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 ALA A 78 Average value of CA-N-C-CB angle is 34.01 Standard deviation is 1.42 * 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 = 1196 old number = 0 * TYR A 6 PHE A 29 PHE A 30 PHE A 33 TYR A 44 Total number of residues that need to be changed and total number of residues: ALA 0 15 CYS 0 2 ASP 0 10 GLU 0 3 PHE 3 4 GLY 0 3 HIS 0 2 ILE 0 1 LEU 0 10 MET 0 2 PRO 0 5 GLN 0 3 ARG 0 7 SER 0 2 THR 0 1 VAL 0 4 TRP 0 2 TYR 2 2 Processing NMR model 2 ** Unrecognized atom type [ O2 ] in residue ALA A 78 Average value of CA-N-C-CB angle is 33.98 Standard deviation is 1.35 * 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 = 1196 old number = 0 * TYR A 6 PHE A 29 PHE A 30 TYR A 44 Total number of residues that need to be changed and total number of residues: ALA 0 15 CYS 0 2 ASP 0 10 GLU 0 3 PHE 2 4 GLY 0 3 HIS 0 2 ILE 0 1 LEU 0 10 MET 0 2 PRO 0 5 GLN 0 3 ARG 0 7 SER 0 2 THR 0 1 VAL 0 4 TRP 0 2 TYR 2 2 Processing NMR model 3 ** Unrecognized atom type [ O2 ] in residue ALA A 78 Average value of CA-N-C-CB angle is 33.95 Standard deviation is 1.36 * 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 = 1196 old number = 0 * TYR A 6 PHE A 29 PHE A 30 TYR A 44 Total number of residues that need to be changed and total number of residues: ALA 0 15 CYS 0 2 ASP 0 10 GLU 0 3 PHE 2 4 GLY 0 3 HIS 0 2 ILE 0 1 LEU 0 10 MET 0 2 PRO 0 5 GLN 0 3 ARG 0 7 SER 0 2 THR 0 1 VAL 0 4 TRP 0 2 TYR 2 2 Processing NMR model 4 ** Unrecognized atom type [ O2 ] in residue ALA A 78 Average value of CA-N-C-CB angle is 34.03 Standard deviation is 1.43 * 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 = 1196 old number = 0 * TYR A 6 PHE A 29 PHE A 30 TYR A 44 Total number of residues that need to be changed and total number of residues: ALA 0 15 CYS 0 2 ASP 0 10 GLU 0 3 PHE 2 4 GLY 0 3 HIS 0 2 ILE 0 1 LEU 0 10 MET 0 2 PRO 0 5 GLN 0 3 ARG 0 7 SER 0 2 THR 0 1 VAL 0 4 TRP 0 2 TYR 2 2 Processing NMR model 5 ** Unrecognized atom type [ O2 ] in residue ALA A 78 Average value of CA-N-C-CB angle is 33.95 Standard deviation is 1.36 * 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 = 1196 old number = 0 * TYR A 6 PHE A 29 PHE A 30 Total number of residues that need to be changed and total number of residues: ALA 0 15 CYS 0 2 ASP 0 10 GLU 0 3 PHE 2 4 GLY 0 3 HIS 0 2 ILE 0 1 LEU 0 10 MET 0 2 PRO 0 5 GLN 0 3 ARG 0 7 SER 0 2 THR 0 1 VAL 0 4 TRP 0 2 TYR 1 2 Processing NMR model 6 ** Unrecognized atom type [ O2 ] in residue ALA A 78 Average value of CA-N-C-CB angle is 33.96 Standard deviation is 1.37 * 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 = 1196 old number = 0 * PHE A 29 PHE A 30 TYR A 44 Total number of residues that need to be changed and total number of residues: ALA 0 15 CYS 0 2 ASP 0 10 GLU 0 3 PHE 2 4 GLY 0 3 HIS 0 2 ILE 0 1 LEU 0 10 MET 0 2 PRO 0 5 GLN 0 3 ARG 0 7 SER 0 2 THR 0 1 VAL 0 4 TRP 0 2 TYR 1 2 Processing NMR model 7 ** Unrecognized atom type [ O2 ] in residue ALA A 78 Average value of CA-N-C-CB angle is 33.96 Standard deviation is 1.37 * 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 = 1196 old number = 0 * PHE A 29 PHE A 30 TYR A 44 Total number of residues that need to be changed and total number of residues: ALA 0 15 CYS 0 2 ASP 0 10 GLU 