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 Average value of CA-N-C-CB angle is 34.50 Standard deviation is 1.00 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 1689 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 3 ASP 0 4 GLU 0 12 PHE 0 3 GLY 0 8 HIS 0 1 ILE 0 4 LYS 0 7 LEU 0 8 MET 0 2 ASN 0 10 PRO 0 5 GLN 0 1 ARG 0 2 SER 0 4 THR 0 10 VAL 0 18 TRP 0 2 TYR 0 4 Processing NMR model 2 Average value of CA-N-C-CB angle is 34.53 Standard deviation is 1.03 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 1689 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 3 ASP 0 4 GLU 0 12 PHE 0 3 GLY 0 8 HIS 0 1 ILE 0 4 LYS 0 7 LEU 0 8 MET 0 2 ASN 0 10 PRO 0 5 GLN 0 1 ARG 0 2 SER 0 4 THR 0 10 VAL 0 18 TRP 0 2 TYR 0 4 Processing NMR model 3 Average value of CA-N-C-CB angle is 34.49 Standard deviation is 1.05 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 1689 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 3 ASP 0 4 GLU 0 12 PHE 0 3 GLY 0 8 HIS 0 1 ILE 0 4 LYS 0 7 LEU 0 8 MET 0 2 ASN 0 10 PRO 0 5 GLN 0 1 ARG 0 2 SER 0 4 THR 0 10 VAL 0 18 TRP 0 2 TYR 0 4 Processing NMR model 4 Average value of CA-N-C-CB angle is 34.49 Standard deviation is 1.05 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 1689 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 3 ASP 0 4 GLU 0 12 PHE 0 3 GLY 0 8 HIS 0 1 ILE 0 4 LYS 0 7 LEU 0 8 MET 0 2 ASN 0 10 PRO 0 5 GLN 0 1 ARG 0 2 SER 0 4 THR 0 10 VAL 0 18 TRP 0 2 TYR 0 4 Processing NMR model 5 Average value of CA-N-C-CB angle is 34.54 Standard deviation is 1.05 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 1689 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 3 ASP 0 4 GLU 0 12 PHE 0 3 GLY 0 8 HIS 0 1 ILE 0 4 LYS 0 7 LEU 0 8 MET 0 2 ASN 0 10 PRO 0 5 GLN 0 1 ARG 0 2 SER 0 4 THR 0 10 VAL 0 18 TRP 0 2 TYR 0 4 Processing NMR model 6 Average value of CA-N-C-CB angle is 34.53 Standard deviation is 0.99 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 1689 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 3 ASP 0 4 GLU 0 12 PHE 0 3 GLY 0 8 HIS 0 1 ILE 0 4 LYS 0 7 LEU 0 8 MET 0 2 ASN 0 10 PRO 0 5 GLN 0 1 ARG 0 2 SER 0 4 THR 0 10 VAL 0 18 TRP 0 2 TYR 0 4 Processing NMR model 7 Average value of CA-N-C-CB angle is 34.53 Standard deviation is 1.04 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 1689 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 3 ASP 0 4 GLU 0 12 PHE 0 3 GLY 0 8 HIS 0 1 ILE 0 4 LYS 0 7 LEU 0 8 MET 0 2 ASN 0 10 PRO 0 5 GLN 0 1 ARG 0 2 SER 0 4 THR 0 10 VAL 0 18 TRP 0 2 TYR 0 4 Processing NMR model 8 Average value of CA-N-C-CB angle is 34.50 Standard deviation is 0.99 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 1689 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 3 ASP 0 4 GLU 0 12 PHE 0 3 GLY 0 8 HIS 0 1 ILE 0 4 LYS 0 7 LEU 0 8 MET 0 2 ASN 0 10 PRO 0 5 GLN 0 1 ARG 0 2 SER 0 4 THR 0 10 VAL 0 18 TRP 0 2 TYR 0 4 Processing NMR model 9 Average value of CA-N-C-CB angle is 34.53 Standard deviation is 1.07 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 1689 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 3 ASP 0 4 GLU 0 12 PHE 0 3 GLY 0 8 HIS 0 1 ILE 0 4 LYS 0 7 LEU 0 8 MET 0 2 ASN 0 10 PRO 0 5 GLN 0 1 ARG 0 2 SER 0 4 THR 0 10 VAL 0 18 TRP 0 2 TYR 0 4 Processing NMR model 10 Average value of CA-N-C-CB angle is 34.51 Standard deviation is 1.05 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 1689 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 3 ASP 0 4 GLU 0 12 PHE 0 3 GLY 0 8 HIS 0 1 ILE 0 4 LYS 0 7 LEU 0 8 MET 0 2 ASN 0 10 PRO 0 5 GLN 0 1 ARG 0 2 SER 0 4 THR 0 10 VAL 0 18 TRP 0 2 TYR 0 4 Processing NMR model 11 Average value of CA-N-C-CB angle is 34.53 Standard deviation