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 166 Average value of CA-N-C-CB angle is 34.28 Standard deviation is 1.15 * Side chain atoms should be swapped for the following residues: * As this is an NMR ensemble the swap has not been made * PHE A 7 PHE A 58 TYR A 61 PHE A 73 TYR A 102 PHE A 125 TYR A 132 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2486 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 14 CYS 0 2 ASP 0 8 GLU 0 16 PHE 4 9 GLY 0 18 HIS 0 8 ILE 0 5 LYS 0 4 LEU 0 18 MET 0 5 ASN 0 2 PRO 0 10 GLN 0 5 ARG 0 5 SER 0 12 THR 0 7 VAL 0 10 TRP 0 1 TYR 3 7 Processing NMR model 2 ** Unrecognized atom type [ O2 ] in residue HIS A 166 Average value of CA-N-C-CB angle is 34.28 Standard deviation is 1.17 * 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 = 2486 old number = 0 * PHE A 3 PHE A 7 PHE A 58 TYR A 61 TYR A 102 PHE A 125 Total number of residues that need to be changed and total number of residues: ALA 0 14 CYS 0 2 ASP 0 8 GLU 0 16 PHE 4 9 GLY 0 18 HIS 0 8 ILE 0 5 LYS 0 4 LEU 0 18 MET 0 5 ASN 0 2 PRO 0 10 GLN 0 5 ARG 0 5 SER 0 12 THR 0 7 VAL 0 10 TRP 0 1 TYR 2 7 Processing NMR model 3 ** Unrecognized atom type [ O2 ] in residue HIS A 166 Average value of CA-N-C-CB angle is 34.28 Standard deviation is 1.24 * Side chain atoms should be swapped for the following residues: * As this is an NMR ensemble the swap has not been made * PHE A 3 PHE A 7 PHE A 35 TYR A 61 PHE A 69 PHE A 75 TYR A 106 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2486 old number = 0 * TYR A 113 PHE A 125 TYR A 135 Total number of residues that need to be changed and total number of residues: ALA 0 14 CYS 0 2 ASP 0 8 GLU 0 16 PHE 6 9 GLY 0 18 HIS 0 8 ILE 0 5 LYS 0 4 LEU 0 18 MET 0 5 ASN 0 2 PRO 0 10 GLN 0 5 ARG 0 5 SER 0 12 THR 0 7 VAL 0 10 TRP 0 1 TYR 4 7 Processing NMR model 4 ** Unrecognized atom type [ O2 ] in residue HIS A 166 Average value of CA-N-C-CB angle is 34.24 Standard deviation is 1.12 * Side chain atoms should be swapped for the following residues: * As this is an NMR ensemble the swap has not been made * PHE A 3 PHE A 7 PHE A 35 TYR A 39 TYR A 61 PHE A 75 TYR A 113 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2486 old number = 0 * PHE A 125 Total number of residues that need to be changed and total number of residues: ALA 0 14 CYS 0 2 ASP 0 8 GLU 0 16 PHE 5 9 GLY 0 18 HIS 0 8 ILE 0 5 LYS 0 4 LEU 0 18 MET 0 5 ASN 0 2 PRO 0 10 GLN 0 5 ARG 0 5 SER 0 12 THR 0 7 VAL 0 10 TRP 0 1 TYR 3 7 Processing NMR model 5 ** Unrecognized atom type [ O2 ] in residue HIS A 166 Average value of CA-N-C-CB angle is 34.27 Standard deviation is 1.14 * 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 = 2486 old number = 0 * PHE A 3 PHE A 7 PHE A 58 TYR A 61 PHE A 125 TYR A 132 Total number of residues that need to be changed and total number of residues: ALA 0 14 CYS 0 2 ASP 0 8 GLU 0 16 