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 76 ** Unrecognized atom type [ O2 ] in residue HIS M 162 Chain break between 76 (M 76 ) and 77 (M 87 ) Average value of CA-N-C-CB angle is 34.23 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 = 2446 old number = 0 * TYR M 7 TYR M 93 Total number of residues that need to be changed and total number of residues: ALA 0 10 CYS 0 2 ASP 0 8 GLU 0 12 PHE 0 2 GLY 0 2 HIS 0 12 ILE 0 10 LYS 0 12 LEU 0 16 MET 0 4 ASN 0 8 PRO 0 6 GLN 0 6 ARG 0 4 SER 0 8 THR 0 6 VAL 0 22 TYR 2 2 Processing NMR model 2 ** Unrecognized atom type [ O2 ] in residue HIS M 76 ** Unrecognized atom type [ O2 ] in residue HIS M 162 Chain break between 76 (M 76 ) and 77 (M 87 ) Average value of CA-N-C-CB angle is 34.18 Standard deviation is 1.04 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2446 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 10 CYS 0 2 ASP 0 8 GLU 0 12 PHE 0 2 GLY 0 2 HIS 0 12 ILE 0 10 LYS 0 12 LEU 0 16 MET 0 4 ASN 0 8 PRO 0 6 GLN 0 6 ARG 0 4 SER 0 8 THR 0 6 VAL 0 22 TYR 0 2 Processing NMR model 3 ** Unrecognized atom type [ O2 ] in residue HIS M 76 ** Unrecognized atom type [ O2 ] in residue HIS M 162 Chain break between 76 (M 76 ) and 77 (M 87 ) Average value of CA-N-C-CB angle is 34.19 Standard deviation is 0.92 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2446 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 10 CYS 0 2 ASP 0 8 GLU 0 12 PHE 0 2 GLY 0 2 HIS 0 12 ILE 0 10 LYS 0 12 LEU 0 16 MET 0 4 ASN 0 8 PRO 0 6 GLN 0 6 ARG 0 4 SER 0 8 THR 0 6 VAL 0 22 TYR 0 2 Processing NMR model 4 ** Unrecognized atom type [ O2 ] in residue HIS M 76 ** Unrecognized atom type [ O2 ] in residue HIS M 162 Chain break between 76 (M 76 ) and 77 (M 87 ) Average value of CA-N-C-CB angle is 34.18 Standard deviation is 1.04 * 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 = 2446 old number = 0 * TYR M 7 TYR M 93 Total number of residues that need to be changed and total number of residues: ALA 0 10 CYS 0 2 ASP 0 8 GLU 0 12 PHE 0 2 GLY 0 2 HIS 0 12 ILE 0 10 LYS 0 12 LEU 0 16 MET 0 4 ASN 0 8 PRO 0 6 GLN 0 6 ARG 0 4 SER 0 8 THR 0 6 VAL 0 22 TYR 2 2 Processing NMR model 5 ** Unrecognized atom type [ O2 ] in residue HIS M 76 ** Unrecognized atom type [ O2 ] in residue HIS M 162 Chain break between 76 (M 76 ) and 77 (M 87 ) Average value of CA-N-C-CB angle is 34.17 Standard deviation is 1.03 * 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 = 2446 old number = 0 * TYR M 7 PHE M 60 TYR M 93 PHE M 146 Total number of residues that need to be changed and total number of residues: ALA 0 10 CYS 0 2 ASP 0 8 GLU 0 12 PHE 2 2 GLY 0 2 HIS 0 12 ILE 0 10 LYS 0 12 LEU 0 16 MET 0 4 ASN 0 8 PRO 0 6 GLN 0 6 ARG 0 4 SER 0 8 THR 0 6 VAL 0 22 TYR 2 2 Processing NMR model 6 ** Unrecognized atom type [ O2 ] in residue HIS M 76 ** Unrecognized atom type [ O2 ] in residue HIS M 162 Chain break between 76 (M 76 ) and 77 (M 87 ) Average value of CA-N-C-CB angle is 34.15 Standard deviation is 1.03 * 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 = 2446 old number = 0 * TYR M 7 TYR M 93 Total number of residues that need to be changed and total number of residues: ALA 0 10 CYS 0 2 ASP 0 8 GLU 0 12 PHE 0 2 GLY 0 2 HIS 0 12 ILE 0 10 LYS 0 12 LEU 0 16 MET 0 4 ASN 0 8 PRO 0 6 GLN 0 6 ARG 0 4 SER 0 8 THR 0 6 VAL 0 22 TYR 2 2 Processing NMR model 7 ** Unrecognized atom type [ O2 ] in residue HIS M 76 ** Unrecognized atom type [ O2 ] in residue HIS M 162 Chain break between 76 (M 76 ) and 77 (M 87 ) Average value of CA-N-C-CB angle is 34.18 Standard deviation is 1.03 * 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 = 2446 old number = 0 * TYR M 7 TYR M 93 Total number of residues that need to be changed and total