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 86 Average value of CA-N-C-CB angle is 34.01 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 = 1363 old number = 0 * TYR A 60 PHE A 74 Total number of residues that need to be changed and total number of residues: ALA 0 8 CYS 0 1 ASP 0 3 GLU 0 8 PHE 1 1 GLY 0 6 HIS 0 9 ILE 0 4 LYS 0 6 LEU 0 6 MET 0 6 ASN 0 3 PRO 0 2 GLN 0 2 ARG 0 7 SER 0 4 THR 0 3 VAL 0 6 TYR 1 1 Processing NMR model 2 ** Unrecognized atom type [ O2 ] in residue SER A 86 Average value of CA-N-C-CB angle is 34.10 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 = 1363 old number = 0 * PHE A 74 Total number of residues that need to be changed and total number of residues: ALA 0 8 CYS 0 1 ASP 0 3 GLU 0 8 PHE 1 1 GLY 0 6 HIS 0 9 ILE 0 4 LYS 0 6 LEU 0 6 MET 0 6 ASN 0 3 PRO 0 2 GLN 0 2 ARG 0 7 SER 0 4 THR 0 3 VAL 0 6 TYR 0 1 Processing NMR model 3 ** Unrecognized atom type [ O2 ] in residue SER A 86 Average value of CA-N-C-CB angle is 34.01 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 = 1363 old number = 0 * PHE A 74 Total number of residues that need to be changed and total number of residues: ALA 0 8 CYS 0 1 ASP 0 3 GLU 0 8 PHE 1 1 GLY 0 6 HIS 0 9 ILE 0 4 LYS 0 6 LEU 0 6 MET 0 6 ASN 0 3 PRO 0 2 GLN 0 2 ARG 0 7 SER 0 4 THR 0 3 VAL 0 6 TYR 0 1 Processing NMR model 4 ** Unrecognized atom type [ O2 ] in residue SER A 86 Average value of CA-N-C-CB angle is 34.00 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 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 1363 old number = 0 * PHE A 74 Total number of residues that need to be changed and total number of residues: ALA 0 8 CYS 0 1 ASP 0 3 GLU 0 8 PHE 1 1 GLY 0 6 HIS 0 9 ILE 0 4 LYS 0 6 LEU 0 6 MET 0 6 ASN 0 3 PRO 0 2 GLN 0 2 ARG 0 7 SER 0 4 THR 0 3 VAL 0 6 TYR 0 1 Processing NMR model 5 ** Unrecognized atom type [ O2 ] in residue SER A 86 Average value of CA-N-C-CB angle is 34.03 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 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 1363 old number = 0 * TYR A 60 ASP A 73 PHE A 74 Total number of residues that need to be changed and total number of residues: ALA 0 8 CYS 0 1 ASP 1 3 GLU 0 8 PHE 1 1 GLY 0 6 HIS 0 9 ILE 0 4 LYS 0 6 LEU 0 6 MET 0 6 ASN 0 3 PRO 0 2 GLN 0 2 ARG 0 7 SER 0 4 THR 0 3 VAL 0 6 TYR 1 1 Processing NMR model 6 ** Unrecognized atom type [ O2 ] in residue SER A 86 Average value of CA-N-C-CB angle is 34.10 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 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 1363 old number = 0 * TYR A 60 PHE A 74 Total number of residues that need to be changed and total number of residues: ALA 0 8 CYS 0 1 ASP 0 3 GLU 0 8 PHE 1 1 GLY 0 6 HIS 0 9 ILE 0 4 LYS 0 6 LEU 0 6 MET 0 6 ASN 0 3 PRO 0 2 GLN 0 2 ARG 0 7 SER 0 4 THR 0 3 VAL 0 6 TYR 1 1 Processing NMR model 7 ** Unrecognized atom type [ O2 ] in residue SER A 86 Average value of CA-N-C-CB angle is 33.97 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 = 1363 old number = 0 * TYR A 60 PHE A 74 Total number of residues that need to be changed and total number