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 166 Average value of CA-N-C-CB angle is 34.34 Standard deviation is 1.33 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2494 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 14 CYS 0 2 ASP 0 8 GLU 0 16 PHE 0 9 GLY 0 18 HIS 0 8 ILE 0 5 LYS 0 4 LEU 0 18 MET 0 5 ASN 0 2 PRO 0 10 GLN 0 5 ARG 0 5 SER 0 12 THR 0 7 VAL 0 10 TRP 0 1 TYR 0 7 Processing NMR model 2 ** Unrecognized atom type [ O2 ] in residue HIS A 166 Average value of CA-N-C-CB angle is 34.41 Standard deviation is 1.28 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2494 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 14 CYS 0 2 ASP 0 8 GLU 0 16 PHE 0 9 GLY 0 18 HIS 0 8 ILE 0 5 LYS 0 4 LEU 0 18 MET 0 5 ASN 0 2 PRO 0 10 GLN 0 5 ARG 0 5 SER 0 12 THR 0 7 VAL 0 10 TRP 0 1 TYR 0 7 Processing NMR model 3 ** Unrecognized atom type [ O2 ] in residue HIS A 166 Average value of CA-N-C-CB angle is 34.37 Standard deviation is 1.30 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2494 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 14 CYS 0 2 ASP 0 8 GLU 0 16 PHE 0 9 GLY 0 18 HIS 0 8 ILE 0 5 LYS 0 4 LEU 0 18 MET 0 5 ASN 0 2 PRO 0 10 GLN 0 5 ARG 0 5 SER 0 12 THR 0 7 VAL 0 10 TRP 0 1 TYR 0 7 Processing NMR model 4 ** Unrecognized atom type [ O2 ] in residue HIS A 166 Average value of CA-N-C-CB angle is 34.42 Standard deviation is 1.29 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2494 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 14 CYS 0 2 ASP 0 8 GLU 0 16 PHE 0 9 GLY 0 18 HIS 0 8 ILE 0 5 LYS 0 4 LEU 0 18 MET 0 5 ASN 0 2 PRO 0 10 GLN 0 5 ARG 0 5 SER 0 12 THR 0 7 VAL 0 10 TRP 0 1 TYR 0 7 Processing NMR model 5 ** Unrecognized atom type [ O2 ] in residue HIS A 166 Average value of CA-N-C-CB angle is 34.39 Standard deviation is 1.21 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2494 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 14 CYS 0 2 ASP 0 8 GLU 0 16 PHE 0 9 GLY 0 18 HIS 0 8 ILE 0 5 LYS 0 4 LEU 0 18 MET 0 5 ASN 0 2 PRO 0 10 GLN 0 5 ARG 0 5 SER 0 12 THR 0 7 VAL 0 10 TRP 0 1 TYR 0 7 Processing NMR model 6 ** Unrecognized atom type [ O2 ] in residue HIS A 166 Average value of CA-N-C-CB angle is 34.46 Standard deviation is 1.19 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2494 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 14 CYS 0 2 ASP 0 8 GLU 0 16 PHE 0 9 GLY 0 18 HIS 0 8 ILE 0 5 LYS 0 4 LEU 0 18 MET 0 5 ASN 0 2 PRO 0 10 GLN 0 5 ARG 0 5 SER 0 12 THR 0 7 VAL 0 10 TRP 0 1 TYR 0 7 Processing NMR model 7 ** Unrecognized atom type [ O2 ] in residue HIS A 166 Average value of CA-N-C-CB angle is 34.39 Standard deviation is 1.28 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2494 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 14 CYS 0 2 ASP 0 8 GLU 0 16 PHE 0 9 GLY 0 18 HIS 0 8 ILE 0 5 LYS 0 4 LEU 0 18 MET 0 5 ASN 0 2 PRO 0 