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 M 71 ** Unrecognized atom type [ O2 ] in residue HIS M 152 Chain break between 71 (M 71 ) and 72 (M 82 ) Average value of CA-N-C-CB angle is 34.13 Standard deviation is 0.71 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2274 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 12 PHE 0 4 GLY 0 12 HIS 0 14 ILE 0 10 LYS 0 12 LEU 0 22 MET 0 2 ASN 0 2 PRO 0 4 GLN 0 8 ARG 0 2 SER 0 8 THR 0 4 VAL 0 12 TYR 0 2 Processing NMR model 2 ** Unrecognized atom type [ O2 ] in residue HIS M 71 ** Unrecognized atom type [ O2 ] in residue HIS M 152 Chain break between 71 (M 71 ) and 72 (M 82 ) Average value of CA-N-C-CB angle is 34.11 Standard deviation is 0.66 * 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 = 2274 old number = 0 * TYR M 62 TYR M 143 Total number of residues that need to be changed and total number of residues: ALA 0 4 ASP 0 8 GLU 0 12 PHE 0 4 GLY 0 12 HIS 0 14 ILE 0 10 LYS 0 12 LEU 0 22 MET 0 2 ASN 0 2 PRO 0 4 GLN 0 8 ARG 0 2 SER 0 8 THR 0 4 VAL 0 12 TYR 2 2 Processing NMR model 3 ** Unrecognized atom type [ O2 ] in residue HIS M 71 ** Unrecognized atom type [ O2 ] in residue HIS M 152 Chain break between 71 (M 71 ) and 72 (M 82 ) Average value of CA-N-C-CB angle is 34.12 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 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2274 old number = 0 * PHE M 6 PHE M 87 Total number of residues that need to be changed and total number of residues: ALA 0 4 ASP 0 8 GLU 0 12 PHE 2 4 GLY 0 12 HIS 0 14 ILE 0 10 LYS 0 12 LEU 0 22 MET 0 2 ASN 0 2 PRO 0 4 GLN 0 8 ARG 0 2 SER 0 8 THR 0 4 VAL 0 12 TYR 0 2 Processing NMR model 4 ** Unrecognized atom type [ O2 ] in residue HIS M 71 ** Unrecognized atom type [ O2 ] in residue HIS M 152 Chain break between 71 (M 71 ) and 72 (M 82 ) Average value of CA-N-C-CB angle is 34.14 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 = 2274 old number = 0 * PHE M 18 TYR M 62 PHE M 99 TYR M 143 Total number of residues that need to be changed and total number of residues: ALA 0 4 ASP 0 8 GLU 0 12 PHE 2 4 GLY 0 12 HIS 0 14 ILE 0 10 LYS 0 12 LEU 0 22 MET 0 2 ASN 0 2 PRO 0 4 GLN 0 8 ARG 0 2 SER 0 8 THR 0 4 VAL 0 12 TYR 2 2 Processing NMR model 5 ** Unrecognized atom type [ O2 ] in residue HIS M 71 ** Unrecognized atom type [ O2 ] in residue HIS M 152 Chain break between 71 (M 71 ) and 72 (M 82 ) Average value of CA-N-C-CB angle is 34.08 Standard deviation is 0.73 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2274 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 12 PHE 0 4 GLY 0 12 HIS 0 14 ILE 0 10 LYS 0 12 LEU 0 22 MET 0 2 ASN 0 2 PRO 0 4 GLN 0 8 ARG 0 2 SER 0 8 THR 0 4 VAL 0 12 TYR 0 2 Processing NMR model 6 ** Unrecognized atom type [ O2 ] in residue HIS M 71 ** Unrecognized atom type [ O2 ] in residue HIS M 152 Chain break between 71 (M 71 ) and 72 (M 82 ) Average value of CA-N-C-CB angle is 34.11 Standard deviation is 0.70 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2274 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 12 PHE 0 4 GLY 0 12 HIS 0 14 ILE 0 10 LYS 0 12 LEU 0 22 MET 0 2 ASN 0 2 PRO 0 4 GLN 0 8 ARG 0 2 SER 0 8 THR 0 4 VAL 0 12 TYR 0 2 Processing NMR model 7 ** Unrecognized atom type [ O2 ] in residue HIS M 71 ** Unrecognized atom type [ O2 ] in residue HIS M 152 Chain break between 71 (M 71 ) and 72 (M 82 ) Average value of CA-N-C-CB angle is 34.12 Standard deviation is 0.68 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2274 