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 34.32 Standard deviation is 0.94 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 1774 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 18 ASP 0 9 GLU 0 11 PHE 0 4 GLY 0 10 HIS 0 3 ILE 0 3 LYS 0 4 LEU 0 17 MET 0 1 ASN 0 1 PRO 0 4 GLN 0 5 ARG 0 7 SER 0 5 THR 0 3 VAL 0 6 TRP 0 3 TYR 0 2 Processing NMR model 2 Average value of CA-N-C-CB angle is 34.37 Standard deviation is 0.92 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 1774 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 18 ASP 0 9 GLU 0 11 PHE 0 4 GLY 0 10 HIS 0 3 ILE 0 3 LYS 0 4 LEU 0 17 MET 0 1 ASN 0 1 PRO 0 4 GLN 0 5 ARG 0 7 SER 0 5 THR 0 3 VAL 0 6 TRP 0 3 TYR 0 2 Processing NMR model 3 Average value of CA-N-C-CB angle is 34.36 Standard deviation is 0.86 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 1774 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 18 ASP 0 9 GLU 0 11 PHE 0 4 GLY 0 10 HIS 0 3 ILE 0 3 LYS 0 4 LEU 0 17 MET 0 1 ASN 0 1 PRO 0 4 GLN 0 5 ARG 0 7 SER 0 5 THR 0 3 VAL 0 6 TRP 0 3 TYR 0 2 Processing NMR model 4 Average value of CA-N-C-CB angle is 34.40 Standard deviation is 0.95 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 1774 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 18 ASP 0 9 GLU 0 11 PHE 0 4 GLY 0 10 HIS 0 3 ILE 0 3 LYS 0 4 LEU 0 17 MET 0 1 ASN 0 1 PRO 0 4 GLN 0 5 ARG 0 7 SER 0 5 THR 0 3 VAL 0 6 TRP 0 3 TYR 0 2 Processing NMR model 5 Average value of CA-N-C-CB angle is 34.28 Standard deviation is 0.95 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 1774 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 18 ASP 0 9 GLU 0 11 PHE 0 4 GLY 0 10 HIS 0 3 ILE 0 3 LYS 0 4 LEU 0 17 MET 0 1 ASN 0 1 PRO 0 4 GLN 0 5 ARG 0 7 SER 0 5 THR 0 3 VAL 0 6 TRP 0 3 TYR 0 2 Processing NMR model 6 Average value of CA-N-C-CB angle is 34.37 Standard deviation is 0.94 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 1774 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 18 ASP 0 9 GLU 0 11 PHE 0 4 GLY 0 10 HIS 0 3 ILE 0 3 LYS 0 4 LEU 0 17 MET 0 1 ASN 0 1 PRO 0 4 GLN 0 5 ARG 0 7 SER 0 5 THR 0 3 VAL 0 6 TRP 0 3 TYR 0 2 Processing NMR model 7 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 = 1774 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 18 ASP 0 9 GLU 0 11 PHE 0 4 GLY 0 10 HIS 0 3 ILE 0 3 LYS 0 4 LEU 0 17 MET 0 1 ASN 0 1 PRO 0 4 GLN 0 5 ARG 0 7 SER 0 5 THR 0 3 VAL 0 6 TRP 0 3 TYR 0 2 Processing NMR model 8 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 = 1774 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 18 ASP 0 9 GLU 0 11 PHE 0 4 GLY 0 10 HIS 0 3 ILE 0 3 LYS 0 4 LEU 0 17 MET 0 1 ASN 0 1 PRO 0 4 GLN 0 5 ARG 0 7 SER 0 5 THR 0 3 VAL 0 6 TRP 0 3 TYR 0 2 Processing NMR model 9 Average value of CA-N-C-CB angle is 34.31 Standard deviation is 0.91 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 1774 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 18 ASP 0 9 GLU 0 11 PHE 0 4 GLY 0 10 HIS 0 3 ILE 0 3 LYS 0 4 LEU 0 17 MET 0 1 ASN 0 1 PRO 0 4 GLN 0 5 ARG 0 7 SER 0 5 THR 0 3 VAL 0 6 TRP 0 3 TYR 0 2 Processing NMR model 10 Average value of CA-N-C-CB angle is 34.37 Standard deviation is 0.96 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 1774 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 18 ASP 0 9 GLU 0 11 PHE 0 4 GLY 0 10 HIS 0 3 ILE 0 3 LYS 0 4 LEU 0 17 MET 0 1 ASN 0 1 PRO 0 4 GLN 0 5 ARG 0 7 SER 0 5 THR 0 3 VAL 0 6 TRP 0 3 TYR 0 2 Processing NMR model 11 Average value of CA-N-C-CB angle is 34.34 Standard