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 88 ** Unrecognized atom type [ O2 ] in residue HIS M 186 Chain break between 88 (M 88 ) and 89 (M 99 ) Average value of CA-N-C-CB angle is 34.24 Standard deviation is 0.62 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2856 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 4 CYS 0 2 ASP 0 12 GLU 0 6 PHE 0 10 GLY 0 12 HIS 0 12 ILE 0 16 LYS 0 14 LEU 0 16 MET 0 8 ASN 0 14 GLN 0 4 ARG 0 8 SER 0 4 THR 0 20 VAL 0 14 Processing NMR model 2 ** Unrecognized atom type [ O2 ] in residue HIS M 88 ** Unrecognized atom type [ O2 ] in residue HIS M 186 Chain break between 88 (M 88 ) and 89 (M 99 ) Average value of CA-N-C-CB angle is 34.28 Standard deviation is 0.59 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2856 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 4 CYS 0 2 ASP 0 12 GLU 0 6 PHE 0 10 GLY 0 12 HIS 0 12 ILE 0 16 LYS 0 14 LEU 0 16 MET 0 8 ASN 0 14 GLN 0 4 ARG 0 8 SER 0 4 THR 0 20 VAL 0 14 Processing NMR model 3 ** Unrecognized atom type [ O2 ] in residue HIS M 88 ** Unrecognized atom type [ O2 ] in residue HIS M 186 Chain break between 88 (M 88 ) and 89 (M 99 ) Average value of CA-N-C-CB angle is 34.21 Standard deviation is 0.57 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2856 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 4 CYS 0 2 ASP 0 12 GLU 0 6 PHE 0 10 GLY 0 12 HIS 0 12 ILE 0 16 LYS 0 14 LEU 0 16 MET 0 8 ASN 0 14 GLN 0 4 ARG 0 8 SER 0 4 THR 0 20 VAL 0 14 Processing NMR model 4 ** Unrecognized atom type [ O2 ] in residue HIS M 88 ** Unrecognized atom type [ O2 ] in residue HIS M 186 Chain break between 88 (M 88 ) and 89 (M 99 ) Average value of CA-N-C-CB angle is 34.17 Standard deviation is 0.63 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2856 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 4 CYS 0 2 ASP 0 12 GLU 0 6 PHE 0 10 GLY 0 12 HIS 0 12 ILE 0 16 LYS 0 14 LEU 0 16 MET 0 8 ASN 0 14 GLN 0 4 ARG 0 8 SER 0 4 THR 0 20 VAL 0 14 Processing NMR model 5 ** Unrecognized atom type [ O2 ] in residue HIS M 88 ** Unrecognized atom type [ O2 ] in residue HIS M 186 Chain break between 88 (M 88 ) and 89 (M 99 ) Average value of CA-N-C-CB angle is 34.19 Standard deviation is 0.71 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2856 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 4 CYS 0 2 ASP 0 12 GLU 0 6 PHE 0 10 GLY 0 12 HIS 0 12 ILE 0 16 LYS 0 14 LEU 0 16 MET 0 8 ASN 0 14 GLN 0 4 ARG 0 8 SER 0 4 THR 0 20 VAL 0 14 Processing NMR model 6 ** Unrecognized atom type [ O2 ] in residue HIS M 88 ** Unrecognized atom type [ O2 ] in residue HIS M 186 Chain break between 88 (M 88 ) and 89 (M 99 ) Average value of CA-N-C-CB angle is 34.20 Standard deviation is 0.57 * 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 = 2856 old number = 0 * PHE M 102 Total number of residues that need to be changed and total number of residues: ALA 0 4 CYS 0 2 ASP 0 12 GLU 0 6 PHE 1 10 GLY 0 12 HIS 0 12 ILE 0 16 LYS 0 14 LEU 0 16 MET 0 8 ASN 0 14 GLN 0 4 ARG 0 8 SER 0 4 THR 0 20 VAL 0 14 Processing NMR model 7 ** Unrecognized atom type [ O2 ] in residue HIS M 88 ** Unrecognized atom type [ O2 ] in residue HIS M 186 Chain break between 88 (M 88 ) and 89 (M 99 ) Average value of CA-N-C-CB angle is 34.22 Standard deviation is 0.64 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2856 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 4 CYS 0 2 ASP 