PHE 4 9 GLY 0 18 HIS 0 8 ILE 0 5 LYS 0 4 LEU 0 18 MET 0 5 ASN 0 2 PRO 0 10 GLN 0 5 ARG 0 5 SER 0 12 THR 0 7 VAL 0 10 TRP 0 1 TYR 2 7 Processing NMR model 6 ** Unrecognized atom type [ O2 ] in residue HIS A 166 Average value of CA-N-C-CB angle is 34.28 Standard deviation is 1.17 * Side chain atoms should be swapped for the following residues: * As this is an NMR ensemble the swap has not been made * PHE A 7 TYR A 61 PHE A 62 PHE A 69 PHE A 73 PHE A 75 TYR A 106 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2486 old number = 0 * PHE A 125 TYR A 135 Total number of residues that need to be changed and total number of residues: ALA 0 14 CYS 0 2 ASP 0 8 GLU 0 16 PHE 6 9 GLY 0 18 HIS 0 8 ILE 0 5 LYS 0 4 LEU 0 18 MET 0 5 ASN 0 2 PRO 0 10 GLN 0 5 ARG 0 5 SER 0 12 THR 0 7 VAL 0 10 TRP 0 1 TYR 3 7 Processing NMR model 7 ** Unrecognized atom type [ O2 ] in residue HIS A 166 Average value of CA-N-C-CB angle is 34.27 Standard deviation is 1.15 * Side chain atoms should be swapped for the following residues: * As this is an NMR ensemble the swap has not been made * PHE A 7 PHE A 35 PHE A 75 TYR A 102 TYR A 106 PHE A 125 TYR A 132 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2486 old number = 0 * TYR A 135 Total number of residues that need to be changed and total number of residues: ALA 0 14 CYS 0 2 ASP 0 8 GLU 0 16 PHE 4 9 GLY 0 18 HIS 0 8 ILE 0 5 LYS 0 4 LEU 0 18 MET 0 5 ASN 0 2 PRO 0 10 GLN 0 5 ARG 0 5 SER 0 12 THR 0 7 VAL 0 10 TRP 0 1 TYR 4 7 Processing NMR model 8 ** Unrecognized atom type [ O2 ] in residue HIS A 166 Average value of CA-N-C-CB angle is 34.24 Standard deviation is 1.18 * 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 = 2486 old number = 0 * PHE A 7 PHE A 58 PHE A 75 PHE A 125 Total number of residues that need to be changed and total number of residues: ALA 0 14 CYS 0 2 ASP 0 8 GLU 0 16 PHE 4 9 GLY 0 18 HIS 0 8 ILE 0 5 LYS 0 4 LEU 0 18 MET 0 5 ASN 0 2 PRO 0 10 GLN 0 5 ARG 0 5 SER 0 12 THR 0 7 VAL 0 10 TRP 0 1 TYR 0 7 Processing NMR model 9 ** Unrecognized atom type [ O2 ] in residue HIS A 166 Average value of CA-N-C-CB angle is 34.27 Standard deviation is 1.17 * 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 = 2486 old number = 0 * PHE A 7 PHE A 75 TYR A 102 PHE A 125 Total number of residues that need to be changed and total number of residues: ALA 0 14 CYS 0 2 ASP 0 8 GLU 0 16 PHE 3 9 GLY 0 18 HIS 0 8 ILE 0 5 LYS 0 4 LEU 0 18 MET 0 5 ASN 0 2 PRO 0 10 GLN 0 5 ARG 0 5 SER 0 12 THR 0 7 VAL 0 10 TRP 0 1 TYR 1 7 Processing NMR model 10 ** Unrecognized atom type [ O2 ] in residue HIS A 166 Average value of CA-N-C-CB angle is 34.27 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 = 2486 old number = 0 * PHE A 58 TYR A 61 PHE A 69 PHE A 75 TYR A 102 PHE A 125 Total number of residues that need to be changed and total number of residues: ALA 0 14 CYS 0 2 ASP 0 8 GLU 