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 GLU A 48 Average value of CA-N-C-CB angle is 33.94 Standard deviation is 0.57 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 786 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 7 GLU 0 7 PHE 0 1 GLY 0 2 ILE 0 4 LYS 0 7 LEU 0 4 MET 0 2 ASN 0 2 GLN 0 3 ARG 0 3 SER 0 3 THR 0 1 VAL 0 1 TYR 0 1 Processing NMR model 2 ** Unrecognized atom type [ O2 ] in residue GLU A 48 Average value of CA-N-C-CB angle is 33.90 Standard deviation is 0.62 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 786 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 7 GLU 0 7 PHE 0 1 GLY 0 2 ILE 0 4 LYS 0 7 LEU 0 4 MET 0 2 ASN 0 2 GLN 0 3 ARG 0 3 SER 0 3 THR 0 1 VAL 0 1 TYR 0 1 Processing NMR model 3 ** Unrecognized atom type [ O2 ] in residue GLU A 48 Average value of CA-N-C-CB angle is 33.89 Standard deviation is 0.59 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 786 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 7 GLU 0 7 PHE 0 1 GLY 0 2 ILE 0 4 LYS 0 7 LEU 0 4 MET 0 2 ASN 0 2 GLN 0 3 ARG 0 3 SER 0 3 THR 0 1 VAL 0 1 TYR 0 1 Processing NMR model 4 ** Unrecognized atom type [ O2 ] in residue GLU A 48 Average value of CA-N-C-CB angle is 33.88 Standard deviation is 0.59 * 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 = 786 old number = 0 * PHE A 41 Total number of residues that need to be changed and total number of residues: ALA 0 7 GLU 0 7 PHE 1 1 GLY 0 2 ILE 0 4 LYS 0 7 LEU 0 4 MET 0 2 ASN 0 2 GLN 0 3 ARG 0 3 SER 0 3 THR 0 1 VAL 0 1 TYR 0 1 Processing NMR model 5 ** Unrecognized atom type [ O2 ] in residue GLU A 48 Average value of CA-N-C-CB angle is 33.89 Standard deviation is 0.63 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 786 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 7 GLU 0 7 PHE 0 1 GLY 0 2 ILE 0 4 LYS 0 7 LEU 0 4 MET 0 2 ASN 0 2 GLN 0 3 ARG 0 3 SER 0 3 THR 0 1 VAL 0 1 TYR 0 1 Processing NMR model 6 ** Unrecognized atom type [ O2 ] in residue GLU A 48 Average value of CA-N-C-CB angle is 33.90 Standard deviation is 0.61 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 786 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 7 GLU 0 7 PHE 0 1 GLY 0 2 ILE 0 4 LYS 0 7 LEU 0 4 MET 0 2 ASN 0 2 GLN 0 3 ARG 0 3 SER 0 3 THR 0 1 VAL 0 1 TYR 0 1 Processing NMR model 7 ** Unrecognized atom type [ O2 ] in residue GLU A 48 Average value of CA-N-C-CB angle is 33.88 Standard deviation is 0.64 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 786 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 7 GLU 0 7 PHE 0 1 GLY 0 2 ILE 0 4 LYS 0 7 LEU 0 4 MET 0 2 ASN 0 2 GLN 0 3 ARG 0 3 SER 0 3 THR 0 1 VAL 0 1 TYR 0 1 Processing NMR model 8 ** Unrecognized atom type [ O2 ] in residue GLU A 48 Average value of CA-N-C-CB angle is 33.90 Standard deviation is 0.62 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 786 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 7 GLU 0 7 PHE 0 1 GLY 0 2 ILE 0 4 LYS 0 7 LEU 0 4 MET 0 2 ASN 0 2 GLN 0 3 ARG 0 3 SER 0 3 THR 0 1 VAL 0 1 TYR 0 1 Processing NMR model 9 ** Unrecognized atom type [ O2 ] in residue GLU A 48 Average value of CA-N-C-CB angle is 33.89 Standard deviation is 0.62 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 786 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 7 GLU 0 7 PHE 0 1 GLY 0 2 ILE 0 4 LYS 0 7 LEU 0 4 MET 0 2 ASN 0 2 GLN 0 3 ARG 0 3 SER 0 3 THR 0 1 VAL 0 1 TYR 0 1 Processing NMR model 10 ** Unrecognized atom type [ O2 ] in residue GLU A 48 Average value of CA-N-C-CB angle is 33.89 Standard deviation is 0.58 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 786 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 7 GLU 0 7 PHE 0 1 GLY 0 2 ILE 0 4 LYS 0 7 LEU 0 4 MET 0 2 ASN 0 2 GLN 0 3 ARG 0 3 SER 0 3 THR 0 1 VAL 0 1 TYR 0 1 Processing NMR model 11 ** Unrecognized atom type [ O2 ] in residue GLU A 48 Average value of CA-N-C-CB angle is 33.87 Standard deviation is 0.59 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 786 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 7 GLU 0 7 PHE 0 1 GLY 0 2 ILE 0 4 LYS 0 7 LEU 0 4 MET 0 2 ASN 0 2 GLN 0 3 ARG 0 3 SER 0 3 THR 0 1 VAL 0 1 TYR 0 1 Processing NMR model 12 ** Unrecognized atom type [ O2 ] in residue GLU A 48 Average value of CA-N-C-CB angle is 33.89 Standard deviation is 0.63 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 786 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 7 GLU 0 7 PHE 0 1 GLY 0 2 ILE 0 4 LYS 0 7 LEU 0 4 MET 0 2 ASN 0 2 GLN 0 3 ARG 0 3 SER 0 3 THR 0 1 VAL 0 1 TYR 0 1 Processing NMR model 13 ** Unrecognized atom type [ O2 ] in residue GLU A 48 Average value of CA-N-C-CB angle is 33.88 Standard deviation is 0.62 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 786 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 7 GLU 0 7 PHE 0 1 GLY 0 2 ILE 0 4 LYS 0 7 LEU 0 4 MET 0 2 ASN 0 2 GLN 0 3 ARG 0 3 SER 0 3 THR 0 1 VAL 0 1 TYR 0 1 Processing NMR model 14 ** Unrecognized atom type [ O2 ] in residue GLU A 48 Average value of CA-N-C-CB angle is 33.86 Standard deviation is 0.57 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 786 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 7 GLU 0 7 PHE 0 1 GLY 0 2 ILE 0 4 LYS 0 7 LEU 0 4 MET 0 2 ASN 0 2 GLN 0 3 ARG 0 3 SER 0 3 THR 0 1 VAL 0 1 TYR 0 1 Processing NMR model 15 ** Unrecognized atom type [ O2 ] in residue GLU A 48 Average value of CA-N-C-CB angle is 33.90 Standard deviation is 0.59 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 786 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 7 GLU 0 7 PHE 0 1 GLY 0 2 ILE 0 4 LYS 0 7 LEU 0 4 MET 0 2 ASN 0 2 GLN 0 3 ARG 0 3 SER 0 3 THR 0 1 VAL 0 1 TYR 0 1 Processing NMR model 16 ** Unrecognized atom type [ O2 ] in residue GLU A 48 Average value of CA-N-C-CB angle is 33.87 Standard deviation is 0.59 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 786 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 7 GLU 0 7 PHE 0 1 GLY 0 2 ILE 0 4 LYS 0 7 LEU 0 4 MET 0 2 ASN 0 2 GLN 0 3 ARG 0 3 SER 0 3 THR 0 1 VAL 0 1 TYR 0 1 Processing NMR model 17 ** Unrecognized atom type [ O2 ] in residue GLU A 48 Average value of CA-N-C-CB angle is 33.92 Standard deviation is 0.51 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 786 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 7 GLU 0 7 PHE 0 1 GLY 0 2 ILE 0 4 LYS 0 7 LEU 0 4 MET 0 2 ASN 0 2 GLN 0 3 ARG 0 3 SER 0 3 THR 0 1 VAL 0 1 TYR 0 1 Processing NMR model 18 ** Unrecognized atom type [ O2 ] in residue GLU A 48 Average value of CA-N-C-CB angle is 33.88 Standard deviation is 0.61 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 786 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 7 GLU 0 7 PHE 0 1 GLY 0 2 ILE 0 4 LYS 0 7 LEU 0 4 MET 0 2 ASN 0 2 GLN 0 3 ARG 0 3 SER 0 3 THR 0 1 VAL 0 1 TYR 0 1 Processing NMR model 19 ** Unrecognized atom type [ O2 ] in residue GLU A 48 Average value of CA-N-C-CB angle is 33.94 Standard deviation is 0.50 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 786 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 7 GLU 0 7 PHE 0 1 GLY 0 2 ILE 0 4 LYS 0 7 LEU 0 4 MET 0 2 ASN 0 2 GLN 0 3 ARG 0 3 SER 0 3 THR 0 1 VAL 0 1 TYR 0 1 Processing NMR model 20 ** Unrecognized atom type [ O2 ] in residue GLU A 48 Average value of CA-N-C-CB angle is 33.89 Standard deviation is 0.57 WARNING: Number of atoms/hetatms in new file differs from old file - new number = 786 old number = 0 Total number of residues that need to be changed and total number of residues: ALA 0 7 GLU 0 7 PHE 0 1 GLY 0 2 ILE 0 4 LYS 0 7 LEU 0 4 MET 0 2 ASN 0 2 GLN 0 3 ARG 0 3 SER 0 3 THR 0 1 VAL 0 1 TYR 0 1 * NMR ensemble comprises 20 model structures * Program completed