0 6 THR 0 3 VAL 0 3 TYR 4 9 Processing NMR model 3 ** Unrecognized atom type [ O2 ] in residue HIS A 121 Average value of CA-N-C-CB angle is 34.11 Standard deviation is 0.80 * Side chain atoms should be swapped for the following residues: * As this is an NMR ensemble the swap has not been made * TYR A 46 TYR A 57 PHE A 68 TYR A 99 TYR A 100 PHE A 108 TYR A 113 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2005 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 4 ASP 0 8 GLU 0 5 PHE 2 7 GLY 0 5 HIS 0 7 ILE 0 8 LYS 0 13 LEU 0 14 MET 0 2 ASN 0 13 PRO 0 4 GLN 0 9 ARG 0 1 SER 0 6 THR 0 3 VAL 0 3 TYR 5 9 Processing NMR model 4 ** Unrecognized atom type [ O2 ] in residue HIS A 121 Average value of CA-N-C-CB angle is 34.10 Standard deviation is 0.80 * Side chain atoms should be swapped for the following residues: * As this is an NMR ensemble the swap has not been made * PHE A 22 TYR A 46 TYR A 57 PHE A 68 PHE A 75 TYR A 100 TYR A 113 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2005 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 4 ASP 0 8 GLU 0 5 PHE 3 7 GLY 0 5 HIS 0 7 ILE 0 8 LYS 0 13 LEU 0 14 MET 0 2 ASN 0 13 PRO 0 4 GLN 0 9 ARG 0 1 SER 0 6 THR 0 3 VAL 0 3 TYR 4 9 Processing NMR model 5 ** Unrecognized atom type [ O2 ] in residue HIS A 121 Average value of CA-N-C-CB angle is 34.09 Standard deviation is 0.71 * Side chain atoms should be swapped for the following residues: * As this is an NMR ensemble the swap has not been made * PHE A 24 TYR A 47 TYR A 57 PHE A 68 PHE A 75 TYR A 100 TYR A 113 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2005 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 4 ASP 0 8 GLU 0 5 PHE 3 7 GLY 0 5 HIS 0 7 ILE 0 8 LYS 0 13 LEU 0 14 MET 0 2 ASN 0 13 PRO 0 4 GLN 0 9 ARG 0 1 SER 0 6 THR 0 3 VAL 0 3 TYR 4 9 Processing NMR model 6 ** Unrecognized atom type [ O2 ] in residue HIS A 121 Average value of CA-N-C-CB angle is 34.13 Standard deviation is 0.81 * Side chain atoms should be swapped for the following residues: * As this is an NMR ensemble the swap has not been made * TYR A 46 TYR A 57 PHE A 68 PHE A 75 TYR A 99 TYR A 100 PHE A 108 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2005 old number = 0 * TYR A 113 Total number of residues that need to be changed and total number of residues: ALA 0 4 ASP 0 8 GLU 0 5 PHE 3 7 GLY 0 5 HIS 0 7 ILE 0 8 LYS 0 13 LEU 0 14 MET 0 2 ASN 0 13 PRO 0 4 GLN 0 9 ARG 0 1 SER 0 6 THR 0 3 VAL 0 3 TYR 5 9 Processing NMR model 7 ** Unrecognized atom type [ O2 ] in residue HIS A 121 Average value of CA-N-C-CB angle is 34.12 Standard deviation is 0.81 * Side chain atoms should be swapped for the following residues: * As this is an NMR ensemble the swap has not been made * TYR A 43 TYR A 46 TYR A 57 PHE A 68 TYR A 99 TYR A 100 TYR A 113 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2005 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 4 ASP 0 8 GLU 0 5 PHE 1 7 GLY 0 5 HIS 0 7 ILE 0 8 LYS 0 13 LEU 0 14 MET 0 2 ASN 0 13 PRO 0 4 GLN 0 9 ARG 0 1 SER 0 6 THR 0 3 VAL 0 3 TYR 6 9 Processing NMR model 8 ** Unrecognized atom type [ O2 ] in residue HIS A 121 Average value of CA-N-C-CB angle is 34.12 Standard deviation is 0.79 * Side chain atoms should be swapped for the following residues: * As this is an NMR ensemble the swap has not been made * TYR A 57 PHE A 68 PHE A 75 TYR A 99 TYR A 100 PHE A 108 TYR A 113 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2005 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 4 