
#######################################################
#                                                     #
#                        LGA                          #
#                  ---------------                    #
#                                                     #
#               Local-Global Alignment                #
#        A Method for Finding 3-D Similarities        #
#               in Protein Structures                 #
#                                                     #
#                  --------------- 06/2006            #
#                                                     #
#      Adam Zemla (adamz@llnl.gov)                    #
#      Lawrence Livermore National Laboratory, CA     #
#                                                     #
#######################################################

# Molecule1: number of CA atoms    5 (   35),  selected    3 , name T0320TS186_3-D2
# Molecule2: number of CA atoms   73 (  604),  selected    3 , name T0320_D2.pdb
# PARAMETERS: T0320TS186_3-D2.T0320_D2.pdb  -3  -ie  -o1  -sda  -d:4  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
# WARNING! The change of the parameter DIST cutoff may give you better result.

  LONGEST_CONTINUOUS_SEGMENT:     3       256 - 258         0.48     0.48
  LCS_AVERAGE:      4.11

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     3       256 - 258         0.48     0.48
  LCS_AVERAGE:      4.11

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     3       256 - 258         0.48     0.48
  LCS_AVERAGE:      4.11

LCS_GDT    MOLECULE-1    MOLECULE-2    LENGTH_OF_THE
LCS_GDT     RESIDUE       RESIDUE         CONTINUOUS
LCS_GDT   NAME NUMBER   NAME NUMBER          SEGMENT     GLOBAL DISTANCE TEST - GDT_DATA_COLUMNS                             NUMBER OF THE RESIDUES:   73
LCS_GDT     G     256     G     256      3    3    3     0    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3 
LCS_GDT     K     257     K     257      3    3    3     1    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3 
LCS_GDT     D     258     D     258      3    3    3     0    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3 
LCS_AVERAGE  LCS_A:   4.11  (   4.11    4.11    4.11 )

GLOBAL_DISTANCE_TEST (the largest set of residues that can fit under specified DISTANCE_CUTOFF)
GDT DIST_CUTOFF  0.50   1.00   1.50   2.00   2.50   3.00   3.50   4.00   4.50   5.00   5.50   6.00   6.50   7.00   7.50   8.00   8.50   9.00   9.50  10.00
GDT NUMBER_CA      1      3      3      3      3      3      3      3      3      3      3      3      3      3      3      3      3      3      3      3 
GDT PERCENT_CA   1.37   4.11   4.11   4.11   4.11   4.11   4.11   4.11   4.11   4.11   4.11   4.11   4.11   4.11   4.11   4.11   4.11   4.11   4.11   4.11
GDT RMS_LOCAL   31.62   0.48   0.48   0.48   0.48   0.48   0.48   0.48   0.48   0.48   0.48   0.48   0.48   0.48   0.48   0.48   0.48   0.48   0.48   0.48
GDT RMS_ALL_CA   0.48   0.48   0.48   0.48   0.48   0.48   0.48   0.48   0.48   0.48   0.48   0.48   0.48   0.48   0.48   0.48   0.48   0.48   0.48   0.48

#      Molecule1      Molecule2       DISTANCE
LGA    G     256      G     256          0.530
LGA    K     257      K     257          0.349
LGA    D     258      D     258          0.531

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)    5   73    4.0      3    0.48     4.110     4.110     0.519

LGA_LOCAL      RMSD =  0.478  Number of atoms =    3  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  0.478  Number of atoms =    3 
Std_ALL_ATOMS  RMSD =  0.478  (standard rmsd on all 3 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.143435 * X  +   0.019779 * Y  +  -0.989462 * Z  +  78.982132
  Y_new =   0.379861 * X  +   0.924320 * Y  +  -0.036589 * Z  + -18.359001
  Z_new =   0.913855 * X  +  -0.381106 * Y  +  -0.140093 * Z  +  -5.006744 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.923060    1.218533  [ DEG:  -110.1832     69.8168 ]
  Theta =  -1.152680   -1.988912  [ DEG:   -66.0437   -113.9563 ]
  Phi   =   1.931843   -1.209749  [ DEG:   110.6865    -69.3135 ]
 
