
#######################################################
#                                                     #
#                        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_4-D3
# Molecule2: number of CA atoms  120 (  972),  selected    5 , name T0356_D3.pdb
# PARAMETERS: T0356AL044_4-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         3.69     3.69
  LCS_AVERAGE:      4.17

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
# WARNING! The change of the parameter DIST cutoff may give you better result.

  LONGEST_CONTINUOUS_SEGMENT:     3       349 - 351         1.49     6.91
  LONGEST_CONTINUOUS_SEGMENT:     3       350 - 353         1.42     4.66
  LONGEST_CONTINUOUS_SEGMENT:     3       351 - 355         1.85     5.54
  LCS_AVERAGE:      2.50

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  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    3    5     0    1    2    3    3    4    4    4    4    4    4    5    5    5    5    5    5    5    5    5 
LCS_GDT     I     351     I     351      0    3    5     0    0    2    3    3    4    4    4    4    4    4    5    5    5    5    5    5    5    5    5 
LCS_GDT     D     353     D     353      0    3    5     0    1    2    3    3    4    4    4    4    4    4    5    5    5    5    5    5    5    5    5 
LCS_GDT     Y     355     Y     355      0    3    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:   2.22  (   0.00    2.50    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      2      3      3      4      4      4      4      4      4      5      5      5      5      5      5      5      5      5 
GDT PERCENT_CA   0.00   0.83   1.67   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  22.39   1.42   1.42   2.06   2.06   2.06   2.06   2.06   2.06   3.69   3.69   3.69   3.69   3.69   3.69   3.69   3.69   3.69
GDT RMS_ALL_CA 1000.00   3.69   6.91   4.66   4.66   4.54   4.54   4.54   4.54   4.54   4.54   3.69   3.69   3.69   3.69   3.69   3.69   3.69   3.69   3.69

#      Molecule1      Molecule2       DISTANCE
LGA    P     349      P     349          9.265
LGA    E     350      E     350          1.424
LGA    I     351      I     351          2.603
LGA    D     353      D     353          0.999
LGA    Y     355      Y     355          2.689

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)    5  120    4.0      4    2.06     2.708     2.822     0.185

LGA_LOCAL      RMSD =  2.063  Number of atoms =    4  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  4.536  Number of atoms =    5 
Std_ALL_ATOMS  RMSD =  3.695  (standard rmsd on all 5 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.980798 * X  +  -0.152323 * Y  +  -0.121787 * Z  + 154.049820
  Y_new =   0.193622 * X  +  -0.835295 * Y  +  -0.514581 * Z  + 164.796860
  Z_new =  -0.023345 * X  +  -0.528280 * Y  +   0.848749 * Z  +  69.518547 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.556744    2.584849  [ DEG:   -31.8991    148.1009 ]
  Theta =   0.023347    3.118245  [ DEG:     1.3377    178.6623 ]
  Phi   =   2.946687   -0.194906  [ DEG:   168.8327    -11.1673 ]
 
# 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_4-D3                               
REMARK     2: T0356_D3.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0356AL044_4-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   2.06   2.822     3.69
REMARK  ---------------------------------------------------------- 
MOLECULE T0356AL044_4-D3
REMARK Aligment from pdb entry: 1yw6_A
ATOM    137  N   PRO   349      49.813  69.626  57.034  1.00  0.00              
ATOM    138  CA  PRO   349      51.058  68.979  57.443  1.00  0.00              
ATOM    139  C   PRO   349      51.965  68.809  56.239  1.00  0.00              
ATOM    140  O   PRO   349      53.186  68.777  56.365  1.00  0.00              
ATOM    141  N   GLU   350      51.495  70.570  52.828  1.00  0.00              
ATOM    142  CA  GLU   350      51.666  71.843  52.150  1.00  0.00              
ATOM    143  C   GLU   350      52.189  72.984  52.982  1.00  0.00              
ATOM    144  O   GLU   350      52.503  74.025  52.424  1.00  0.00              
ATOM    145  N   ILE   351      53.788  71.996  56.343  1.00  0.00              
ATOM    146  CA  ILE   351      54.569  71.364  57.390  1.00  0.00              
ATOM    147  C   ILE   351      54.035  71.682  58.768  1.00  0.00              
ATOM    148  O   ILE   351      54.804  71.919  59.708  1.00  0.00              
ATOM    149  N   ASP   353      52.710  71.693  58.879  1.00  0.00              
ATOM    150  CA  ASP   353      52.051  71.998  60.132  1.00  0.00              
ATOM    151  C   ASP   353      52.043  70.755  60.964  1.00  0.00              
ATOM    152  O   ASP   353      51.929  69.654  60.432  1.00  0.00              
ATOM    153  N   TYR   355      52.211  70.917  62.266  1.00  0.00              
ATOM    154  CA  TYR   355      52.166  69.758  63.138  1.00  0.00              
ATOM    155  C   TYR   355      50.671  69.545  63.295  1.00  0.00              
ATOM    156  O   TYR   355      50.075  70.012  64.248  1.00  0.00              
END