is 1.04 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 1689 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 3 ASP 0 4 GLU 0 12 PHE 0 3 GLY 0 8 HIS 0 1 ILE 0 4 LYS 0 7 LEU 0 8 MET 0 2 ASN 0 10 PRO 0 5 GLN 0 1 ARG 0 2 SER 0 4 THR 0 10 VAL 0 18 TRP 0 2 TYR 0 4 Processing NMR model 12 Average value of CA-N-C-CB angle is 34.53 Standard deviation is 1.04 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 1689 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 3 ASP 0 4 GLU 0 12 PHE 0 3 GLY 0 8 HIS 0 1 ILE 0 4 LYS 0 7 LEU 0 8 MET 0 2 ASN 0 10 PRO 0 5 GLN 0 1 ARG 0 2 SER 0 4 THR 0 10 VAL 0 18 TRP 0 2 TYR 0 4 Processing NMR model 13 Average value of CA-N-C-CB angle is 34.53 Standard deviation is 0.99 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 1689 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 3 ASP 0 4 GLU 0 12 PHE 0 3 GLY 0 8 HIS 0 1 ILE 0 4 LYS 0 7 LEU 0 8 MET 0 2 ASN 0 10 PRO 0 5 GLN 0 1 ARG 0 2 SER 0 4 THR 0 10 VAL 0 18 TRP 0 2 TYR 0 4 Processing NMR model 14 Average value of CA-N-C-CB angle is 34.51 Standard deviation is 1.07 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 1689 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 3 ASP 0 4 GLU 0 12 PHE 0 3 GLY 0 8 HIS 0 1 ILE 0 4 LYS 0 7 LEU 0 8 MET 0 2 ASN 0 10 PRO 0 5 GLN 0 1 ARG 0 2 SER 0 4 THR 0 10 VAL 0 18 TRP 0 2 TYR 0 4 Processing NMR model 15 Average value of CA-N-C-CB angle is 34.53 Standard deviation is 1.03 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 1689 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 3 ASP 0 4 GLU 0 12 PHE 0 3 GLY 0 8 HIS 0 1 ILE 0 4 LYS 0 7 LEU 0 8 MET 0 2 ASN 0 10 PRO 0 5 GLN 0 1 ARG 0 2 SER 0 4 THR 0 10 VAL 0 18 TRP 0 2 TYR 0 4 Processing NMR model 16 Average value of CA-N-C-CB angle is 34.48 Standard deviation is 1.06 * 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 = 1689 old number = 0 * ASP A 14 Total number of residues that need to be changed and total number of residues: ALA 0 3 ASP 1 4 GLU 0 12 PHE 0 3 GLY 0 8 HIS 0 1 ILE 0 4 LYS 0 7 LEU 0 8 MET 0 2 ASN 0 10 PRO 0 5 GLN 0 1 ARG 0 2 SER 0 4 THR 0 10 VAL 0 18 TRP 0 2 TYR 0 4 Processing NMR model 17 Average value of CA-N-C-CB angle is 34.50 Standard deviation is 1.07 * 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 = 1689 old number = 0 * GLU A 61 Total number of residues that need to be changed and total number of residues: ALA 0 3 ASP 0 4 GLU 1 12 PHE 0 3 GLY 0 8 HIS 0 1 ILE 0 4 LYS 0 7 LEU 0 8 MET 0 2 ASN 0 10 PRO 0 5 GLN 0 1 ARG 0 2 SER 0 4 THR 0 10 VAL 0 18 TRP 0 2 TYR 0 4 Processing NMR model 18 Average value of CA-N-C-CB angle is 34.50 Standard deviation is 1.04 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 1689 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 3 ASP 0 4 GLU 0 12 PHE 0 3 GLY 0 8 HIS 0 1 ILE 0 4 LYS 0 7 LEU 0 8 MET 0 2 ASN 0 10 PRO 0 5 GLN 0 1 ARG 0 2 SER 0 4 THR 0 10 VAL 0 18 TRP 0 2 TYR 0 4 Processing NMR model 19 Average value of CA-N-C-CB angle is 34.50 Standard deviation is 1.02 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 1689 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 3 ASP 0 4 GLU 0 12 PHE 0 3 GLY 0 8 HIS 0 1 ILE 0 4 LYS 0 7 LEU 0 8 MET 0 2 ASN 0 10 PRO 0 5 GLN 0 1 ARG 0 2 SER 0 4 THR 0 10 VAL 0 18 TRP 0 2 TYR 0 4 Processing NMR model 20 Average value of CA-N-C-CB angle is 34.53 Standard deviation is 1.06 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 1689 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 3 ASP 0 4 GLU 0 12 PHE 0 3 GLY 0 8 HIS 0 1 ILE 0 4 LYS 0 7 LEU 0 8 MET 0 2 ASN 0 10 PRO 0 5 GLN 0 1 ARG 0 2 SER 0 4 THR 0 10 VAL 0 18 TRP 0 2 TYR 0 4 * NMR ensemble comprises 20 model structures * Program completed