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 THR A 122 Average value of CA-N-C-CB angle is 34.14 Standard deviation is 0.95 * 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 = 1890 old number = 0 * TYR A 57 PHE A 119 Total number of residues that need to be changed and total number of residues: ALA 0 6 CYS 0 1 ASP 0 6 GLU 0 7 PHE 1 2 GLY 0 11 HIS 0 7 ILE 0 8 LYS 0 9 LEU 0 4 MET 0 4 ASN 0 6 PRO 0 3 GLN 0 6 ARG 0 4 SER 0 9 THR 0 12 VAL 0 10 TRP 0 4 TYR 1 3 Processing NMR model 2 ** Unrecognized atom type [ O2 ] in residue THR A 122 Average value of CA-N-C-CB angle is 34.13 Standard deviation is 0.91 * 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 = 1890 old number = 0 * PHE A 26 TYR A 61 Total number of residues that need to be changed and total number of residues: ALA 0 6 CYS 0 1 ASP 0 6 GLU 0 7 PHE 1 2 GLY 0 11 HIS 0 7 ILE 0 8 LYS 0 9 LEU 0 4 MET 0 4 ASN 0 6 PRO 0 3 GLN 0 6 ARG 0 4 SER 0 9 THR 0 12 VAL 0 10 TRP 0 4 TYR 1 3 Processing NMR model 3 ** Unrecognized atom type [ O2 ] in residue THR A 122 Average value of CA-N-C-CB angle is 34.18 Standard deviation is 0.98 * 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 = 1890 old number = 0 * PHE A 26 TYR A 61 PHE A 119 Total number of residues that need to be changed and total number of residues: ALA 0 6 CYS 0 1 ASP 0 6 GLU 0 7 PHE 2 2 GLY 0 11 HIS 0 7 ILE 0 8 LYS 0 9 LEU 0 4 MET 0 4 ASN 0 6 PRO 0 3 GLN 0 6 ARG 0 4 SER 0 9 THR 0 12 VAL 0 10 TRP 0 4 TYR 1 3 Processing NMR model 4 ** Unrecognized atom type [ O2 ] in residue THR A 122 Average value of CA-N-C-CB angle is 34.14 Standard deviation is 0.91 * 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 = 1890 old number = 0 * PHE A 26 TYR A 61 PHE A 119 Total number of residues that need to be changed and total number of residues: ALA 0 6 CYS 0 1 ASP 0 6 GLU 0 7 PHE 2 2 GLY 0 11 HIS 0 7 ILE 0 8 LYS 0 9 LEU 0 4 MET 0 4 ASN 0 6 PRO 0 3 GLN 0 6 ARG 0 4 SER 0 9 THR 0 12 VAL 0 10 TRP 0 4 TYR 1 3 Processing NMR model 5 ** Unrecognized atom type [ O2 ] in residue THR A 122 Average value of CA-N-C-CB angle is 34.18 Standard deviation is 1.08 * 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 = 1890 old number = 0 * TYR A 57 Total number of residues that need to be changed and total number of residues: ALA 0 6 CYS 0 1 ASP 0 6 GLU 0 7 PHE 0 2 GLY 0 11 HIS 0 7 ILE 0 8 LYS 0 9 LEU 0 4 MET 0 4 ASN 0 6 PRO 0 3 GLN 0 6 ARG 0 4 SER 0 9 THR 0 12 VAL 0 10 TRP 0 4 TYR 1 3 Processing NMR model 6 ** Unrecognized atom type [ O2 ] in residue THR A 122 Average value of CA-N-C-CB angle is 34.13 Standard deviation is 0.88 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 1890 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 6 CYS 0 1 ASP 0 6 GLU 0 7 PHE 0 2 GLY 0 11 HIS 0 7 ILE 0 8 LYS 0 9 LEU 0 4 MET 0 4 ASN 0 6 PRO 0 3 GLN 0 6 ARG 0 4 SER 0 9 THR 0 12 VAL 0 10 TRP 0 4 TYR 0 3 Processing NMR model 7 ** Unrecognized atom type [ O2 ] in residue THR A 122 Average value of CA-N-C-CB angle is 34.19 Standard deviation is 1.02 * 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 = 1890 old number = 0 * PHE A 26 TYR A 57 Total number of residues that need to be changed and total number of residues: ALA 0 6 CYS 0 1 