
#######################################################
#                                                     #
#                        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 (   20),  selected    5 , name T0299AL243_5-D2
# Molecule2: number of CA atoms   89 (  757),  selected    5 , name T0299_D2.pdb
# PARAMETERS: T0299AL243_5-D2.T0299_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
  LONGEST_CONTINUOUS_SEGMENT:     5        79 - 83          1.01     1.01
  LCS_AVERAGE:      5.62

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5        79 - 83          1.01     1.01
  LCS_AVERAGE:      5.62

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4        79 - 82          0.25     1.56
  LCS_AVERAGE:      4.27

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:   89
LCS_GDT     L      79     L      79      4    5    5     4    4    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5 
LCS_GDT     E      80     E      80      4    5    5     4    4    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5 
LCS_GDT     D      81     D      81      4    5    5     4    4    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5 
LCS_GDT     F      82     F      82      4    5    5     4    4    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5 
LCS_GDT     E      83     E      83      3    5    5     0    3    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5 
LCS_AVERAGE  LCS_A:   5.17  (   4.27    5.62    5.62 )

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      4      4      5      5      5      5      5      5      5      5      5      5      5      5      5      5      5      5      5      5 
GDT PERCENT_CA   4.49   4.49   5.62   5.62   5.62   5.62   5.62   5.62   5.62   5.62   5.62   5.62   5.62   5.62   5.62   5.62   5.62   5.62   5.62   5.62
GDT RMS_LOCAL    0.25   0.25   1.01   1.01   1.01   1.01   1.01   1.01   1.01   1.01   1.01   1.01   1.01   1.01   1.01   1.01   1.01   1.01   1.01   1.01
GDT RMS_ALL_CA   1.56   1.56   1.01   1.01   1.01   1.01   1.01   1.01   1.01   1.01   1.01   1.01   1.01   1.01   1.01   1.01   1.01   1.01   1.01   1.01

#      Molecule1      Molecule2       DISTANCE
LGA    L      79      L      79          0.710
LGA    E      80      E      80          1.275
LGA    D      81      D      81          0.443
LGA    F      82      F      82          0.769
LGA    E      83      E      83          1.474

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)    5   89    4.0      5    1.01     5.337     5.529     0.451

LGA_LOCAL      RMSD =  1.009  Number of atoms =    5  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  1.009  Number of atoms =    5 
Std_ALL_ATOMS  RMSD =  1.009  (standard rmsd on all 5 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.082795 * X  +   0.043744 * Y  +  -0.995606 * Z  +  16.272173
  Y_new =  -0.980016 * X  +  -0.177744 * Y  +  -0.089309 * Z  +  99.194649
  Z_new =  -0.180869 * X  +   0.983104 * Y  +   0.028154 * Z  + -34.586594 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.542166   -1.599426  [ DEG:    88.3596    -91.6404 ]
  Theta =   0.181870    2.959723  [ DEG:    10.4204    169.5796 ]
  Phi   =  -1.486513    1.655080  [ DEG:   -85.1709     94.8291 ]
 
# 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: T0299AL243_5-D2                               
REMARK     2: T0299_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0299AL243_5-D2.T0299_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:    5   89   4.0    5   1.01   5.529     1.01
REMARK  ---------------------------------------------------------- 
MOLECULE T0299AL243_5-D2
REMARK Aligment from pdb entry: 1dy3A
ATOM    273  N   LEU    79     -10.222  57.354  -6.732  1.00  0.00              
ATOM    274  CA  LEU    79     -10.737  56.960  -5.424  1.00  0.00              
ATOM    275  C   LEU    79     -10.767  58.172  -4.503  1.00  0.00              
ATOM    276  O   LEU    79     -10.237  59.213  -4.863  1.00  0.00              
ATOM    277  N   GLU    80     -11.313  58.020  -3.299  1.00  0.00              
ATOM    278  CA  GLU    80     -11.377  59.147  -2.354  1.00  0.00              
ATOM    279  C   GLU    80      -9.994  59.558  -1.911  1.00  0.00              
ATOM    280  O   GLU    80      -9.726  60.744  -1.662  1.00  0.00              
ATOM    281  N   ASP    81      -9.029  58.614  -1.848  1.00  0.00              
ATOM    282  CA  ASP    81      -7.684  58.972  -1.452  1.00  0.00              
ATOM    283  C   ASP    81      -6.802  59.386  -2.636  1.00  0.00              
ATOM    284  O   ASP    81      -5.852  60.142  -2.461  1.00  0.00              
ATOM    285  N   PHE    82      -7.088  58.816  -3.801  1.00  0.00              
ATOM    286  CA  PHE    82      -6.173  59.070  -4.921  1.00  0.00              
ATOM    287  C   PHE    82      -6.805  59.245  -6.272  1.00  0.00              
ATOM    288  O   PHE    82      -7.599  58.430  -6.759  1.00  0.00              
ATOM    289  N   GLU    83      -6.492  60.398  -6.870  1.00  0.00              
ATOM    290  CA  GLU    83      -6.958  60.754  -8.217  1.00  0.00              
ATOM    291  C   GLU    83      -5.701  60.932  -9.062  1.00  0.00              
ATOM    292  O   GLU    83      -4.845  61.766  -8.781  1.00  0.00              
END
