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 34.37 Standard deviation is 0.75 * 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 = 1527 old number = 0 * ASP A 33 Total number of residues that need to be changed and total number of residues: ALA 0 5 ASP 1 6 GLU 0 9 PHE 0 3 GLY 0 10 ILE 0 8 LYS 0 11 LEU 0 9 MET 0 2 ASN 0 5 PRO 0 2 GLN 0 2 ARG 0 2 SER 0 9 THR 0 4 VAL 0 6 TRP 0 1 TYR 0 4 Processing NMR model 2 Average value of CA-N-C-CB angle is 34.34 Standard deviation is 0.88 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 1527 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 5 ASP 0 6 GLU 0 9 PHE 0 3 GLY 0 10 ILE 0 8 LYS 0 11 LEU 0 9 MET 0 2 ASN 0 5 PRO 0 2 GLN 0 2 ARG 0 2 SER 0 9 THR 0 4 VAL 0 6 TRP 0 1 TYR 0 4 Processing NMR model 3 Average value of CA-N-C-CB angle is 34.39 Standard deviation is 0.72 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 1527 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 5 ASP 0 6 GLU 0 9 PHE 0 3 GLY 0 10 ILE 0 8 LYS 0 11 LEU 0 9 MET 0 2 ASN 0 5 PRO 0 2 GLN 0 2 ARG 0 2 SER 0 9 THR 0 4 VAL 0 6 TRP 0 1 TYR 0 4 Processing NMR model 4 Average value of CA-N-C-CB angle is 34.36 Standard deviation is 0.81 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 1527 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 5 ASP 0 6 GLU 0 9 PHE 0 3 GLY 0 10 ILE 0 8 LYS 0 11 LEU 0 9 MET 0 2 ASN 0 5 PRO 0 2 GLN 0 2 ARG 0 2 SER 0 9 THR 0 4 VAL 0 6 TRP 0 1 TYR 0 4 Processing NMR model 5 Average value of CA-N-C-CB angle is 34.38 Standard deviation is 0.81 * 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 = 1527 old number = 0 * GLU A 71 Total number of residues that need to be changed and total number of residues: ALA 0 5 ASP 0 6 GLU 1 9 PHE 0 3 GLY 0 10 ILE 0 8 LYS 0 11 LEU 0 9 MET 0 2 ASN 0 5 PRO 0 2 GLN 0 2 ARG 0 2 SER 0 9 THR 0 4 VAL 0 6 TRP 0 1 TYR 0 4 Processing NMR model 6 Average value of CA-N-C-CB angle is 34.30 Standard deviation is 0.81 * 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 = 1527 old number = 0 * GLU A 19 Total number of residues that need to be changed and total number of residues: ALA 0 5 ASP 0 6 GLU 1 9 PHE 0 3 GLY 0 10 ILE 0 8 LYS 0 11 LEU 0 9 MET 0 2 ASN 0 5 PRO 0 2 GLN 0 2 ARG 0 2 SER 0 9 THR 0 4 VAL 0 6 TRP 0 1 TYR 0 4 Processing NMR model 7 Average value of CA-N-C-CB angle is 34.40 Standard deviation is 0.79 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 1527 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 5 ASP 0 6 GLU 0 9 PHE 0 3 GLY 0 10 ILE 0 8 LYS 0 11 LEU 0 9 MET 0 2 ASN 0 5 PRO 0 2 GLN 0 2 ARG 0 2 SER 0 9 THR 0 4 VAL 0 6 TRP 0 1 TYR 0 4 Processing NMR model 8 Average value of CA-N-C-CB angle is 34.34 Standard deviation is 0.82 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 1527 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 5 ASP 0 6 GLU 0 9 PHE 0 3 GLY 0 10 ILE 0 8 LYS 0 11 LEU 0 9 MET 0 2 ASN 0 5 PRO 0 2 GLN 0 2 ARG 0 2 SER 0 9 THR 0 4 VAL 0 6 TRP 0 1 TYR 0 4 Processing NMR model 9 Average value of CA-N-C-CB angle is 34.35 Standard deviation is 0.77 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 1527 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 5 ASP 0 6 GLU 0 9 PHE 0 3 GLY 0 10 ILE 0 8 LYS 0 11 LEU 0 9 MET 0 2 ASN 0 5 PRO 0 2 GLN 0 2 ARG 0 2 SER 0 9 THR 0 4 VAL 0 6 TRP 0 1 TYR 0 4 Processing NMR model 10 Average value of CA-N-C-CB angle is 34.48 Standard deviation is 0.79 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 1527 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 5 ASP 0 6 GLU 0 9 PHE 0 3 GLY 0 10 ILE 0 8 LYS 0 11 LEU 0 9 MET 0 2 ASN 0 5 PRO 0 2 GLN 