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 129 Average value of CA-N-C-CB angle is 34.23 Standard deviation is 0.73 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2138 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 9 CYS 0 1 ASP 0 2 GLU 0 18 PHE 0 4 GLY 0 3 HIS 0 8 ILE 0 7 LYS 0 16 LEU 0 15 MET 0 1 ASN 0 10 PRO 0 1 GLN 0 1 ARG 0 3 SER 0 10 THR 0 4 VAL 0 9 TRP 0 3 TYR 0 4 Processing NMR model 2 ** Unrecognized atom type [ O2 ] in residue HIS A 129 Average value of CA-N-C-CB angle is 34.16 Standard deviation is 0.76 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2138 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 9 CYS 0 1 ASP 0 2 GLU 0 18 PHE 0 4 GLY 0 3 HIS 0 8 ILE 0 7 LYS 0 16 LEU 0 15 MET 0 1 ASN 0 10 PRO 0 1 GLN 0 1 ARG 0 3 SER 0 10 THR 0 4 VAL 0 9 TRP 0 3 TYR 0 4 Processing NMR model 3 ** Unrecognized atom type [ O2 ] in residue HIS A 129 Average value of CA-N-C-CB angle is 34.19 Standard deviation is 0.68 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2138 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 9 CYS 0 1 ASP 0 2 GLU 0 18 PHE 0 4 GLY 0 3 HIS 0 8 ILE 0 7 LYS 0 16 LEU 0 15 MET 0 1 ASN 0 10 PRO 0 1 GLN 0 1 ARG 0 3 SER 0 10 THR 0 4 VAL 0 9 TRP 0 3 TYR 0 4 Processing NMR model 4 ** Unrecognized atom type [ O2 ] in residue HIS A 129 Average value of CA-N-C-CB angle is 34.23 Standard deviation is 0.66 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2138 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 9 CYS 0 1 ASP 0 2 GLU 0 18 PHE 0 4 GLY 0 3 HIS 0 8 ILE 0 7 LYS 0 16 LEU 0 15 MET 0 1 ASN 0 10 PRO 0 1 GLN 0 1 ARG 0 3 SER 0 10 THR 0 4 VAL 0 9 TRP 0 3 TYR 0 4 Processing NMR model 5 ** Unrecognized atom type [ O2 ] in residue HIS A 129 Average value of CA-N-C-CB angle is 34.16 Standard deviation is 0.69 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2138 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 9 CYS 0 1 ASP 0 2 GLU 0 18 PHE 0 4 GLY 0 3 HIS 0 8 ILE 0 7 LYS 0 16 LEU 0 15 MET 0 1 ASN 0 10 PRO 0 1 GLN 0 1 ARG 0 3 SER 0 10 THR 0 4 VAL 0 9 TRP 0 3 TYR 0 4 Processing NMR model 6 ** Unrecognized atom type [ O2 ] in residue HIS A 129 Average value of CA-N-C-CB angle is 34.26 Standard deviation is 0.79 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2138 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 9 CYS 0 1 ASP 0 2 GLU 0 18 PHE 0 4 GLY 0 3 HIS 0 8 ILE 0 7 LYS 0 16 LEU 0 15 MET 0 1 ASN 0 10 PRO 0 1 GLN 0 1 ARG 0 3 SER 0 10 THR 0 4 VAL 0 9 TRP 0 3 TYR 0 4 Processing NMR model 7 ** Unrecognized atom type [ O2 ] in residue HIS A 129 Average value of CA-N-C-CB angle is 34.17 Standard deviation is 0.72 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2138 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 9 CYS 0 1 ASP 0 2 GLU 0 18 PHE 0 4 GLY 0 3 HIS 0 8 ILE 0 7 LYS 0 16 LEU 0 15 MET 0 1 ASN 0 10 PRO 0 1 GLN 0 1 