of residues: ALA 0 8 CYS 0 1 ASP 0 3 GLU 0 8 PHE 1 1 GLY 0 6 HIS 0 9 ILE 0 4 LYS 0 6 LEU 0 6 MET 0 6 ASN 0 3 PRO 0 2 GLN 0 2 ARG 0 7 SER 0 4 THR 0 3 VAL 0 6 TYR 1 1 Processing NMR model 8 ** Unrecognized atom type [ O2 ] in residue SER A 86 Average value of CA-N-C-CB angle is 34.08 Standard deviation is 1.09 * 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 = 1363 old number = 0 * TYR A 60 Total number of residues that need to be changed and total number of residues: ALA 0 8 CYS 0 1 ASP 0 3 GLU 0 8 PHE 0 1 GLY 0 6 HIS 0 9 ILE 0 4 LYS 0 6 LEU 0 6 MET 0 6 ASN 0 3 PRO 0 2 GLN 0 2 ARG 0 7 SER 0 4 THR 0 3 VAL 0 6 TYR 1 1 Processing NMR model 9 ** Unrecognized atom type [ O2 ] in residue SER A 86 Average value of CA-N-C-CB angle is 34.06 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 = 1363 old number = 0 * PHE A 74 Total number of residues that need to be changed and total number of residues: ALA 0 8 CYS 0 1 ASP 0 3 GLU 0 8 PHE 1 1 GLY 0 6 HIS 0 9 ILE 0 4 LYS 0 6 LEU 0 6 MET 0 6 ASN 0 3 PRO 0 2 GLN 0 2 ARG 0 7 SER 0 4 THR 0 3 VAL 0 6 TYR 0 1 Processing NMR model 10 ** Unrecognized atom type [ O2 ] in residue SER A 86 Average value of CA-N-C-CB angle is 34.04 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 = 1363 old number = 0 * TYR A 60 PHE A 74 Total number of residues that need to be changed and total number of residues: ALA 0 8 CYS 0 1 ASP 0 3 GLU 0 8 PHE 1 1 GLY 0 6 HIS 0 9 ILE 0 4 LYS 0 6 LEU 0 6 MET 0 6 ASN 0 3 PRO 0 2 GLN 0 2 ARG 0 7 SER 0 4 THR 0 3 VAL 0 6 TYR 1 1 Processing NMR model 11 ** Unrecognized atom type [ O2 ] in residue SER A 86 Average value of CA-N-C-CB angle is 33.99 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 = 1363 old number = 0 * TYR A 60 ASP A 73 PHE A 74 Total number of residues that need to be changed and total number of residues: ALA 0 8 CYS 0 1 ASP 1 3 GLU 0 8 PHE 1 1 GLY 0 6 HIS 0 9 ILE 0 4 LYS 0 6 LEU 0 6 MET 0 6 ASN 0 3 PRO 0 2 GLN 0 2 ARG 0 7 SER 0 4 THR 0 3 VAL 0 6 TYR 1 1 Processing NMR model 12 ** Unrecognized atom type [ O2 ] in residue SER A 86 Average value of CA-N-C-CB angle is 34.01 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 = 1363 old number = 0 * PHE A 74 Total number of residues that need to be changed and total number of residues: ALA 0 8 CYS 0 1 ASP 0 3 GLU 0 8 PHE 1 1 GLY 0 6 HIS 0 9 ILE 0 4 LYS 0 6 LEU 0 6 MET 0 6 ASN 0 3 PRO 0 2 GLN 0 2 ARG 0 7 SER 0 4 THR 0 3 VAL 0 6 TYR 0 1 Processing NMR model 13 ** Unrecognized atom type [ O2 ] in residue SER A 86 Average value of CA-N-C-CB angle is 34.10 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 = 1363 old number = 0 * TYR A 60 PHE A 74 Total number of residues that need to be changed and total number of residues: ALA 0 8 CYS 0 1 ASP 0 3 GLU 0 8 PHE 1 1 GLY 0 6 HIS 0 9 ILE 0 4 LYS 0 6 LEU 0 6 MET 0 6 ASN 0 3 PRO 0 2 GLN 0 2 ARG 0 7 SER 0 4 THR 0 3 VAL 0 6 TYR 1 1 Processing NMR model 14 ** Unrecognized atom type [ O2 ] in residue SER A 86 Average value of CA-N-C-CB angle is 34.09 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 = 1363 old number = 0 * ASP A 73 PHE A 