
#######################################################
#                                                     #
#                        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   14 (  108),  selected   14 , name T0318TS319_4-D2
# Molecule2: number of CA atoms  335 ( 2465),  selected   14 , name T0318_D2.pdb
# PARAMETERS: T0318TS319_4-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:    14       156 - 169         0.49     0.49
  LCS_AVERAGE:      4.18

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    14       156 - 169         0.49     0.49
  LCS_AVERAGE:      4.18

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    14       156 - 169         0.49     0.49
  LCS_AVERAGE:      4.18

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     14   14   14     7   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14 
LCS_GDT     N     157     N     157     14   14   14    11   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14 
LCS_GDT     E     158     E     158     14   14   14    11   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14 
LCS_GDT     D     159     D     159     14   14   14    11   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14 
LCS_GDT     A     160     A     160     14   14   14    11   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14 
LCS_GDT     V     161     V     161     14   14   14    11   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14 
LCS_GDT     F     162     F     162     14   14   14    11   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14 
LCS_GDT     L     163     L     163     14   14   14    11   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14 
LCS_GDT     T     164     T     164     14   14   14    11   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14 
LCS_GDT     D     165     D     165     14   14   14    11   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14 
LCS_GDT     L     166     L     166     14   14   14    11   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14 
LCS_GDT     S     167     S     167     14   14   14    11   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14 
LCS_GDT     E     168     E     168     14   14   14    11   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14 
LCS_GDT     S     169     S     169     14   14   14     5   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14   14 
LCS_AVERAGE  LCS_A:   4.18  (   4.18    4.18    4.18 )

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     11     14     14     14     14     14     14     14     14     14     14     14     14     14     14     14     14     14     14     14 
GDT PERCENT_CA   3.28   4.18   4.18   4.18   4.18   4.18   4.18   4.18   4.18   4.18   4.18   4.18   4.18   4.18   4.18   4.18   4.18   4.18   4.18   4.18
GDT RMS_LOCAL    0.25   0.49   0.49   0.49   0.49   0.49   0.49   0.49   0.49   0.49   0.49   0.49   0.49   0.49   0.49   0.49   0.49   0.49   0.49   0.49
GDT RMS_ALL_CA   0.55   0.49   0.49   0.49   0.49   0.49   0.49   0.49   0.49   0.49   0.49   0.49   0.49   0.49   0.49   0.49   0.49   0.49   0.49   0.49

#      Molecule1      Molecule2       DISTANCE
LGA    T     156      T     156          0.998
LGA    N     157      N     157          0.163
LGA    E     158      E     158          0.469
LGA    D     159      D     159          0.197
LGA    A     160      A     160          0.267
LGA    V     161      V     161          0.183
LGA    F     162      F     162          0.375
LGA    L     163      L     163          0.349
LGA    T     164      T     164          0.356
LGA    D     165      D     165          0.274
LGA    L     166      L     166          0.459
LGA    S     167      S     167          0.442
LGA    E     168      E     168          0.582
LGA    S     169      S     169          0.864

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   14  335    4.0     14    0.49     4.179     4.179     2.379

LGA_LOCAL      RMSD =  0.489  Number of atoms =   14  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  0.489  Number of atoms =   14 
Std_ALL_ATOMS  RMSD =  0.489  (standard rmsd on all 14 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.516885 * X  +   0.531600 * Y  +  -0.670993 * Z  + -21.049818
  Y_new =  -0.448765 * X  +   0.835751 * Y  +   0.316435 * Z  +  33.837894
  Z_new =   0.728999 * X  +   0.137558 * Y  +   0.670550 * Z  +  15.015738 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.202334   -2.939258  [ DEG:    11.5929   -168.4071 ]
  Theta =  -0.816859   -2.324734  [ DEG:   -46.8026   -133.1974 ]
  Phi   =  -0.714972    2.426621  [ DEG:   -40.9649    139.0351 ]
 
