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 34.16 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 = 2524 old number = 0 * TYR M 7 TYR M 97 Total number of residues that need to be changed and total number of residues: ALA 0 18 CYS 0 2 ASP 0 2 GLU 0 14 PHE 0 2 GLY 0 2 HIS 0 16 ILE 0 6 LYS 0 12 LEU 0 20 MET 0 4 ASN 0 6 PRO 0 4 GLN 0 10 ARG 0 4 SER 0 16 THR 0 6 VAL 0 14 TYR 2 2 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 34.15 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 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2524 old number = 0 * TYR M 7 TYR M 97 Total number of residues that need to be changed and total number of residues: ALA 0 18 CYS 0 2 ASP 0 2 GLU 0 14 PHE 0 2 GLY 0 2 HIS 0 16 ILE 0 6 LYS 0 12 LEU 0 20 MET 0 4 ASN 0 6 PRO 0 4 GLN 0 10 ARG 0 4 SER 0 16 THR 0 6 VAL 0 14 TYR 2 2 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 34.21 Standard deviation is 0.90 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2524 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 18 CYS 0 2 ASP 0 2 GLU 0 14 PHE 0 2 GLY 0 2 HIS 0 16 ILE 0 6 LYS 0 12 LEU 0 20 MET 0 4 ASN 0 6 PRO 0 4 GLN 0 10 ARG 0 4 SER 0 16 THR 0 6 VAL 0 14 TYR 0 2 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 34.18 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 = 2524 old number = 0 * TYR M 7 TYR M 97 Total number of residues that need to be changed and total number of residues: ALA 0 18 CYS 0 2 ASP 0 2 GLU 0 14 PHE 0 2 GLY 0 2 HIS 0 16 ILE 0 6 LYS 0 12 LEU 0 20 MET 0 4 ASN 0 6 PRO 0 4 GLN 0 10 ARG 0 4 SER 0 16 THR 0 6 VAL 0 14 TYR 2 2 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 34.16 Standard deviation is 0.87 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2524 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 18 CYS 0 2 ASP 0 2 GLU 0 14 PHE 0 2 GLY 0 2 HIS 0 16 ILE 0 6 LYS 0 12 LEU 0 20 MET 0 4 ASN 0 6 PRO 0 4 GLN 0 10 ARG 0 4 SER 0 16 THR 0 6 VAL 0 14 TYR 0 2 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 34.15 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 = 2524 old number = 0 * TYR M 7 PHE M 61 TYR M 97 PHE M 151 Total number of residues that need to be changed and total number of residues: ALA 0 18 CYS 0 2 ASP 0 2 GLU 0 14 PHE 2 2 GLY 0 2 HIS 0 16 ILE 0 6 LYS 0 12 LEU 0 20 MET 0 4 ASN 0 6 PRO 0 4 GLN 0 10 ARG 0 4 SER 0 16 THR 0 6 VAL 0 14 TYR 2 2 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 34.17 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 = 2524 old number = 0 * TYR M 7 TYR M 97 Total number of residues that need to be changed and total number of residues: ALA 0 18 CYS 0 2 ASP 0 2 GLU 0 14 PHE 0 2 GLY 0 2 HIS 0 16 ILE 0 6 LYS 0 12 LEU 0 20 MET 0 4 ASN 0 6 PRO 0 4 GLN 0 10 ARG 0 4 SER 0 16 THR 0 6 VAL 0 14 TYR 2 2 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 34.17 Standard deviation is 0.82 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2524 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 18 CYS 0 2 ASP 0 2 GLU 0 14 PHE 0 2 GLY 0 2 HIS 0 16 ILE 0 6 LYS 0 12 LEU 0 20 MET 0 4 ASN 0 6 PRO 0 4 GLN 0 10 ARG 0 4 SER 0 16 THR 0 6 VAL 0 14 TYR 0 2 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 34.17 Standard deviation is 0.88 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2524 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 18 CYS 0 2 ASP 0 2 GLU 0 14 PHE 0 2 GLY 0 2 HIS 0 16 ILE 0 6 LYS 0 12 LEU 0 20 MET 0 4 ASN 0 6 PRO 0 4 GLN 0 10 ARG 0 4 SER 0 16 THR 0 6 VAL 0 14 TYR 0 2 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 34.16 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 