
#######################################################
#                                                     #
#                        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 (   44),  selected    5 , name T0316TS650_1_3-D2
# Molecule2: number of CA atoms   60 (  457),  selected    5 , name T0316_D2.pdb
# PARAMETERS: T0316TS650_1_3-D2.T0316_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       279 - 283         1.72     1.72
  LCS_AVERAGE:      8.33

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5       279 - 283         1.72     1.72
  LCS_AVERAGE:      8.33

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4       279 - 282         0.82     2.47
  LONGEST_CONTINUOUS_SEGMENT:     4       280 - 283         0.97     2.39
  LCS_AVERAGE:      6.67

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:   60
LCS_GDT     Y     279     Y     279      4    5    5     3    4    4    4    4    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5 
LCS_GDT     H     280     H     280      4    5    5     3    4    4    4    4    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5 
LCS_GDT     D     281     D     281      4    5    5     3    4    4    4    4    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5 
LCS_GDT     S     282     S     282      4    5    5     3    4    4    4    4    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5 
LCS_GDT     L     283     L     283      4    5    5     0    3    4    4    4    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5 
LCS_AVERAGE  LCS_A:   7.78  (   6.67    8.33    8.33 )

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      4      4      4      4      5      5      5      5      5      5      5      5      5      5      5      5      5      5      5 
GDT PERCENT_CA   5.00   6.67   6.67   6.67   6.67   8.33   8.33   8.33   8.33   8.33   8.33   8.33   8.33   8.33   8.33   8.33   8.33   8.33   8.33   8.33
GDT RMS_LOCAL    0.10   0.82   0.82   0.82   0.82   1.72   1.72   1.72   1.72   1.72   1.72   1.72   1.72   1.72   1.72   1.72   1.72   1.72   1.72   1.72
GDT RMS_ALL_CA   3.71   2.47   2.47   2.47   2.47   1.72   1.72   1.72   1.72   1.72   1.72   1.72   1.72   1.72   1.72   1.72   1.72   1.72   1.72   1.72

#      Molecule1      Molecule2       DISTANCE
LGA    Y     279      Y     279          2.255
LGA    H     280      H     280          1.472
LGA    D     281      D     281          0.647
LGA    S     282      S     282          0.658
LGA    L     283      L     283          2.594

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)    5   60    4.0      5    1.72     7.500     7.851     0.274

LGA_LOCAL      RMSD =  1.722  Number of atoms =    5  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  1.722  Number of atoms =    5 
Std_ALL_ATOMS  RMSD =  1.722  (standard rmsd on all 5 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.676880 * X  +  -0.718312 * Y  +  -0.160813 * Z  +  39.064518
  Y_new =   0.325737 * X  +  -0.488211 * Y  +   0.809658 * Z  + -20.228531
  Z_new =  -0.660098 * X  +   0.495659 * Y  +   0.564441 * Z  +  22.817356 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.720606   -2.420987  [ DEG:    41.2877   -138.7123 ]
  Theta =   0.720949    2.420644  [ DEG:    41.3073    138.6927 ]
  Phi   =   2.693071   -0.448521  [ DEG:   154.3016    -25.6984 ]
 