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 12 PHE 0 4 GLY 0 12 HIS 0 14 ILE 0 10 LYS 0 12 LEU 0 22 MET 0 2 ASN 0 2 PRO 0 4 GLN 0 8 ARG 0 2 SER 0 8 THR 0 4 VAL 0 12 TYR 0 2 Processing NMR model 8 ** Unrecognized atom type [ O2 ] in residue HIS M 71 ** Unrecognized atom type [ O2 ] in residue HIS M 152 Chain break between 71 (M 71 ) and 72 (M 82 ) Average value of CA-N-C-CB angle is 34.16 Standard deviation is 0.63 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2274 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 12 PHE 0 4 GLY 0 12 HIS 0 14 ILE 0 10 LYS 0 12 LEU 0 22 MET 0 2 ASN 0 2 PRO 0 4 GLN 0 8 ARG 0 2 SER 0 8 THR 0 4 VAL 0 12 TYR 0 2 Processing NMR model 9 ** Unrecognized atom type [ O2 ] in residue HIS M 71 ** Unrecognized atom type [ O2 ] in residue HIS M 152 Chain break between 71 (M 71 ) and 72 (M 82 ) Average value of CA-N-C-CB angle is 34.18 Standard deviation is 0.65 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2274 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 12 PHE 0 4 GLY 0 12 HIS 0 14 ILE 0 10 LYS 0 12 LEU 0 22 MET 0 2 ASN 0 2 PRO 0 4 GLN 0 8 ARG 0 2 SER 0 8 THR 0 4 VAL 0 12 TYR 0 2 Processing NMR model 10 ** Unrecognized atom type [ O2 ] in residue HIS M 71 ** Unrecognized atom type [ O2 ] in residue HIS M 152 Chain break between 71 (M 71 ) and 72 (M 82 ) Average value of CA-N-C-CB angle is 34.12 Standard deviation is 0.69 * 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 = 2274 old number = 0 * PHE M 18 TYR M 62 PHE M 99 TYR M 143 Total number of residues that need to be changed and total number of residues: ALA 0 4 ASP 0 8 GLU 0 12 PHE 2 4 GLY 0 12 HIS 0 14 ILE 0 10 LYS 0 12 LEU 0 22 MET 0 2 ASN 0 2 PRO 0 4 GLN 0 8 ARG 0 2 SER 0 8 THR 0 4 VAL 0 12 TYR 2 2 Processing NMR model 11 ** Unrecognized atom type [ O2 ] in residue HIS M 71 ** Unrecognized atom type [ O2 ] in residue HIS M 152 Chain break between 71 (M 71 ) and 72 (M 82 ) Average value of CA-N-C-CB angle is 34.10 Standard deviation is 0.70 * 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 = 2274 old number = 0 * PHE M 6 PHE M 87 Total number of residues that need to be changed and total number of residues: ALA 0 4 ASP 0 8 GLU 0 12 PHE 2 4 GLY 0 12 HIS 0 14 ILE 0 10 LYS 0 12 LEU 0 22 MET 0 2 ASN 0 2 PRO 0 4 GLN 0 8 ARG 0 2 SER 0 8 THR 0 4 VAL 0 12 TYR 0 2 Processing NMR model 12 ** Unrecognized atom type [ O2 ] in residue HIS M 71 ** Unrecognized atom type [ O2 ] in residue HIS M 152 Chain break between 71 (M 71 ) and 72 (M 82 ) Average value of CA-N-C-CB angle is 34.12 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 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2274 old number = 0 * PHE M 6 PHE M 87 Total number of residues that need to be changed and total number of residues: ALA 0 4 ASP 0 8 GLU 0 12 PHE 2 4 GLY 0 12 HIS 0 14 ILE 0 10 LYS 0 12 LEU 0 22 MET 0 2 ASN 0 2 PRO 0 4 GLN 0 8 ARG 0 2 SER 0 8 THR 0 4 VAL 0 12 TYR 0 2 Processing NMR model 13 ** Unrecognized atom type [ O2 ] in residue HIS M 71 ** Unrecognized atom type [ O2 ] in residue HIS M 152 Chain break between 71 (M 71 ) and 72 (M 82 ) Average value of CA-N-C-CB angle is 34.13 Standard deviation is 0.68 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2274 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 12 PHE 0 4 GLY 0 12 HIS 0 14 ILE 0 10 LYS 0 12 LEU 0 22 MET 0 2 ASN 0 2 PRO 0 4 GLN 0 8 ARG 0 2 SER 0 8 THR 0 4 VAL 0 12 TYR 0 2 Processing NMR model 14 ** Unrecognized atom type [ O2 ] in residue HIS M 71 ** Unrecognized atom type [ O2 ] in residue HIS M 152 Chain break between 71 (M 71 ) and 72 (M 82 ) Average value of CA-N-C-CB angle is 34.09 Standard deviation is 0.72 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2274 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 12 PHE 0 4 GLY 0 12 HIS 0 14 ILE 0 10 LYS 0 12 LEU 0 22 MET 0 2 ASN 0 2 PRO 0 4 GLN 0 8 ARG 0 2 SER 0 8 THR 0 4 VAL 0 12 TYR 0 2 Processing NMR model 15 ** Unrecognized atom type [ O2 ] in residue HIS M 71 ** Unrecognized atom type [ O2 ] in residue HIS M 152 Chain break between 71 (M 71 ) and 72 (M 82 ) Average value of CA-N-C-CB angle is 34.09 Standard deviation is 0.69 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2274 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 12 PHE 0 4 GLY 0 12 HIS 0 14 ILE 0 10 LYS 0 12 LEU 0 22 MET 0 2 ASN 0 2 PRO 0 4 GLN 0 8 ARG 0 2 SER 0 8 THR 0 4 VAL 0 12 TYR 0 2 Processing NMR model 16 ** Unrecognized atom type [ O2 ] in residue HIS M 71 ** Unrecognized atom type [ O2 ] in residue HIS M 152 Chain break between 71 (M 71 ) and 72 (M 82 ) Average value of CA-N-C-CB angle is 34.08 Standard deviation is 0.69 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2274 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 12 PHE 0 4 GLY 0 12 HIS 0 14 ILE 0 10 LYS 0 12 LEU 0 22 MET 0 2 ASN 0 2 PRO 0 4 GLN 0 8 ARG 0 2 SER 0 8 THR 0 4 VAL 0 12 TYR 0 2 Processing NMR model 17 ** Unrecognized atom type [ O2 ] in residue HIS M 71 ** Unrecognized atom type [ O2 ] in residue HIS M 152 Chain break between 71 (M 71 ) and 72 (M 82 ) Average value of CA-N-C-CB angle is 34.15 Standard deviation is 0.78 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2274 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 12 PHE 0 4 GLY 0 12 HIS 0 14 ILE 0 10 LYS 0 12 LEU 0 22 MET 0 2 ASN 0 2 PRO 0 4 GLN 0 8 ARG 0 2 SER 0 8 THR 0 4 VAL 0 12 TYR 0 2 Processing NMR model 18 ** Unrecognized atom type [ O2 ] in residue HIS M 71 ** Unrecognized atom type [ O2 ] in residue HIS M 152 Chain break between 71 (M 71 ) and 72 (M 82 ) Average value of CA-N-C-CB angle is 34.10 Standard deviation is 0.76 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2274 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 12 PHE 0 4 GLY 0 12 HIS 0 14 ILE 0 10 LYS 0 12 LEU 0 22 MET 0 2 ASN 0 2 PRO 0 4 GLN 0 8 ARG 0 2 SER 0 8 THR 0 4 VAL 0 12 TYR 0 2 Processing NMR model 19 ** Unrecognized atom type [ O2 ] in residue HIS M 71 ** Unrecognized atom type [ O2 ] in residue HIS M 152 Chain break between 71 (M 71 ) and 72 (M 82 ) Average value of CA-N-C-CB angle is 34.08 Standard deviation is 0.79 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2274 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 12 PHE 0 4 GLY 0 12 HIS 0 14 ILE 0 10 LYS 0 12 LEU 0 22 MET 0 2 ASN 0 2 PRO 0 4 GLN 0 8 ARG 0 2 SER 0 8 THR 0 4 VAL 0 12 TYR 0 2 Processing NMR model 20 ** Unrecognized atom type [ O2 ] in residue HIS M 71 ** Unrecognized atom type [ O2 ] in residue HIS M 152 Chain break between 71 (M 71 ) and 72 (M 82 ) Average value of CA-N-C-CB angle is 34.07 Standard deviation is 0.71 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2274 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 12 PHE 0 4 GLY 0 12 HIS 0 14 ILE 0 10 LYS 0 12 LEU 0 22 MET 0 2 ASN 0 2 PRO 0 4 GLN 0 8 ARG 0 2 SER 0 8 THR 0 4 VAL 0 12 TYR 0 2 * NMR ensemble comprises 20 model structures * Program completed