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 SER A 143 Average value of CA-N-C-CB angle is 34.15 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 = 2250 old number = 0 * PHE A 38 PHE A 45 PHE A 49 PHE A 53 TYR A 113 PHE A 125 Total number of residues that need to be changed and total number of residues: ALA 0 6 CYS 0 2 ASP 0 6 GLU 0 15 PHE 5 9 GLY 0 6 HIS 0 7 ILE 0 13 LYS 0 7 LEU 0 9 MET 0 2 ASN 0 4 PRO 0 5 GLN 0 6 ARG 0 4 SER 0 16 THR 0 10 VAL 0 12 TRP 0 2 TYR 1 2 Processing NMR model 2 ** Unrecognized atom type [ O2 ] in residue SER A 143 Average value of CA-N-C-CB angle is 34.20 Standard deviation is 0.98 * 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 = 2250 old number = 0 * PHE A 38 PHE A 45 PHE A 49 PHE A 68 PHE A 122 PHE A 125 Total number of residues that need to be changed and total number of residues: ALA 0 6 CYS 0 2 ASP 0 6 GLU 0 15 PHE 6 9 GLY 0 6 HIS 0 7 ILE 0 13 LYS 0 7 LEU 0 9 MET 0 2 ASN 0 4 PRO 0 5 GLN 0 6 ARG 0 4 SER 0 16 THR 0 10 VAL 0 12 TRP 0 2 TYR 0 2 Processing NMR model 3 ** Unrecognized atom type [ O2 ] in residue SER A 143 Average value of CA-N-C-CB angle is 34.19 Standard deviation is 1.02 * Side chain atoms should be swapped for the following residues: * As this is an NMR ensemble the swap has not been made * PHE A 38 PHE A 45 PHE A 49 PHE A 53 PHE A 68 PHE A 122 PHE A 125 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2250 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 6 CYS 0 2 ASP 0 6 GLU 0 15 PHE 7 9 GLY 0 6 HIS 0 7 ILE 0 13 LYS 0 7 LEU 0 9 MET 0 2 ASN 0 4 PRO 0 5 GLN 0 6 ARG 0 4 SER 0 16 THR 0 10 VAL 0 12 TRP 0 2 TYR 0 2 Processing NMR model 4 ** Unrecognized atom type [ O2 ] in residue SER A 143 Average value of CA-N-C-CB angle is 34.17 Standard deviation is 1.08 * Side chain atoms should be swapped for the following residues: * As this is an NMR ensemble the swap has not been made * PHE A 38 PHE A 45 PHE A 49 PHE A 53 PHE A 68 PHE A 122 PHE A 125 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2250 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 6 CYS 0 2 ASP 0 6 GLU 0 15 PHE 7 9 GLY 0 6 HIS 0 7 ILE 0 13 LYS 0 7 LEU 0 9 MET 0 2 ASN 0 4 PRO 0 5 GLN 0 6 ARG 0 4 SER 0 16 THR 0 10 VAL 0 12 TRP 0 2 TYR 0 2 Processing NMR model 5 ** Unrecognized atom type [ O2 ] in residue SER A 143 Average value of CA-N-C-CB angle is 34.19 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 = 2250 old number = 0 * PHE A 38 PHE A 45 PHE A 49 PHE A 53 TYR A 67 PHE A 68 Total number of residues that need to be changed and total number of residues: ALA 0 6 CYS 0 2 ASP 0 6 GLU 0 15 PHE 5 9 GLY 0 6 HIS 0 7 ILE 0 13 LYS 0 7 LEU 0 9 MET 0 2 ASN 0 4 PRO 0 5 GLN 0 6 ARG 0 4 SER 0 16 THR 0 10 VAL 0 12 TRP 0 2 TYR 1 2 Processing NMR model 6 ** Unrecognized atom type [ O2 ] in residue SER A 143 Average value of CA-N-C-CB angle is 34.17 Standard deviation is 1.05 * 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 = 2250 old number = 0 * PHE A 38 PHE A 49 PHE A 53 PHE A 68 PHE A 122 PHE A 125 Total number of residues that need to be changed and total number of residues: ALA 0 6 CYS 0 2 ASP 0 6 GLU 0 15 PHE 6 9 GLY 0 6 HIS 0 7 ILE 0 13 LYS 0 7 LEU 0 9 MET 0 2 ASN 0 4 PRO 0 5 GLN 0 6 ARG 0 4 SER 0 16 THR 0 10 VAL 0 12 TRP 0 2 TYR 0 2 Processing NMR model 7 ** Unrecognized atom type [ O2 ] in residue SER A 143 Average value of CA-N-C-CB angle is 34.16 Standard deviation is 1.02 * Side chain atoms should be swapped for the following residues: * As this is an NMR ensemble the swap has not been made * PHE A 38 PHE