74 Total number of residues that need to be changed and total number of residues: ALA 0 8 CYS 0 1 ASP 1 3 GLU 0 8 PHE 1 1 GLY 0 6 HIS 0 9 ILE 0 4 LYS 0 6 LEU 0 6 MET 0 6 ASN 0 3 PRO 0 2 GLN 0 2 ARG 0 7 SER 0 4 THR 0 3 VAL 0 6 TYR 0 1 Processing NMR model 15 ** Unrecognized atom type [ O2 ] in residue SER A 86 Average value of CA-N-C-CB angle is 34.08 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 = 1363 old number = 0 * TYR A 60 ASP A 73 PHE A 74 Total number of residues that need to be changed and total number of residues: ALA 0 8 CYS 0 1 ASP 1 3 GLU 0 8 PHE 1 1 GLY 0 6 HIS 0 9 ILE 0 4 LYS 0 6 LEU 0 6 MET 0 6 ASN 0 3 PRO 0 2 GLN 0 2 ARG 0 7 SER 0 4 THR 0 3 VAL 0 6 TYR 1 1 Processing NMR model 16 ** Unrecognized atom type [ O2 ] in residue SER A 86 Average value of CA-N-C-CB angle is 34.00 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 = 1363 old number = 0 * PHE A 74 Total number of residues that need to be changed and total number of residues: ALA 0 8 CYS 0 1 ASP 0 3 GLU 0 8 PHE 1 1 GLY 0 6 HIS 0 9 ILE 0 4 LYS 0 6 LEU 0 6 MET 0 6 ASN 0 3 PRO 0 2 GLN 0 2 ARG 0 7 SER 0 4 THR 0 3 VAL 0 6 TYR 0 1 Processing NMR model 17 ** Unrecognized atom type [ O2 ] in residue SER A 86 Average value of CA-N-C-CB angle is 34.05 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 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 1363 old number = 0 * PHE A 74 Total number of residues that need to be changed and total number of residues: ALA 0 8 CYS 0 1 ASP 0 3 GLU 0 8 PHE 1 1 GLY 0 6 HIS 0 9 ILE 0 4 LYS 0 6 LEU 0 6 MET 0 6 ASN 0 3 PRO 0 2 GLN 0 2 ARG 0 7 SER 0 4 THR 0 3 VAL 0 6 TYR 0 1 Processing NMR model 18 ** Unrecognized atom type [ O2 ] in residue SER A 86 Average value of CA-N-C-CB angle is 34.11 Standard deviation is 1.13 * 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 = 1363 old number = 0 * TYR A 60 PHE A 74 Total number of residues that need to be changed and total number of residues: ALA 0 8 CYS 0 1 ASP 0 3 GLU 0 8 PHE 1 1 GLY 0 6 HIS 0 9 ILE 0 4 LYS 0 6 LEU 0 6 MET 0 6 ASN 0 3 PRO 0 2 GLN 0 2 ARG 0 7 SER 0 4 THR 0 3 VAL 0 6 TYR 1 1 Processing NMR model 19 ** Unrecognized atom type [ O2 ] in residue SER A 86 Average value of CA-N-C-CB angle is 34.01 Standard deviation is 1.09 * 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 = 1363 old number = 0 * PHE A 74 Total number of residues that need to be changed and total number of residues: ALA 0 8 CYS 0 1 ASP 0 3 GLU 0 8 PHE 1 1 GLY 0 6 HIS 0 9 ILE 0 4 LYS 0 6 LEU 0 6 MET 0 6 ASN 0 3 PRO 0 2 GLN 0 2 ARG 0 7 SER 0 4 THR 0 3 VAL 0 6 TYR 0 1 Processing NMR model 20 ** Unrecognized atom type [ O2 ] in residue SER A 86 Average value of CA-N-C-CB angle is 33.97 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 = 1363 old number = 0 * TYR A 60 PHE A 74 Total number of residues that need to be changed and total number of residues: ALA 0 8 CYS 0 1 ASP 0 3 GLU 0 8 PHE 1 1 GLY 0 6 HIS 0 9 ILE 0 4 LYS 0 6 LEU 0 6 MET 0 6 ASN 0 3 PRO 0 2 GLN 0 2 ARG 0 7 SER 0 4 THR 0 3 VAL 0 6 TYR 1 1 * NMR ensemble comprises 20 model structures * Program completed