0 16 PHE 4 9 GLY 0 18 HIS 0 8 ILE 0 5 LYS 0 4 LEU 0 18 MET 0 5 ASN 0 2 PRO 0 10 GLN 0 5 ARG 0 5 SER 0 12 THR 0 7 VAL 0 10 TRP 0 1 TYR 2 7 Processing NMR model 11 ** Unrecognized atom type [ O2 ] in residue HIS A 166 Average value of CA-N-C-CB angle is 34.27 Standard deviation is 1.17 * 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 = 2486 old number = 0 * PHE A 3 TYR A 39 PHE A 58 PHE A 75 TYR A 106 TYR A 113 Total number of residues that need to be changed and total number of residues: ALA 0 14 CYS 0 2 ASP 0 8 GLU 0 16 PHE 3 9 GLY 0 18 HIS 0 8 ILE 0 5 LYS 0 4 LEU 0 18 MET 0 5 ASN 0 2 PRO 0 10 GLN 0 5 ARG 0 5 SER 0 12 THR 0 7 VAL 0 10 TRP 0 1 TYR 3 7 Processing NMR model 12 ** Unrecognized atom type [ O2 ] in residue HIS A 166 Average value of CA-N-C-CB angle is 34.28 Standard deviation is 1.17 * 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 = 2486 old number = 0 * PHE A 3 PHE A 7 PHE A 75 TYR A 102 PHE A 125 Total number of residues that need to be changed and total number of residues: ALA 0 14 CYS 0 2 ASP 0 8 GLU 0 16 PHE 4 9 GLY 0 18 HIS 0 8 ILE 0 5 LYS 0 4 LEU 0 18 MET 0 5 ASN 0 2 PRO 0 10 GLN 0 5 ARG 0 5 SER 0 12 THR 0 7 VAL 0 10 TRP 0 1 TYR 1 7 Processing NMR model 13 ** Unrecognized atom type [ O2 ] in residue HIS A 166 Average value of CA-N-C-CB angle is 34.25 Standard deviation is 1.20 * Side chain atoms should be swapped for the following residues: * As this is an NMR ensemble the swap has not been made * PHE A 3 PHE A 35 PHE A 58 TYR A 61 PHE A 69 PHE A 125 TYR A 135 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2486 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 14 CYS 0 2 ASP 0 8 GLU 0 16 PHE 5 9 GLY 0 18 HIS 0 8 ILE 0 5 LYS 0 4 LEU 0 18 MET 0 5 ASN 0 2 PRO 0 10 GLN 0 5 ARG 0 5 SER 0 12 THR 0 7 VAL 0 10 TRP 0 1 TYR 2 7 Processing NMR model 14 ** Unrecognized atom type [ O2 ] in residue HIS A 166 Average value of CA-N-C-CB angle is 34.28 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 * PHE A 7 PHE A 58 PHE A 62 PHE A 69 PHE A 73 PHE A 75 PHE A 125 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2486 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 14 CYS 0 2 ASP 0 8 GLU 0 16 PHE 7 9 GLY 0 18 HIS 0 8 ILE 0 5 LYS 0 4 LEU 0 18 MET 0 5 ASN 0 2 PRO 0 10 GLN 0 5 ARG 0 5 SER 0 12 THR 0 7 VAL 0 10 TRP 0 1 TYR 0 7 Processing NMR model 15 ** Unrecognized atom type [ O2 ] in residue HIS A 166 Average value of CA-N-C-CB angle is 34.29 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 * PHE A 3 PHE A 7 PHE A 58 TYR A 61 PHE A 69 PHE A 75 TYR A 106 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2486 old number = 0 * PHE A 125 Total number of residues that need to be changed and total number of residues: ALA 0 14 CYS 0 2 ASP 0 8 GLU 0 16 PHE 6 9 GLY 0 18 HIS 0 8 ILE 0 5 LYS 0 4 LEU 0 18 MET 0 5 ASN 0 2 PRO 0 10 GLN 0 5 ARG 0 5 SER 0 12 THR 0 7 VAL 