number of residues: ALA 0 10 CYS 0 2 ASP 0 8 GLU 0 12 PHE 0 2 GLY 0 2 HIS 0 12 ILE 0 10 LYS 0 12 LEU 0 16 MET 0 4 ASN 0 8 PRO 0 6 GLN 0 6 ARG 0 4 SER 0 8 THR 0 6 VAL 0 22 TYR 2 2 Processing NMR model 8 ** Unrecognized atom type [ O2 ] in residue HIS M 76 ** Unrecognized atom type [ O2 ] in residue HIS M 162 Chain break between 76 (M 76 ) and 77 (M 87 ) Average value of CA-N-C-CB angle is 34.20 Standard deviation is 1.01 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2446 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 10 CYS 0 2 ASP 0 8 GLU 0 12 PHE 0 2 GLY 0 2 HIS 0 12 ILE 0 10 LYS 0 12 LEU 0 16 MET 0 4 ASN 0 8 PRO 0 6 GLN 0 6 ARG 0 4 SER 0 8 THR 0 6 VAL 0 22 TYR 0 2 Processing NMR model 9 ** Unrecognized atom type [ O2 ] in residue HIS M 76 ** Unrecognized atom type [ O2 ] in residue HIS M 162 Chain break between 76 (M 76 ) and 77 (M 87 ) Average value of CA-N-C-CB angle is 34.18 Standard deviation is 1.04 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2446 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 10 CYS 0 2 ASP 0 8 GLU 0 12 PHE 0 2 GLY 0 2 HIS 0 12 ILE 0 10 LYS 0 12 LEU 0 16 MET 0 4 ASN 0 8 PRO 0 6 GLN 0 6 ARG 0 4 SER 0 8 THR 0 6 VAL 0 22 TYR 0 2 Processing NMR model 10 ** Unrecognized atom type [ O2 ] in residue HIS M 76 ** Unrecognized atom type [ O2 ] in residue HIS M 162 Chain break between 76 (M 76 ) and 77 (M 87 ) Average value of CA-N-C-CB angle is 34.20 Standard deviation is 0.99 * 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 = 2446 old number = 0 * TYR M 7 TYR M 93 Total number of residues that need to be changed and total number of residues: ALA 0 10 CYS 0 2 ASP 0 8 GLU 0 12 PHE 0 2 GLY 0 2 HIS 0 12 ILE 0 10 LYS 0 12 LEU 0 16 MET 0 4 ASN 0 8 PRO 0 6 GLN 0 6 ARG 0 4 SER 0 8 THR 0 6 VAL 0 22 TYR 2 2 Processing NMR model 11 ** Unrecognized atom type [ O2 ] in residue HIS M 76 ** Unrecognized atom type [ O2 ] in residue HIS M 162 Chain break between 76 (M 76 ) and 77 (M 87 ) Average value of CA-N-C-CB angle is 34.18 Standard deviation is 1.08 * 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 = 2446 old number = 0 * TYR M 7 TYR M 93 Total number of residues that need to be changed and total number of residues: ALA 0 10 CYS 0 2 ASP 0 8 GLU 0 12 PHE 0 2 GLY 0 2 HIS 0 12 ILE 0 10 LYS 0 12 LEU 0 16 MET 0 4 ASN 0 8 PRO 0 6 GLN 0 6 ARG 0 4 SER 0 8 THR 0 6 VAL 0 22 TYR 2 2 Processing NMR model 12 ** Unrecognized atom type [ O2 ] in residue HIS M 76 ** Unrecognized atom type [ O2 ] in residue HIS M 162 Chain break between 76 (M 76 ) and 77 (M 87 ) Average value of CA-N-C-CB angle is 34.22 Standard deviation is 0.98 * 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 = 2446 old number = 0 * TYR M 7 TYR M 93 Total number of residues that need to be changed and total number of residues: ALA 0 10 CYS 0 2 ASP 0 8 GLU 0 12 PHE 0 2 GLY 0 2 HIS 0 12 ILE 0 10 LYS 0 12 LEU 0 16 MET 0 4 ASN 0 8 PRO 0 6 GLN 0 6 ARG 0 4 SER 0 8 THR 0 6 VAL 0 22 TYR 2 2 Processing NMR model 13 ** Unrecognized atom type [ O2 ] in residue HIS M 76 ** Unrecognized atom type [ O2 ] in residue HIS M 162 Chain break between 76 (M 76 ) and 77 (M 87 ) Average value of CA-N-C-CB angle is 34.23 Standard deviation is 1.03 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2446 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 10 CYS 0 2 ASP 0 8 GLU 0 12 PHE 0 2 GLY 0 2 HIS 0 12 ILE 0 10 LYS 0 12 LEU 0 16 MET 0 4 ASN 0 8 PRO 0 6 GLN 0 6 ARG 0 4 SER 0 8 THR 0 6 VAL 0 22 TYR 0 2 Processing NMR model 14 ** Unrecognized atom type [ O2 ] in residue HIS M 76 ** Unrecognized atom type [ O2 ] in residue HIS M 162 Chain break between 76 (M 76 ) and 77 (M 87 ) Average value of CA-N-C-CB angle is 34.19 Standard deviation is 1.09 