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 80 ** Unrecognized atom type [ O2 ] in residue HIS M 170 Chain break between 80 (M 80 ) and 81 (M 91 ) Average value of CA-N-C-CB angle is 34.01 Standard deviation is 0.67 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2658 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 6 ASP 0 6 GLU 0 14 PHE 0 4 GLY 0 2 HIS 0 18 ILE 0 8 LYS 0 14 LEU 0 14 MET 0 6 ASN 0 10 PRO 0 2 GLN 0 10 ARG 0 6 SER 0 14 THR 0 4 VAL 0 14 TYR 0 8 Processing NMR model 2 ** Unrecognized atom type [ O2 ] in residue HIS M 80 ** Unrecognized atom type [ O2 ] in residue HIS M 170 Chain break between 80 (M 80 ) and 81 (M 91 ) Average value of CA-N-C-CB angle is 34.07 Standard deviation is 0.77 * 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 = 2658 old number = 0 * TYR M 33 TYR M 63 TYR M 123 TYR M 153 Total number of residues that need to be changed and total number of residues: ALA 0 6 ASP 0 6 GLU 0 14 PHE 0 4 GLY 0 2 HIS 0 18 ILE 0 8 LYS 0 14 LEU 0 14 MET 0 6 ASN 0 10 PRO 0 2 GLN 0 10 ARG 0 6 SER 0 14 THR 0 4 VAL 0 14 TYR 4 8 Processing NMR model 3 ** Unrecognized atom type [ O2 ] in residue HIS M 80 ** Unrecognized atom type [ O2 ] in residue HIS M 170 Chain break between 80 (M 80 ) and 81 (M 91 ) Average value of CA-N-C-CB angle is 34.10 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 = 2658 old number = 0 * TYR M 33 TYR M 34 TYR M 123 TYR M 124 Total number of residues that need to be changed and total number of residues: ALA 0 6 ASP 0 6 GLU 0 14 PHE 0 4 GLY 0 2 HIS 0 18 ILE 0 8 LYS 0 14 LEU 0 14 MET 0 6 ASN 0 10 PRO 0 2 GLN 0 10 ARG 0 6 SER 0 14 THR 0 4 VAL 0 14 TYR 4 8 Processing NMR model 4 ** Unrecognized atom type [ O2 ] in residue HIS M 80 ** Unrecognized atom type [ O2 ] in residue HIS M 170 Chain break between 80 (M 80 ) and 81 (M 91 ) Average value of CA-N-C-CB angle is 34.07 Standard deviation is 0.73 * 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 = 2658 old number = 0 * TYR M 33 TYR M 123 Total number of residues that need to be changed and total number of residues: ALA 0 6 ASP 0 6 GLU 0 14 PHE 0 4 GLY 0 2 HIS 0 18 ILE 0 8 LYS 0 14 LEU 0 14 MET 0 6 ASN 0 10 PRO 0 2 GLN 0 10 ARG 0 6 SER 0 14 THR 0 4 VAL 0 14 TYR 2 8 Processing NMR model 5 ** Unrecognized atom type [ O2 ] in residue HIS M 80 ** Unrecognized atom type [ O2 ] in residue HIS M 170 Chain break between 80 (M 80 ) and 81 (M 91 ) Average value of CA-N-C-CB angle is 34.05 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 = 2658 old number = 0 * PHE M 5 TYR M 63 PHE M 95 TYR M 153 Total number of residues that need to be changed and total number of residues: ALA 0 6 ASP 0 6 GLU 0 14 PHE 2 4 GLY 0 2 HIS 0 18 ILE 0 8 LYS 0 14 LEU 0 14 MET 0 6 ASN 0 10 PRO 0 2 GLN 0 10 ARG 0 6 SER 0 14 THR 0 4 VAL 0 14 TYR 2 8 Processing NMR model 6 ** Unrecognized atom type [ O2 ] in residue HIS M 80 ** Unrecognized atom type [ O2 ] in residue HIS M 170 Chain break between 80 (M 80 ) and 81 (M 91 ) 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 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2658 old number = 0 * TYR M 33 TYR M 63 TYR M 123 TYR M 153 Total number of residues that need to be changed and total number of residues: ALA 0 6 ASP 0 6 GLU 0 14 PHE 0 4 GLY 0 2 HIS 0 18 ILE 0 8 LYS 0 14 LEU 0 14 MET 0 6 ASN 0 10 PRO 0 2 GLN 0 10 ARG 0 6 SER 0 14 THR 0 4 VAL 0 14 TYR 4 8 Processing NMR model 7 ** Unrecognized atom type [ O2 ] in residue HIS M 80 ** Unrecognized atom type [ O2 ] in residue HIS M 170 Chain break between 80 (M 80 ) and 81 (M 91 ) Average value of CA-N-C-CB angle is 34.01 Standard deviation is 0.68 * 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 = 2658 old number = 0 * TYR M 33 TYR M 34 TYR M 123 TYR M 124 Total number of residues that need to be changed and total number of residues: ALA 0 6 ASP 0 6 GLU 0 14 PHE 0 4 GLY 0 2 HIS 0 18 ILE 0 8 LYS 0 14 LEU 0 14 MET 0 6 ASN 0 10 PRO 0 2 GLN 0 10 ARG 0 6 SER 0 14 THR 0 4 VAL 0 14 TYR 4 8 Processing NMR model 8 ** Unrecognized atom type [ O2 ] in residue HIS M 80 ** Unrecognized atom type [ O2 ] in residue HIS M 170 Chain break between 80 (M 80 ) and 81 (M 91 ) Average value of CA-N-C-CB angle is 34.15 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 = 2658 old number = 0 * TYR M 63 TYR M 153 Total number of residues that need to be changed and total number of residues: ALA 0 6 ASP 0 6 GLU 0 14 PHE 0 4 GLY 0 2 HIS 0 18 ILE 0 8 LYS 0 14 LEU 0 14 MET 0 6 ASN 0 10 PRO 0 2 GLN 0 10 ARG 0 6 SER 0 14 THR 0 4 VAL 0 14 TYR 2 8 Processing NMR model 9 ** Unrecognized atom type [ O2 ] in residue HIS M 80 ** Unrecognized atom type [ O2 ] in residue HIS M 170 Chain break between 80 (M 80 ) and 81 (M 91 ) Average value of CA-N-C-CB angle is 34.07 Standard deviation is 0.72 * 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 = 2658 old number = 0 * TYR M 34 TYR M 124 Total number of residues that need to be changed and total number of residues: ALA 0 6 ASP 0 6 GLU 0 14 PHE 0 4 GLY 0 2 HIS 0 18 ILE 0 8 LYS 0 14 LEU 0 14 MET 0 6 ASN 0 10 PRO 0 2 GLN 0 10 ARG 0 6 SER 0 14 THR 0 4 VAL 0 14 TYR 2 8 Processing NMR model 10 ** Unrecognized atom type [ O2 ] in residue HIS M 80 ** Unrecognized atom type [ O2 ] in residue HIS M 170 Chain break between 80 (M 80 ) and 81 (M 91 ) Average value of CA-N-C-CB angle is 34.08 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 * PHE M 5 TYR M 33 TYR M 34 TYR M 63 PHE M 95 TYR M 123 TYR M 124 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2658 old number = 0 * TYR M 153 Total number of residues that need to be changed and total number of residues: ALA 0 6 ASP 0 6 GLU 0 14 PHE 2 4 GLY 0 2 HIS 0 18 ILE 0 8 LYS 0 14 LEU 0 14 MET 0 6 ASN 0 10 PRO 0 2 GLN 0 10 ARG 0 6 SER 0 14 THR 0 4 VAL 0 14 TYR 6 8 Processing NMR model 11 ** Unrecognized atom