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 82 ** Unrecognized atom type [ O2 ] in residue HIS M 174 Chain break between 82 (M 82 ) and 83 (M 93 ) Average value of CA-N-C-CB angle is 34.29 Standard deviation is 0.94 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2646 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 10 ASP 0 6 GLU 0 20 PHE 0 12 GLY 0 10 HIS 0 16 ILE 0 8 LYS 0 16 LEU 0 10 MET 0 8 ASN 0 10 PRO 0 4 GLN 0 2 ARG 0 4 SER 0 8 THR 0 12 VAL 0 4 TRP 0 4 Processing NMR model 2 ** Unrecognized atom type [ O2 ] in residue HIS M 82 ** Unrecognized atom type [ O2 ] in residue HIS M 174 Chain break between 82 (M 82 ) and 83 (M 93 ) Average value of CA-N-C-CB angle is 34.32 Standard deviation is 0.87 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2646 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 10 ASP 0 6 GLU 0 20 PHE 0 12 GLY 0 10 HIS 0 16 ILE 0 8 LYS 0 16 LEU 0 10 MET 0 8 ASN 0 10 PRO 0 4 GLN 0 2 ARG 0 4 SER 0 8 THR 0 12 VAL 0 4 TRP 0 4 Processing NMR model 3 ** Unrecognized atom type [ O2 ] in residue HIS M 82 ** Unrecognized atom type [ O2 ] in residue HIS M 174 Chain break between 82 (M 82 ) and 83 (M 93 ) Average value of CA-N-C-CB angle is 34.25 Standard deviation is 0.98 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2646 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 10 ASP 0 6 GLU 0 20 PHE 0 12 GLY 0 10 HIS 0 16 ILE 0 8 LYS 0 16 LEU 0 10 MET 0 8 ASN 0 10 PRO 0 4 GLN 0 2 ARG 0 4 SER 0 8 THR 0 12 VAL 0 4 TRP 0 4 Processing NMR model 4 ** Unrecognized atom type [ O2 ] in residue HIS M 82 ** Unrecognized atom type [ O2 ] in residue HIS M 174 Chain break between 82 (M 82 ) and 83 (M 93 ) Average value of CA-N-C-CB angle is 34.24 Standard deviation is 1.04 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2646 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 10 ASP 0 6 GLU 0 20 PHE 0 12 GLY 0 10 HIS 0 16 ILE 0 8 LYS 0 16 LEU 0 10 MET 0 8 ASN 0 10 PRO 0 4 GLN 0 2 ARG 0 4 SER 0 8 THR 0 12 VAL 0 4 TRP 0 4 Processing NMR model 5 ** Unrecognized atom type [ O2 ] in residue HIS M 82 ** Unrecognized atom type [ O2 ] in residue HIS M 174 Chain break between 82 (M 82 ) and 83 (M 93 ) Average value of CA-N-C-CB angle is 34.32 Standard deviation is 0.85 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2646 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 10 ASP 0 6 GLU 0 20 PHE 0 12 GLY 0 10 HIS 0 16 ILE 0 8 LYS 0 16 LEU 0 10 MET 0 8 ASN 0 10 PRO 0 4 GLN 0 2 ARG 0 4 SER 0 8 THR 0 12 VAL 0 4 TRP 0 4 Processing NMR model 6 ** Unrecognized atom type [ O2 ] in residue HIS M 82 ** Unrecognized atom type [ O2 ] in residue HIS M 174 Chain break between 82 (M 82 ) and 83 (M 93 ) Average value of CA-N-C-CB angle is 34.17 Standard deviation is 0.97 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2646 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 10 ASP 0 6 GLU 0 20 PHE 0 12 GLY 0 10 HIS 0 16 ILE 0 8 LYS 0 16 LEU 0 10 MET 0 8 ASN 0 10 PRO 0 4 GLN 0 2 ARG 0 4 SER 0 8 THR 0 12 VAL 0 4 TRP 0 4 Processing NMR model 7 ** Unrecognized atom type [ O2 ] in residue HIS M 82 ** Unrecognized atom type [ O2 ] in residue HIS M 174 Chain break between 82 (M 82 ) and 83 (M 93 ) Average value of CA-N-C-CB angle is 34.25 Standard deviation is 1.05 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2646 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 10 ASP 0 6 GLU 0 20 PHE 0 12 