0 3 PHE 2 4 GLY 0 3 HIS 0 2 ILE 0 1 LEU 0 10 MET 0 2 PRO 0 5 GLN 0 3 ARG 0 7 SER 0 2 THR 0 1 VAL 0 4 TRP 0 2 TYR 1 2 Processing NMR model 8 ** Unrecognized atom type [ O2 ] in residue ALA A 78 Average value of CA-N-C-CB angle is 33.96 Standard deviation is 1.36 * 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 = 1196 old number = 0 * PHE A 29 PHE A 30 TYR A 44 Total number of residues that need to be changed and total number of residues: ALA 0 15 CYS 0 2 ASP 0 10 GLU 0 3 PHE 2 4 GLY 0 3 HIS 0 2 ILE 0 1 LEU 0 10 MET 0 2 PRO 0 5 GLN 0 3 ARG 0 7 SER 0 2 THR 0 1 VAL 0 4 TRP 0 2 TYR 1 2 Processing NMR model 9 ** Unrecognized atom type [ O2 ] in residue ALA A 78 Average value of CA-N-C-CB angle is 33.96 Standard deviation is 1.36 * 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 = 1196 old number = 0 * PHE A 29 PHE A 30 TYR A 44 Total number of residues that need to be changed and total number of residues: ALA 0 15 CYS 0 2 ASP 0 10 GLU 0 3 PHE 2 4 GLY 0 3 HIS 0 2 ILE 0 1 LEU 0 10 MET 0 2 PRO 0 5 GLN 0 3 ARG 0 7 SER 0 2 THR 0 1 VAL 0 4 TRP 0 2 TYR 1 2 Processing NMR model 10 ** Unrecognized atom type [ O2 ] in residue ALA A 78 Average value of CA-N-C-CB angle is 33.97 Standard deviation is 1.35 * 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 = 1196 old number = 0 * PHE A 29 PHE A 30 TYR A 44 Total number of residues that need to be changed and total number of residues: ALA 0 15 CYS 0 2 ASP 0 10 GLU 0 3 PHE 2 4 GLY 0 3 HIS 0 2 ILE 0 1 LEU 0 10 MET 0 2 PRO 0 5 GLN 0 3 ARG 0 7 SER 0 2 THR 0 1 VAL 0 4 TRP 0 2 TYR 1 2 Processing NMR model 11 ** Unrecognized atom type [ O2 ] in residue ALA A 78 Average value of CA-N-C-CB angle is 33.96 Standard deviation is 1.36 * 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 = 1196 old number = 0 * TYR A 6 PHE A 29 PHE A 30 TYR A 44 Total number of residues that need to be changed and total number of residues: ALA 0 15 CYS 0 2 ASP 0 10 GLU 0 3 PHE 2 4 GLY 0 3 HIS 0 2 ILE 0 1 LEU 0 10 MET 0 2 PRO 0 5 GLN 0 3 ARG 0 7 SER 0 2 THR 0 1 VAL 0 4 TRP 0 2 TYR 2 2 Processing NMR model 12 ** Unrecognized atom type [ O2 ] in residue ALA A 78 Average value of CA-N-C-CB angle is 33.96 Standard deviation is 1.36 * 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 = 1196 old number = 0 * TYR A 6 PHE A 29 PHE A 30 PHE A 33 TYR A 44 Total number of residues that need to be changed and total number of residues: ALA 0 15 CYS 0 2 ASP 0 10 GLU 0 3 PHE 3 4 GLY 0 3 HIS 0 2 ILE 0 1 LEU 0 10 MET 0 2 PRO 0 5 GLN 0 3 ARG 0 7 SER 0 2 THR 0 1 VAL 0 4 TRP 0 2 TYR 2 2 Processing NMR model 13 ** Unrecognized atom type [ O2 ] in residue ALA A 78 Average value of CA-N-C-CB angle is 33.96 Standard deviation is 1.37 * 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 = 1196 old number = 0 * TYR A 6 PHE A 29 PHE A 30 TYR A 44 Total number of residues that need to be changed and total number of residues: ALA 0 15 CYS 0 2 ASP 0 10 GLU 0 3 PHE 2 4 GLY 0 3 HIS 0 2 ILE 0 1 LEU 0 10 MET 0 2 PRO 0 5 GLN 0 3 ARG 0 7 SER 0 2 THR 0 1 VAL 0 4 TRP 0 2 TYR 2 2 Processing NMR model 14 ** Unrecognized atom type [ O2 ] in residue ALA A 78 Average value of CA-N-C-CB angle is 34.01 Standard deviation is 1.45 * 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 = 1196 old number = 0 * TYR A 6 