type [ O2 ] in residue HIS M 80 ** Unrecognized atom type [ O2 ] in residue HIS M 170 Chain break between 80 (M 80 ) and 81 (M 91 ) 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 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2658 old number = 0 * PHE M 5 TYR M 34 PHE M 95 TYR M 124 Total number of residues that need to be changed and total number of residues: ALA 0 6 ASP 0 6 GLU 0 14 PHE 2 4 GLY 0 2 HIS 0 18 ILE 0 8 LYS 0 14 LEU 0 14 MET 0 6 ASN 0 10 PRO 0 2 GLN 0 10 ARG 0 6 SER 0 14 THR 0 4 VAL 0 14 TYR 2 8 Processing NMR model 12 ** Unrecognized atom type [ O2 ] in residue HIS M 80 ** Unrecognized atom type [ O2 ] in residue HIS M 170 Chain break between 80 (M 80 ) and 81 (M 91 ) 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 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2658 old number = 0 * PHE M 5 TYR M 33 PHE M 95 TYR M 123 Total number of residues that need to be changed and total number of residues: ALA 0 6 ASP 0 6 GLU 0 14 PHE 2 4 GLY 0 2 HIS 0 18 ILE 0 8 LYS 0 14 LEU 0 14 MET 0 6 ASN 0 10 PRO 0 2 GLN 0 10 ARG 0 6 SER 0 14 THR 0 4 VAL 0 14 TYR 2 8 Processing NMR model 13 ** Unrecognized atom type [ O2 ] in residue HIS M 80 ** Unrecognized atom type [ O2 ] in residue HIS M 170 Chain break between 80 (M 80 ) and 81 (M 91 ) Average value of CA-N-C-CB angle is 34.09 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 = 2658 old number = 0 * TYR M 33 TYR M 123 Total number of residues that need to be changed and total number of residues: ALA 0 6 ASP 0 6 GLU 0 14 PHE 0 4 GLY 0 2 HIS 0 18 ILE 0 8 LYS 0 14 LEU 0 14 MET 0 6 ASN 0 10 PRO 0 2 GLN 0 10 ARG 0 6 SER 0 14 THR 0 4 VAL 0 14 TYR 2 8 Processing NMR model 14 ** Unrecognized atom type [ O2 ] in residue HIS M 80 ** Unrecognized atom type [ O2 ] in residue HIS M 170 Chain break between 80 (M 80 ) and 81 (M 91 ) Average value of CA-N-C-CB angle is 34.14 Standard deviation is 0.83 * 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 = 2658 old number = 0 * PHE M 10 TYR M 34 PHE M 100 TYR M 124 Total number of residues that need to be changed and total number of residues: ALA 0 6 ASP 0 6 GLU 0 14 PHE 2 4 GLY 0 2 HIS 0 18 ILE 0 8 LYS 0 14 LEU 0 14 MET 0 6 ASN 0 10 PRO 0 2 GLN 0 10 ARG 0 6 SER 0 14 THR 0 4 VAL 0 14 TYR 2 8 Processing NMR model 15 ** Unrecognized atom type [ O2 ] in residue HIS M 80 ** Unrecognized atom type [ O2 ] in residue HIS M 170 Chain break between 80 (M 80 ) and 81 (M 91 ) Average value of CA-N-C-CB angle is 34.11 Standard deviation is 0.77 * 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 = 2658 old number = 0 * PHE M 5 PHE M 95 Total number of residues that need to be changed and total number of residues: ALA 0 6 ASP 0 6 GLU 0 14 PHE 2 4 GLY 0 2 HIS 0 18 ILE 0 8 LYS 0 14 LEU 0 14 MET 0 6 ASN 0 10 PRO 0 2 GLN 0 10 ARG 0 6 SER 0 14 THR 0 4 VAL 0 14 TYR 0 8 Processing NMR model 16 ** Unrecognized atom type [ O2 ] in residue