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 HIS A 114 Average value of CA-N-C-CB angle is 34.31 Standard deviation is 1.07 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 1802 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 3 CYS 0 1 ASP 0 9 GLU 0 8 PHE 0 2 GLY 0 10 HIS 0 8 ILE 0 10 LYS 0 13 LEU 0 5 MET 0 3 ASN 0 6 PRO 0 5 GLN 0 5 ARG 0 3 SER 0 5 THR 0 6 VAL 0 10 TRP 0 1 TYR 0 1 Processing NMR model 2 ** Unrecognized atom type [ O2 ] in residue HIS A 114 Average value of CA-N-C-CB angle is 34.40 Standard deviation is 1.02 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 1802 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 3 CYS 0 1 ASP 0 9 GLU 0 8 PHE 0 2 GLY 0 10 HIS 0 8 ILE 0 10 LYS 0 13 LEU 0 5 MET 0 3 ASN 0 6 PRO 0 5 GLN 0 5 ARG 0 3 SER 0 5 THR 0 6 VAL 0 10 TRP 0 1 TYR 0 1 Processing NMR model 3 ** Unrecognized atom type [ O2 ] in residue HIS A 114 Average value of CA-N-C-CB angle is 34.41 Standard deviation is 1.02 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 1802 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 3 CYS 0 1 ASP 0 9 GLU 0 8 PHE 0 2 GLY 0 10 HIS 0 8 ILE 0 10 LYS 0 13 LEU 0 5 MET 0 3 ASN 0 6 PRO 0 5 GLN 0 5 ARG 0 3 SER 0 5 THR 0 6 VAL 0 10 TRP 0 1 TYR 0 1 Processing NMR model 4 ** Unrecognized atom type [ O2 ] in residue HIS A 114 Average value of CA-N-C-CB angle is 34.44 Standard deviation is 1.00 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 1802 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 3 CYS 0 1 ASP 0 9 GLU 0 8 PHE 0 2 GLY 0 10 HIS 0 8 ILE 0 10 LYS 0 13 LEU 0 5 MET 0 3 ASN 0 6 PRO 0 5 GLN 0 5 ARG 0 3 SER 0 5 THR 0 6 VAL 0 10 TRP 0 1 TYR 0 1 Processing NMR model 5 ** Unrecognized atom type [ O2 ] in residue HIS A 114 Average value of CA-N-C-CB angle is 34.40 Standard deviation is 1.01 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 1802 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 3 CYS 0 1 ASP 0 9 GLU 0 8 PHE 0 2 GLY 0 10 HIS 0 8 ILE 0 10 LYS 0 13 LEU 0 5 MET 0 3 ASN 0 6 PRO 0 5 GLN 0 5 ARG 0 3 SER 0 5 THR 0 6 VAL 0 10 TRP 0 1 TYR 0 1 Processing NMR model 6 ** Unrecognized atom type [ O2 ] in residue HIS A 114 Average value of CA-N-C-CB angle is 34.39 Standard deviation is 0.99 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 1802 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 3 CYS 0 1 ASP 0 9 GLU 0 8 PHE 0 2 GLY 0 10 HIS 0 8 ILE 0 10 LYS 0 13 LEU 0 5 MET 0 3 ASN 0 6 PRO 0 5 GLN 0 5 ARG 0 3 SER 0 5 THR 0 6 VAL 0 10 TRP 0 1 TYR 0 1 Processing NMR model 7 ** Unrecognized atom type [ O2 ] in residue HIS A 114 Average value of CA-N-C-CB angle is 34.46 Standard deviation is 1.04 * 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 = 1802 old number = 0 * ASP A 99 Total number of residues that need to be changed and total number of residues: ALA 0 3 CYS 0 1 