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 71 ** Unrecognized atom type [ O2 ] in residue HIS M 152 Chain break between 71 (M 71 ) and 72 (M 82 ) 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 = 2288 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 4 ASP 0 8 GLU 0 12 PHE 0 4 GLY 0 12 HIS 0 14 ILE 0 10 LYS 0 12 LEU 0 22 MET 0 2 ASN 0 2 PRO 0 4 GLN 0 8 ARG 0 2 SER 0 8 THR 0 4 VAL 0 12 TYR 0 2 Processing NMR model 2 ** Unrecognized atom type [ O2 ] in residue HIS M 71 ** Unrecognized atom type [ O2 ] in residue HIS M 152 Chain break between 71 (M 71 ) and 72 (M 82 ) Average value of CA-N-C-CB angle is 34.36 Standard deviation is 0.93 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2288 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 4 ASP 0 8 GLU 0 12 PHE 0 4 GLY 0 12 HIS 0 14 ILE 0 10 LYS 0 12 LEU 0 22 MET 0 2 ASN 0 2 PRO 0 4 GLN 0 8 ARG 0 2 SER 0 8 THR 0 4 VAL 0 12 TYR 0 2 Processing NMR model 3 ** Unrecognized atom type [ O2 ] in residue HIS M 71 ** Unrecognized atom type [ O2 ] in residue HIS M 152 Chain break between 71 (M 71 ) and 72 (M 82 ) Average value of CA-N-C-CB angle is 34.27 Standard deviation is 1.03 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2288 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 4 ASP 0 8 GLU 0 12 PHE 0 4 GLY 0 12 HIS 0 14 ILE 0 10 LYS 0 12 LEU 0 22 MET 0 2 ASN 0 2 PRO 0 4 GLN 0 8 ARG 0 2 SER 0 8 THR 0 4 VAL 0 12 TYR 0 2 Processing NMR model 4 ** Unrecognized atom type [ O2 ] in residue HIS M 71 ** Unrecognized atom type [ O2 ] in residue HIS M 152 Chain break between 71 (M 71 ) and 72 (M 82 ) Average value of CA-N-C-CB angle is 34.30 Standard deviation is 0.93 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2288 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 4 ASP 0 8 GLU 0 12 PHE 0 4 GLY 0 12 HIS 0 14 ILE 0 10 LYS 0 12 LEU 0 22 MET 0 2 ASN 0 2 PRO 0 4 GLN 0 8 ARG 0 2 SER 0 8 THR 0 4 VAL 0 12 TYR 0 2 Processing NMR model 5 ** Unrecognized atom type [ O2 ] in residue HIS M 71 ** Unrecognized atom type [ O2 ] in residue HIS M 152 Chain break between 71 (M 71 ) and 72 (M 82 ) Average value of CA-N-C-CB angle is 34.30 Standard deviation is 0.93 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2288 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 4 ASP 0 8 GLU 0 12 PHE 0 4 GLY 0 12 HIS 0 14 ILE 0 10 LYS 0 12 LEU 0 22 MET 0 2 ASN 0 2 PRO 0 4 GLN 0 8 ARG 0 2 SER 0 8 THR 0 4 VAL 0 12 TYR 0 2 Processing NMR model 6 ** Unrecognized atom type [ O2 ] in residue HIS M 71 ** Unrecognized atom type [ O2 ] in residue HIS M 152 Chain break between 71 (M 71 ) and 72 (M 82 ) Average value of CA-N-C-CB angle is 34.32 Standard deviation is 0.96 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2288 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 4 ASP 0 8 GLU 0 12 PHE 0 4 GLY 0 12 HIS 0 14 ILE 0 10 LYS 0 12 LEU 0 22 MET 0 2 ASN 0 2 PRO 0 4 GLN 0 8 ARG 0 2 SER 0 8 THR 0 4 VAL 0 12 TYR 0 2 Processing NMR model 7 ** Unrecognized atom type [ O2 ] in residue HIS M 71 ** Unrecognized atom type [ O2 ] in residue HIS M 152 Chain break between 71 (M 71 ) and 72 (M 82 ) Average value of CA-N-C-CB angle is 34.28 Standard deviation is 0.94 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2288 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 4 ASP 0 8 GLU 0 12 PHE 0 4 GLY 0 12 HIS 0 14 ILE 0 10 LYS 0 12 LEU 0 22 MET 0 2 