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 202 Average value of CA-N-C-CB angle is 34.12 Standard deviation is 1.24 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 3140 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 16 CYS 0 3 ASP 0 9 GLU 0 15 PHE 0 7 GLY 0 17 HIS 0 8 ILE 0 9 LYS 0 11 LEU 0 28 MET 0 1 ASN 0 9 PRO 0 9 GLN 0 16 ARG 0 4 SER 0 12 THR 0 6 VAL 0 12 TRP 0 3 TYR 0 7 Processing NMR model 2 ** Unrecognized atom type [ O2 ] in residue HIS A 202 Average value of CA-N-C-CB angle is 34.02 Standard deviation is 1.26 * 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 = 3140 old number = 0 * TYR A 118 Total number of residues that need to be changed and total number of residues: ALA 0 16 CYS 0 3 ASP 0 9 GLU 0 15 PHE 0 7 GLY 0 17 HIS 0 8 ILE 0 9 LYS 0 11 LEU 0 28 MET 0 1 ASN 0 9 PRO 0 9 GLN 0 16 ARG 0 4 SER 0 12 THR 0 6 VAL 0 12 TRP 0 3 TYR 1 7 Processing NMR model 3 ** Unrecognized atom type [ O2 ] in residue HIS A 202 Average value of CA-N-C-CB angle is 34.09 Standard deviation is 1.19 * 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 = 3140 old number = 0 * ASP A 89 Total number of residues that need to be changed and total number of residues: ALA 0 16 CYS 0 3 ASP 1 9 GLU 0 15 PHE 0 7 GLY 0 17 HIS 0 8 ILE 0 9 LYS 0 11 LEU 0 28 MET 0 1 ASN 0 9 PRO 0 9 GLN 0 16 ARG 0 4 SER 0 12 THR 0 6 VAL 0 12 TRP 0 3 TYR 0 7 Processing NMR model 4 ** Unrecognized atom type [ O2 ] in residue HIS A 202 Average value of CA-N-C-CB angle is 34.08 Standard deviation is 1.21 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 3140 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 16 CYS 0 3 ASP 0 9 GLU 0 15 PHE 0 7 GLY 0 17 HIS 0 8 ILE 0 9 LYS 0 11 LEU 0 28 MET 0 1 ASN 0 9 PRO 0 9 GLN 0 16 ARG 0 4 SER 0 12 THR 0 6 VAL 0 12 TRP 0 3 TYR 0 7 Processing NMR model 5 ** Unrecognized atom type [ O2 ] in residue HIS A 202 Average value of CA-N-C-CB angle is 34.06 Standard deviation is 1.20 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 3140 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 16 CYS 0 3 ASP 0 9 GLU 0 15 PHE 0 7 GLY 0 17 HIS 0 8 ILE 0 9 LYS 0 11 LEU 0 28 MET 0 1 ASN 0 9 PRO 0 9 GLN 0 16 ARG 0 4 SER 0 12 THR 0 6 VAL 0 12 TRP 0 3 TYR 0 7 Processing NMR model 6 ** Unrecognized atom type [ O2 ] in residue HIS A 202 Average value of CA-N-C-CB angle is 34.08 Standard deviation is 1.28 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 3140 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 16 CYS 0 3 ASP 0 9 GLU 0 15 PHE 0 7 GLY 0 17 HIS 0 8 ILE 0 9 LYS 0 11 LEU 0 28 MET 0 1 ASN 0 9 PRO 0 9 GLN 0 16 ARG 0 4 SER 0 12 THR 0 6 VAL 0 12 TRP 0 3 TYR 0 7 Processing NMR model 7 ** Unrecognized atom type [ O2 ] in residue HIS A 202 Average value of CA-N-C-CB angle is 34.05 Standard deviation is 1.32 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 3140 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 16 CYS 0 3 ASP 0 9 GLU 0 15 PHE 0 7 GLY 0 17 HIS 0 8 ILE 0 9 LYS 0 11 LEU 0 28 MET 0 1 ASN 0 9 PRO 0 9 