A 45 PHE A 49 PHE A 53 PHE A 68 TYR A 113 PHE A 122 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2250 old number = 0 * PHE A 125 Total number of residues that need to be changed and total number of residues: ALA 0 6 CYS 0 2 ASP 0 6 GLU 0 15 PHE 7 9 GLY 0 6 HIS 0 7 ILE 0 13 LYS 0 7 LEU 0 9 MET 0 2 ASN 0 4 PRO 0 5 GLN 0 6 ARG 0 4 SER 0 16 THR 0 10 VAL 0 12 TRP 0 2 TYR 1 2 Processing NMR model 8 ** Unrecognized atom type [ O2 ] in residue SER A 143 Average value of CA-N-C-CB angle is 34.18 Standard deviation is 1.00 * Side chain atoms should be swapped for the following residues: * As this is an NMR ensemble the swap has not been made * PHE A 38 PHE A 45 PHE A 49 PHE A 53 PHE A 68 PHE A 122 PHE A 125 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2250 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 6 CYS 0 2 ASP 0 6 GLU 0 15 PHE 7 9 GLY 0 6 HIS 0 7 ILE 0 13 LYS 0 7 LEU 0 9 MET 0 2 ASN 0 4 PRO 0 5 GLN 0 6 ARG 0 4 SER 0 16 THR 0 10 VAL 0 12 TRP 0 2 TYR 0 2 Processing NMR model 9 ** Unrecognized atom type [ O2 ] in residue SER A 143 Average value of CA-N-C-CB angle is 34.13 Standard deviation is 0.97 * Side chain atoms should be swapped for the following residues: * As this is an NMR ensemble the swap has not been made * PHE A 38 PHE A 45 TYR A 67 PHE A 68 PHE A 85 PHE A 122 PHE A 125 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2250 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 6 CYS 0 2 ASP 0 6 GLU 0 15 PHE 6 9 GLY 0 6 HIS 0 7 ILE 0 13 LYS 0 7 LEU 0 9 MET 0 2 ASN 0 4 PRO 0 5 GLN 0 6 ARG 0 4 SER 0 16 THR 0 10 VAL 0 12 TRP 0 2 TYR 1 2 Processing NMR model 10 ** Unrecognized atom type [ O2 ] in residue SER A 143 Average value of CA-N-C-CB angle is 34.16 Standard deviation is 1.01 * Side chain atoms should be swapped for the following residues: * As this is an NMR ensemble the swap has not been made * PHE A 38 PHE A 45 PHE A 49 TYR A 67 PHE A 68 PHE A 122 PHE A 125 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2250 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 6 CYS 0 2 ASP 0 6 GLU 0 15 PHE 6 9 GLY 0 6 HIS 0 7 ILE 0 13 LYS 0 7 LEU 0 9 MET 0 2 ASN 0 4 PRO 0 5 GLN 0 6 ARG 0 4 SER 0 16 THR 0 10 VAL 0 12 TRP 0 2 TYR 1 2 Processing NMR model 11 ** Unrecognized atom type [ O2 ] in residue SER A 143 Average value of CA-N-C-CB angle is 34.17 Standard deviation is 1.02 * Side chain atoms should be swapped for the following residues: * As this is an NMR ensemble the swap has not been made * PHE A 38 PHE A 45 PHE A 49 PHE A 53 PHE A 68 PHE A 122 PHE A 125 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2250 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 6 CYS 0 2 ASP 0 6 GLU 0 15 PHE 7 9 GLY 0 6 HIS 0 7 ILE 0 13 LYS 0 7 LEU 0 9 MET 0 2 ASN 0 4 PRO 0 5 GLN 0 6 ARG 0 4 SER 0 16 THR 0 10 VAL 0 12 TRP 0 2 TYR 0 2 Processing NMR model 12 ** Unrecognized atom type [ O2 ] in residue SER A 143 Average value of CA-N-C-CB angle is 34.16 Standard deviation is 1.03 * Side chain atoms should be swapped for the following residues: * As this is an NMR ensemble the swap has not been made * PHE A 38 PHE A 45 PHE A 49 PHE A 53 PHE A 68 PHE A 122 PHE A 125 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2250 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 6 CYS 0 2 ASP 0 6 GLU 0 15 PHE 7 9 GLY 0 6 HIS 0 7 ILE 0 13 LYS 0 7 LEU 0 9 MET 0 2 ASN 0 4 PRO 0 5 GLN 0 6 ARG 0 4 SER 0 16 THR 0 10 VAL 0 12 TRP 0 2 TYR 0 2 Processing NMR model 13 ** Unrecognized atom type [ O2 ] in residue SER A 143 Average value of CA-N-C-CB angle is 