# 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: T0318TS319_4-D2                               
REMARK     2: T0318_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0318TS319_4-D2.T0318_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   14  335   4.0   14   0.49   4.179     0.49
REMARK  ---------------------------------------------------------- 
MOLECULE T0318TS319_4-D2
PFRMAT TS
TARGET T0318
MODEL 4
PARENT N/A
ATOM   1185  N   THR   156      28.920  27.213  14.534  1.00191.53       1SG1186
ATOM   1186  CA  THR   156      27.690  27.908  14.733  1.00191.53       1SG1187
ATOM   1187  CB  THR   156      27.618  28.571  16.075  1.00191.53       1SG1188
ATOM   1188  OG1 THR   156      26.378  29.245  16.231  1.00191.53       1SG1189
ATOM   1189  CG2 THR   156      28.801  29.542  16.209  1.00191.53       1SG1190
ATOM   1190  C   THR   156      27.712  28.961  13.681  1.00191.53       1SG1191
ATOM   1191  O   THR   156      27.359  30.116  13.910  1.00191.53       1SG1192
ATOM   1192  N   ASN   157      28.145  28.547  12.477  1.00 81.69       1SG1193
ATOM   1193  CA  ASN   157      28.293  29.426  11.358  1.00 81.69       1SG1194
ATOM   1194  CB  ASN   157      28.997  28.752  10.167  1.00 81.69       1SG1195
ATOM   1195  CG  ASN   157      29.384  29.842   9.177  1.00 81.69       1SG1196
ATOM   1196  OD1 ASN   157      28.625  30.180   8.270  1.00 81.69       1SG1197
ATOM   1197  ND2 ASN   157      30.599  30.421   9.364  1.00 81.69       1SG1198
ATOM   1198  C   ASN   157      26.950  29.884  10.899  1.00 81.69       1SG1199
ATOM   1199  O   ASN   157      26.767  31.055  10.565  1.00 81.69       1SG1200
ATOM   1200  N   GLU   158      25.964  28.969  10.878  1.00107.95       1SG1201
ATOM   1201  CA  GLU   158      24.675  29.320  10.361  1.00107.95       1SG1202
ATOM   1202  CB  GLU   158      23.685  28.140  10.338  1.00107.95       1SG1203
ATOM   1203  CG  GLU   158      23.352  27.564  11.717  1.00107.95       1SG1204
ATOM   1204  CD  GLU   158      24.480  26.637  12.145  1.00107.95       1SG1205
ATOM   1205  OE1 GLU   158      25.429  26.442  11.339  1.00107.95       1SG1206
ATOM   1206  OE2 GLU   158      24.405  26.109  13.287  1.00107.95       1SG1207
ATOM   1207  C   GLU   158      24.079  30.392  11.209  1.00107.95       1SG1208
ATOM   1208  O   GLU   158      23.549  31.378  10.697  1.00107.95       1SG1209
ATOM   1209  N   ASP   159      24.169  30.244  12.539  1.00 52.67       1SG1210
ATOM   1210  CA  ASP   159      23.563  31.230  13.376  1.00 52.67       1SG1211
ATOM   1211  CB  ASP   159      23.682  30.912  14.877  1.00 52.67       1SG1212
ATOM   1212  CG  ASP   159      22.761  29.740  15.190  1.00 52.67       1SG1213
ATOM   1213  OD1 ASP   159      22.068  29.263  14.250  1.00 52.67       1SG1214
ATOM   1214  OD2 ASP   159      22.730  29.310  16.374  1.00 52.67       1SG1215
ATOM   1215  C   ASP   159      24.239  32.534  13.125  1.00 52.67       1SG1216
ATOM   1216  O   ASP   159      23.577  33.549  12.942  1.00 52.67       1SG1217