0 10 TRP 0 1 TYR 2 7 Processing NMR model 16 ** Unrecognized atom type [ O2 ] in residue HIS A 166 Average value of CA-N-C-CB angle is 34.29 Standard deviation is 1.14 * 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 = 2486 old number = 0 * PHE A 7 PHE A 58 TYR A 61 PHE A 75 TYR A 106 PHE A 125 Total number of residues that need to be changed and total number of residues: ALA 0 14 CYS 0 2 ASP 0 8 GLU 0 16 PHE 4 9 GLY 0 18 HIS 0 8 ILE 0 5 LYS 0 4 LEU 0 18 MET 0 5 ASN 0 2 PRO 0 10 GLN 0 5 ARG 0 5 SER 0 12 THR 0 7 VAL 0 10 TRP 0 1 TYR 2 7 Processing NMR model 17 ** Unrecognized atom type [ O2 ] in residue HIS A 166 Average value of CA-N-C-CB angle is 34.25 Standard deviation is 1.14 * Side chain atoms should be swapped for the following residues: * As this is an NMR ensemble the swap has not been made * PHE A 7 PHE A 35 PHE A 58 TYR A 61 PHE A 75 TYR A 106 PHE A 125 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2486 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 14 CYS 0 2 ASP 0 8 GLU 0 16 PHE 5 9 GLY 0 18 HIS 0 8 ILE 0 5 LYS 0 4 LEU 0 18 MET 0 5 ASN 0 2 PRO 0 10 GLN 0 5 ARG 0 5 SER 0 12 THR 0 7 VAL 0 10 TRP 0 1 TYR 2 7 Processing NMR model 18 ** Unrecognized atom type [ O2 ] in residue HIS A 166 Average value of CA-N-C-CB angle is 34.30 Standard deviation is 1.12 * 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 = 2486 old number = 0 * TYR A 39 PHE A 69 PHE A 75 TYR A 102 PHE A 125 TYR A 132 Total number of residues that need to be changed and total number of residues: ALA 0 14 CYS 0 2 ASP 0 8 GLU 0 16 PHE 3 9 GLY 0 18 HIS 0 8 ILE 0 5 LYS 0 4 LEU 0 18 MET 0 5 ASN 0 2 PRO 0 10 GLN 0 5 ARG 0 5 SER 0 12 THR 0 7 VAL 0 10 TRP 0 1 TYR 3 7 Processing NMR model 19 ** Unrecognized atom type [ O2 ] in residue HIS A 166 Average value of CA-N-C-CB angle is 34.27 Standard deviation is 1.16 * 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 = 2486 old number = 0 * PHE A 3 PHE A 7 PHE A 58 TYR A 61 PHE A 125 TYR A 132 Total number of residues that need to be changed and total number of residues: ALA 0 14 CYS 0 2 ASP 0 8 GLU 0 16 PHE 4 9 GLY 0 18 HIS 0 8 ILE 0 5 LYS 0 4 LEU 0 18 MET 0 5 ASN 0 2 PRO 0 10 GLN 0 5 ARG 0 5 SER 0 12 THR 0 7 VAL 0 10 TRP 0 1 TYR 2 7 Processing NMR model 20 ** Unrecognized atom type [ O2 ] in residue HIS A 166 Average value of CA-N-C-CB angle is 34.28 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 * PHE A 7 PHE A 58 TYR A 61 PHE A 75 TYR A 106 TYR A 113 PHE A 125 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 2486 old number = 0 * TYR A 135 Total number of residues that need to be changed and total number of residues: ALA 0 14 CYS 0 2 ASP 0 8 GLU 0 16 PHE 4 9 GLY 0 18 HIS 0 8 ILE 0 5 LYS 0 4 LEU 0 18 MET 0 5 ASN 0 2 PRO 0 10 GLN 0 5 ARG 0 5 SER 0 12 THR 0 7 VAL 0 10 TRP 0 1 TYR 4 7 * NMR ensemble comprises 20 model structures * Program completed