GLN 0 16 ARG 0 4 SER 0 12 THR 0 6 VAL 0 12 TRP 0 3 TYR 0 7 Processing NMR model 8 ** Unrecognized atom type [ O2 ] in residue HIS A 202 Average value of CA-N-C-CB angle is 34.08 Standard deviation is 1.28 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 3140 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 16 CYS 0 3 ASP 0 9 GLU 0 15 PHE 0 7 GLY 0 17 HIS 0 8 ILE 0 9 LYS 0 11 LEU 0 28 MET 0 1 ASN 0 9 PRO 0 9 GLN 0 16 ARG 0 4 SER 0 12 THR 0 6 VAL 0 12 TRP 0 3 TYR 0 7 Processing NMR model 9 ** Unrecognized atom type [ O2 ] in residue HIS A 202 Average value of CA-N-C-CB angle is 34.07 Standard deviation is 1.20 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 3140 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 16 CYS 0 3 ASP 0 9 GLU 0 15 PHE 0 7 GLY 0 17 HIS 0 8 ILE 0 9 LYS 0 11 LEU 0 28 MET 0 1 ASN 0 9 PRO 0 9 GLN 0 16 ARG 0 4 SER 0 12 THR 0 6 VAL 0 12 TRP 0 3 TYR 0 7 Processing NMR model 10 ** Unrecognized atom type [ O2 ] in residue HIS A 202 Average value of CA-N-C-CB angle is 34.02 Standard deviation is 1.24 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 3140 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 16 CYS 0 3 ASP 0 9 GLU 0 15 PHE 0 7 GLY 0 17 HIS 0 8 ILE 0 9 LYS 0 11 LEU 0 28 MET 0 1 ASN 0 9 PRO 0 9 GLN 0 16 ARG 0 4 SER 0 12 THR 0 6 VAL 0 12 TRP 0 3 TYR 0 7 Processing NMR model 11 ** Unrecognized atom type [ O2 ] in residue HIS A 202 Average value of CA-N-C-CB angle is 34.15 Standard deviation is 1.29 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 3140 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 16 CYS 0 3 ASP 0 9 GLU 0 15 PHE 0 7 GLY 0 17 HIS 0 8 ILE 0 9 LYS 0 11 LEU 0 28 MET 0 1 ASN 0 9 PRO 0 9 GLN 0 16 ARG 0 4 SER 0 12 THR 0 6 VAL 0 12 TRP 0 3 TYR 0 7 Processing NMR model 12 ** Unrecognized atom type [ O2 ] in residue HIS A 202 Average value of CA-N-C-CB angle is 34.04 Standard deviation is 1.22 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 3140 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 16 CYS 0 3 ASP 0 9 GLU 0 15 PHE 0 7 GLY 0 17 HIS 0 8 ILE 0 9 LYS 0 11 LEU 0 28 MET 0 1 ASN 0 9 PRO 0 9 GLN 0 16 ARG 0 4 SER 0 12 THR 0 6 VAL 0 12 TRP 0 3 TYR 0 7 Processing NMR model 13 ** Unrecognized atom type [ O2 ] in residue HIS A 202 Average value of CA-N-C-CB angle is 34.01 Standard deviation is 1.25 * 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 = 3140 old number = 0 * ASP A 89 Total number of residues that need to be changed and total number of residues: ALA 0 16 CYS 0 3 ASP 1 9 GLU 0 15 PHE 0 7 GLY 0 17 HIS 0 8 ILE 0 9 LYS 0 11 LEU 0 28 MET 0 1 ASN 0 9 PRO 0 9 GLN 0 16 ARG 0 4 SER 0 12 THR 0 6 VAL 0 12 TRP 0 3 TYR 0 7 Processing NMR model 14 ** Unrecognized atom type [ O2 ] in residue HIS A 202 Average value of CA-N-C-CB angle is 34.17 Standard deviation is 1.11 * 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 = 3140 old number = 0 * GLU A 154 Total number of residues that need to be changed and total number of residues: ALA 0 16 CYS 0 3 ASP 0 9 