ATOM   1217  N   ALA   160      25.577  32.536  13.016  1.00 53.15       1SG1218
ATOM   1218  CA  ALA   160      26.289  33.778  12.919  1.00 53.15       1SG1219
ATOM   1219  CB  ALA   160      27.812  33.602  12.784  1.00 53.15       1SG1220
ATOM   1220  C   ALA   160      25.821  34.555  11.728  1.00 53.15       1SG1221
ATOM   1221  O   ALA   160      25.701  35.777  11.796  1.00 53.15       1SG1222
ATOM   1222  N   VAL   161      25.535  33.878  10.604  1.00 34.35       1SG1223
ATOM   1223  CA  VAL   161      25.144  34.587   9.418  1.00 34.35       1SG1224
ATOM   1224  CB  VAL   161      24.864  33.668   8.264  1.00 34.35       1SG1225
ATOM   1225  CG1 VAL   161      24.343  34.500   7.082  1.00 34.35       1SG1226
ATOM   1226  CG2 VAL   161      26.146  32.875   7.953  1.00 34.35       1SG1227
ATOM   1227  C   VAL   161      23.894  35.371   9.692  1.00 34.35       1SG1228
ATOM   1228  O   VAL   161      23.800  36.544   9.334  1.00 34.35       1SG1229
ATOM   1229  N   PHE   162      22.903  34.746  10.355  1.00 97.85       1SG1230
ATOM   1230  CA  PHE   162      21.653  35.401  10.631  1.00 97.85       1SG1231
ATOM   1231  CB  PHE   162      20.618  34.470  11.286  1.00 97.85       1SG1232
ATOM   1232  CG  PHE   162      20.225  33.482  10.242  1.00 97.85       1SG1233
ATOM   1233  CD1 PHE   162      20.985  32.356  10.020  1.00 97.85       1SG1234
ATOM   1234  CD2 PHE   162      19.100  33.686   9.477  1.00 97.85       1SG1235
ATOM   1235  CE1 PHE   162      20.622  31.448   9.054  1.00 97.85       1SG1236
ATOM   1236  CE2 PHE   162      18.732  32.780   8.509  1.00 97.85       1SG1237
ATOM   1237  CZ  PHE   162      19.496  31.658   8.296  1.00 97.85       1SG1238
ATOM   1238  C   PHE   162      21.916  36.544  11.551  1.00 97.85       1SG1239
ATOM   1239  O   PHE   162      21.349  37.626  11.416  1.00 97.85       1SG1240
ATOM   1240  N   LEU   163      22.832  36.319  12.498  1.00124.90       1SG1241
ATOM   1241  CA  LEU   163      23.227  37.261  13.495  1.00124.90       1SG1242
ATOM   1242  CB  LEU   163      24.382  36.635  14.273  1.00124.90       1SG1243
ATOM   1243  CG  LEU   163      23.933  35.747  15.448  1.00124.90       1SG1244
ATOM   1244  CD2 LEU   163      25.120  34.898  15.921  1.00124.90       1SG1245
ATOM   1245  CD1 LEU   163      22.707  34.892  15.126  1.00124.90       1SG1246
ATOM   1246  C   LEU   163      23.683  38.509  12.808  1.00124.90       1SG1247
ATOM   1247  O   LEU   163      23.335  39.613  13.227  1.00124.90       1SG1248
ATOM   1248  N   THR   164      24.452  38.373  11.715  1.00 39.53       1SG1249
ATOM   1249  CA  THR   164      24.908  39.532  11.007  1.00 39.53       1SG1250
ATOM   1250  CB  THR   164      25.684  39.204   9.763  1.00 39.53       1SG1251
ATOM   1251  OG1 THR   164      26.807  38.391  10.060  1.00 39.53       1SG1252
ATOM   1252  CG2 THR   164      26.134  40.528   9.118  1.00 39.53       1SG1253
ATOM   1253  C   THR   164      23.706  40.265  10.509  1.00 39.53       1SG1254
ATOM   1254  O   THR   164      23.616  41.486  10.621  1.00 39.53       1SG1255
