
#######################################################
#                                                     #
#                        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   10 (   79),  selected   10 , name T0318TS021_3_1-D2
# Molecule2: number of CA atoms  335 ( 2465),  selected   10 , name T0318_D2.pdb
# PARAMETERS: T0318TS021_3_1-D2.T0318_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:    10       156 - 165         1.26     1.26
  LCS_AVERAGE:      2.99

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    10       156 - 165         1.26     1.26
  LCS_AVERAGE:      2.99

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     9       156 - 164         0.97     1.41
  LONGEST_CONTINUOUS_SEGMENT:     9       157 - 165         0.79     1.44
  LCS_AVERAGE:      2.69

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:  335
LCS_GDT     T     156     T     156      9   10   10     3    4    6    9    9   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10 
LCS_GDT     N     157     N     157      9   10   10     8    8    8    9    9   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10 
LCS_GDT     E     158     E     158      9   10   10     8    8    8    9    9   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10 
LCS_GDT     D     159     D     159      9   10   10     8    8    8    9    9   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10 
LCS_GDT     A     160     A     160      9   10   10     8    8    8    9    9   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10 
LCS_GDT     V     161     V     161      9   10   10     8    8    8    9    9   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10 
LCS_GDT     F     162     F     162      9   10   10     8    8    8    9    9   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10 
LCS_GDT     L     163     L     163      9   10   10     8    8    8    9    9   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10 
LCS_GDT     T     164     T     164      9   10   10     8    8    8    9    9   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10 
LCS_GDT     D     165     D     165      9   10   10     0    3    4    9    9   10   10   10   10   10   10   10   10   10   10   10   10   10   10   10 
LCS_AVERAGE  LCS_A:   2.89  (   2.69    2.99    2.99 )

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      8      8      8      9      9     10     10     10     10     10     10     10     10     10     10     10     10     10     10     10 
GDT PERCENT_CA   2.39   2.39   2.39   2.69   2.69   2.99   2.99   2.99   2.99   2.99   2.99   2.99   2.99   2.99   2.99   2.99   2.99   2.99   2.99   2.99
GDT RMS_LOCAL    0.36   0.36   0.36   0.79   0.79   1.26   1.26   1.26   1.26   1.26   1.26   1.26   1.26   1.26   1.26   1.26   1.26   1.26   1.26   1.26
GDT RMS_ALL_CA   1.40   1.40   1.40   1.44   1.44   1.26   1.26   1.26   1.26   1.26   1.26   1.26   1.26   1.26   1.26   1.26   1.26   1.26   1.26   1.26

#      Molecule1      Molecule2       DISTANCE
LGA    T     156      T     156          2.636
LGA    N     157      N     157          0.847
LGA    E     158      E     158          0.764
LGA    D     159      D     159          0.581
LGA    A     160      A     160          0.624
LGA    V     161      V     161          0.546
LGA    F     162      F     162          0.638
LGA    L     163      L     163          0.866
LGA    T     164      T     164          0.759
LGA    D     165      D     165          2.196

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   10  335    4.0     10    1.26     2.761     2.853     0.736

LGA_LOCAL      RMSD =  1.258  Number of atoms =   10  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  1.258  Number of atoms =   10 
Std_ALL_ATOMS  RMSD =  1.258  (standard rmsd on all 10 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.388531 * X  +  -0.882165 * Y  +   0.266135 * Z  +  35.056049
  Y_new =   0.859327 * X  +   0.242656 * Y  +  -0.450196 * Z  +  30.853285
  Z_new =   0.332568 * X  +   0.403612 * Y  +   0.852347 * Z  + -25.335260 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.442248   -2.699344  [ DEG:    25.3390   -154.6610 ]
  Theta =  -0.339025   -2.802568  [ DEG:   -19.4247   -160.5753 ]
  Phi   =   1.146168   -1.995424  [ DEG:    65.6706   -114.3294 ]
 