# 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: T0316TS650_1_3-D2                             
REMARK     2: T0316_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0316TS650_1_3-D2.T0316_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:    5   60   4.0    5   1.72   7.851     1.72
REMARK  ---------------------------------------------------------- 
MOLECULE T0316TS650_1_3-D2
REMARK PARENT number 3
PFRMAT TS
TARGET T0316
PARENT 1EXM_A
ATOM   2176  N   TYR   279      18.755  16.379 -19.779  1.00  0.00              
ATOM   2177  CA  TYR   279      19.602  16.646 -20.960  1.00  0.00              
ATOM   2178  CB  TYR   279      19.757  18.159 -21.183  1.00  0.00              
ATOM   2179  CG  TYR   279      20.708  18.339 -22.317  1.00  0.00              
ATOM   2180  CD1 TYR   279      20.287  18.191 -23.620  1.00  0.00              
ATOM   2181  CD2 TYR   279      22.024  18.662 -22.077  1.00  0.00              
ATOM   2182  CE1 TYR   279      21.166  18.361 -24.662  1.00  0.00              
ATOM   2183  CE2 TYR   279      22.911  18.835 -23.116  1.00  0.00              
ATOM   2184  CZ  TYR   279      22.481  18.685 -24.411  1.00  0.00              
ATOM   2185  OH  TYR   279      23.383  18.860 -25.482  1.00  0.00              
ATOM   2186  C   TYR   279      20.967  16.056 -20.828  1.00  0.00              
ATOM   2187  O   TYR   279      21.345  15.188 -21.613  1.00  0.00              
ATOM   2188  N   HIS   280      21.742  16.499 -19.817  1.00  0.00              
ATOM   2189  CA  HIS   280      23.084  16.008 -19.708  1.00  0.00              
ATOM   2190  ND1 HIS   280      24.641  18.834 -17.622  1.00  0.00              
ATOM   2191  CG  HIS   280      23.960  18.080 -18.550  1.00  0.00              
ATOM   2192  CB  HIS   280      23.859  16.585 -18.508  1.00  0.00              
ATOM   2193  NE2 HIS   280      23.763  20.270 -19.071  1.00  0.00              
ATOM   2194  CD2 HIS   280      23.426  18.977 -19.431  1.00  0.00              
ATOM   2195  CE1 HIS   280      24.493  20.132 -17.980  1.00  0.00              
ATOM   2196  C   HIS   280      23.024  14.526 -19.546  1.00  0.00              
ATOM   2197  O   HIS   280      22.477  14.009 -18.571  1.00  0.00              
ATOM   2198  N   ASP   281      23.570  13.811 -20.549  1.00  0.00              
ATOM   2199  CA  ASP   281      23.614  12.379 -20.568  1.00  0.00              
ATOM   2200  CB  ASP   281      24.087  11.825 -21.923  1.00  0.00              
ATOM   2201  CG  ASP   281      23.960  10.311 -21.876  1.00  0.00              
ATOM   2202  OD1 ASP   281      23.195   9.816 -21.008  1.00  0.00              
ATOM   2203  OD2 ASP   281      24.616   9.633 -22.711  1.00  0.00              
ATOM   2204  C   ASP   281      24.583  11.874 -19.549  1.00  0.00              
ATOM   2205  O   ASP   281      24.274  10.952 -18.796  1.00  0.00              
ATOM   2206  N   SER   282      25.787  12.479 -19.485  1.00  0.00              
ATOM   2207  CA  SER   282      26.787  11.944 -18.606  1.00  0.00              
ATOM   2208  CB  SER   282      27.990  11.338 -19.350  1.00  0.00              
ATOM   2209  OG  SER   282      28.716  12.363 -20.016  1.00  0.00              
ATOM   2210  C   SER   282      27.333  13.048 -17.772  1.00  0.00              
ATOM   2211  O   SER   282      27.382  14.202 -18.196  1.00  0.00              
ATOM   2212  N   LEU   283      27.749  12.703 -16.539  1.00  0.00              
ATOM   2213  CA  LEU   283      28.315  13.673 -15.653  1.00  0.00              
ATOM   2214  CB  LEU   283      27.310  14.246 -14.636  1.00  0.00              
ATOM   2215  CG  LEU   283      26.424  13.201 -13.917  1.00  0.00              
ATOM   2216  CD1 LEU   283      27.232  12.219 -13.054  1.00  0.00              
ATOM   2217  CD2 LEU   283      25.326  13.904 -13.108  1.00  0.00              
ATOM   2218  C   LEU   283      29.399  13.014 -14.873  1.00  0.00              
ATOM   2219  O   LEU   283      29.423  11.795 -14.715  1.00  0.00              
TER
END