ATOM   1255  N   ASP   165      22.739  39.519   9.944  1.00 76.78       1SG1256
ATOM   1256  CA  ASP   165      21.594  40.134   9.339  1.00 76.78       1SG1257
ATOM   1257  CB  ASP   165      20.643  39.110   8.690  1.00 76.78       1SG1258
ATOM   1258  CG  ASP   165      19.533  39.853   7.953  1.00 76.78       1SG1259
ATOM   1259  OD1 ASP   165      19.552  41.112   7.930  1.00 76.78       1SG1260
ATOM   1260  OD2 ASP   165      18.641  39.157   7.397  1.00 76.78       1SG1261
ATOM   1261  C   ASP   165      20.805  40.895  10.357  1.00 76.78       1SG1262
ATOM   1262  O   ASP   165      20.457  42.053  10.131  1.00 76.78       1SG1263
ATOM   1263  N   LEU   166      20.508  40.280  11.517  1.00 74.83       1SG1264
ATOM   1264  CA  LEU   166      19.701  40.972  12.478  1.00 74.83       1SG1265
ATOM   1265  CB  LEU   166      19.361  40.132  13.725  1.00 74.83       1SG1266
ATOM   1266  CG  LEU   166      18.330  39.012  13.478  1.00 74.83       1SG1267
ATOM   1267  CD2 LEU   166      17.847  38.390  14.796  1.00 74.83       1SG1268
ATOM   1268  CD1 LEU   166      18.853  37.961  12.493  1.00 74.83       1SG1269
ATOM   1269  C   LEU   166      20.429  42.185  12.947  1.00 74.83       1SG1270
ATOM   1270  O   LEU   166      19.849  43.266  13.044  1.00 74.83       1SG1271
ATOM   1271  N   SER   167      21.737  42.042  13.228  1.00 30.60       1SG1272
ATOM   1272  CA  SER   167      22.502  43.131  13.759  1.00 30.60       1SG1273
ATOM   1273  CB  SER   167      23.948  42.729  14.090  1.00 30.60       1SG1274
ATOM   1274  OG  SER   167      24.590  42.244  12.922  1.00 30.60       1SG1275
ATOM   1275  C   SER   167      22.537  44.256  12.776  1.00 30.60       1SG1276
ATOM   1276  O   SER   167      22.459  45.421  13.165  1.00 30.60       1SG1277
ATOM   1277  N   GLU   168      22.648  43.950  11.471  1.00 23.61       1SG1278
ATOM   1278  CA  GLU   168      22.697  45.020  10.519  1.00 23.61       1SG1279
ATOM   1279  CB  GLU   168      22.860  44.537   9.066  1.00 23.61       1SG1280
ATOM   1280  CG  GLU   168      24.222  43.896   8.790  1.00 23.61       1SG1281
ATOM   1281  CD  GLU   168      24.272  43.489   7.323  1.00 23.61       1SG1282
ATOM   1282  OE1 GLU   168      23.581  42.506   6.946  1.00 23.61       1SG1283
ATOM   1283  OE2 GLU   168      25.005  44.168   6.555  1.00 23.61       1SG1284
ATOM   1284  C   GLU   168      21.400  45.749  10.614  1.00 23.61       1SG1285
ATOM   1285  O   GLU   168      21.359  46.979  10.579  1.00 23.61       1SG1286
ATOM   1286  N   SER   169      20.294  44.995  10.748  1.00 49.49       1SG1287
ATOM   1287  CA  SER   169      19.009  45.612  10.858  1.00 49.49       1SG1288
ATOM   1288  CB  SER   169      17.847  44.615  10.728  1.00 49.49       1SG1289
ATOM   1289  OG  SER   169      17.824  44.057   9.423  1.00 49.49       1SG1290
ATOM   1290  C   SER   169      18.930  46.242  12.245  1.00 49.49       1SG1291
ATOM   1291  O   SER   169      18.059  45.808  13.046  1.00 49.49       1SG1292
ATOM   1292  OXT SER   169      19.738  47.168  12.523  1.00 49.49       1SG1293
TER
END