# 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: T0318TS021_3_1-D2                             
REMARK     2: T0318_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0318TS021_3_1-D2.T0318_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   10  335   4.0   10   1.26   2.853     1.26
REMARK  ---------------------------------------------------------- 
MOLECULE T0318TS021_3_1-D2
REMARK PARENT number 1
PFRMAT TS
TARGET T0318
PARENT N/A
ATOM   1209  N   THR   156      29.721  29.937  15.056  1.00332.23       1SG1210
ATOM   1210  CA  THR   156      28.378  29.603  14.679  1.00332.23       1SG1211
ATOM   1211  CB  THR   156      27.371  30.577  15.198  1.00332.23       1SG1212
ATOM   1212  OG1 THR   156      26.114  30.330  14.598  1.00332.23       1SG1213
ATOM   1213  CG2 THR   156      27.855  32.008  14.927  1.00332.23       1SG1214
ATOM   1214  C   THR   156      28.320  29.617  13.190  1.00332.23       1SG1215
ATOM   1215  O   THR   156      28.435  30.674  12.576  1.00332.23       1SG1216
ATOM   1216  N   ASN   157      28.160  28.451  12.546  1.00236.00       1SG1217
ATOM   1217  CA  ASN   157      28.126  28.534  11.119  1.00236.00       1SG1218
ATOM   1218  CB  ASN   157      28.279  27.147  10.463  1.00236.00       1SG1219
ATOM   1219  CG  ASN   157      27.249  26.193  11.060  1.00236.00       1SG1220
ATOM   1220  OD1 ASN   157      26.177  25.971  10.500  1.00236.00       1SG1221
ATOM   1221  ND2 ASN   157      27.584  25.612  12.243  1.00236.00       1SG1222
ATOM   1222  C   ASN   157      26.876  29.204  10.613  1.00236.00       1SG1223
ATOM   1223  O   ASN   157      26.918  30.332  10.125  1.00236.00       1SG1224
ATOM   1224  N   GLU   158      25.718  28.531  10.760  1.00 94.60       1SG1225
ATOM   1225  CA  GLU   158      24.460  28.998  10.251  1.00 94.60       1SG1226
ATOM   1226  CB  GLU   158      23.394  27.894  10.189  1.00 94.60       1SG1227
ATOM   1227  CG  GLU   158      23.717  26.806   9.163  1.00 94.60       1SG1228
ATOM   1228  CD  GLU   158      22.600  25.775   9.193  1.00 94.60       1SG1229
ATOM   1229  OE1 GLU   158      21.638  25.962   9.985  1.00 94.60       1SG1230
ATOM   1230  OE2 GLU   158      22.692  24.784   8.418  1.00 94.60       1SG1231
ATOM   1231  C   GLU   158      23.919  30.087  11.099  1.00 94.60       1SG1232
ATOM   1232  O   GLU   158      23.429  31.100  10.602  1.00 94.60       1SG1233
ATOM   1233  N   ASP   159      24.012  29.907  12.424  1.00139.57       1SG1234
ATOM   1234  CA  ASP   159      23.401  30.870  13.280  1.00139.57       1SG1235
ATOM   1235  CB  ASP   159      23.357  30.475  14.766  1.00139.57       1SG1236
ATOM   1236  CG  ASP   159      22.322  29.369  14.909  1.00139.57       1SG1237
ATOM   1237  OD1 ASP   159      21.655  29.053  13.888  1.00139.57       1SG1238
ATOM   1238  OD2 ASP   159      22.177  28.833  16.040  1.00139.57       1SG1239
ATOM   1239  C   ASP   159      24.095  32.179  13.113  1.00139.57       1SG1240
ATOM   1240  O   ASP   159      23.461  33.224  13.209  1.00139.57       1SG1241
ATOM   1241  N   ALA   160      25.406  32.173  12.814  1.00115.69       1SG1242
ATOM   1242  CA  ALA   160      26.116  33.419  12.743  1.00115.69       1SG1243
ATOM   1243  CB  ALA   160      27.574  33.258  12.283  1.00115.69       1SG1244
ATOM   1244  C   ALA   160      25.491  34.307  11.718  1.00115.69       1SG1245
ATOM   1245  O   ALA   160      25.266  35.489  11.975  1.00115.69       1SG1246
