
#######################################################
#                                                     #
#                        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 T0356AL044_5-D3
# Molecule2: number of CA atoms  120 (  972),  selected    5 , name T0356_D3.pdb
# PARAMETERS: T0356AL044_5-D3.T0356_D3.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       349 - 355         3.63     3.63
  LCS_AVERAGE:      4.17

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4       350 - 355         1.93     4.48
  LCS_AVERAGE:      3.17

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
# WARNING! The change of the parameter DIST cutoff may give you better result.

  LCS_AVERAGE:      0.00

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:  120
LCS_GDT     P     349     P     349      0    3    5     0    0    2    3    3    3    4    4    4    4    4    5    5    5    5    5    5    5    5    5 
LCS_GDT     E     350     E     350      0    4    5     0    1    3    3    3    4    4    4    4    4    4    5    5    5    5    5    5    5    5    5 
LCS_GDT     I     351     I     351      0    4    5     0    1    3    3    3    4    4    4    4    4    4    5    5    5    5    5    5    5    5    5 
LCS_GDT     D     353     D     353      0    4    5     0    1    3    3    3    4    4    4    4    4    4    5    5    5    5    5    5    5    5    5 
LCS_GDT     Y     355     Y     355      0    4    5     0    0    0    0    3    4    4    4    4    4    4    5    5    5    5    5    5    5    5    5 
LCS_AVERAGE  LCS_A:   2.44  (   0.00    3.17    4.17 )

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      0      1      3      3      3      4      4      4      4      4      4      5      5      5      5      5      5      5      5      5 
GDT PERCENT_CA   0.00   0.83   2.50   2.50   2.50   3.33   3.33   3.33   3.33   3.33   3.33   4.17   4.17   4.17   4.17   4.17   4.17   4.17   4.17   4.17
GDT RMS_LOCAL  1000.00  31.63   1.14   1.14   1.14   1.93   1.93   1.93   1.93   1.93   1.93   3.63   3.63   3.63   3.63   3.63   3.63   3.63   3.63   3.63
GDT RMS_ALL_CA 1000.00   3.63   4.90   4.90   4.90   4.48   4.48   4.48   4.48   4.48   4.48   3.63   3.63   3.63   3.63   3.63   3.63   3.63   3.63   3.63

#      Molecule1      Molecule2       DISTANCE
LGA    P     349      P     349          9.250
LGA    E     350      E     350          1.450
LGA    I     351      I     351          2.276
LGA    D     353      D     353          0.952
LGA    Y     355      Y     355          2.580

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)    5  120    4.0      4    1.93     2.708     3.050     0.197

LGA_LOCAL      RMSD =  1.926  Number of atoms =    4  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  4.481  Number of atoms =    5 
Std_ALL_ATOMS  RMSD =  3.627  (standard rmsd on all 5 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.255823 * X  +  -0.625181 * Y  +  -0.737363 * Z  + 125.739731
  Y_new =  -0.779562 * X  +  -0.584480 * Y  +   0.225093 * Z  +  76.531242
  Z_new =  -0.571697 * X  +   0.517236 * Y  +  -0.636890 * Z  + 152.383591 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.459501   -0.682092  [ DEG:   140.9190    -39.0810 ]
  Theta =   0.608573    2.533019  [ DEG:    34.8687    145.1313 ]
  Phi   =  -1.253706    1.887886  [ DEG:   -71.8321    108.1679 ]
 
# 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: T0356AL044_5-D3                               
REMARK     2: T0356_D3.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0356AL044_5-D3.T0356_D3.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:    5  120   4.0    4   1.93   3.050     3.63
REMARK  ---------------------------------------------------------- 
MOLECULE T0356AL044_5-D3
REMARK Aligment from pdb entry: 1yw4_A
ATOM    125  N   PRO   349      50.441  68.607  57.145  1.00  0.00              
ATOM    126  CA  PRO   349      51.805  68.423  57.629  1.00  0.00              
ATOM    127  C   PRO   349      52.839  68.737  56.542  1.00  0.00              
ATOM    128  O   PRO   349      53.826  69.419  56.801  1.00  0.00              
ATOM    129  N   GLU   350      52.178  70.058  53.006  1.00  0.00              
ATOM    130  CA  GLU   350      51.907  71.271  52.249  1.00  0.00              
ATOM    131  C   GLU   350      51.919  72.522  53.112  1.00  0.00              
ATOM    132  O   GLU   350      52.461  73.546  52.710  1.00  0.00              
ATOM    133  N   ILE   351      53.134  72.416  56.154  1.00  0.00              
ATOM    134  CA  ILE   351      54.208  72.120  57.090  1.00  0.00              
ATOM    135  C   ILE   351      53.797  72.389  58.532  1.00  0.00              
ATOM    136  O   ILE   351      54.487  73.076  59.277  1.00  0.00              
ATOM    137  N   ASP   353      52.655  71.835  58.925  1.00  0.00              
ATOM    138  CA  ASP   353      52.176  72.010  60.288  1.00  0.00              
ATOM    139  C   ASP   353      52.300  70.699  61.048  1.00  0.00              
ATOM    140  O   ASP   353      52.587  69.656  60.462  1.00  0.00              
ATOM    141  N   TYR   355      52.108  70.760  62.359  1.00  0.00              
ATOM    142  CA  TYR   355      52.161  69.561  63.183  1.00  0.00              
ATOM    143  C   TYR   355      50.753  68.996  63.137  1.00  0.00              
ATOM    144  O   TYR   355      49.876  69.416  63.882  1.00  0.00              
END