HIS M 80 ** Unrecognized atom type [ O2 ] in residue HIS M 170 Chain break between 80 (M 80 ) and 81 (M 91 ) Average value of CA-N-C-CB angle is 34.08 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 = 2658 old number = 0 * TYR M 33 TYR M 63 TYR M 123 TYR M 153 Total number of residues that need to be changed and total number of residues: ALA 0 6 ASP 0 6 GLU 0 14 PHE 0 4 GLY 0 2 HIS 0 18 ILE 0 8 LYS 0 14 LEU 0 14 MET 0 6 ASN 0 10 PRO 0 2 GLN 0 10 ARG 0 6 SER 0 14 THR 0 4 VAL 0 14 TYR 4 8 Processing NMR model 17 ** Unrecognized atom type [ O2 ] in residue HIS M 80 ** Unrecognized atom type [ O2 ] in residue HIS M 170 Chain break between 80 (M 80 ) and 81 (M 91 ) 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 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2658 old number = 0 * PHE M 10 TYR M 33 TYR M 34 PHE M 100 TYR M 123 TYR M 124 Total number of residues that need to be changed and total number of residues: ALA 0 6 ASP 0 6 GLU 0 14 PHE 2 4 GLY 0 2 HIS 0 18 ILE 0 8 LYS 0 14 LEU 0 14 MET 0 6 ASN 0 10 PRO 0 2 GLN 0 10 ARG 0 6 SER 0 14 THR 0 4 VAL 0 14 TYR 4 8 Processing NMR model 18 ** Unrecognized atom type [ O2 ] in residue HIS M 80 ** Unrecognized atom type [ O2 ] in residue HIS M 170 Chain break between 80 (M 80 ) and 81 (M 91 ) Average value of CA-N-C-CB angle is 34.10 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 = 2658 old number = 0 * PHE M 10 TYR M 34 PHE M 100 TYR M 124 Total number of residues that need to be changed and total number of residues: ALA 0 6 ASP 0 6 GLU 0 14 PHE 2 4 GLY 0 2 HIS 0 18 ILE 0 8 LYS 0 14 LEU 0 14 MET 0 6 ASN 0 10 PRO 0 2 GLN 0 10 ARG 0 6 SER 0 14 THR 0 4 VAL 0 14 TYR 2 8 Processing NMR model 19 ** Unrecognized atom type [ O2 ] in residue HIS M 80 ** Unrecognized atom type [ O2 ] in residue HIS M 170 Chain break between 80 (M 80 ) and 81 (M 91 ) Average value of CA-N-C-CB angle is 34.08 Standard deviation is 0.73 * 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 = 2658 old number = 0 * TYR M 33 TYR M 123 Total number of residues that need to be changed and total number of residues: ALA 0 6 ASP 0 6 GLU 0 14 PHE 0 4 GLY 0 2 HIS 0 18 ILE 0 8 LYS 0 14 LEU 0 14 MET 0 6 ASN 0 10 PRO 0 2 GLN 0 10 ARG 0 6 SER 0 14 THR 0 4 VAL 0 14 TYR 2 8 Processing NMR model 20 ** Unrecognized atom type [ O2 ] in residue HIS M 80 ** Unrecognized atom type [ O2 ] in residue HIS M 170 Chain break between 80 (M 80 ) and 81 (M 91 ) Average value of CA-N-C-CB angle is 34.08 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 = 2658 old number = 0 * PHE M 10 TYR M 33 TYR M 34 PHE M 100 TYR M 123 TYR M 124 Total number of residues that need to be changed and total number of residues: ALA 0 6 ASP 0 6 GLU 0 14 PHE 2 4 GLY 0 2 HIS 0 18 ILE 0 8 LYS 0 14 LEU 0 14 MET 0 6 ASN 0 10 PRO 0 2 GLN 0 10 ARG 0 6 SER 0 14 THR 0 4 VAL 0 14 TYR 4 8 * NMR ensemble comprises 20 model structures * Program completed