ASP 0 8 GLU 0 5 PHE 3 7 GLY 0 5 HIS 0 7 ILE 0 8 LYS 0 13 LEU 0 14 MET 0 2 ASN 0 13 PRO 0 4 GLN 0 9 ARG 0 1 SER 0 6 THR 0 3 VAL 0 3 TYR 4 9 Processing NMR model 9 ** Unrecognized atom type [ O2 ] in residue HIS A 121 Average value of CA-N-C-CB angle is 34.09 Standard deviation is 0.80 * 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 = 2005 old number = 0 * TYR A 46 TYR A 57 PHE A 68 TYR A 99 TYR A 100 Total number of residues that need to be changed and total number of residues: ALA 0 4 ASP 0 8 GLU 0 5 PHE 1 7 GLY 0 5 HIS 0 7 ILE 0 8 LYS 0 13 LEU 0 14 MET 0 2 ASN 0 13 PRO 0 4 GLN 0 9 ARG 0 1 SER 0 6 THR 0 3 VAL 0 3 TYR 4 9 Processing NMR model 10 ** Unrecognized atom type [ O2 ] in residue HIS A 121 Average value of CA-N-C-CB angle is 34.12 Standard deviation is 0.75 * Side chain atoms should be swapped for the following residues: * As this is an NMR ensemble the swap has not been made * TYR A 43 TYR A 46 TYR A 57 PHE A 68 TYR A 100 PHE A 108 TYR A 113 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2005 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 4 ASP 0 8 GLU 0 5 PHE 2 7 GLY 0 5 HIS 0 7 ILE 0 8 LYS 0 13 LEU 0 14 MET 0 2 ASN 0 13 PRO 0 4 GLN 0 9 ARG 0 1 SER 0 6 THR 0 3 VAL 0 3 TYR 5 9 Processing NMR model 11 ** Unrecognized atom type [ O2 ] in residue HIS A 121 Average value of CA-N-C-CB angle is 34.10 Standard deviation is 0.74 * 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 = 2005 old number = 0 * TYR A 47 TYR A 57 PHE A 75 TYR A 100 PHE A 108 Total number of residues that need to be changed and total number of residues: ALA 0 4 ASP 0 8 GLU 0 5 PHE 2 7 GLY 0 5 HIS 0 7 ILE 0 8 LYS 0 13 LEU 0 14 MET 0 2 ASN 0 13 PRO 0 4 GLN 0 9 ARG 0 1 SER 0 6 THR 0 3 VAL 0 3 TYR 3 9 Processing NMR model 12 ** Unrecognized atom type [ O2 ] in residue HIS A 121 Average value of CA-N-C-CB angle is 34.09 Standard deviation is 0.76 * 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 = 2005 old number = 0 * TYR A 46 TYR A 100 PHE A 108 TYR A 113 Total number of residues that need to be changed and total number of residues: ALA 0 4 ASP 0 8 GLU 0 5 PHE 1 7 GLY 0 5 HIS 0 7 ILE 0 8 LYS 0 13 LEU 0 14 MET 0 2 ASN 0 13 PRO 0 4 GLN 0 9 ARG 0 1 SER 0 6 THR 0 3 VAL 0 3 TYR 3 9 Processing NMR model 13 ** Unrecognized atom type [ O2 ] in residue HIS A 121 Average value of CA-N-C-CB angle is 34.12 Standard deviation is 0.80 * Side chain atoms should be swapped for the following residues: * As this is an NMR ensemble the swap has not been made * PHE A 24 TYR A 34 TYR A 47 TYR A 57 TYR A 99 TYR A 100 TYR A 113 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2005 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 4 ASP 0 8 GLU 0 5 PHE 1 7 GLY 0 5 HIS 0 7 ILE 0 8 LYS 0 13 LEU 0 14 MET 0 2 ASN 0 13 PRO 0 4 GLN 0 9 ARG 0 1 SER 0 6 THR 0 3 VAL 0 3 TYR 6 9 Processing NMR model 14 ** Unrecognized atom type [ O2 ] in residue HIS A 121 Average value of CA-N-C-CB angle is 34.07 Standard deviation is 0.74 * Side chain atoms should be swapped for the following residues: * As this is an NMR ensemble the swap has not been made * PHE A 24 TYR A 34 TYR A 47 TYR A 57 PHE A 68 PHE A 75 TYR A 99 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2005 old number = 0 * TYR A 100 PHE A 108 Total number of residues that need to be changed and total number of residues: ALA 0 4 ASP 0 8 GLU 0 5 PHE 4 7 GLY 0 5 HIS 0 7 ILE 0 8 LYS 0 13 LEU 0 14 MET 0 2 ASN 0 13 PRO 0 4 GLN 0 9 ARG 0 1 SER 0 6 THR 0 3 VAL 0 3 TYR 5 9 Processing