0 12 GLU 0 6 PHE 0 10 GLY 0 12 HIS 0 12 ILE 0 16 LYS 0 14 LEU 0 16 MET 0 8 ASN 0 14 GLN 0 4 ARG 0 8 SER 0 4 THR 0 20 VAL 0 14 Processing NMR model 8 ** Unrecognized atom type [ O2 ] in residue HIS M 88 ** Unrecognized atom type [ O2 ] in residue HIS M 186 Chain break between 88 (M 88 ) and 89 (M 99 ) Average value of CA-N-C-CB angle is 34.17 Standard deviation is 0.62 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2856 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 4 CYS 0 2 ASP 0 12 GLU 0 6 PHE 0 10 GLY 0 12 HIS 0 12 ILE 0 16 LYS 0 14 LEU 0 16 MET 0 8 ASN 0 14 GLN 0 4 ARG 0 8 SER 0 4 THR 0 20 VAL 0 14 Processing NMR model 9 ** Unrecognized atom type [ O2 ] in residue HIS M 88 ** Unrecognized atom type [ O2 ] in residue HIS M 186 Chain break between 88 (M 88 ) and 89 (M 99 ) Average value of CA-N-C-CB angle is 34.23 Standard deviation is 0.58 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2856 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 4 CYS 0 2 ASP 0 12 GLU 0 6 PHE 0 10 GLY 0 12 HIS 0 12 ILE 0 16 LYS 0 14 LEU 0 16 MET 0 8 ASN 0 14 GLN 0 4 ARG 0 8 SER 0 4 THR 0 20 VAL 0 14 Processing NMR model 10 ** Unrecognized atom type [ O2 ] in residue HIS M 88 ** Unrecognized atom type [ O2 ] in residue HIS M 186 Chain break between 88 (M 88 ) and 89 (M 99 ) Average value of CA-N-C-CB angle is 34.21 Standard deviation is 0.63 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2856 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 4 CYS 0 2 ASP 0 12 GLU 0 6 PHE 0 10 GLY 0 12 HIS 0 12 ILE 0 16 LYS 0 14 LEU 0 16 MET 0 8 ASN 0 14 GLN 0 4 ARG 0 8 SER 0 4 THR 0 20 VAL 0 14 Processing NMR model 11 ** Unrecognized atom type [ O2 ] in residue HIS M 88 ** Unrecognized atom type [ O2 ] in residue HIS M 186 Chain break between 88 (M 88 ) and 89 (M 99 ) Average value of CA-N-C-CB angle is 34.16 Standard deviation is 0.62 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2856 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 4 CYS 0 2 ASP 0 12 GLU 0 6 PHE 0 10 GLY 0 12 HIS 0 12 ILE 0 16 LYS 0 14 LEU 0 16 MET 0 8 ASN 0 14 GLN 0 4 ARG 0 8 SER 0 4 THR 0 20 VAL 0 14 Processing NMR model 12 ** Unrecognized atom type [ O2 ] in residue HIS M 88 ** Unrecognized atom type [ O2 ] in residue HIS M 186 Chain break between 88 (M 88 ) and 89 (M 99 ) Average value of CA-N-C-CB angle is 34.17 Standard deviation is 0.59 * 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 = 2856 old number = 0 * PHE M 102 Total number of residues that need to be changed and total number of residues: ALA 0 4 CYS 0 2 ASP 0 12 GLU 0 6 PHE 1 10 GLY 0 12 HIS 0 12 ILE 0 16 LYS 0 14 LEU 0 16 MET 0 8 ASN 0 14 GLN 0 4 ARG 0 8 SER 0 4 THR 0 20 VAL 0 14 Processing NMR model 13 ** Unrecognized atom type [ O2 ] in residue HIS M 88 ** Unrecognized atom type [ O2 ] in residue HIS M 186 Chain break between 88 (M 88 ) and 89 (M 99 ) Average value of CA-N-C-CB angle is 34.20 Standard deviation is 0.61 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2856 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 4 CYS 0 2 ASP 0 12 GLU 0 6 PHE 0 10 GLY 0 12 HIS 0 12 ILE 0 16 LYS 0 14 LEU 0 16 MET 0 8 ASN 0 14 GLN 0 4 ARG 0 8 SER 0 4 THR 0 20 VAL 0 14 Processing NMR model 14 ** Unrecognized atom type [ O2 ] in residue HIS M 88 ** Unrecognized atom type [ O2 ] in residue HIS M 186 Chain break between 88 (M 88 ) and 89 (M 99 ) Average value of CA-N-C-CB angle is 34.22 