
#######################################################
#                                                     #
#                        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 T0338TS021_1-D2
# Molecule2: number of CA atoms  113 (  914),  selected    5 , name T0338_D2.pdb
# PARAMETERS: T0338TS021_1-D2.T0338_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       144 - 148         2.08     2.08
  LCS_AVERAGE:      4.42

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4       145 - 148         0.62     3.18
  LCS_AVERAGE:      3.36

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4       145 - 148         0.62     3.18
  LCS_AVERAGE:      3.36

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:  113
LCS_GDT     E     144     E     144      3    3    5     0    2    3    3    3    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5 
LCS_GDT     H     145     H     145      4    4    5     3    4    4    4    4    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5 
LCS_GDT     P     146     P     146      4    4    5     3    4    4    4    4    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5 
LCS_GDT     H     147     H     147      4    4    5     3    4    4    4    4    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5 
LCS_GDT     T     148     T     148      4    4    5     0    4    4    4    4    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5 
LCS_AVERAGE  LCS_A:   3.72  (   3.36    3.36    4.42 )

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      4      4      4      4      5      5      5      5      5      5      5      5      5      5      5      5      5      5      5 
GDT PERCENT_CA   2.65   3.54   3.54   3.54   3.54   4.42   4.42   4.42   4.42   4.42   4.42   4.42   4.42   4.42   4.42   4.42   4.42   4.42   4.42   4.42
GDT RMS_LOCAL    0.15   0.62   0.62   0.62   0.62   2.08   2.08   2.08   2.08   2.08   2.08   2.08   2.08   2.08   2.08   2.08   2.08   2.08   2.08   2.08
GDT RMS_ALL_CA   3.35   3.18   3.18   3.18   3.18   2.08   2.08   2.08   2.08   2.08   2.08   2.08   2.08   2.08   2.08   2.08   2.08   2.08   2.08   2.08

#      Molecule1      Molecule2       DISTANCE
LGA    E     144      E     144          2.901
LGA    H     145      H     145          2.527
LGA    P     146      P     146          1.223
LGA    H     147      H     147          2.253
LGA    T     148      T     148          0.593

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)    5  113    4.0      5    2.08     3.982     3.903     0.229

LGA_LOCAL      RMSD =  2.085  Number of atoms =    5  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  2.085  Number of atoms =    5 
Std_ALL_ATOMS  RMSD =  2.085  (standard rmsd on all 5 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.114626 * X  +  -0.837925 * Y  +   0.533613 * Z  + -10.232658
  Y_new =  -0.976003 * X  +  -0.005123 * Y  +  -0.217699 * Z  +  -2.387017
  Z_new =   0.185149 * X  +  -0.545762 * Y  +  -0.817230 * Z  +  76.300484 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.552793    0.588800  [ DEG:  -146.2642     33.7358 ]
  Theta =  -0.186223   -2.955369  [ DEG:   -10.6698   -169.3302 ]
  Phi   =  -1.687705    1.453888  [ DEG:   -96.6984     83.3016 ]
 