ATOM   1246  N   VAL   161      25.154  33.749  10.542  1.00138.64       1SG1247
ATOM   1247  CA  VAL   161      24.697  34.577   9.464  1.00138.64       1SG1248
ATOM   1248  CB  VAL   161      24.424  33.806   8.202  1.00138.64       1SG1249
ATOM   1249  CG1 VAL   161      23.291  32.798   8.451  1.00138.64       1SG1250
ATOM   1250  CG2 VAL   161      24.118  34.814   7.081  1.00138.64       1SG1251
ATOM   1251  C   VAL   161      23.453  35.322   9.834  1.00138.64       1SG1252
ATOM   1252  O   VAL   161      23.371  36.531   9.625  1.00138.64       1SG1253
ATOM   1253  N   PHE   162      22.456  34.637  10.422  1.00 75.09       1SG1254
ATOM   1254  CA  PHE   162      21.220  35.305  10.713  1.00 75.09       1SG1255
ATOM   1255  CB  PHE   162      20.173  34.383  11.360  1.00 75.09       1SG1256
ATOM   1256  CG  PHE   162      19.815  33.330  10.369  1.00 75.09       1SG1257
ATOM   1257  CD1 PHE   162      20.552  32.172  10.287  1.00 75.09       1SG1258
ATOM   1258  CD2 PHE   162      18.745  33.500   9.520  1.00 75.09       1SG1259
ATOM   1259  CE1 PHE   162      20.225  31.196   9.376  1.00 75.09       1SG1260
ATOM   1260  CE2 PHE   162      18.415  32.528   8.606  1.00 75.09       1SG1261
ATOM   1261  CZ  PHE   162      19.156  31.373   8.533  1.00 75.09       1SG1262
ATOM   1262  C   PHE   162      21.495  36.398  11.686  1.00 75.09       1SG1263
ATOM   1263  O   PHE   162      21.034  37.529  11.528  1.00 75.09       1SG1264
ATOM   1264  N   LEU   163      22.285  36.073  12.717  1.00159.10       1SG1265
ATOM   1265  CA  LEU   163      22.599  36.987  13.770  1.00159.10       1SG1266
ATOM   1266  CB  LEU   163      23.421  36.279  14.858  1.00159.10       1SG1267
ATOM   1267  CG  LEU   163      22.558  35.332  15.730  1.00159.10       1SG1268
ATOM   1268  CD1 LEU   163      21.669  34.392  14.903  1.00159.10       1SG1269
ATOM   1269  CD2 LEU   163      23.430  34.575  16.741  1.00159.10       1SG1270
ATOM   1270  C   LEU   163      23.334  38.156  13.196  1.00159.10       1SG1271
ATOM   1271  O   LEU   163      23.063  39.300  13.558  1.00159.10       1SG1272
ATOM   1272  N   THR   164      24.268  37.915  12.260  1.00241.62       1SG1273
ATOM   1273  CA  THR   164      24.962  39.032  11.692  1.00241.62       1SG1274
ATOM   1274  CB  THR   164      26.195  38.656  10.924  1.00241.62       1SG1275
ATOM   1275  OG1 THR   164      26.934  39.821  10.588  1.00241.62       1SG1276
ATOM   1276  CG2 THR   164      25.778  37.907   9.648  1.00241.62       1SG1277
ATOM   1277  C   THR   164      24.014  39.689  10.747  1.00241.62       1SG1278
ATOM   1278  O   THR   164      22.954  39.149  10.437  1.00241.62       1SG1279
ATOM   1279  N   ASP   165      24.357  40.901  10.283  1.00 98.94       1SG1280
ATOM   1280  CA  ASP   165      23.479  41.585   9.382  1.00 98.94       1SG1281
ATOM   1281  CB  ASP   165      23.896  43.042   9.115  1.00 98.94       1SG1282
ATOM   1282  CG  ASP   165      22.807  43.716   8.290  1.00 98.94       1SG1283
ATOM   1283  OD1 ASP   165      21.852  43.011   7.866  1.00 98.94       1SG1284
ATOM   1284  OD2 ASP   165      22.918  44.953   8.072  1.00 98.94       1SG1285
ATOM   1285  C   ASP   165      23.518  40.841   8.055  1.00 98.94       1SG1286
ATOM   1286  O   ASP   165      22.430  40.390   7.605  1.00 98.94       1SG1287
ATOM   1287  OXT ASP   165      24.628  40.719   7.472  1.00 98.94       1SG1288
TER
END