GLY 0 10 HIS 0 16 ILE 0 8 LYS 0 16 LEU 0 10 MET 0 8 ASN 0 10 PRO 0 4 GLN 0 2 ARG 0 4 SER 0 8 THR 0 12 VAL 0 4 TRP 0 4 Processing NMR model 8 ** Unrecognized atom type [ O2 ] in residue HIS M 82 ** Unrecognized atom type [ O2 ] in residue HIS M 174 Chain break between 82 (M 82 ) and 83 (M 93 ) Average value of CA-N-C-CB angle is 34.19 Standard deviation is 1.00 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2646 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 10 ASP 0 6 GLU 0 20 PHE 0 12 GLY 0 10 HIS 0 16 ILE 0 8 LYS 0 16 LEU 0 10 MET 0 8 ASN 0 10 PRO 0 4 GLN 0 2 ARG 0 4 SER 0 8 THR 0 12 VAL 0 4 TRP 0 4 Processing NMR model 9 ** Unrecognized atom type [ O2 ] in residue HIS M 82 ** Unrecognized atom type [ O2 ] in residue HIS M 174 Chain break between 82 (M 82 ) and 83 (M 93 ) Average value of CA-N-C-CB angle is 34.25 Standard deviation is 0.96 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2646 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 10 ASP 0 6 GLU 0 20 PHE 0 12 GLY 0 10 HIS 0 16 ILE 0 8 LYS 0 16 LEU 0 10 MET 0 8 ASN 0 10 PRO 0 4 GLN 0 2 ARG 0 4 SER 0 8 THR 0 12 VAL 0 4 TRP 0 4 Processing NMR model 10 ** Unrecognized atom type [ O2 ] in residue HIS M 82 ** Unrecognized atom type [ O2 ] in residue HIS M 174 Chain break between 82 (M 82 ) and 83 (M 93 ) Average value of CA-N-C-CB angle is 34.19 Standard deviation is 0.96 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2646 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 10 ASP 0 6 GLU 0 20 PHE 0 12 GLY 0 10 HIS 0 16 ILE 0 8 LYS 0 16 LEU 0 10 MET 0 8 ASN 0 10 PRO 0 4 GLN 0 2 ARG 0 4 SER 0 8 THR 0 12 VAL 0 4 TRP 0 4 Processing NMR model 11 ** Unrecognized atom type [ O2 ] in residue HIS M 82 ** Unrecognized atom type [ O2 ] in residue HIS M 174 Chain break between 82 (M 82 ) and 83 (M 93 ) Average value of CA-N-C-CB angle is 34.21 Standard deviation is 0.98 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2646 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 10 ASP 0 6 GLU 0 20 PHE 0 12 GLY 0 10 HIS 0 16 ILE 0 8 LYS 0 16 LEU 0 10 MET 0 8 ASN 0 10 PRO 0 4 GLN 0 2 ARG 0 4 SER 0 8 THR 0 12 VAL 0 4 TRP 0 4 Processing NMR model 12 ** Unrecognized atom type [ O2 ] in residue HIS M 82 ** Unrecognized atom type [ O2 ] in residue HIS M 174 Chain break between 82 (M 82 ) and 83 (M 93 ) Average value of CA-N-C-CB angle is 34.20 Standard deviation is 1.00 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2646 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 10 ASP 0 6 GLU 0 20 PHE 0 12 GLY 0 10 HIS 0 16 ILE 0 8 LYS 0 16 LEU 0 10 MET 0 8 ASN 0 10 PRO 0 4 GLN 0 2 ARG 0 4 SER 0 8 THR 0 12 VAL 0 4 TRP 0 4 Processing NMR model 13 ** Unrecognized atom type [ O2 ] in residue HIS M 82 ** Unrecognized atom type [ O2 ] in residue HIS M 174 Chain break between 82 (M 82 ) and 83 (M 93 ) Average value of CA-N-C-CB angle is 34.20 Standard deviation is 0.95 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2646 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 10 ASP 0 6 GLU 0 20 PHE 0 12 GLY 0 10 HIS 0 16 ILE 0 8 LYS 0 16 LEU 0 10 MET 0 8 ASN 0 10 PRO 0 4 GLN 0 2 ARG 0 4 SER 0 8 THR 0 12 VAL 0 4 TRP 0 4 Processing NMR model 14 ** Unrecognized atom type [ O2 ] in residue HIS M 82 ** Unrecognized atom type [ O2 ] in residue HIS M 174 Chain break between 82 (M 82 ) and 83 (M 93 ) Average value of CA-N-C-CB angle is 34.29 Standard deviation is 