10 GLN 0 5 ARG 0 5 SER 0 12 THR 0 7 VAL 0 10 TRP 0 1 TYR 0 7 Processing NMR model 8 ** Unrecognized atom type [ O2 ] in residue HIS A 166 Average value of CA-N-C-CB angle is 34.37 Standard deviation is 1.26 * 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 = 2494 old number = 0 * GLU A 36 Total number of residues that need to be changed and total number of residues: ALA 0 14 CYS 0 2 ASP 0 8 GLU 1 16 PHE 0 9 GLY 0 18 HIS 0 8 ILE 0 5 LYS 0 4 LEU 0 18 MET 0 5 ASN 0 2 PRO 0 10 GLN 0 5 ARG 0 5 SER 0 12 THR 0 7 VAL 0 10 TRP 0 1 TYR 0 7 Processing NMR model 9 ** Unrecognized atom type [ O2 ] in residue HIS A 166 Average value of CA-N-C-CB angle is 34.38 Standard deviation is 1.31 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2494 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 14 CYS 0 2 ASP 0 8 GLU 0 16 PHE 0 9 GLY 0 18 HIS 0 8 ILE 0 5 LYS 0 4 LEU 0 18 MET 0 5 ASN 0 2 PRO 0 10 GLN 0 5 ARG 0 5 SER 0 12 THR 0 7 VAL 0 10 TRP 0 1 TYR 0 7 Processing NMR model 10 ** Unrecognized atom type [ O2 ] in residue HIS A 166 Average value of CA-N-C-CB angle is 34.42 Standard deviation is 1.24 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2494 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 14 CYS 0 2 ASP 0 8 GLU 0 16 PHE 0 9 GLY 0 18 HIS 0 8 ILE 0 5 LYS 0 4 LEU 0 18 MET 0 5 ASN 0 2 PRO 0 10 GLN 0 5 ARG 0 5 SER 0 12 THR 0 7 VAL 0 10 TRP 0 1 TYR 0 7 Processing NMR model 11 ** Unrecognized atom type [ O2 ] in residue HIS A 166 Average value of CA-N-C-CB angle is 34.44 Standard deviation is 1.23 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2494 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 14 CYS 0 2 ASP 0 8 GLU 0 16 PHE 0 9 GLY 0 18 HIS 0 8 ILE 0 5 LYS 0 4 LEU 0 18 MET 0 5 ASN 0 2 PRO 0 10 GLN 0 5 ARG 0 5 SER 0 12 THR 0 7 VAL 0 10 TRP 0 1 TYR 0 7 Processing NMR model 12 ** Unrecognized atom type [ O2 ] in residue HIS A 166 Average value of CA-N-C-CB angle is 34.42 Standard deviation is 1.25 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2494 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 14 CYS 0 2 ASP 0 8 GLU 0 16 PHE 0 9 GLY 0 18 HIS 0 8 ILE 0 5 LYS 0 4 LEU 0 18 MET 0 5 ASN 0 2 PRO 0 10 GLN 0 5 ARG 0 5 SER 0 12 THR 0 7 VAL 0 10 TRP 0 1 TYR 0 7 Processing NMR model 13 ** Unrecognized atom type [ O2 ] in residue HIS A 166 Average value of CA-N-C-CB angle is 34.41 Standard deviation is 1.26 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2494 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 14 CYS 0 2 ASP 0 8 GLU 0 16 PHE 0 9 GLY 0 18 HIS 0 8 ILE 0 5 LYS 0 4 LEU 0 18 MET 0 5 ASN 0 2 PRO 0 10 GLN 0 5 ARG 0 5 SER 0 12 THR 0 7 VAL 0 10 TRP 0 1 TYR 0 7 Processing NMR model 14 ** Unrecognized atom type [ O2 ] in residue HIS A 166 Average value of CA-N-C-CB angle is 34.37 Standard deviation is 1.31 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2494 