GLU 1 15 PHE 0 7 GLY 0 17 HIS 0 8 ILE 0 9 LYS 0 11 LEU 0 28 MET 0 1 ASN 0 9 PRO 0 9 GLN 0 16 ARG 0 4 SER 0 12 THR 0 6 VAL 0 12 TRP 0 3 TYR 0 7 Processing NMR model 15 ** Unrecognized atom type [ O2 ] in residue HIS A 202 Average value of CA-N-C-CB angle is 34.16 Standard deviation is 1.21 * 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 = 3140 old number = 0 * GLU A 196 Total number of residues that need to be changed and total number of residues: ALA 0 16 CYS 0 3 ASP 0 9 GLU 1 15 PHE 0 7 GLY 0 17 HIS 0 8 ILE 0 9 LYS 0 11 LEU 0 28 MET 0 1 ASN 0 9 PRO 0 9 GLN 0 16 ARG 0 4 SER 0 12 THR 0 6 VAL 0 12 TRP 0 3 TYR 0 7 Processing NMR model 16 ** Unrecognized atom type [ O2 ] in residue HIS A 202 Average value of CA-N-C-CB angle is 34.13 Standard deviation is 1.23 * 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 = 3140 old number = 0 * GLU A 4 Total number of residues that need to be changed and total number of residues: ALA 0 16 CYS 0 3 ASP 0 9 GLU 1 15 PHE 0 7 GLY 0 17 HIS 0 8 ILE 0 9 LYS 0 11 LEU 0 28 MET 0 1 ASN 0 9 PRO 0 9 GLN 0 16 ARG 0 4 SER 0 12 THR 0 6 VAL 0 12 TRP 0 3 TYR 0 7 Processing NMR model 17 ** Unrecognized atom type [ O2 ] in residue HIS A 202 Average value of CA-N-C-CB angle is 34.12 Standard deviation is 1.17 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 3140 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 16 CYS 0 3 ASP 0 9 GLU 0 15 PHE 0 7 GLY 0 17 HIS 0 8 ILE 0 9 LYS 0 11 LEU 0 28 MET 0 1 ASN 0 9 PRO 0 9 GLN 0 16 ARG 0 4 SER 0 12 THR 0 6 VAL 0 12 TRP 0 3 TYR 0 7 Processing NMR model 18 ** Unrecognized atom type [ O2 ] in residue HIS A 202 Average value of CA-N-C-CB angle is 34.06 Standard deviation is 1.22 * 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 = 3140 old number = 0 * GLU A 53 Total number of residues that need to be changed and total number of residues: ALA 0 16 CYS 0 3 ASP 0 9 GLU 1 15 PHE 0 7 GLY 0 17 HIS 0 8 ILE 0 9 LYS 0 11 LEU 0 28 MET 0 1 ASN 0 9 PRO 0 9 GLN 0 16 ARG 0 4 SER 0 12 THR 0 6 VAL 0 12 TRP 0 3 TYR 0 7 Processing NMR model 19 ** Unrecognized atom type [ O2 ] in residue HIS A 202 Average value of CA-N-C-CB angle is 34.11 Standard deviation is 1.24 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 3140 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 16 CYS 0 3 ASP 0 9 GLU 0 15 PHE 0 7 GLY 0 17 HIS 0 8 ILE 0 9 LYS 0 11 LEU 0 28 MET 0 1 ASN 0 9 PRO 0 9 GLN 0 16 ARG 0 4 SER 0 12 THR 0 6 VAL 0 12 TRP 0 3 TYR 0 7 Processing NMR model 20 ** Unrecognized atom type [ O2 ] in residue HIS A 202 Average value of CA-N-C-CB angle is 34.14 Standard deviation is 1.22 * 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 = 3140 old number = 0 * GLU A 40 TYR A 139 Total number of residues that need to be changed and total number of residues: ALA 0 16 CYS 0 3 ASP 0 9 GLU 1 15 PHE 0 7 GLY 0 17 HIS 0 8 ILE 0 9 LYS 0 11 LEU 0 28 MET 0 1 ASN 0 9 PRO 0 9 GLN 0 16 ARG 0 4 SER 0 12 THR 0 6 VAL 0 12 TRP 0 3 TYR 1 7 * NMR ensemble comprises 20 model structures * Program completed