# 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: T0338TS021_1-D2                               
REMARK     2: T0338_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0338TS021_1-D2.T0338_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:    5  113   4.0    5   2.08   3.903     2.08
REMARK  ---------------------------------------------------------- 
MOLECULE T0338TS021_1-D2
PFRMAT TS
TARGET T0338
MODEL 1
PARENT N/A
ATOM   1159  N   GLU   144     -28.243  20.059  60.501  1.00441.44       1SG1160
ATOM   1160  CA  GLU   144     -26.864  19.746  60.745  1.00441.44       1SG1161
ATOM   1161  CB  GLU   144     -26.119  20.655  61.740  1.00441.44       1SG1162
ATOM   1162  CG  GLU   144     -24.617  20.378  61.803  1.00441.44       1SG1163
ATOM   1163  CD  GLU   144     -23.994  20.909  60.520  1.00441.44       1SG1164
ATOM   1164  OE1 GLU   144     -24.757  21.429  59.662  1.00441.44       1SG1165
ATOM   1165  OE2 GLU   144     -22.747  20.801  60.381  1.00441.44       1SG1166
ATOM   1166  C   GLU   144     -26.854  18.368  61.300  1.00441.44       1SG1167
ATOM   1167  O   GLU   144     -27.771  17.979  62.022  1.00441.44       1SG1168
ATOM   1168  N   HIS   145     -25.820  17.578  60.968  1.00149.75       1SG1169
ATOM   1169  CA  HIS   145     -25.798  16.265  61.525  1.00149.75       1SG1170
ATOM   1170  ND1 HIS   145     -23.672  14.117  63.004  1.00149.75       1SG1171
ATOM   1171  CG  HIS   145     -24.489  14.163  61.897  1.00149.75       1SG1172
ATOM   1172  CB  HIS   145     -24.633  15.384  61.040  1.00149.75       1SG1173
ATOM   1173  NE2 HIS   145     -24.664  12.135  62.863  1.00149.75       1SG1174
ATOM   1174  CD2 HIS   145     -25.087  12.945  61.824  1.00149.75       1SG1175
ATOM   1175  CE1 HIS   145     -23.816  12.881  63.545  1.00149.75       1SG1176
ATOM   1176  C   HIS   145     -25.709  16.409  63.001  1.00149.75       1SG1177
ATOM   1177  O   HIS   145     -26.432  15.759  63.753  1.00149.75       1SG1178
ATOM   1178  N   PRO   146     -24.849  17.249  63.465  1.00134.43       1SG1179
ATOM   1179  CA  PRO   146     -24.801  17.442  64.872  1.00134.43       1SG1180
ATOM   1180  CD  PRO   146     -23.583  17.570  62.826  1.00134.43       1SG1181
ATOM   1181  CB  PRO   146     -23.439  18.072  65.181  1.00134.43       1SG1182
ATOM   1182  CG  PRO   146     -22.905  18.532  63.813  1.00134.43       1SG1183
ATOM   1183  C   PRO   146     -25.983  18.277  65.269  1.00134.43       1SG1184
ATOM   1184  O   PRO   146     -26.175  18.491  66.461  1.00134.43       1SG1185
ATOM   1185  N   HIS   147     -26.784  18.798  64.317  1.00116.07       1SG1186
ATOM   1186  CA  HIS   147     -27.881  19.626  64.746  1.00116.07       1SG1187
ATOM   1187  ND1 HIS   147     -30.487  21.828  64.353  1.00116.07       1SG1188
ATOM   1188  CG  HIS   147     -29.110  21.818  64.387  1.00116.07       1SG1189
ATOM   1189  CB  HIS   147     -28.247  20.757  63.769  1.00116.07       1SG1190
ATOM   1190  NE2 HIS   147     -29.868  23.647  65.472  1.00116.07       1SG1191
ATOM   1191  CD2 HIS   147     -28.750  22.936  65.076  1.00116.07       1SG1192
ATOM   1192  CE1 HIS   147     -30.887  22.943  65.015  1.00116.07       1SG1193
ATOM   1193  C   HIS   147     -29.102  18.778  64.941  1.00116.07       1SG1194
ATOM   1194  O   HIS   147     -29.126  17.611  64.555  1.00116.07       1SG1195
ATOM   1195  N   THR   148     -30.134  19.350  65.602  1.00147.19       1SG1196
ATOM   1196  CA  THR   148     -31.384  18.696  65.861  1.00147.19       1SG1197
ATOM   1197  CB  THR   148     -31.305  17.623  66.902  1.00147.19       1SG1198
ATOM   1198  OG1 THR   148     -32.512  16.876  66.932  1.00147.19       1SG1199
ATOM   1199  CG2 THR   148     -31.059  18.286  68.268  1.00147.19       1SG1200
ATOM   1200  C   THR   148     -32.306  19.749  66.467  1.00147.19       1SG1201
ATOM   1201  O   THR   148     -33.499  19.410  66.698  1.00147.19       1SG1202
ATOM   1202  OXT THR   148     -31.836  20.891  66.712  1.00147.19       1SG1203
TER
END