ARG 0 3 SER 0 10 THR 0 4 VAL 0 9 TRP 0 3 TYR 0 4 Processing NMR model 8 ** Unrecognized atom type [ O2 ] in residue HIS A 129 Average value of CA-N-C-CB angle is 34.27 Standard deviation is 0.69 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2138 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 9 CYS 0 1 ASP 0 2 GLU 0 18 PHE 0 4 GLY 0 3 HIS 0 8 ILE 0 7 LYS 0 16 LEU 0 15 MET 0 1 ASN 0 10 PRO 0 1 GLN 0 1 ARG 0 3 SER 0 10 THR 0 4 VAL 0 9 TRP 0 3 TYR 0 4 Processing NMR model 9 ** Unrecognized atom type [ O2 ] in residue HIS A 129 Average value of CA-N-C-CB angle is 34.21 Standard deviation is 0.64 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2138 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 9 CYS 0 1 ASP 0 2 GLU 0 18 PHE 0 4 GLY 0 3 HIS 0 8 ILE 0 7 LYS 0 16 LEU 0 15 MET 0 1 ASN 0 10 PRO 0 1 GLN 0 1 ARG 0 3 SER 0 10 THR 0 4 VAL 0 9 TRP 0 3 TYR 0 4 Processing NMR model 10 ** Unrecognized atom type [ O2 ] in residue HIS A 129 Average value of CA-N-C-CB angle is 34.19 Standard deviation is 0.77 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2138 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 9 CYS 0 1 ASP 0 2 GLU 0 18 PHE 0 4 GLY 0 3 HIS 0 8 ILE 0 7 LYS 0 16 LEU 0 15 MET 0 1 ASN 0 10 PRO 0 1 GLN 0 1 ARG 0 3 SER 0 10 THR 0 4 VAL 0 9 TRP 0 3 TYR 0 4 Processing NMR model 11 ** Unrecognized atom type [ O2 ] in residue HIS A 129 Average value of CA-N-C-CB angle is 34.32 Standard deviation is 0.72 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2138 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 9 CYS 0 1 ASP 0 2 GLU 0 18 PHE 0 4 GLY 0 3 HIS 0 8 ILE 0 7 LYS 0 16 LEU 0 15 MET 0 1 ASN 0 10 PRO 0 1 GLN 0 1 ARG 0 3 SER 0 10 THR 0 4 VAL 0 9 TRP 0 3 TYR 0 4 Processing NMR model 12 ** Unrecognized atom type [ O2 ] in residue HIS A 129 Average value of CA-N-C-CB angle is 34.17 Standard deviation is 0.72 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2138 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 9 CYS 0 1 ASP 0 2 GLU 0 18 PHE 0 4 GLY 0 3 HIS 0 8 ILE 0 7 LYS 0 16 LEU 0 15 MET 0 1 ASN 0 10 PRO 0 1 GLN 0 1 ARG 0 3 SER 0 10 THR 0 4 VAL 0 9 TRP 0 3 TYR 0 4 Processing NMR model 13 ** Unrecognized atom type [ O2 ] in residue HIS A 129 Average value of CA-N-C-CB angle is 34.24 Standard deviation is 0.72 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2138 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 9 CYS 0 1 ASP 0 2 GLU 0 18 PHE 0 4 GLY 0 3 HIS 0 8 ILE 0 7 LYS 0 16 LEU 0 15 MET 0 1 ASN 0 10 PRO 0 1 GLN 0 1 ARG 0 3 SER 0 10 THR 0 4 VAL 0 9 TRP 0 3 TYR 0 4 Processing NMR model 14 ** Unrecognized atom type [ O2 ] in residue HIS A 129 Average value of CA-N-C-CB angle is 34.27 Standard deviation is 0.67 * 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 = 2138 old number = 0 * PHE A 117 Total number of residues that need to be changed and total