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 99 Average value of CA-N-C-CB angle is 33.91 Standard deviation is 1.08 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 1566 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 10 ASP 0 11 GLU 0 13 PHE 0 2 GLY 0 5 HIS 0 9 ILE 0 2 LYS 0 5 LEU 0 12 ASN 0 1 PRO 0 3 GLN 0 4 ARG 0 5 SER 0 2 THR 0 6 VAL 0 3 TYR 0 6 Processing NMR model 2 ** Unrecognized atom type [ O2 ] in residue HIS A 99 Average value of CA-N-C-CB angle is 33.91 Standard deviation is 1.18 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 1566 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 10 ASP 0 11 GLU 0 13 PHE 0 2 GLY 0 5 HIS 0 9 ILE 0 2 LYS 0 5 LEU 0 12 ASN 0 1 PRO 0 3 GLN 0 4 ARG 0 5 SER 0 2 THR 0 6 VAL 0 3 TYR 0 6 Processing NMR model 3 ** Unrecognized atom type [ O2 ] in residue HIS A 99 Average value of CA-N-C-CB angle is 33.97 Standard deviation is 1.15 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 1566 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 10 ASP 0 11 GLU 0 13 PHE 0 2 GLY 0 5 HIS 0 9 ILE 0 2 LYS 0 5 LEU 0 12 ASN 0 1 PRO 0 3 GLN 0 4 ARG 0 5 SER 0 2 THR 0 6 VAL 0 3 TYR 0 6 Processing NMR model 4 ** Unrecognized atom type [ O2 ] in residue HIS A 99 Average value of CA-N-C-CB angle is 33.93 Standard deviation is 1.13 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 1566 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 10 ASP 0 11 GLU 0 13 PHE 0 2 GLY 0 5 HIS 0 9 ILE 0 2 LYS 0 5 LEU 0 12 ASN 0 1 PRO 0 3 GLN 0 4 ARG 0 5 SER 0 2 THR 0 6 VAL 0 3 TYR 0 6 Processing NMR model 5 ** Unrecognized atom type [ O2 ] in residue HIS A 99 Average value of CA-N-C-CB angle is 33.92 Standard deviation is 1.09 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 1566 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 10 ASP 0 11 GLU 0 13 PHE 0 2 GLY 0 5 HIS 0 9 ILE 0 2 LYS 0 5 LEU 0 12 ASN 0 1 PRO 0 3 GLN 0 4 ARG 0 5 SER 0 2 THR 0 6 VAL 0 3 TYR 0 6 Processing NMR model 6 ** Unrecognized atom type [ O2 ] in residue HIS A 99 Average value of CA-N-C-CB angle is 33.93 Standard deviation is 1.14 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 1566 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 10 ASP 0 11 GLU 0 13 PHE 0 2 GLY 0 5 HIS 0 9 ILE 0 2 LYS 0 5 LEU 0 12 ASN 0 1 PRO 0 3 GLN 0 4 ARG 0 5 SER 0 2 THR 0 6 VAL 0 3 TYR 0 6 Processing NMR model 7 ** Unrecognized atom type [ O2 ] in residue HIS A 99 Average value of CA-N-C-CB angle is 33.95 Standard deviation is 1.04 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 1566 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 10 ASP 0 11 GLU 0 13 PHE 0 2 GLY 0 5 HIS 0 9 ILE 0 2 LYS 0 5 LEU 0 12 ASN 0 1 PRO 0 3 GLN 0 4 ARG 0 5 SER 0 2 THR 0 6 VAL 0 3 TYR 0 6 Processing NMR model 8 ** Unrecognized atom type [ O2 ] in residue HIS A 99 Average value of CA-N-C-CB angle is 33.96 Standard deviation is 1.08 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 1566 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 10 ASP 0 11 GLU 0 13 PHE 0 2 GLY 0 5 HIS 0 9 ILE 0 2 LYS 0 5 LEU 0 12 ASN 0 1 PRO 0 3 GLN 0 4 ARG 0 5 SER 0 2 THR 0 6 VAL 0 3 TYR 0 6 Processing NMR model 9 ** Unrecognized atom type [ O2 ] in residue HIS A 99 Average value of CA-N-C-CB angle is 33.97 Standard deviation is 1.08 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 1566 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 10 ASP 0 11 GLU 0 13 PHE 0 2 GLY 0 5 HIS 0 9 ILE 0 2 LYS 0 5 LEU 0 12 ASN 0 1 PRO 0 3 GLN 0 4 ARG 0 5 SER 0 2 THR 0 6 VAL 0 3 TYR 0 6 Processing NMR model 10 ** Unrecognized atom type [ O2 ] in residue HIS A 99 Average value of CA-N-C-CB angle is 33.90 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 = 1566 old number = 0 * GLU A 90 Total number of residues that need to be changed and total number of residues: ALA 0 10 ASP 0 11 GLU 1 13 PHE 0 2 GLY 0 5 HIS 0 9 ILE 0 2 LYS 0 5 LEU 0 12 ASN 0 1 PRO 0 3 GLN 0 4 ARG 0 5 SER 0 2 THR 0 6 VAL 0 3 TYR 0 6 Processing NMR model 11 ** Unrecognized atom type [ O2 ] in residue HIS A 99 Average value