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 125 Average value of CA-N-C-CB angle is 35.67 Standard deviation is 0.73 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2070 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 6 ASP 0 11 GLU 0 7 PHE 0 4 GLY 0 6 HIS 0 11 ILE 0 9 LYS 0 12 LEU 0 11 MET 0 3 ASN 0 5 PRO 0 8 GLN 0 5 ARG 0 5 SER 0 4 THR 0 3 VAL 0 6 TRP 0 3 TYR 0 6 Processing NMR model 2 ** Unrecognized atom type [ O2 ] in residue HIS A 125 Average value of CA-N-C-CB angle is 35.65 Standard deviation is 0.71 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2070 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 6 ASP 0 11 GLU 0 7 PHE 0 4 GLY 0 6 HIS 0 11 ILE 0 9 LYS 0 12 LEU 0 11 MET 0 3 ASN 0 5 PRO 0 8 GLN 0 5 ARG 0 5 SER 0 4 THR 0 3 VAL 0 6 TRP 0 3 TYR 0 6 Processing NMR model 3 ** Unrecognized atom type [ O2 ] in residue HIS A 125 Average value of CA-N-C-CB angle is 35.67 Standard deviation is 0.73 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2070 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 6 ASP 0 11 GLU 0 7 PHE 0 4 GLY 0 6 HIS 0 11 ILE 0 9 LYS 0 12 LEU 0 11 MET 0 3 ASN 0 5 PRO 0 8 GLN 0 5 ARG 0 5 SER 0 4 THR 0 3 VAL 0 6 TRP 0 3 TYR 0 6 Processing NMR model 4 ** Unrecognized atom type [ O2 ] in residue HIS A 125 Average value of CA-N-C-CB angle is 35.70 Standard deviation is 0.76 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2070 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 6 ASP 0 11 GLU 0 7 PHE 0 4 GLY 0 6 HIS 0 11 ILE 0 9 LYS 0 12 LEU 0 11 MET 0 3 ASN 0 5 PRO 0 8 GLN 0 5 ARG 0 5 SER 0 4 THR 0 3 VAL 0 6 TRP 0 3 TYR 0 6 Processing NMR model 5 ** Unrecognized atom type [ O2 ] in residue HIS A 125 Average value of CA-N-C-CB angle is 35.62 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 = 2070 old number = 0 * PHE A 25 Total number of residues that need to be changed and total number of residues: ALA 0 6 ASP 0 11 GLU 0 7 PHE 1 4 GLY 0 6 HIS 0 11 ILE 0 9 LYS 0 12 LEU 0 11 MET 0 3 ASN 0 5 PRO 0 8 GLN 0 5 ARG 0 5 SER 0 4 THR 0 3 VAL 0 6 TRP 0 3 TYR 0 6 Processing NMR model 6 ** Unrecognized atom type [ O2 ] in residue HIS A 125 Average value of CA-N-C-CB angle is 35.69 Standard deviation is 0.72 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2070 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 6 ASP 0 11 GLU 0 7 PHE 0 4 GLY 0 6 HIS 0 11 ILE 0 9 LYS 0 12 LEU 0 11 MET 0 3 ASN 0 5 PRO 0 8 GLN 0 5 ARG 0 5 SER 0 4 THR 0 3 VAL 0 6 TRP 0 3 TYR 0 6 Processing NMR model 7 ** Unrecognized atom type [ O2 ] in residue HIS A 125 Average value of CA-N-C-CB angle is 35.68 Standard deviation is 0.78 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2070 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 6 ASP 0 11 GLU 0 7 PHE 0 4 GLY 0 6 HIS 0 11 ILE 0 9 LYS 0 12 LEU 0 11 MET 0 3 ASN 0 5 PRO 0 8 GLN 0 5 ARG 0 5 SER 0 4 THR 0 3 VAL 0 6 TRP 0 3 TYR 0 6 Processing NMR model 8 ** Unrecognized atom type [ O2 ] in residue HIS A 125 Average value of CA-N-C-CB angle is 35.63 Standard deviation is 0.77 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2070 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 6 ASP 0 11 GLU 0 7 PHE 0 4 GLY 0 6 HIS 0 11 ILE 0 9 LYS 0 12 LEU 0 11 MET 0 3 ASN 0 5 PRO 0 8 GLN 0 5 ARG 0 5 SER 0 4 THR 0 3 VAL 0 6 TRP 0 3 TYR 0 6 Processing NMR model 9 ** Unrecognized atom type [ O2 ] in residue HIS A 125 Average value of CA-N-C-CB angle is 35.60 Standard deviation is 0.72 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2070 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 6 ASP 0 11 GLU 0 7 PHE 0 4 GLY 0 6 HIS 0 11 ILE 0 9 LYS 0 12 LEU 0 11 MET 0 3 ASN 0 5 PRO 0 8 GLN 0 5 ARG 0 5 SER 0 4 THR 0 3 VAL 0 6 TRP 0 3 TYR 0 6 Processing NMR model 10 ** Unrecognized atom type [ O2 ] in residue HIS A 125 Average value of CA-N-C-CB angle is 35.59 Standard deviation is 0.75 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2070 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 6 ASP 0 11 GLU 0 7 PHE 0 4 GLY 0 6 HIS 0 11 ILE 0 9 LYS 0 12 LEU 0 11 MET 0 3 ASN 0 5 PRO 0 8 GLN 0 5 ARG 0 5 SER 0 4 THR 0 3 VAL 0 6 TRP 0 3 TYR 0 6 Processing NMR model 11 ** Unrecognized atom type [ O2 ] in residue HIS A 125 Average value of CA-N-C-CB angle is 35.67 Standard deviation is 0.71 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2070 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 6 ASP 0 11 GLU 0 7 PHE 0 4 GLY 0 6 HIS 0 11 ILE 0 9 LYS 0 12 LEU 0 11 MET 0 3 ASN 0 5 PRO 0 8 GLN 0 5 ARG 0 5 SER 0 4 THR 0 3 VAL 0 6 TRP 0 3 TYR 0 6 Processing NMR model 12 ** Unrecognized atom type [ O2 ] in residue HIS A 125 Average value of CA-N-C-CB angle is 35.66 Standard deviation is 0.73 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2070 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 6 ASP 0 11 GLU 0 7 PHE 0 4 GLY 0 6 HIS 0 11 ILE 0 9 LYS 0 12 LEU 0 11 MET 0 3 ASN 0 5 PRO 0 8 GLN 0 5 ARG 0 5 SER 0 4 THR 0 3 VAL 0 6 TRP 0 3 TYR 0 6 Processing NMR model 13 ** Unrecognized atom type [ O2 ] in residue HIS A 125 Average value of CA-N-C-CB angle is 35.64 Standard deviation is 0.74 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2070 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 6 ASP 0 11 GLU 0 7 PHE 0 4 GLY 0 6 HIS 0 11 ILE 0 9 LYS 0 12 LEU 0 11 MET 0 3 ASN 0 5 PRO 0 8 GLN 0 5 ARG 0 5 SER 0 4 THR 0 3 VAL 0 6 TRP 0 3 TYR 0 6 Processing NMR model 14 ** Unrecognized atom type [ O2 ] in residue HIS A 125 Average value of CA-N-C-CB angle is 35.67 Standard deviation is 0.73 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2070 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 6 ASP 0 11 GLU 0 7 PHE 0 4 GLY 0 6 HIS 0 11 ILE 0 9 LYS 0 12 LEU 0 11 MET 0 3 ASN 0 5 PRO 0 8 GLN 0 5 ARG 0 5 SER 0 4 THR 0 3 VAL 0 6 TRP 0 3 TYR 0 6 Processing NMR model 15 ** Unrecognized atom type [ O2 ] in residue HIS A 125 Average value of CA-N-C-CB angle is 35.62 Standard deviation is 0.73 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2070 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 6 ASP 0 11 GLU 0 7 PHE 0 4 GLY 0 6 HIS 0 11 ILE 0 9 LYS 0 12 LEU 0 11 MET 0 3 ASN 0 5 PRO 0 8 GLN 0 5 ARG 0 5 SER 0 4 THR 0 3 VAL 0 6 TRP 0 3 TYR 0 6 Processing NMR model 16 ** Unrecognized atom type [ O2 ] in residue HIS A 125 Average value of CA-N-C-CB angle is 35.61 Standard deviation is 0.71 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2070 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 6 ASP 0 11 GLU 0 7 PHE 0 4 GLY 0 6 HIS 0 11 ILE 0 9 LYS 0 12 LEU 0 11 MET 0 3 ASN 0 5 PRO 0 8 GLN 0 5 ARG 0 5 SER 0 4 THR 0 3 VAL 0 6 TRP 0 3 TYR 0 6 Processing NMR model 17 ** Unrecognized atom type [ O2 ] in residue HIS A 125 Average value of CA-N-C-CB angle is 35.70 Standard deviation is 0.80 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2070 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 6 ASP 0 11 GLU 0 7 PHE 0 4 GLY 0 6 HIS 0 11 ILE 0 9 LYS 0 12 LEU 0 11 MET 0 3 ASN 0 5 PRO 0 8 GLN 0 5 ARG 0 5 SER 0 4 THR 0 3 VAL 0 6 TRP 0 3 TYR 0 6 Processing NMR model 18 ** Unrecognized atom type [ O2 ] in residue HIS A 125 Average value of CA-N-C-CB angle is 35.55 Standard deviation is 0.72 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2070 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 6 ASP 0 11 GLU 0 7 PHE 0 4 GLY 0 6 HIS 0 11 ILE 0 9 LYS 0 12 LEU 0 11 MET 0 3 ASN 0 5 PRO 0 8 GLN 0 5 ARG 0 5 SER 0 4 THR 0 3 VAL 0 6 TRP 0 3 TYR 0 6 Processing NMR model 19 ** Unrecognized atom type [ O2 ] in residue HIS A 125 Average value of CA-N-C-CB angle is 35.67 Standard deviation is 0.80 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2070 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 6 ASP 0 11 GLU 0 7 PHE 0 4 GLY 0 6 HIS 0 11 ILE 0 9 LYS 0 12 LEU 0 11 MET 0 3 ASN 0 5 PRO 0 8 GLN 0 5 ARG 0 5 SER 0 4 THR 0 3 VAL 0 6 TRP 0 3 TYR 0 6 Processing NMR model 20 ** Unrecognized atom type [ O2 ] in residue HIS A 125 Average value of CA-N-C-CB angle is 35.66 Standard deviation is 0.76 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2070 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 6 ASP 0 11 GLU 0 7 PHE 0 4 GLY 0 6 HIS 0 11 ILE 0 9 LYS 0 12 LEU 0 11 MET 0 3 ASN 0 5 PRO 0 8 GLN 0 5 ARG 0 5 SER 0 4 THR 0 3 VAL 0 6 TRP 0 3 TYR 0 6 * NMR ensemble comprises 20 model structures * Program completed