number of residues: ALA 0 9 CYS 0 1 ASP 0 2 GLU 0 18 PHE 1 4 GLY 0 3 HIS 0 8 ILE 0 7 LYS 0 16 LEU 0 15 MET 0 1 ASN 0 10 PRO 0 1 GLN 0 1 ARG 0 3 SER 0 10 THR 0 4 VAL 0 9 TRP 0 3 TYR 0 4 Processing NMR model 15 ** Unrecognized atom type [ O2 ] in residue HIS A 129 Average value of CA-N-C-CB angle is 34.23 Standard deviation is 0.70 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2138 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 9 CYS 0 1 ASP 0 2 GLU 0 18 PHE 0 4 GLY 0 3 HIS 0 8 ILE 0 7 LYS 0 16 LEU 0 15 MET 0 1 ASN 0 10 PRO 0 1 GLN 0 1 ARG 0 3 SER 0 10 THR 0 4 VAL 0 9 TRP 0 3 TYR 0 4 Processing NMR model 16 ** Unrecognized atom type [ O2 ] in residue HIS A 129 Average value of CA-N-C-CB angle is 34.23 Standard deviation is 0.74 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2138 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 9 CYS 0 1 ASP 0 2 GLU 0 18 PHE 0 4 GLY 0 3 HIS 0 8 ILE 0 7 LYS 0 16 LEU 0 15 MET 0 1 ASN 0 10 PRO 0 1 GLN 0 1 ARG 0 3 SER 0 10 THR 0 4 VAL 0 9 TRP 0 3 TYR 0 4 Processing NMR model 17 ** Unrecognized atom type [ O2 ] in residue HIS A 129 Average value of CA-N-C-CB angle is 34.21 Standard deviation is 0.69 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2138 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 9 CYS 0 1 ASP 0 2 GLU 0 18 PHE 0 4 GLY 0 3 HIS 0 8 ILE 0 7 LYS 0 16 LEU 0 15 MET 0 1 ASN 0 10 PRO 0 1 GLN 0 1 ARG 0 3 SER 0 10 THR 0 4 VAL 0 9 TRP 0 3 TYR 0 4 Processing NMR model 18 ** Unrecognized atom type [ O2 ] in residue HIS A 129 Average value of CA-N-C-CB angle is 34.26 Standard deviation is 0.68 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2138 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 9 CYS 0 1 ASP 0 2 GLU 0 18 PHE 0 4 GLY 0 3 HIS 0 8 ILE 0 7 LYS 0 16 LEU 0 15 MET 0 1 ASN 0 10 PRO 0 1 GLN 0 1 ARG 0 3 SER 0 10 THR 0 4 VAL 0 9 TRP 0 3 TYR 0 4 Processing NMR model 19 ** Unrecognized atom type [ O2 ] in residue HIS A 129 Average value of CA-N-C-CB angle is 34.26 Standard deviation is 0.67 * 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 = 2138 old number = 0 * GLU A 92 Total number of residues that need to be changed and total number of residues: ALA 0 9 CYS 0 1 ASP 0 2 GLU 1 18 PHE 0 4 GLY 0 3 HIS 0 8 ILE 0 7 LYS 0 16 LEU 0 15 MET 0 1 ASN 0 10 PRO 0 1 GLN 0 1 ARG 0 3 SER 0 10 THR 0 4 VAL 0 9 TRP 0 3 TYR 0 4 Processing NMR model 20 ** Unrecognized atom type [ O2 ] in residue HIS A 129 Average value of CA-N-C-CB angle is 34.22 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 = 2138 old number = 0 * GLU A 44 Total number of residues that need to be changed and total number of residues: ALA 0 9 CYS 0 1 ASP 0 2 GLU 1 18 PHE 0 4 GLY 0 3 HIS 0 8 ILE 0 7 LYS 0 16 LEU 0 15 MET 0 1 ASN 0 10 PRO 0 1 GLN 0 1 ARG 0 3 SER 0 10 THR 0 4 VAL 0 9 TRP 0 3 TYR 0 4 * NMR ensemble comprises 20 model structures * Program completed