ASP 0 6 GLU 0 7 PHE 1 2 GLY 0 11 HIS 0 7 ILE 0 8 LYS 0 9 LEU 0 4 MET 0 4 ASN 0 6 PRO 0 3 GLN 0 6 ARG 0 4 SER 0 9 THR 0 12 VAL 0 10 TRP 0 4 TYR 1 3 Processing NMR model 8 ** Unrecognized atom type [ O2 ] in residue THR A 122 Average value of CA-N-C-CB angle is 34.09 Standard deviation is 0.84 * 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 = 1890 old number = 0 * PHE A 119 Total number of residues that need to be changed and total number of residues: ALA 0 6 CYS 0 1 ASP 0 6 GLU 0 7 PHE 1 2 GLY 0 11 HIS 0 7 ILE 0 8 LYS 0 9 LEU 0 4 MET 0 4 ASN 0 6 PRO 0 3 GLN 0 6 ARG 0 4 SER 0 9 THR 0 12 VAL 0 10 TRP 0 4 TYR 0 3 Processing NMR model 9 ** Unrecognized atom type [ O2 ] in residue THR A 122 Average value of CA-N-C-CB angle is 34.12 Standard deviation is 0.98 * 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 = 1890 old number = 0 * PHE A 26 TYR A 57 TYR A 61 Total number of residues that need to be changed and total number of residues: ALA 0 6 CYS 0 1 ASP 0 6 GLU 0 7 PHE 1 2 GLY 0 11 HIS 0 7 ILE 0 8 LYS 0 9 LEU 0 4 MET 0 4 ASN 0 6 PRO 0 3 GLN 0 6 ARG 0 4 SER 0 9 THR 0 12 VAL 0 10 TRP 0 4 TYR 2 3 Processing NMR model 10 ** Unrecognized atom type [ O2 ] in residue THR A 122 Average value of CA-N-C-CB angle is 34.14 Standard deviation is 1.02 * 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 = 1890 old number = 0 * PHE A 26 TYR A 61 Total number of residues that need to be changed and total number of residues: ALA 0 6 CYS 0 1 ASP 0 6 GLU 0 7 PHE 1 2 GLY 0 11 HIS 0 7 ILE 0 8 LYS 0 9 LEU 0 4 MET 0 4 ASN 0 6 PRO 0 3 GLN 0 6 ARG 0 4 SER 0 9 THR 0 12 VAL 0 10 TRP 0 4 TYR 1 3 Processing NMR model 11 ** Unrecognized atom type [ O2 ] in residue THR A 122 Average value of CA-N-C-CB angle is 34.10 Standard deviation is 0.86 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 1890 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 6 CYS 0 1 ASP 0 6 GLU 0 7 PHE 0 2 GLY 0 11 HIS 0 7 ILE 0 8 LYS 0 9 LEU 0 4 MET 0 4 ASN 0 6 PRO 0 3 GLN 0 6 ARG 0 4 SER 0 9 THR 0 12 VAL 0 10 TRP 0 4 TYR 0 3 Processing NMR model 12 ** Unrecognized atom type [ O2 ] in residue THR A 122 Average value of CA-N-C-CB angle is 34.12 Standard deviation is 0.88 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 1890 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 6 CYS 0 1 ASP 0 6 GLU 0 7 PHE 0 2 GLY 0 11 HIS 0 7 ILE 0 8 LYS 0 9 LEU 0 4 MET 0 4 ASN 0 6 PRO 0 3 GLN 0 6 ARG 0 4 SER 0 9 THR 0 12 VAL 0 10 TRP 0 4 TYR 0 3 Processing NMR model 13 ** Unrecognized atom type [ O2 ] in residue THR A 122 Average value of CA-N-C-CB angle is 34.13 Standard deviation is 0.97 * 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 = 1890 old number = 0 * PHE A 26 TYR A 61 Total number of residues that need to be changed and total number of residues: ALA 0 6 CYS 0 1 ASP 0 6 GLU 0 7 PHE 1 2 GLY 0 11 HIS 0 7 ILE 0 8 LYS 0 9 LEU 0 4 MET 0 4 ASN 0 6 PRO 0 3 GLN 0 6 ARG 0 4 SER 0 9 THR 0 12 VAL 0 10 TRP 0 4 TYR 1 3 Processing NMR model 14 ** Unrecognized atom type [ O2 ] in residue THR A 122 Average value of CA-N-C-CB angle is 34.12 Standard deviation is 0.83 * 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 = 1890 old number = 0 * PHE A 119 Total number of