NMR model 15 ** Unrecognized atom type [ O2 ] in residue HIS A 121 Average value of CA-N-C-CB angle is 34.13 Standard deviation is 0.82 * 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 = 2005 old number = 0 * PHE A 22 TYR A 34 TYR A 47 TYR A 57 PHE A 75 TYR A 100 Total number of residues that need to be changed and total number of residues: ALA 0 4 ASP 0 8 GLU 0 5 PHE 2 7 GLY 0 5 HIS 0 7 ILE 0 8 LYS 0 13 LEU 0 14 MET 0 2 ASN 0 13 PRO 0 4 GLN 0 9 ARG 0 1 SER 0 6 THR 0 3 VAL 0 3 TYR 4 9 Processing NMR model 16 ** Unrecognized atom type [ O2 ] in residue HIS A 121 Average value of CA-N-C-CB angle is 34.09 Standard deviation is 0.78 * 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 = 2005 old number = 0 * TYR A 47 TYR A 57 PHE A 68 TYR A 100 TYR A 113 Total number of residues that need to be changed and total number of residues: ALA 0 4 ASP 0 8 GLU 0 5 PHE 1 7 GLY 0 5 HIS 0 7 ILE 0 8 LYS 0 13 LEU 0 14 MET 0 2 ASN 0 13 PRO 0 4 GLN 0 9 ARG 0 1 SER 0 6 THR 0 3 VAL 0 3 TYR 4 9 Processing NMR model 17 ** Unrecognized atom type [ O2 ] in residue HIS A 121 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 * PHE A 24 TYR A 34 TYR A 47 TYR A 57 PHE A 75 TYR A 100 PHE A 108 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2005 old number = 0 * TYR A 113 Total number of residues that need to be changed and total number of residues: ALA 0 4 ASP 0 8 GLU 0 5 PHE 3 7 GLY 0 5 HIS 0 7 ILE 0 8 LYS 0 13 LEU 0 14 MET 0 2 ASN 0 13 PRO 0 4 GLN 0 9 ARG 0 1 SER 0 6 THR 0 3 VAL 0 3 TYR 5 9 Processing NMR model 18 ** Unrecognized atom type [ O2 ] in residue HIS A 121 Average value of CA-N-C-CB angle is 34.07 Standard deviation is 0.74 * Side chain atoms should be swapped for the following residues: * As this is an NMR ensemble the swap has not been made * TYR A 46 TYR A 47 TYR A 57 PHE A 68 PHE A 75 TYR A 99 TYR A 100 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2005 old number = 0 * PHE A 108 TYR A 113 Total number of residues that need to be changed and total number of residues: ALA 0 4 ASP 0 8 GLU 0 5 PHE 3 7 GLY 0 5 HIS 0 7 ILE 0 8 LYS 0 13 LEU 0 14 MET 0 2 ASN 0 13 PRO 0 4 GLN 0 9 ARG 0 1 SER 0 6 THR 0 3 VAL 0 3 TYR 6 9 Processing NMR model 19 ** Unrecognized atom type [ O2 ] in residue HIS A 121 Average value of CA-N-C-CB angle is 34.10 Standard deviation is 0.80 * Side chain atoms should be swapped for the following residues: * As this is an NMR ensemble the swap has not been made * PHE A 22 PHE A 24 TYR A 46 TYR A 57 PHE A 68 TYR A 99 TYR A 100 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2005 old number = 0 * PHE A 108 TYR A 113 Total number of residues that need to be changed and total number of residues: ALA 0 4 ASP 0 8 GLU 0 5 PHE 4 7 GLY 0 5 HIS 0 7 ILE 0 8 LYS 0 13 LEU 0 14 MET 0 2 ASN 0 13 PRO 0 4 GLN 0 9 ARG 0 1 SER 0 6 THR 0 3 VAL 0 3 TYR 5 9 Processing NMR model 20 ** Unrecognized atom type [ O2 ] in residue HIS A 121 Average value of CA-N-C-CB angle is 34.09 Standard deviation is 0.75 * Side chain atoms should be swapped for the following residues: * As this is an NMR ensemble the swap has not been made * TYR A 46 TYR A 57 PHE A 68 PHE A 75 TYR A 100 PHE A 108 TYR A 113 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2005 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 4 ASP 0 8 GLU 0 5 PHE 3 7 GLY 0 5 HIS 0 7 ILE 0 8 LYS 0 13 LEU 0 14 MET 0 2 ASN 0 13 PRO 0 4 GLN 0 9 ARG 0 1 SER 0 6 THR 0 3 VAL 0 3 TYR 4 9 * NMR ensemble comprises 20 model structures * Program completed