34.13 Standard deviation is 0.93 * Side chain atoms should be swapped for the following residues: * As this is an NMR ensemble the swap has not been made * PHE A 45 PHE A 49 PHE A 53 PHE A 68 TYR A 113 PHE A 122 PHE A 125 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2250 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 6 CYS 0 2 ASP 0 6 GLU 0 15 PHE 6 9 GLY 0 6 HIS 0 7 ILE 0 13 LYS 0 7 LEU 0 9 MET 0 2 ASN 0 4 PRO 0 5 GLN 0 6 ARG 0 4 SER 0 16 THR 0 10 VAL 0 12 TRP 0 2 TYR 1 2 Processing NMR model 14 ** Unrecognized atom type [ O2 ] in residue SER A 143 Average value of CA-N-C-CB angle is 34.11 Standard deviation is 0.90 * Side chain atoms should be swapped for the following residues: * As this is an NMR ensemble the swap has not been made * PHE A 38 PHE A 45 PHE A 49 TYR A 67 PHE A 68 PHE A 85 PHE A 125 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2250 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 6 CYS 0 2 ASP 0 6 GLU 0 15 PHE 6 9 GLY 0 6 HIS 0 7 ILE 0 13 LYS 0 7 LEU 0 9 MET 0 2 ASN 0 4 PRO 0 5 GLN 0 6 ARG 0 4 SER 0 16 THR 0 10 VAL 0 12 TRP 0 2 TYR 1 2 Processing NMR model 15 ** Unrecognized atom type [ O2 ] in residue SER A 143 Average value of CA-N-C-CB angle is 34.12 Standard deviation is 0.92 * Side chain atoms should be swapped for the following residues: * As this is an NMR ensemble the swap has not been made * PHE A 38 PHE A 45 PHE A 49 PHE A 53 TYR A 67 PHE A 85 PHE A 122 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2250 old number = 0 * PHE A 125 Total number of residues that need to be changed and total number of residues: ALA 0 6 CYS 0 2 ASP 0 6 GLU 0 15 PHE 7 9 GLY 0 6 HIS 0 7 ILE 0 13 LYS 0 7 LEU 0 9 MET 0 2 ASN 0 4 PRO 0 5 GLN 0 6 ARG 0 4 SER 0 16 THR 0 10 VAL 0 12 TRP 0 2 TYR 1 2 Processing NMR model 16 ** Unrecognized atom type [ O2 ] in residue SER A 143 Average value of CA-N-C-CB angle is 34.18 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 * PHE A 38 PHE A 45 PHE A 49 PHE A 53 TYR A 67 PHE A 68 PHE A 122 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2250 old number = 0 * PHE A 125 Total number of residues that need to be changed and total number of residues: ALA 0 6 CYS 0 2 ASP 0 6 GLU 0 15 PHE 7 9 GLY 0 6 HIS 0 7 ILE 0 13 LYS 0 7 LEU 0 9 MET 0 2 ASN 0 4 PRO 0 5 GLN 0 6 ARG 0 4 SER 0 16 THR 0 10 VAL 0 12 TRP 0 2 TYR 1 2 Processing NMR model 17 ** Unrecognized atom type [ O2 ] in residue SER A 143 Average value of CA-N-C-CB angle is 34.16 Standard deviation is 1.02 * Side chain atoms should be swapped for the following residues: * As this is an NMR ensemble the swap has not been made * PHE A 38 PHE A 45 PHE A 49 PHE A 53 PHE A 68 PHE A 122 PHE A 125 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2250 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 6 CYS 0 2 ASP 0 6 GLU 0 15 PHE 7 9 GLY 0 6 HIS 0 7 ILE 0 13 LYS 0 7 LEU 0 9 MET 0 2 ASN 0 4 PRO 0 5 GLN 0 6 ARG 0 4 SER 0 16 THR 0 10 VAL 0 12 TRP 0 2 TYR 0 2 Processing NMR model 18 ** Unrecognized atom type [ O2 ] in residue SER A 143 Average value of CA-N-C-CB angle is 34.17 Standard deviation is 1.06 * 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 = 2250 old number = 0 * PHE A 38 PHE A 45 PHE A 53 TYR A 67 PHE A 68 PHE A 125 Total number of residues that need to be changed and total number of residues: ALA 0 6 CYS 0 2 ASP 0 6 GLU 0 15 PHE 5 9 GLY 0 6 HIS 0 7 ILE 0 13 LYS 0 7 LEU 0 9 MET 0 2 ASN 0 4 PRO 0 5 GLN 0 6 ARG 0 4 SER 0 16 THR 0 10 VAL 0 12 TRP 0 2 TYR 1 2 * NMR ensemble comprises 18 model structures * Program completed