Standard deviation is 0.64 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2856 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 4 CYS 0 2 ASP 0 12 GLU 0 6 PHE 0 10 GLY 0 12 HIS 0 12 ILE 0 16 LYS 0 14 LEU 0 16 MET 0 8 ASN 0 14 GLN 0 4 ARG 0 8 SER 0 4 THR 0 20 VAL 0 14 Processing NMR model 15 ** Unrecognized atom type [ O2 ] in residue HIS M 88 ** Unrecognized atom type [ O2 ] in residue HIS M 186 Chain break between 88 (M 88 ) and 89 (M 99 ) Average value of CA-N-C-CB angle is 34.17 Standard deviation is 0.61 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2856 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 4 CYS 0 2 ASP 0 12 GLU 0 6 PHE 0 10 GLY 0 12 HIS 0 12 ILE 0 16 LYS 0 14 LEU 0 16 MET 0 8 ASN 0 14 GLN 0 4 ARG 0 8 SER 0 4 THR 0 20 VAL 0 14 Processing NMR model 16 ** Unrecognized atom type [ O2 ] in residue HIS M 88 ** Unrecognized atom type [ O2 ] in residue HIS M 186 Chain break between 88 (M 88 ) and 89 (M 99 ) Average value of CA-N-C-CB angle is 34.20 Standard deviation is 0.58 * 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 = 2856 old number = 0 * ASP M 30 ASP M 57 Total number of residues that need to be changed and total number of residues: ALA 0 4 CYS 0 2 ASP 2 12 GLU 0 6 PHE 0 10 GLY 0 12 HIS 0 12 ILE 0 16 LYS 0 14 LEU 0 16 MET 0 8 ASN 0 14 GLN 0 4 ARG 0 8 SER 0 4 THR 0 20 VAL 0 14 Processing NMR model 17 ** Unrecognized atom type [ O2 ] in residue HIS M 88 ** Unrecognized atom type [ O2 ] in residue HIS M 186 Chain break between 88 (M 88 ) and 89 (M 99 ) Average value of CA-N-C-CB angle is 34.22 Standard deviation is 0.59 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2856 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 4 CYS 0 2 ASP 0 12 GLU 0 6 PHE 0 10 GLY 0 12 HIS 0 12 ILE 0 16 LYS 0 14 LEU 0 16 MET 0 8 ASN 0 14 GLN 0 4 ARG 0 8 SER 0 4 THR 0 20 VAL 0 14 Processing NMR model 18 ** Unrecognized atom type [ O2 ] in residue HIS M 88 ** Unrecognized atom type [ O2 ] in residue HIS M 186 Chain break between 88 (M 88 ) and 89 (M 99 ) Average value of CA-N-C-CB angle is 34.20 Standard deviation is 0.60 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2856 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 4 CYS 0 2 ASP 0 12 GLU 0 6 PHE 0 10 GLY 0 12 HIS 0 12 ILE 0 16 LYS 0 14 LEU 0 16 MET 0 8 ASN 0 14 GLN 0 4 ARG 0 8 SER 0 4 THR 0 20 VAL 0 14 Processing NMR model 19 ** Unrecognized atom type [ O2 ] in residue HIS M 88 ** Unrecognized atom type [ O2 ] in residue HIS M 186 Chain break between 88 (M 88 ) and 89 (M 99 ) Average value of CA-N-C-CB angle is 34.19 Standard deviation is 0.59 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2856 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 4 CYS 0 2 ASP 0 12 GLU 0 6 PHE 0 10 GLY 0 12 HIS 0 12 ILE 0 16 LYS 0 14 LEU 0 16 MET 0 8 ASN 0 14 GLN 0 4 ARG 0 8 SER 0 4 THR 0 20 VAL 0 14 Processing NMR model 20 ** Unrecognized atom type [ O2 ] in residue HIS M 88 ** Unrecognized atom type [ O2 ] in residue HIS M 186 Chain break between 88 (M 88 ) and 89 (M 99 ) Average value of CA-N-C-CB angle is 34.24 Standard deviation is 0.62 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2856 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 4 CYS 0 2 ASP 0 12 GLU 0 6 PHE 0 10 GLY 0 12 HIS 0 12 ILE 0 16 LYS 0 14 LEU 0 16 MET 0 8 ASN 0 14 GLN 0 4 ARG 0 8 SER 0 4 THR 0 20 VAL 0 14 * NMR ensemble comprises 20 model structures * Program completed