0.99 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2646 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 10 ASP 0 6 GLU 0 20 PHE 0 12 GLY 0 10 HIS 0 16 ILE 0 8 LYS 0 16 LEU 0 10 MET 0 8 ASN 0 10 PRO 0 4 GLN 0 2 ARG 0 4 SER 0 8 THR 0 12 VAL 0 4 TRP 0 4 Processing NMR model 15 ** Unrecognized atom type [ O2 ] in residue HIS M 82 ** Unrecognized atom type [ O2 ] in residue HIS M 174 Chain break between 82 (M 82 ) and 83 (M 93 ) Average value of CA-N-C-CB angle is 34.27 Standard deviation is 0.92 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2646 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 10 ASP 0 6 GLU 0 20 PHE 0 12 GLY 0 10 HIS 0 16 ILE 0 8 LYS 0 16 LEU 0 10 MET 0 8 ASN 0 10 PRO 0 4 GLN 0 2 ARG 0 4 SER 0 8 THR 0 12 VAL 0 4 TRP 0 4 Processing NMR model 16 ** Unrecognized atom type [ O2 ] in residue HIS M 82 ** Unrecognized atom type [ O2 ] in residue HIS M 174 Chain break between 82 (M 82 ) and 83 (M 93 ) Average value of CA-N-C-CB angle is 34.22 Standard deviation is 0.98 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2646 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 10 ASP 0 6 GLU 0 20 PHE 0 12 GLY 0 10 HIS 0 16 ILE 0 8 LYS 0 16 LEU 0 10 MET 0 8 ASN 0 10 PRO 0 4 GLN 0 2 ARG 0 4 SER 0 8 THR 0 12 VAL 0 4 TRP 0 4 Processing NMR model 17 ** Unrecognized atom type [ O2 ] in residue HIS M 82 ** Unrecognized atom type [ O2 ] in residue HIS M 174 Chain break between 82 (M 82 ) and 83 (M 93 ) Average value of CA-N-C-CB angle is 34.25 Standard deviation is 0.89 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2646 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 10 ASP 0 6 GLU 0 20 PHE 0 12 GLY 0 10 HIS 0 16 ILE 0 8 LYS 0 16 LEU 0 10 MET 0 8 ASN 0 10 PRO 0 4 GLN 0 2 ARG 0 4 SER 0 8 THR 0 12 VAL 0 4 TRP 0 4 Processing NMR model 18 ** Unrecognized atom type [ O2 ] in residue HIS M 82 ** Unrecognized atom type [ O2 ] in residue HIS M 174 Chain break between 82 (M 82 ) and 83 (M 93 ) Average value of CA-N-C-CB angle is 34.22 Standard deviation is 0.95 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2646 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 10 ASP 0 6 GLU 0 20 PHE 0 12 GLY 0 10 HIS 0 16 ILE 0 8 LYS 0 16 LEU 0 10 MET 0 8 ASN 0 10 PRO 0 4 GLN 0 2 ARG 0 4 SER 0 8 THR 0 12 VAL 0 4 TRP 0 4 Processing NMR model 19 ** Unrecognized atom type [ O2 ] in residue HIS M 82 ** Unrecognized atom type [ O2 ] in residue HIS M 174 Chain break between 82 (M 82 ) and 83 (M 93 ) Average value of CA-N-C-CB angle is 34.21 Standard deviation is 0.96 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2646 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 10 ASP 0 6 GLU 0 20 PHE 0 12 GLY 0 10 HIS 0 16 ILE 0 8 LYS 0 16 LEU 0 10 MET 0 8 ASN 0 10 PRO 0 4 GLN 0 2 ARG 0 4 SER 0 8 THR 0 12 VAL 0 4 TRP 0 4 Processing NMR model 20 ** Unrecognized atom type [ O2 ] in residue HIS M 82 ** Unrecognized atom type [ O2 ] in residue HIS M 174 Chain break between 82 (M 82 ) and 83 (M 93 ) Average value of CA-N-C-CB angle is 34.25 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 = 2646 old number = 0 * GLU M 20 Total number of residues that need to be changed and total number of residues: ALA 0 10 ASP 0 6 GLU 1 20 PHE 0 12 GLY 0 10 HIS 0 16 ILE 0 8 LYS 0 16 LEU 0 10 MET 0 8 ASN 0 10 PRO 0 4 GLN 0 2 ARG 0 4 SER 0 8 THR 0 12 VAL 0 4 TRP 0 4 * NMR ensemble comprises 20 model structures * Program completed