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 14 CYS 0 2 ASP 0 8 GLU 0 16 PHE 0 9 GLY 0 18 HIS 0 8 ILE 0 5 LYS 0 4 LEU 0 18 MET 0 5 ASN 0 2 PRO 0 10 GLN 0 5 ARG 0 5 SER 0 12 THR 0 7 VAL 0 10 TRP 0 1 TYR 0 7 Processing NMR model 15 ** Unrecognized atom type [ O2 ] in residue HIS A 166 Average value of CA-N-C-CB angle is 34.34 Standard deviation is 1.32 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2494 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 14 CYS 0 2 ASP 0 8 GLU 0 16 PHE 0 9 GLY 0 18 HIS 0 8 ILE 0 5 LYS 0 4 LEU 0 18 MET 0 5 ASN 0 2 PRO 0 10 GLN 0 5 ARG 0 5 SER 0 12 THR 0 7 VAL 0 10 TRP 0 1 TYR 0 7 Processing NMR model 16 ** Unrecognized atom type [ O2 ] in residue HIS A 166 Average value of CA-N-C-CB angle is 34.43 Standard deviation is 1.23 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2494 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 14 CYS 0 2 ASP 0 8 GLU 0 16 PHE 0 9 GLY 0 18 HIS 0 8 ILE 0 5 LYS 0 4 LEU 0 18 MET 0 5 ASN 0 2 PRO 0 10 GLN 0 5 ARG 0 5 SER 0 12 THR 0 7 VAL 0 10 TRP 0 1 TYR 0 7 Processing NMR model 17 ** Unrecognized atom type [ O2 ] in residue HIS A 166 Average value of CA-N-C-CB angle is 34.43 Standard deviation is 1.36 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2494 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 14 CYS 0 2 ASP 0 8 GLU 0 16 PHE 0 9 GLY 0 18 HIS 0 8 ILE 0 5 LYS 0 4 LEU 0 18 MET 0 5 ASN 0 2 PRO 0 10 GLN 0 5 ARG 0 5 SER 0 12 THR 0 7 VAL 0 10 TRP 0 1 TYR 0 7 Processing NMR model 18 ** Unrecognized atom type [ O2 ] in residue HIS A 166 Average value of CA-N-C-CB angle is 34.40 Standard deviation is 1.28 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2494 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 14 CYS 0 2 ASP 0 8 GLU 0 16 PHE 0 9 GLY 0 18 HIS 0 8 ILE 0 5 LYS 0 4 LEU 0 18 MET 0 5 ASN 0 2 PRO 0 10 GLN 0 5 ARG 0 5 SER 0 12 THR 0 7 VAL 0 10 TRP 0 1 TYR 0 7 Processing NMR model 19 ** Unrecognized atom type [ O2 ] in residue HIS A 166 Average value of CA-N-C-CB angle is 34.34 Standard deviation is 1.27 * 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 = 2494 old number = 0 * GLU A 157 Total number of residues that need to be changed and total number of residues: ALA 0 14 CYS 0 2 ASP 0 8 GLU 1 16 PHE 0 9 GLY 0 18 HIS 0 8 ILE 0 5 LYS 0 4 LEU 0 18 MET 0 5 ASN 0 2 PRO 0 10 GLN 0 5 ARG 0 5 SER 0 12 THR 0 7 VAL 0 10 TRP 0 1 TYR 0 7 Processing NMR model 20 ** Unrecognized atom type [ O2 ] in residue HIS A 166 Average value of CA-N-C-CB angle is 34.34 Standard deviation is 1.30 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2494 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 14 CYS 0 2 ASP 0 8 GLU 0 16 PHE 0 9 GLY 0 18 HIS 0 8 ILE 0 5 LYS 0 4 LEU 0 18 MET 0 5 ASN 0 2 PRO 0 10 GLN 0 5 ARG 0 5 SER 0 12 THR 0 7 VAL 0 10 TRP 0 1 TYR 0 7 * NMR ensemble comprises 20 model structures * Program completed