
#######################################################
#                                                     #
#                        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    3 (   12),  selected    3 , name T0356AL243_3-D1
# Molecule2: number of CA atoms  124 (  963),  selected    3 , name T0356_D1.pdb
# PARAMETERS: T0356AL243_3-D1.T0356_D1.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       314 - 316         0.03     0.03
  LCS_AVERAGE:      2.42

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     3       314 - 316         0.03     0.03
  LCS_AVERAGE:      2.42

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     3       314 - 316         0.03     0.03
  LCS_AVERAGE:      2.42

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:  124
LCS_GDT     D     314     D     314      3    3    3     3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3 
LCS_GDT     A     315     A     315      3    3    3     3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3 
LCS_GDT     I     316     I     316      3    3    3     3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3 
LCS_AVERAGE  LCS_A:   2.42  (   2.42    2.42    2.42 )

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      3      3      3      3      3      3      3      3      3      3      3      3      3      3      3      3      3      3      3      3 
GDT PERCENT_CA   2.42   2.42   2.42   2.42   2.42   2.42   2.42   2.42   2.42   2.42   2.42   2.42   2.42   2.42   2.42   2.42   2.42   2.42   2.42   2.42
GDT RMS_LOCAL    0.03   0.03   0.03   0.03   0.03   0.03   0.03   0.03   0.03   0.03   0.03   0.03   0.03   0.03   0.03   0.03   0.03   0.03   0.03   0.03
GDT RMS_ALL_CA   0.03   0.03   0.03   0.03   0.03   0.03   0.03   0.03   0.03   0.03   0.03   0.03   0.03   0.03   0.03   0.03   0.03   0.03   0.03   0.03

#      Molecule1      Molecule2       DISTANCE
LGA    D     314      D     314          0.025
LGA    A     315      A     315          0.035
LGA    I     316      I     316          0.010

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)    3  124    4.0      3    0.03     2.419     2.419     2.332

LGA_LOCAL      RMSD =  0.029  Number of atoms =    3  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  0.026  Number of atoms =    3 
Std_ALL_ATOMS  RMSD =  0.029  (standard rmsd on all 3 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.541081 * X  +   0.366585 * Y  +  -0.756866 * Z  +  98.964035
  Y_new =  -0.151943 * X  +   0.842566 * Y  +   0.516717 * Z  +  26.624741
  Z_new =   0.827130 * X  +   0.394586 * Y  +  -0.400196 * Z  +  56.489487 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.363253   -0.778340  [ DEG:   135.4044    -44.5956 ]
  Theta =  -0.973982   -2.167610  [ DEG:   -55.8051   -124.1949 ]
  Phi   =  -2.867830    0.273763  [ DEG:  -164.3145     15.6855 ]
 
# 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: T0356AL243_3-D1                               
REMARK     2: T0356_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0356AL243_3-D1.T0356_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:    3  124   4.0    3   0.03   2.419     0.03
REMARK  ---------------------------------------------------------- 
MOLECULE T0356AL243_3-D1
REMARK Aligment from pdb entry: 1ejeA
ATOM    245  N   ASP   314      78.352  75.929  96.721  1.00  0.00              
ATOM    246  CA  ASP   314      77.069  75.349  97.116  1.00  0.00              
ATOM    247  C   ASP   314      76.335  74.826  95.879  1.00  0.00              
ATOM    248  O   ASP   314      75.271  75.329  95.512  1.00  0.00              
ATOM    249  N   ALA   315      76.892  73.792  95.228  1.00  0.00              
ATOM    250  CA  ALA   315      76.297  73.199  94.023  1.00  0.00              
ATOM    251  C   ALA   315      74.887  72.695  94.259  1.00  0.00              
ATOM    252  O   ALA   315      74.590  72.164  95.325  1.00  0.00              
ATOM    253  N   ILE   316      74.026  72.856  93.260  1.00  0.00              
ATOM    254  CA  ILE   316      72.648  72.390  93.350  1.00  0.00              
ATOM    255  C   ILE   316      72.579  70.925  92.918  1.00  0.00              
ATOM    256  O   ILE   316      73.099  70.557  91.866  1.00  0.00              
END