0 2 ARG 0 2 SER 0 9 THR 0 4 VAL 0 6 TRP 0 1 TYR 0 4 Processing NMR model 11 Average value of CA-N-C-CB angle is 34.33 Standard deviation is 0.83 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 1527 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 5 ASP 0 6 GLU 0 9 PHE 0 3 GLY 0 10 ILE 0 8 LYS 0 11 LEU 0 9 MET 0 2 ASN 0 5 PRO 0 2 GLN 0 2 ARG 0 2 SER 0 9 THR 0 4 VAL 0 6 TRP 0 1 TYR 0 4 Processing NMR model 12 Average value of CA-N-C-CB angle is 34.32 Standard deviation is 0.81 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 1527 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 5 ASP 0 6 GLU 0 9 PHE 0 3 GLY 0 10 ILE 0 8 LYS 0 11 LEU 0 9 MET 0 2 ASN 0 5 PRO 0 2 GLN 0 2 ARG 0 2 SER 0 9 THR 0 4 VAL 0 6 TRP 0 1 TYR 0 4 Processing NMR model 13 Average value of CA-N-C-CB angle is 34.37 Standard deviation is 0.84 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 1527 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 5 ASP 0 6 GLU 0 9 PHE 0 3 GLY 0 10 ILE 0 8 LYS 0 11 LEU 0 9 MET 0 2 ASN 0 5 PRO 0 2 GLN 0 2 ARG 0 2 SER 0 9 THR 0 4 VAL 0 6 TRP 0 1 TYR 0 4 Processing NMR model 14 Average value of CA-N-C-CB angle is 34.38 Standard deviation is 0.78 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 1527 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 5 ASP 0 6 GLU 0 9 PHE 0 3 GLY 0 10 ILE 0 8 LYS 0 11 LEU 0 9 MET 0 2 ASN 0 5 PRO 0 2 GLN 0 2 ARG 0 2 SER 0 9 THR 0 4 VAL 0 6 TRP 0 1 TYR 0 4 Processing NMR model 15 Average value of CA-N-C-CB angle is 34.40 Standard deviation is 0.80 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 1527 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 5 ASP 0 6 GLU 0 9 PHE 0 3 GLY 0 10 ILE 0 8 LYS 0 11 LEU 0 9 MET 0 2 ASN 0 5 PRO 0 2 GLN 0 2 ARG 0 2 SER 0 9 THR 0 4 VAL 0 6 TRP 0 1 TYR 0 4 Processing NMR model 16 Average value of CA-N-C-CB angle is 34.36 Standard deviation is 0.77 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 1527 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 5 ASP 0 6 GLU 0 9 PHE 0 3 GLY 0 10 ILE 0 8 LYS 0 11 LEU 0 9 MET 0 2 ASN 0 5 PRO 0 2 GLN 0 2 ARG 0 2 SER 0 9 THR 0 4 VAL 0 6 TRP 0 1 TYR 0 4 Processing NMR model 17 Average value of CA-N-C-CB angle is 34.28 Standard deviation is 0.79 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 1527 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 5 ASP 0 6 GLU 0 9 PHE 0 3 GLY 0 10 ILE 0 8 LYS 0 11 LEU 0 9 MET 0 2 ASN 0 5 PRO 0 2 GLN 0 2 ARG 0 2 SER 0 9 THR 0 4 VAL 0 6 TRP 0 1 TYR 0 4 Processing NMR model 18 Average value of CA-N-C-CB angle is 34.38 Standard deviation is 0.78 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 1527 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 5 ASP 0 6 GLU 0 9 PHE 0 3 GLY 0 10 ILE 0 8 LYS 0 11 LEU 0 9 MET 0 2 ASN 0 5 PRO 0 2 GLN 0 2 ARG 0 2 SER 0 9 THR 0 4 VAL 0 6 TRP 0 1 TYR 0 4 Processing NMR model 19 Average value of CA-N-C-CB angle is 34.47 Standard deviation is 0.77 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 1527 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 5 ASP 0 6 GLU 0 9 PHE 0 3 GLY 0 10 ILE 0 8 LYS 0 11 LEU 0 9 MET 0 2 ASN 0 5 PRO 0 2 GLN 0 2 ARG 0 2 SER 0 9 THR 0 4 VAL 0 6 TRP 0 1 TYR 0 4 Processing NMR model 20 Average value of CA-N-C-CB angle is 34.40 Standard deviation is 0.85 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 1527 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 5 ASP 0 6 GLU 0 9 PHE 0 3 GLY 0 10 ILE 0 8 LYS 0 11 LEU 0 9 MET 0 2 ASN 0 5 PRO 0 2 GLN 0 2 ARG 0 2 SER 0 9 THR 0 4 VAL 0 6 TRP 0 1 TYR 0 4 * NMR ensemble comprises 20 model structures * Program completed