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 Chain break between 80 (M 80 ) and 81 (M 91 ) Average value of CA-N-C-CB angle is 35.03 Standard deviation is 0.45 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2676 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 6 ASP 0 6 GLU 0 14 PHE 0 4 GLY 0 2 HIS 0 18 ILE 0 8 LYS 0 14 LEU 0 14 MET 0 6 ASN 0 10 PRO 0 2 GLN 0 10 ARG 0 6 SER 0 14 THR 0 4 VAL 0 14 TYR 0 8 Processing NMR model 2 Chain break between 80 (M 80 ) and 81 (M 91 ) Average value of CA-N-C-CB angle is 34.99 Standard deviation is 0.52 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2676 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 6 ASP 0 6 GLU 0 14 PHE 0 4 GLY 0 2 HIS 0 18 ILE 0 8 LYS 0 14 LEU 0 14 MET 0 6 ASN 0 10 PRO 0 2 GLN 0 10 ARG 0 6 SER 0 14 THR 0 4 VAL 0 14 TYR 0 8 Processing NMR model 3 Chain break between 80 (M 80 ) and 81 (M 91 ) Average value of CA-N-C-CB angle is 34.96 Standard deviation is 0.53 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2676 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 6 ASP 0 6 GLU 0 14 PHE 0 4 GLY 0 2 HIS 0 18 ILE 0 8 LYS 0 14 LEU 0 14 MET 0 6 ASN 0 10 PRO 0 2 GLN 0 10 ARG 0 6 SER 0 14 THR 0 4 VAL 0 14 TYR 0 8 Processing NMR model 4 Chain break between 80 (M 80 ) and 81 (M 91 ) Average value of CA-N-C-CB angle is 35.05 Standard deviation is 0.50 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2676 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 6 ASP 0 6 GLU 0 14 PHE 0 4 GLY 0 2 HIS 0 18 ILE 0 8 LYS 0 14 LEU 0 14 MET 0 6 ASN 0 10 PRO 0 2 GLN 0 10 ARG 0 6 SER 0 14 THR 0 4 VAL 0 14 TYR 0 8 Processing NMR model 5 Chain break between 80 (M 80 ) and 81 (M 91 ) Average value of CA-N-C-CB angle is 35.00 Standard deviation is 0.48 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2676 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 6 ASP 0 6 GLU 0 14 PHE 0 4 GLY 0 2 HIS 0 18 ILE 0 8 LYS 0 14 LEU 0 14 MET 0 6 ASN 0 10 PRO 0 2 GLN 0 10 ARG 0 6 SER 0 14 THR 0 4 VAL 0 14 TYR 0 8 Processing NMR model 6 Chain break between 80 (M 80 ) and 81 (M 91 ) Average value of CA-N-C-CB angle is 35.00 Standard deviation is 0.49 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2676 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 6 ASP 0 6 GLU 0 14 PHE 0 4 GLY 0 2 HIS 0 18 ILE 0 8 LYS 0 14 LEU 0 14 MET 0 6 ASN 0 10 PRO 0 2 GLN 0 10 ARG 0 6 SER 0 14 THR 0 4 VAL 0 14 TYR 0 8 Processing NMR model 7 Chain break between 80 (M 80 ) and 81 (M 91 ) Average value of CA-N-C-CB angle is 34.92 Standard deviation is 0.54 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2676 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 6 ASP 0 6 GLU 0 14 PHE 0 4 GLY 0 2 HIS 0 18 ILE 0 8 LYS 0 14 LEU 0 14 MET 0 6 ASN 0 10 PRO 0 2 GLN 0 10 ARG 0 6 SER 0 14 THR 0 4 VAL 0 14 TYR 0 8 Processing NMR model 8 Chain break between 80 (M 80 ) and 81 (M 91 ) Average value of CA-N-C-CB angle is 34.95 Standard deviation is 0.46 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2676 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 6 ASP 0 6 GLU 0 14 PHE 0 4 GLY 0 2 HIS 0 18 ILE 0 8 LYS 0 14 LEU 0 14 MET 0 6 ASN 0 10 PRO 0 2 GLN 0 10 ARG 0 6 SER 0 14 THR 0 4 VAL 0 14 TYR 0 8 Processing NMR model 9 Chain break between 80 (M 80 ) and 81 (M 91 ) Average value of CA-N-C-CB angle is 35.02 Standard deviation is 0.48 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2676 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 6 ASP 0 6 GLU 0 14 PHE 0 4 GLY 0 2 HIS 0 18 ILE 0 8 LYS 0 14 LEU 0 14 MET 0 6 ASN 0 10 PRO 0 2 GLN 0 10 ARG 0 6 SER 0 14 THR 0 4 VAL 0 14 TYR 0 8 Processing NMR model 10 Chain break between 80 (M 80 ) and 81 (M 91 ) Average value of CA-N-C-CB angle is 35.03 Standard deviation is 0.44 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2676 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 6 ASP 0 6 GLU 0 14 PHE 0 4 GLY 0 2 HIS 0 18 ILE 0 8 LYS 0 14 LEU 0 14 MET 0 6 ASN 0 10 PRO 0 2 GLN 0 10 ARG 0 6 SER 0 14 THR 0 4 VAL 0 14 TYR 0 8 Processing NMR model 11 Chain break between 80 (M 80 ) and 81 (M 91 ) Average value of CA-N-C-CB angle is 35.00 Standard deviation is 0.44 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2676 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 6 ASP 0 6 GLU 0 14 PHE 0 4 GLY 0 2 HIS 0 18 ILE 0 8 LYS 0 14 LEU 0 14 MET 0 6 ASN 0 10 PRO 0 2 GLN 0 10 ARG 0 6 SER 0 14 THR 0 4 VAL 0 14 TYR 0 8 Processing NMR model 12 Chain break between 80 (M 80 ) and 81 (M 91 ) Average value of CA-N-C-CB angle is 35.00 Standard deviation is 0.49 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2676 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 6 ASP 0 6 GLU 0 14 PHE 0 4 GLY 0 2 HIS 0 18 ILE 0 8 LYS 0 14 LEU 0 14 MET 0 6 ASN 0 10 PRO 0 2 GLN 0 10 ARG 0 6 SER 0 14 THR 0 4 VAL 0 14 TYR 0 8 Processing NMR model 13 Chain break between 80 (M 80 ) and 81 (M 91 ) Average value of CA-N-C-CB angle is 34.95 Standard deviation is 0.52 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2676 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 6 ASP 0 6 GLU 0 14 PHE 0 4 GLY 0 2 HIS 0 18 ILE 0 8 LYS 0 14 LEU 0 14 MET 0 6 ASN 0 10 PRO 0 2 GLN 0 10 ARG 0 6 SER 0 14 THR 0 4 VAL 0 14 TYR 0 8 Processing NMR model 14 Chain break between 80 (M 80 ) and 81 (M 91 ) Average value of CA-N-C-CB angle is 35.03 Standard deviation is 0.47 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2676 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 6 ASP 0 6 GLU 0 14 PHE 0 4 GLY 0 2 HIS 0 18 ILE 0 8 LYS 0 14 LEU 0 14 MET 0 6 ASN 0 10 PRO 0 2 GLN 0 10 ARG 0 6 SER 0 14 THR 0 4 VAL 0 14 TYR 0 8 Processing NMR model 15 Chain break between 80 (M 80 ) and 81 (M 91 ) Average value of CA-N-C-CB angle is 35.01 Standard deviation is 0.53 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2676 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 6 ASP 0 6 GLU 0 14 PHE 0 4 GLY 0 2 HIS 0 18 ILE 0 8 LYS 0 14 LEU 0 14 MET 0 6 ASN 0 10 PRO 0 2 GLN 0 10 ARG 0 6 SER 0 14 THR 0 4 VAL 0 14 TYR 0 8 Processing NMR model 16 Chain break between 80 (M 80 ) and 81 (M 91 ) Average value of CA-N-C-CB angle is 34.94 Standard deviation is 0.54 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2676 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 6 ASP 0 6 GLU 0 14 PHE 0 4 GLY 0 2 HIS 0 18 ILE 0 8 LYS 0 14 LEU 0 14 MET 0 6 ASN 0 10 PRO 0 2 GLN 0 10 ARG 0 6 SER 0 14 THR 0 4 VAL 0 14 TYR 0 8 Processing NMR model 17 Chain break between 80 (M 80 ) and 81 (M 91 ) Average value of CA-N-C-CB angle is 35.04 Standard deviation is 0.51 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2676 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 6 ASP 0 6 GLU 0 14 PHE 0 4 GLY 0 2 HIS 0 18 ILE 0 8 LYS 0 14 LEU 0 14 MET 0 6 ASN 0 10 PRO 0 2 GLN 0 10 ARG 0 6 SER 0 14 THR 0 4 VAL 0 14 TYR 0 8 Processing NMR model 18 Chain break between 80 (M 80 ) and 81 (M 91 ) Average value of CA-N-C-CB angle is 35.05 Standard deviation is 0.43 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2676 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 6 ASP 0 6 GLU 0 14 PHE 0 4 GLY 0 2 HIS 0 18 ILE 0 8 LYS 0 14 LEU 0 14 MET 0 6 ASN 0 10 PRO 0 2 GLN 0 10 ARG 0 6 SER 0 14 THR 0 4 VAL 0 14 TYR 0 8 Processing NMR model 19 Chain break between 80 (M 80 ) and 81 (M 91 ) Average value of CA-N-C-CB angle is 35.06 Standard deviation is 0.44 * 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 = 2676 old number = 0 * TYR M 33 Total number of residues that need to be changed and total number of residues: ALA 0 6 ASP 0 6 GLU 0 14 PHE 0 4 GLY 0 2 HIS 0 18 ILE 0 8 LYS 0 14 LEU 0 14 MET 0 6 ASN 0 10 PRO 0 2 GLN 0 10 ARG 0 6 SER 0 14 THR 0 4 VAL 0 14 TYR 1 8 Processing NMR model 20 Chain break between 80 (M 80 ) and 81 (M 91 ) Average value of CA-N-C-CB angle is 35.08 Standard deviation is 0.46 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2676 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 6 ASP 0 6 GLU 0 14 PHE 0 4 GLY 0 2 HIS 0 18 ILE 0 8 LYS 0 14 LEU 0 14 MET 0 6 ASN 0 10 PRO 0 2 GLN 0 10 ARG 0 6 SER 0 14 THR 0 4 VAL 0 14 TYR 0 8 * NMR ensemble comprises 20 model structures * Program completed