PHE A 29 PHE A 30 TYR A 44 Total number of residues that need to be changed and total number of residues: ALA 0 15 CYS 0 2 ASP 0 10 GLU 0 3 PHE 2 4 GLY 0 3 HIS 0 2 ILE 0 1 LEU 0 10 MET 0 2 PRO 0 5 GLN 0 3 ARG 0 7 SER 0 2 THR 0 1 VAL 0 4 TRP 0 2 TYR 2 2 Processing NMR model 15 ** Unrecognized atom type [ O2 ] in residue ALA A 78 Average value of CA-N-C-CB angle is 33.90 Standard deviation is 1.25 * 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 = 1196 old number = 0 * TYR A 6 PHE A 29 PHE A 30 PHE A 33 Total number of residues that need to be changed and total number of residues: ALA 0 15 CYS 0 2 ASP 0 10 GLU 0 3 PHE 3 4 GLY 0 3 HIS 0 2 ILE 0 1 LEU 0 10 MET 0 2 PRO 0 5 GLN 0 3 ARG 0 7 SER 0 2 THR 0 1 VAL 0 4 TRP 0 2 TYR 1 2 Processing NMR model 16 ** Unrecognized atom type [ O2 ] in residue ALA A 78 Average value of CA-N-C-CB angle is 33.90 Standard deviation is 1.25 * 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 = 1196 old number = 0 * TYR A 6 PHE A 29 PHE A 30 TYR A 44 Total number of residues that need to be changed and total number of residues: ALA 0 15 CYS 0 2 ASP 0 10 GLU 0 3 PHE 2 4 GLY 0 3 HIS 0 2 ILE 0 1 LEU 0 10 MET 0 2 PRO 0 5 GLN 0 3 ARG 0 7 SER 0 2 THR 0 1 VAL 0 4 TRP 0 2 TYR 2 2 Processing NMR model 17 ** Unrecognized atom type [ O2 ] in residue ALA A 78 Average value of CA-N-C-CB angle is 33.96 Standard deviation is 1.36 * 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 = 1196 old number = 0 * TYR A 6 PHE A 29 PHE A 30 PHE A 33 TYR A 44 Total number of residues that need to be changed and total number of residues: ALA 0 15 CYS 0 2 ASP 0 10 GLU 0 3 PHE 3 4 GLY 0 3 HIS 0 2 ILE 0 1 LEU 0 10 MET 0 2 PRO 0 5 GLN 0 3 ARG 0 7 SER 0 2 THR 0 1 VAL 0 4 TRP 0 2 TYR 2 2 Processing NMR model 18 ** Unrecognized atom type [ O2 ] in residue ALA A 78 Average value of CA-N-C-CB angle is 33.96 Standard deviation is 1.37 * 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 = 1196 old number = 0 * TYR A 6 PHE A 29 PHE A 30 TYR A 44 Total number of residues that need to be changed and total number of residues: ALA 0 15 CYS 0 2 ASP 0 10 GLU 0 3 PHE 2 4 GLY 0 3 HIS 0 2 ILE 0 1 LEU 0 10 MET 0 2 PRO 0 5 GLN 0 3 ARG 0 7 SER 0 2 THR 0 1 VAL 0 4 TRP 0 2 TYR 2 2 Processing NMR model 19 ** Unrecognized atom type [ O2 ] in residue ALA A 78 Average value of CA-N-C-CB angle is 33.98 Standard deviation is 1.36 * 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 = 1196 old number = 0 * TYR A 6 PHE A 29 PHE A 30 PHE A 33 TYR A 44 Total number of residues that need to be changed and total number of residues: ALA 0 15 CYS 0 2 ASP 0 10 GLU 0 3 PHE 3 4 GLY 0 3 HIS 0 2 ILE 0 1 LEU 0 10 MET 0 2 PRO 0 5 GLN 0 3 ARG 0 7 SER 0 2 THR 0 1 VAL 0 4 TRP 0 2 TYR 2 2 Processing NMR model 20 ** Unrecognized atom type [ O2 ] in residue ALA A 78 Average value of CA-N-C-CB angle is 33.96 Standard deviation is 1.37 * 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 = 1196 old number = 0 * TYR A 6 PHE A 29 PHE A 30 TYR A 44 Total number of residues that need to be changed and total number of residues: ALA 0 15 CYS 0 2 ASP 0 10 GLU 0 3 PHE 2 4 GLY 0 3 HIS 0 2 ILE 0 1 LEU 0 10 MET 0 2 PRO 0 5 GLN 0 3 ARG 0 7 SER 0 2 THR 0 1 VAL 0 4 TRP 0 2 TYR 2 2 * NMR ensemble comprises 20 model structures * Program completed