residues that need to be changed and total number of residues: ALA 0 6 CYS 0 1 ASP 0 6 GLU 0 7 PHE 1 2 GLY 0 11 HIS 0 7 ILE 0 8 LYS 0 9 LEU 0 4 MET 0 4 ASN 0 6 PRO 0 3 GLN 0 6 ARG 0 4 SER 0 9 THR 0 12 VAL 0 10 TRP 0 4 TYR 0 3 Processing NMR model 15 ** Unrecognized atom type [ O2 ] in residue THR A 122 Average value of CA-N-C-CB angle is 34.14 Standard deviation is 0.98 * 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 = 1890 old number = 0 * PHE A 26 PHE A 119 Total number of residues that need to be changed and total number of residues: ALA 0 6 CYS 0 1 ASP 0 6 GLU 0 7 PHE 2 2 GLY 0 11 HIS 0 7 ILE 0 8 LYS 0 9 LEU 0 4 MET 0 4 ASN 0 6 PRO 0 3 GLN 0 6 ARG 0 4 SER 0 9 THR 0 12 VAL 0 10 TRP 0 4 TYR 0 3 Processing NMR model 16 ** Unrecognized atom type [ O2 ] in residue THR A 122 Average value of CA-N-C-CB angle is 34.13 Standard deviation is 1.01 * 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 = 1890 old number = 0 * TYR A 57 PHE A 119 Total number of residues that need to be changed and total number of residues: ALA 0 6 CYS 0 1 ASP 0 6 GLU 0 7 PHE 1 2 GLY 0 11 HIS 0 7 ILE 0 8 LYS 0 9 LEU 0 4 MET 0 4 ASN 0 6 PRO 0 3 GLN 0 6 ARG 0 4 SER 0 9 THR 0 12 VAL 0 10 TRP 0 4 TYR 1 3 Processing NMR model 17 ** Unrecognized atom type [ O2 ] in residue THR A 122 Average value of CA-N-C-CB angle is 34.11 Standard deviation is 0.90 * 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 = 1890 old number = 0 * PHE A 119 Total number of residues that need to be changed and total number of residues: ALA 0 6 CYS 0 1 ASP 0 6 GLU 0 7 PHE 1 2 GLY 0 11 HIS 0 7 ILE 0 8 LYS 0 9 LEU 0 4 MET 0 4 ASN 0 6 PRO 0 3 GLN 0 6 ARG 0 4 SER 0 9 THR 0 12 VAL 0 10 TRP 0 4 TYR 0 3 Processing NMR model 18 ** Unrecognized atom type [ O2 ] in residue THR A 122 Average value of CA-N-C-CB angle is 34.14 Standard deviation is 1.00 * 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 = 1890 old number = 0 * TYR A 61 Total number of residues that need to be changed and total number of residues: ALA 0 6 CYS 0 1 ASP 0 6 GLU 0 7 PHE 0 2 GLY 0 11 HIS 0 7 ILE 0 8 LYS 0 9 LEU 0 4 MET 0 4 ASN 0 6 PRO 0 3 GLN 0 6 ARG 0 4 SER 0 9 THR 0 12 VAL 0 10 TRP 0 4 TYR 1 3 Processing NMR model 19 ** Unrecognized atom type [ O2 ] in residue THR A 122 Average value of CA-N-C-CB angle is 34.16 Standard deviation is 0.94 * 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 = 1890 old number = 0 * PHE A 26 TYR A 61 Total number of residues that need to be changed and total number of residues: ALA 0 6 CYS 0 1 ASP 0 6 GLU 0 7 PHE 1 2 GLY 0 11 HIS 0 7 ILE 0 8 LYS 0 9 LEU 0 4 MET 0 4 ASN 0 6 PRO 0 3 GLN 0 6 ARG 0 4 SER 0 9 THR 0 12 VAL 0 10 TRP 0 4 TYR 1 3 Processing NMR model 20 ** Unrecognized atom type [ O2 ] in residue THR A 122 Average value of CA-N-C-CB angle is 34.12 Standard deviation is 0.92 * 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 = 1890 old number = 0 * PHE A 26 Total number of residues that need to be changed and total number of residues: ALA 0 6 CYS 0 1 ASP 0 6 GLU 0 7 PHE 1 2 GLY 0 11 HIS 0 7 ILE 0 8 LYS 0 9 LEU 0 4 MET 0 4 ASN 0 6 PRO 0 3 GLN 0 6 ARG 0 4 SER 0 9 THR 0 12 VAL 0 10 TRP 0 4 TYR 0 3 * NMR ensemble comprises 20 model structures * Program completed