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2446 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 10 CYS 0 2 ASP 0 8 GLU 0 12 PHE 0 2 GLY 0 2 HIS 0 12 ILE 0 10 LYS 0 12 LEU 0 16 MET 0 4 ASN 0 8 PRO 0 6 GLN 0 6 ARG 0 4 SER 0 8 THR 0 6 VAL 0 22 TYR 0 2 Processing NMR model 15 ** Unrecognized atom type [ O2 ] in residue HIS M 76 ** Unrecognized atom type [ O2 ] in residue HIS M 162 Chain break between 76 (M 76 ) and 77 (M 87 ) Average value of CA-N-C-CB angle is 34.18 Standard deviation is 1.03 * 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 = 2446 old number = 0 * PHE M 60 PHE M 146 Total number of residues that need to be changed and total number of residues: ALA 0 10 CYS 0 2 ASP 0 8 GLU 0 12 PHE 2 2 GLY 0 2 HIS 0 12 ILE 0 10 LYS 0 12 LEU 0 16 MET 0 4 ASN 0 8 PRO 0 6 GLN 0 6 ARG 0 4 SER 0 8 THR 0 6 VAL 0 22 TYR 0 2 Processing NMR model 16 ** Unrecognized atom type [ O2 ] in residue HIS M 76 ** Unrecognized atom type [ O2 ] in residue HIS M 162 Chain break between 76 (M 76 ) and 77 (M 87 ) Average value of CA-N-C-CB angle is 34.21 Standard deviation is 1.05 * 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 = 2446 old number = 0 * PHE M 60 PHE M 146 Total number of residues that need to be changed and total number of residues: ALA 0 10 CYS 0 2 ASP 0 8 GLU 0 12 PHE 2 2 GLY 0 2 HIS 0 12 ILE 0 10 LYS 0 12 LEU 0 16 MET 0 4 ASN 0 8 PRO 0 6 GLN 0 6 ARG 0 4 SER 0 8 THR 0 6 VAL 0 22 TYR 0 2 Processing NMR model 17 ** Unrecognized atom type [ O2 ] in residue HIS M 76 ** Unrecognized atom type [ O2 ] in residue HIS M 162 Chain break between 76 (M 76 ) and 77 (M 87 ) Average value of CA-N-C-CB angle is 34.18 Standard deviation is 1.01 * 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 = 2446 old number = 0 * TYR M 7 TYR M 93 Total number of residues that need to be changed and total number of residues: ALA 0 10 CYS 0 2 ASP 0 8 GLU 0 12 PHE 0 2 GLY 0 2 HIS 0 12 ILE 0 10 LYS 0 12 LEU 0 16 MET 0 4 ASN 0 8 PRO 0 6 GLN 0 6 ARG 0 4 SER 0 8 THR 0 6 VAL 0 22 TYR 2 2 Processing NMR model 18 ** Unrecognized atom type [ O2 ] in residue HIS M 76 ** Unrecognized atom type [ O2 ] in residue HIS M 162 Chain break between 76 (M 76 ) and 77 (M 87 ) Average value of CA-N-C-CB angle is 34.19 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 = 2446 old number = 0 * TYR M 7 TYR M 93 Total number of residues that need to be changed and total number of residues: ALA 0 10 CYS 0 2 ASP 0 8 GLU 0 12 PHE 0 2 GLY 0 2 HIS 0 12 ILE 0 10 LYS 0 12 LEU 0 16 MET 0 4 ASN 0 8 PRO 0 6 GLN 0 6 ARG 0 4 SER 0 8 THR 0 6 VAL 0 22 TYR 2 2 Processing NMR model 19 ** Unrecognized atom type [ O2 ] in residue HIS M 76 ** Unrecognized atom type [ O2 ] in residue HIS M 162 Chain break between 76 (M 76 ) and 77 (M 87 ) Average value of CA-N-C-CB angle is 34.21 Standard deviation is 1.09 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2446 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 10 CYS 0 2 ASP 0 8 GLU 0 12 PHE 0 2 GLY 0 2 HIS 0 12 ILE 0 10 LYS 0 12 LEU 0 16 MET 0 4 ASN 0 8 PRO 0 6 GLN 0 6 ARG 0 4 SER 0 8 THR 0 6 VAL 0 22 TYR 0 2 Processing NMR model 20 ** Unrecognized atom type [ O2 ] in residue HIS M 76 ** Unrecognized atom type [ O2 ] in residue HIS M 162 Chain break between 76 (M 76 ) and 77 (M 87 ) Average value of CA-N-C-CB angle is 34.16 Standard deviation is 1.06 * 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 = 2446 old number = 0 * TYR M 7 TYR M 93 Total number of residues that need to be changed and total number of residues: ALA 0 10 CYS 0 2 ASP 0 8 GLU 0 12 PHE 0 2 GLY 0 2 HIS 0 12 ILE 0 10 LYS 0 12 LEU 0 16 MET 0 4 ASN 0 8 PRO 0 6 GLN 0 6 ARG 0 4 SER 0 8 THR 0 6 VAL 0 22 TYR 2 2 * NMR ensemble comprises 20 model structures * Program completed