deviation is 0.93 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 1774 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 18 ASP 0 9 GLU 0 11 PHE 0 4 GLY 0 10 HIS 0 3 ILE 0 3 LYS 0 4 LEU 0 17 MET 0 1 ASN 0 1 PRO 0 4 GLN 0 5 ARG 0 7 SER 0 5 THR 0 3 VAL 0 6 TRP 0 3 TYR 0 2 Processing NMR model 12 Average value of CA-N-C-CB angle is 34.31 Standard deviation is 1.04 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 1774 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 18 ASP 0 9 GLU 0 11 PHE 0 4 GLY 0 10 HIS 0 3 ILE 0 3 LYS 0 4 LEU 0 17 MET 0 1 ASN 0 1 PRO 0 4 GLN 0 5 ARG 0 7 SER 0 5 THR 0 3 VAL 0 6 TRP 0 3 TYR 0 2 Processing NMR model 13 Average value of CA-N-C-CB angle is 34.30 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 = 1774 old number = 0 * ASP A 69 Total number of residues that need to be changed and total number of residues: ALA 0 18 ASP 1 9 GLU 0 11 PHE 0 4 GLY 0 10 HIS 0 3 ILE 0 3 LYS 0 4 LEU 0 17 MET 0 1 ASN 0 1 PRO 0 4 GLN 0 5 ARG 0 7 SER 0 5 THR 0 3 VAL 0 6 TRP 0 3 TYR 0 2 Processing NMR model 14 Average value of CA-N-C-CB angle is 34.28 Standard deviation is 0.95 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 1774 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 18 ASP 0 9 GLU 0 11 PHE 0 4 GLY 0 10 HIS 0 3 ILE 0 3 LYS 0 4 LEU 0 17 MET 0 1 ASN 0 1 PRO 0 4 GLN 0 5 ARG 0 7 SER 0 5 THR 0 3 VAL 0 6 TRP 0 3 TYR 0 2 Processing NMR model 15 Average value of CA-N-C-CB angle is 34.32 Standard deviation is 0.95 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 1774 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 18 ASP 0 9 GLU 0 11 PHE 0 4 GLY 0 10 HIS 0 3 ILE 0 3 LYS 0 4 LEU 0 17 MET 0 1 ASN 0 1 PRO 0 4 GLN 0 5 ARG 0 7 SER 0 5 THR 0 3 VAL 0 6 TRP 0 3 TYR 0 2 Processing NMR model 16 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 = 1774 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 18 ASP 0 9 GLU 0 11 PHE 0 4 GLY 0 10 HIS 0 3 ILE 0 3 LYS 0 4 LEU 0 17 MET 0 1 ASN 0 1 PRO 0 4 GLN 0 5 ARG 0 7 SER 0 5 THR 0 3 VAL 0 6 TRP 0 3 TYR 0 2 Processing NMR model 17 Average value of CA-N-C-CB angle is 34.39 Standard deviation is 0.96 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 1774 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 18 ASP 0 9 GLU 0 11 PHE 0 4 GLY 0 10 HIS 0 3 ILE 0 3 LYS 0 4 LEU 0 17 MET 0 1 ASN 0 1 PRO 0 4 GLN 0 5 ARG 0 7 SER 0 5 THR 0 3 VAL 0 6 TRP 0 3 TYR 0 2 Processing NMR model 18 Average value of CA-N-C-CB angle is 34.30 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 = 1774 old number = 0 * GLU A 116 Total number of residues that need to be changed and total number of residues: ALA 0 18 ASP 0 9 GLU 1 11 PHE 0 4 GLY 0 10 HIS 0 3 ILE 0 3 LYS 0 4 LEU 0 17 MET 0 1 ASN 0 1 PRO 0 4 GLN 0 5 ARG 0 7 SER 0 5 THR 0 3 VAL 0 6 TRP 0 3 TYR 0 2 Processing NMR model 19 Average value of CA-N-C-CB angle is 34.27 Standard deviation is 0.93 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 1774 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 18 ASP 0 9 GLU 0 11 PHE 0 4 GLY 0 10 HIS 0 3 ILE 0 3 LYS 0 4 LEU 0 17 MET 0 1 ASN 0 1 PRO 0 4 GLN 0 5 ARG 0 7 SER 0 5 THR 0 3 VAL 0 6 TRP 0 3 TYR 0 2 Processing NMR model 20 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 = 1774 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 18 ASP 0 9 GLU 0 11 PHE 0 4 GLY 0 10 HIS 0 3 ILE 0 3 LYS 0 4 LEU 0 17 MET 0 1 ASN 0 1 PRO 0 4 GLN 0 5 ARG 0 7 SER 0 5 THR 0 3 VAL 0 6 TRP 0 3 TYR 0 2 * NMR ensemble comprises 20 model structures * Program completed