ASP 1 9 GLU 0 8 PHE 0 2 GLY 0 10 HIS 0 8 ILE 0 10 LYS 0 13 LEU 0 5 MET 0 3 ASN 0 6 PRO 0 5 GLN 0 5 ARG 0 3 SER 0 5 THR 0 6 VAL 0 10 TRP 0 1 TYR 0 1 Processing NMR model 8 ** Unrecognized atom type [ O2 ] in residue HIS A 114 Average value of CA-N-C-CB angle is 34.42 Standard deviation is 0.99 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 1802 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 3 CYS 0 1 ASP 0 9 GLU 0 8 PHE 0 2 GLY 0 10 HIS 0 8 ILE 0 10 LYS 0 13 LEU 0 5 MET 0 3 ASN 0 6 PRO 0 5 GLN 0 5 ARG 0 3 SER 0 5 THR 0 6 VAL 0 10 TRP 0 1 TYR 0 1 Processing NMR model 9 ** Unrecognized atom type [ O2 ] in residue HIS A 114 Average value of CA-N-C-CB angle is 34.42 Standard deviation is 1.00 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 1802 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 3 CYS 0 1 ASP 0 9 GLU 0 8 PHE 0 2 GLY 0 10 HIS 0 8 ILE 0 10 LYS 0 13 LEU 0 5 MET 0 3 ASN 0 6 PRO 0 5 GLN 0 5 ARG 0 3 SER 0 5 THR 0 6 VAL 0 10 TRP 0 1 TYR 0 1 Processing NMR model 10 ** Unrecognized atom type [ O2 ] in residue HIS A 114 Average value of CA-N-C-CB angle is 34.46 Standard deviation is 1.00 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 1802 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 3 CYS 0 1 ASP 0 9 GLU 0 8 PHE 0 2 GLY 0 10 HIS 0 8 ILE 0 10 LYS 0 13 LEU 0 5 MET 0 3 ASN 0 6 PRO 0 5 GLN 0 5 ARG 0 3 SER 0 5 THR 0 6 VAL 0 10 TRP 0 1 TYR 0 1 Processing NMR model 11 ** Unrecognized atom type [ O2 ] in residue HIS A 114 Average value of CA-N-C-CB angle is 34.47 Standard deviation is 0.96 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 1802 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 3 CYS 0 1 ASP 0 9 GLU 0 8 PHE 0 2 GLY 0 10 HIS 0 8 ILE 0 10 LYS 0 13 LEU 0 5 MET 0 3 ASN 0 6 PRO 0 5 GLN 0 5 ARG 0 3 SER 0 5 THR 0 6 VAL 0 10 TRP 0 1 TYR 0 1 Processing NMR model 12 ** Unrecognized atom type [ O2 ] in residue HIS A 114 Average value of CA-N-C-CB angle is 34.41 Standard deviation is 1.02 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 1802 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 3 CYS 0 1 ASP 0 9 GLU 0 8 PHE 0 2 GLY 0 10 HIS 0 8 ILE 0 10 LYS 0 13 LEU 0 5 MET 0 3 ASN 0 6 PRO 0 5 GLN 0 5 ARG 0 3 SER 0 5 THR 0 6 VAL 0 10 TRP 0 1 TYR 0 1 Processing NMR model 13 ** Unrecognized atom type [ O2 ] in residue HIS A 114 Average value of CA-N-C-CB angle is 34.42 Standard deviation is 1.03 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 1802 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 3 CYS 0 1 ASP 0 9 GLU 0 8 PHE 0 2 GLY 0 10 HIS 0 8 ILE 0 10 LYS 0 13 LEU 0 5 MET 0 3 ASN 0 6 PRO 0 5 GLN 0 5 ARG 0 3 SER 0 5 THR 0 6 VAL 0 10 TRP 0 1 TYR 0 1 Processing NMR model 14 ** Unrecognized atom type [ O2 ] in residue HIS A 114 Average value of CA-N-C-CB angle is 34.40 Standard deviation is 0.98 