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2524 old number = 0 * TYR M 7 TYR M 97 Total number of residues that need to be changed and total number of residues: ALA 0 18 CYS 0 2 ASP 0 2 GLU 0 14 PHE 0 2 GLY 0 2 HIS 0 16 ILE 0 6 LYS 0 12 LEU 0 20 MET 0 4 ASN 0 6 PRO 0 4 GLN 0 10 ARG 0 4 SER 0 16 THR 0 6 VAL 0 14 TYR 2 2 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 34.16 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 = 2524 old number = 0 * TYR M 7 PHE M 61 TYR M 97 PHE M 151 Total number of residues that need to be changed and total number of residues: ALA 0 18 CYS 0 2 ASP 0 2 GLU 0 14 PHE 2 2 GLY 0 2 HIS 0 16 ILE 0 6 LYS 0 12 LEU 0 20 MET 0 4 ASN 0 6 PRO 0 4 GLN 0 10 ARG 0 4 SER 0 16 THR 0 6 VAL 0 14 TYR 2 2 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 34.18 Standard deviation is 0.83 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2524 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 18 CYS 0 2 ASP 0 2 GLU 0 14 PHE 0 2 GLY 0 2 HIS 0 16 ILE 0 6 LYS 0 12 LEU 0 20 MET 0 4 ASN 0 6 PRO 0 4 GLN 0 10 ARG 0 4 SER 0 16 THR 0 6 VAL 0 14 TYR 0 2 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 34.11 Standard deviation is 0.92 * 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 = 2524 old number = 0 * PHE M 61 PHE M 151 Total number of residues that need to be changed and total number of residues: ALA 0 18 CYS 0 2 ASP 0 2 GLU 0 14 PHE 2 2 GLY 0 2 HIS 0 16 ILE 0 6 LYS 0 12 LEU 0 20 MET 0 4 ASN 0 6 PRO 0 4 GLN 0 10 ARG 0 4 SER 0 16 THR 0 6 VAL 0 14 TYR 0 2 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 34.19 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 = 2524 old number = 0 * PHE M 61 PHE M 151 Total number of residues that need to be changed and total number of residues: ALA 0 18 CYS 0 2 ASP 0 2 GLU 0 14 PHE 2 2 GLY 0 2 HIS 0 16 ILE 0 6 LYS 0 12 LEU 0 20 MET 0 4 ASN 0 6 PRO 0 4 GLN 0 10 ARG 0 4 SER 0 16 THR 0 6 VAL 0 14 TYR 0 2 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 34.17 Standard deviation is 0.82 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2524 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 18 CYS 0 2 ASP 0 2 GLU 0 14 PHE 0 2 GLY 0 2 HIS 0 16 ILE 0 6 LYS 0 12 LEU 0 20 MET 0 4 ASN 0 6 PRO 0 4 GLN 0 10 ARG 0 4 SER 0 16 THR 0 6 VAL 0 14 TYR 0 2 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 34.19 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 = 2524 old number = 0 * TYR M 7 TYR M 97 Total number of residues that need to be changed and total number of residues: ALA 0 18 CYS 0 2 ASP 0 2 GLU 0 14 PHE 0 2 GLY 0 2 HIS 0 16 ILE 0 6 LYS 0 12 LEU 0 20 MET 0 4 ASN 0 6 PRO 0 4 GLN 0 10 ARG 0 4 SER 0 16 THR 0 6 VAL 0 14 TYR 2 2 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 34.18 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 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2524 old number = 0 * TYR M 7 TYR M 97 Total number of residues that need to be changed and total number of residues: ALA 0 18 CYS 0 2 ASP 0 2 GLU 0 14 PHE 0 2 GLY 0 2 HIS 0 16 ILE 0 6 LYS 0 12 LEU 0 20 MET 0 4 ASN 0 6 PRO 0 4 GLN 0 10 ARG 0 4 SER 0 16 THR 0 6 VAL 0 14 TYR 2 2 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 34.15 Standard deviation is 0.91 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2524 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 18 CYS 0 2 ASP 0 2 GLU 0 14 PHE 0 2 GLY 0 2 HIS 0 16 ILE 0 6 LYS 0 12 LEU 0 20 MET 0 4 ASN 0 6 PRO 0 4 GLN 0 10 ARG 0 4 SER 0 16 THR 0 6 VAL 0 14 TYR 0 2 * NMR ensemble comprises 18 model structures * Program completed