of CA-N-C-CB angle is 33.95 Standard deviation is 1.13 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 1566 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 10 ASP 0 11 GLU 0 13 PHE 0 2 GLY 0 5 HIS 0 9 ILE 0 2 LYS 0 5 LEU 0 12 ASN 0 1 PRO 0 3 GLN 0 4 ARG 0 5 SER 0 2 THR 0 6 VAL 0 3 TYR 0 6 Processing NMR model 12 ** Unrecognized atom type [ O2 ] in residue HIS A 99 Average value of CA-N-C-CB angle is 33.98 Standard deviation is 1.03 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 1566 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 10 ASP 0 11 GLU 0 13 PHE 0 2 GLY 0 5 HIS 0 9 ILE 0 2 LYS 0 5 LEU 0 12 ASN 0 1 PRO 0 3 GLN 0 4 ARG 0 5 SER 0 2 THR 0 6 VAL 0 3 TYR 0 6 Processing NMR model 13 ** Unrecognized atom type [ O2 ] in residue HIS A 99 Average value of CA-N-C-CB angle is 34.00 Standard deviation is 1.17 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 1566 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 10 ASP 0 11 GLU 0 13 PHE 0 2 GLY 0 5 HIS 0 9 ILE 0 2 LYS 0 5 LEU 0 12 ASN 0 1 PRO 0 3 GLN 0 4 ARG 0 5 SER 0 2 THR 0 6 VAL 0 3 TYR 0 6 Processing NMR model 14 ** Unrecognized atom type [ O2 ] in residue HIS A 99 Average value of CA-N-C-CB angle is 33.98 Standard deviation is 1.10 * 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 = 1566 old number = 0 * ASP A 84 Total number of residues that need to be changed and total number of residues: ALA 0 10 ASP 1 11 GLU 0 13 PHE 0 2 GLY 0 5 HIS 0 9 ILE 0 2 LYS 0 5 LEU 0 12 ASN 0 1 PRO 0 3 GLN 0 4 ARG 0 5 SER 0 2 THR 0 6 VAL 0 3 TYR 0 6 Processing NMR model 15 ** Unrecognized atom type [ O2 ] in residue HIS A 99 Average value of CA-N-C-CB angle is 34.03 Standard deviation is 1.06 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 1566 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 10 ASP 0 11 GLU 0 13 PHE 0 2 GLY 0 5 HIS 0 9 ILE 0 2 LYS 0 5 LEU 0 12 ASN 0 1 PRO 0 3 GLN 0 4 ARG 0 5 SER 0 2 THR 0 6 VAL 0 3 TYR 0 6 Processing NMR model 16 ** Unrecognized atom type [ O2 ] in residue HIS A 99 Average value of CA-N-C-CB angle is 33.96 Standard deviation is 1.14 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 1566 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 10 ASP 0 11 GLU 0 13 PHE 0 2 GLY 0 5 HIS 0 9 ILE 0 2 LYS 0 5 LEU 0 12 ASN 0 1 PRO 0 3 GLN 0 4 ARG 0 5 SER 0 2 THR 0 6 VAL 0 3 TYR 0 6 Processing NMR model 17 ** Unrecognized atom type [ O2 ] in residue HIS A 99 Average value of CA-N-C-CB angle is 33.96 Standard deviation is 1.10 * 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 = 1566 old number = 0 * TYR A 39 Total number of residues that need to be changed and total number of residues: ALA 0 10 ASP 0 11 GLU 0 13 PHE 0 2 GLY 0 5 HIS 0 9 ILE 0 2 LYS 0 5 LEU 0 12 ASN 0 1 PRO 0 3 GLN 0 4 ARG 0 5 SER 0 2 THR 0 6 VAL 0 3 TYR 1 6 Processing NMR model 18 ** Unrecognized atom type [ O2 ] in residue HIS A 99 Average value of CA-N-C-CB angle is 33.96 Standard deviation is 1.04 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 1566 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 10 ASP 0 11 GLU 0 13 PHE 0 2 GLY 0 5 HIS 0 9 ILE 0 2 LYS 0 5 LEU 0 12 ASN 0 1 PRO 0 3 GLN 0 4 ARG 0 5 SER 0 2 THR 0 6 VAL 0 3 TYR 0 6 Processing NMR model 19 ** Unrecognized atom type [ O2 ] in residue HIS A 99 Average value of CA-N-C-CB angle is 33.96 Standard deviation is 1.21 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 1566 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 10 ASP 0 11 GLU 0 13 PHE 0 2 GLY 0 5 HIS 0 9 ILE 0 2 LYS 0 5 LEU 0 12 ASN 0 1 PRO 0 3 GLN 0 4 ARG 0 5 SER 0 2 THR 0 6 VAL 0 3 TYR 0 6 Processing NMR model 20 ** Unrecognized atom type [ O2 ] in residue HIS A 99 Average value of CA-N-C-CB angle is 33.90 Standard deviation is 1.04 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 1566 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 10 ASP 0 11 GLU 0 13 PHE 0 2 GLY 0 5 HIS 0 9 ILE 0 2 LYS 0 5 LEU 0 12 ASN 0 1 PRO 0 3 GLN 0 4 ARG 0 5 SER 0 2 THR 0 6 VAL 0 3 TYR 0 6 * NMR ensemble comprises 20 model structures * Program completed