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 1802 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 3 CYS 0 1 ASP 0 9 GLU 0 8 PHE 0 2 GLY 0 10 HIS 0 8 ILE 0 10 LYS 0 13 LEU 0 5 MET 0 3 ASN 0 6 PRO 0 5 GLN 0 5 ARG 0 3 SER 0 5 THR 0 6 VAL 0 10 TRP 0 1 TYR 0 1 Processing NMR model 15 ** Unrecognized atom type [ O2 ] in residue HIS A 114 Average value of CA-N-C-CB angle is 34.45 Standard deviation is 0.98 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 1802 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 3 CYS 0 1 ASP 0 9 GLU 0 8 PHE 0 2 GLY 0 10 HIS 0 8 ILE 0 10 LYS 0 13 LEU 0 5 MET 0 3 ASN 0 6 PRO 0 5 GLN 0 5 ARG 0 3 SER 0 5 THR 0 6 VAL 0 10 TRP 0 1 TYR 0 1 Processing NMR model 16 ** Unrecognized atom type [ O2 ] in residue HIS A 114 Average value of CA-N-C-CB angle is 34.46 Standard deviation is 1.02 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 1802 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 3 CYS 0 1 ASP 0 9 GLU 0 8 PHE 0 2 GLY 0 10 HIS 0 8 ILE 0 10 LYS 0 13 LEU 0 5 MET 0 3 ASN 0 6 PRO 0 5 GLN 0 5 ARG 0 3 SER 0 5 THR 0 6 VAL 0 10 TRP 0 1 TYR 0 1 Processing NMR model 17 ** Unrecognized atom type [ O2 ] in residue HIS A 114 Average value of CA-N-C-CB angle is 34.50 Standard deviation is 0.96 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 1802 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 3 CYS 0 1 ASP 0 9 GLU 0 8 PHE 0 2 GLY 0 10 HIS 0 8 ILE 0 10 LYS 0 13 LEU 0 5 MET 0 3 ASN 0 6 PRO 0 5 GLN 0 5 ARG 0 3 SER 0 5 THR 0 6 VAL 0 10 TRP 0 1 TYR 0 1 Processing NMR model 18 ** Unrecognized atom type [ O2 ] in residue HIS A 114 Average value of CA-N-C-CB angle is 34.43 Standard deviation is 1.02 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 1802 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 3 CYS 0 1 ASP 0 9 GLU 0 8 PHE 0 2 GLY 0 10 HIS 0 8 ILE 0 10 LYS 0 13 LEU 0 5 MET 0 3 ASN 0 6 PRO 0 5 GLN 0 5 ARG 0 3 SER 0 5 THR 0 6 VAL 0 10 TRP 0 1 TYR 0 1 Processing NMR model 19 ** Unrecognized atom type [ O2 ] in residue HIS A 114 Average value of CA-N-C-CB angle is 34.43 Standard deviation is 0.94 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 1802 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 3 CYS 0 1 ASP 0 9 GLU 0 8 PHE 0 2 GLY 0 10 HIS 0 8 ILE 0 10 LYS 0 13 LEU 0 5 MET 0 3 ASN 0 6 PRO 0 5 GLN 0 5 ARG 0 3 SER 0 5 THR 0 6 VAL 0 10 TRP 0 1 TYR 0 1 Processing NMR model 20 ** Unrecognized atom type [ O2 ] in residue HIS A 114 Average value of CA-N-C-CB angle is 34.48 Standard deviation is 0.96 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 1802 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 3 CYS 0 1 ASP 0 9 GLU 0 8 PHE 0 2 GLY 0 10 HIS 0 8 ILE 0 10 LYS 0 13 LEU 0 5 MET 0 3 ASN 0 6 PRO 0 5 GLN 0 5 ARG 0 3 SER 0 5 THR 0 6 VAL 0 10 TRP 0 1 TYR 0 1 * NMR ensemble comprises 20 model structures * Program completed