ASN 0 2 PRO 0 4 GLN 0 8 ARG 0 2 SER 0 8 THR 0 4 VAL 0 12 TYR 0 2 Processing NMR model 8 ** Unrecognized atom type [ O2 ] in residue HIS M 71 ** Unrecognized atom type [ O2 ] in residue HIS M 152 Chain break between 71 (M 71 ) and 72 (M 82 ) Average value of CA-N-C-CB angle is 34.33 Standard deviation is 0.96 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2288 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 4 ASP 0 8 GLU 0 12 PHE 0 4 GLY 0 12 HIS 0 14 ILE 0 10 LYS 0 12 LEU 0 22 MET 0 2 ASN 0 2 PRO 0 4 GLN 0 8 ARG 0 2 SER 0 8 THR 0 4 VAL 0 12 TYR 0 2 Processing NMR model 9 ** Unrecognized atom type [ O2 ] in residue HIS M 71 ** Unrecognized atom type [ O2 ] in residue HIS M 152 Chain break between 71 (M 71 ) and 72 (M 82 ) Average value of CA-N-C-CB angle is 34.25 Standard deviation is 0.99 * 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 = 2288 old number = 0 * PHE M 18 Total number of residues that need to be changed and total number of residues: ALA 0 4 ASP 0 8 GLU 0 12 PHE 1 4 GLY 0 12 HIS 0 14 ILE 0 10 LYS 0 12 LEU 0 22 MET 0 2 ASN 0 2 PRO 0 4 GLN 0 8 ARG 0 2 SER 0 8 THR 0 4 VAL 0 12 TYR 0 2 Processing NMR model 10 ** Unrecognized atom type [ O2 ] in residue HIS M 71 ** Unrecognized atom type [ O2 ] in residue HIS M 152 Chain break between 71 (M 71 ) and 72 (M 82 ) Average value of CA-N-C-CB angle is 34.30 Standard deviation is 0.94 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2288 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 4 ASP 0 8 GLU 0 12 PHE 0 4 GLY 0 12 HIS 0 14 ILE 0 10 LYS 0 12 LEU 0 22 MET 0 2 ASN 0 2 PRO 0 4 GLN 0 8 ARG 0 2 SER 0 8 THR 0 4 VAL 0 12 TYR 0 2 Processing NMR model 11 ** Unrecognized atom type [ O2 ] in residue HIS M 71 ** Unrecognized atom type [ O2 ] in residue HIS M 152 Chain break between 71 (M 71 ) and 72 (M 82 ) Average value of CA-N-C-CB angle is 34.39 Standard deviation is 0.90 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2288 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 4 ASP 0 8 GLU 0 12 PHE 0 4 GLY 0 12 HIS 0 14 ILE 0 10 LYS 0 12 LEU 0 22 MET 0 2 ASN 0 2 PRO 0 4 GLN 0 8 ARG 0 2 SER 0 8 THR 0 4 VAL 0 12 TYR 0 2 Processing NMR model 12 ** Unrecognized atom type [ O2 ] in residue HIS M 71 ** Unrecognized atom type [ O2 ] in residue HIS M 152 Chain break between 71 (M 71 ) and 72 (M 82 ) Average value of CA-N-C-CB angle is 34.28 Standard deviation is 0.97 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2288 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 4 ASP 0 8 GLU 0 12 PHE 0 4 GLY 0 12 HIS 0 14 ILE 0 10 LYS 0 12 LEU 0 22 MET 0 2 ASN 0 2 PRO 0 4 GLN 0 8 ARG 0 2 SER 0 8 THR 0 4 VAL 0 12 TYR 0 2 Processing NMR model 13 ** Unrecognized atom type [ O2 ] in residue HIS M 71 ** Unrecognized atom type [ O2 ] in residue HIS M 152 Chain break between 71 (M 71 ) and 72 (M 82 ) Average value of CA-N-C-CB angle is 34.28 Standard deviation is 0.91 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2288 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 4 ASP 0 8 GLU 0 12 PHE 0 4 GLY 0 12 HIS 0 14 ILE 0 10 LYS 0 12 LEU 0 22 MET 0 2 ASN 0 2 PRO 0 4 GLN 0 8 ARG 0 2 SER 0 8 THR 0 4 VAL 0 12 TYR 0 2 Processing NMR model 14 ** Unrecognized atom type [ O2 ] in residue HIS M 71 ** Unrecognized atom type [ O2 ] in residue HIS M 152 Chain break between 71 (M 71 ) and 72 (M 82 ) Average value of CA-N-C-CB angle is 34.29 