# END of job
REMARK  ---------------------------------------------------------- 
REMARK   Citing LGA: 
REMARK   Zemla A., LGA - a Method for Finding 3D Similarities in  
REMARK   Protein Structures, Nucleic Acids Research, 2003, V. 31, 
REMARK   No. 13, pp. 3370-3374. 
REMARK  ---------------------------------------------------------- 
REMARK   Superimposed MOLECULES (1=>2)   Output: 1 molecule      
REMARK     1: T0320TS186_3-D2                               
REMARK     2: T0320_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0320TS186_3-D2.T0320_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:    5   73   4.0    3   0.48   4.110     0.48
REMARK  ---------------------------------------------------------- 
MOLECULE T0320TS186_3-D2
PFRMAT TS
TARGET T0320
MODEL  3
PARENT 1cz1_A
ATOM   1700  N   GLY   256      -4.038  30.651  16.213  1.00  0.00
ATOM   1701  CA  GLY   256      -3.783  31.925  15.558  1.00  0.00
ATOM   1702  C   GLY   256      -4.189  31.853  14.090  1.00  0.00
ATOM   1703  O   GLY   256      -4.391  32.887  13.462  1.00  0.00
ATOM   1704  N   LYS   257      -4.287  30.647  13.535  1.00  0.00
ATOM   1705  CA  LYS   257      -4.600  30.572  12.106  1.00  0.00
ATOM   1706  C   LYS   257      -6.058  30.233  11.806  1.00  0.00
ATOM   1707  O   LYS   257      -6.504  30.520  10.693  1.00  0.00
ATOM   1708  CB  LYS   257      -3.753  29.493  11.428  1.00  0.00
ATOM   1709  CG  LYS   257      -2.312  29.905  11.174  1.00  0.00
ATOM   1710  CD  LYS   257      -1.494  29.869  12.454  1.00  0.00
ATOM   1711  CE  LYS   257      -0.056  30.294  12.203  1.00  0.00
ATOM   1712  NZ  LYS   257       0.036  31.723  11.792  1.00  0.00
ATOM   1713  N   ASP   258      -6.726  29.558  12.718  1.00  0.00
ATOM   1714  CA  ASP   258      -8.146  29.218  12.503  1.00  0.00
ATOM   1715  C   ASP   258      -8.336  28.155  11.440  1.00  0.00
ATOM   1716  O   ASP   258      -9.254  28.245  10.616  1.00  0.00
ATOM   1717  CB  ASP   258      -8.932  30.453  12.057  1.00  0.00
ATOM   1718  CG  ASP   258      -8.960  31.538  13.115  1.00  0.00
ATOM   1719  OD1 ASP   258      -9.337  31.235  14.268  1.00  0.00
ATOM   1720  OD2 ASP   258      -8.607  32.692  12.794  1.00  0.00
ATOM   1721  N   ALA   259      -7.523  27.110  11.425  1.00  0.00
ATOM   1722  CA  ALA   259      -7.648  26.073  10.406  1.00  0.00
ATOM   1723  C   ALA   259      -8.938  25.268  10.619  1.00  0.00
ATOM   1724  O   ALA   259      -9.348  25.084  11.765  1.00  0.00
ATOM   1725  CB  ALA   259      -6.465  25.119  10.473  1.00  0.00
ATOM   1726  N   GLU   260      -9.546  24.822   9.538  1.00  0.00
ATOM   1727  CA  GLU   260     -10.771  24.038   9.602  1.00  0.00
ATOM   1728  C   GLU   260     -10.476  22.603   9.101  1.00  0.00
ATOM   1729  O   GLU   260     -11.106  21.690   9.665  1.00  0.00
ATOM   1730  CB  GLU   260     -11.855  24.665   8.724  1.00  0.00
ATOM   1731  CG  GLU   260     -12.388  25.990   9.245  1.00  0.00
ATOM   1732  CD  GLU   260     -13.273  26.699   8.239  1.00  0.00
ATOM   1733  OE1 GLU   260     -13.436  26.174   7.117  1.00  0.00
ATOM   1734  OE2 GLU   260     -13.804  27.779   8.572  1.00  0.00
TER
END