Standard deviation is 0.91 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2288 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 4 ASP 0 8 GLU 0 12 PHE 0 4 GLY 0 12 HIS 0 14 ILE 0 10 LYS 0 12 LEU 0 22 MET 0 2 ASN 0 2 PRO 0 4 GLN 0 8 ARG 0 2 SER 0 8 THR 0 4 VAL 0 12 TYR 0 2 Processing NMR model 15 ** Unrecognized atom type [ O2 ] in residue HIS M 71 ** Unrecognized atom type [ O2 ] in residue HIS M 152 Chain break between 71 (M 71 ) and 72 (M 82 ) Average value of CA-N-C-CB angle is 34.33 Standard deviation is 1.01 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2288 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 4 ASP 0 8 GLU 0 12 PHE 0 4 GLY 0 12 HIS 0 14 ILE 0 10 LYS 0 12 LEU 0 22 MET 0 2 ASN 0 2 PRO 0 4 GLN 0 8 ARG 0 2 SER 0 8 THR 0 4 VAL 0 12 TYR 0 2 Processing NMR model 16 ** Unrecognized atom type [ O2 ] in residue HIS M 71 ** Unrecognized atom type [ O2 ] in residue HIS M 152 Chain break between 71 (M 71 ) and 72 (M 82 ) Average value of CA-N-C-CB angle is 34.28 Standard deviation is 0.98 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2288 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 4 ASP 0 8 GLU 0 12 PHE 0 4 GLY 0 12 HIS 0 14 ILE 0 10 LYS 0 12 LEU 0 22 MET 0 2 ASN 0 2 PRO 0 4 GLN 0 8 ARG 0 2 SER 0 8 THR 0 4 VAL 0 12 TYR 0 2 Processing NMR model 17 ** Unrecognized atom type [ O2 ] in residue HIS M 71 ** Unrecognized atom type [ O2 ] in residue HIS M 152 Chain break between 71 (M 71 ) and 72 (M 82 ) Average value of CA-N-C-CB angle is 34.32 Standard deviation is 0.92 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2288 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 4 ASP 0 8 GLU 0 12 PHE 0 4 GLY 0 12 HIS 0 14 ILE 0 10 LYS 0 12 LEU 0 22 MET 0 2 ASN 0 2 PRO 0 4 GLN 0 8 ARG 0 2 SER 0 8 THR 0 4 VAL 0 12 TYR 0 2 Processing NMR model 18 ** Unrecognized atom type [ O2 ] in residue HIS M 71 ** Unrecognized atom type [ O2 ] in residue HIS M 152 Chain break between 71 (M 71 ) and 72 (M 82 ) Average value of CA-N-C-CB angle is 34.28 Standard deviation is 0.99 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2288 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 4 ASP 0 8 GLU 0 12 PHE 0 4 GLY 0 12 HIS 0 14 ILE 0 10 LYS 0 12 LEU 0 22 MET 0 2 ASN 0 2 PRO 0 4 GLN 0 8 ARG 0 2 SER 0 8 THR 0 4 VAL 0 12 TYR 0 2 Processing NMR model 19 ** Unrecognized atom type [ O2 ] in residue HIS M 71 ** Unrecognized atom type [ O2 ] in residue HIS M 152 Chain break between 71 (M 71 ) and 72 (M 82 ) Average value of CA-N-C-CB angle is 34.30 Standard deviation is 0.93 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2288 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 4 ASP 0 8 GLU 0 12 PHE 0 4 GLY 0 12 HIS 0 14 ILE 0 10 LYS 0 12 LEU 0 22 MET 0 2 ASN 0 2 PRO 0 4 GLN 0 8 ARG 0 2 SER 0 8 THR 0 4 VAL 0 12 TYR 0 2 Processing NMR model 20 ** Unrecognized atom type [ O2 ] in residue HIS M 71 ** Unrecognized atom type [ O2 ] in residue HIS M 152 Chain break between 71 (M 71 ) and 72 (M 82 ) Average value of CA-N-C-CB angle is 34.28 Standard deviation is 0.96 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2288 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 4 ASP 0 8 GLU 0 12 PHE 0 4 GLY 0 12 HIS 0 14 ILE 0 10 LYS 0 12 LEU 0 22 MET 0 2 ASN 0 2 PRO 0 4 GLN 0 8 ARG 0 2 SER 0 8 THR 0 4 VAL 0 12 TYR 0 2 * NMR ensemble comprises 20 model structures * Program completed