
#######################################################
#                                                     #
#                        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_1_1-D2
# Molecule2: number of CA atoms  335 ( 2465),  selected   10 , name T0318_D2.pdb
# PARAMETERS: T0318TS021_1_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         4.28     4.28
  LCS_AVERAGE:      2.99

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5       159 - 163         1.71     5.81
  LONGEST_CONTINUOUS_SEGMENT:     5       160 - 164         1.57     6.94
  LONGEST_CONTINUOUS_SEGMENT:     5       161 - 165         1.83     8.44
  LCS_AVERAGE:      1.40

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4       156 - 159         0.59     5.32
  LONGEST_CONTINUOUS_SEGMENT:     4       159 - 162         0.80     5.95
  LONGEST_CONTINUOUS_SEGMENT:     4       161 - 164         0.53     7.65
  LCS_AVERAGE:      1.16

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      4    4   10     3    4    5    5    5    6    7    7    7    8    9    9   10   10   10   10   10   10   10   10 
LCS_GDT     N     157     N     157      4    4   10     3    4    5    5    5    6    7    7    7    8    9    9   10   10   10   10   10   10   10   10 
LCS_GDT     E     158     E     158      4    4   10     3    4    5    5    5    6    7    7    7    8    9    9   10   10   10   10   10   10   10   10 
LCS_GDT     D     159     D     159      4    5   10     3    4    5    5    5    6    7    7    7    8    9    9   10   10   10   10   10   10   10   10 
LCS_GDT     A     160     A     160      4    5   10     3    3    4    5    5    5    7    7    7    7    9    9   10   10   10   10   10   10   10   10 
LCS_GDT     V     161     V     161      4    5   10     3    4    4    5    5    5    7    7    7    8    9    9   10   10   10   10   10   10   10   10 
LCS_GDT     F     162     F     162      4    5   10     3    4    4    5    5    6    7    7    7    8    9    9   10   10   10   10   10   10   10   10 
LCS_GDT     L     163     L     163      4    5   10     3    4    5    5    5    6    6    7    7    8    9    9   10   10   10   10   10   10   10   10 
LCS_GDT     T     164     T     164      4    5   10     3    4    4    4    5    5    6    7    7    8    9    9   10   10   10   10   10   10   10   10 
LCS_GDT     D     165     D     165      3    5   10     0    3    3    3    3    5    6    6    7    7    7    8   10   10   10   10   10   10   10   10 
LCS_AVERAGE  LCS_A:   1.85  (   1.16    1.40    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      3      4      5      5      5      6      7      7      7      8      9      9     10     10     10     10     10     10     10     10 
GDT PERCENT_CA   0.90   1.19   1.49   1.49   1.49   1.79   2.09   2.09   2.09   2.39   2.69   2.69   2.99   2.99   2.99   2.99   2.99   2.99   2.99   2.99
GDT RMS_LOCAL    0.06   0.53   0.96   0.96   0.96   1.73   2.80   2.51   2.51   3.18   3.59   3.59   4.28   4.28   4.28   4.28   4.28   4.28   4.28   4.28
GDT RMS_ALL_CA   5.44   7.65   4.96   4.96   4.96   4.95   5.98   4.47   4.47   4.52   4.61   4.61   4.28   4.28   4.28   4.28   4.28   4.28   4.28   4.28

#      Molecule1      Molecule2       DISTANCE
LGA    T     156      T     156          1.819
LGA    N     157      N     157          2.724
LGA    E     158      E     158          3.561
LGA    D     159      D     159          1.521
LGA    A     160      A     160          6.656
LGA    V     161      V     161          6.289
LGA    F     162      F     162          3.190
LGA    L     163      L     163          0.286
LGA    T     164      T     164          3.521
LGA    D     165      D     165          7.503

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   10  335    4.0      7    2.51     1.940     1.871     0.268

LGA_LOCAL      RMSD =  2.509  Number of atoms =    7  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  4.342  Number of atoms =   10 
Std_ALL_ATOMS  RMSD =  4.278  (standard rmsd on all 10 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.639616 * X  +   0.116714 * Y  +  -0.759782 * Z  +  29.340660
  Y_new =   0.279295 * X  +   0.885571 * Y  +   0.371159 * Z  +   8.734513
  Z_new =   0.716160 * X  +  -0.449603 * Y  +   0.533828 * Z  +  10.516577 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.699963    2.441630  [ DEG:   -40.1049    139.8951 ]
  Theta =  -0.798285   -2.343308  [ DEG:   -45.7383   -134.2617 ]
  Phi   =   0.411706   -2.729887  [ DEG:    23.5890   -156.4110 ]
 
# 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_1_1-D2                             
REMARK     2: T0318_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0318TS021_1_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    7   2.51   1.871     4.28
REMARK  ---------------------------------------------------------- 
MOLECULE T0318TS021_1_1-D2
REMARK PARENT number 1
PFRMAT TS
TARGET T0318
PARENT N/A
ATOM   1209  N   THR   156      26.153  26.606  12.466  1.00455.85       1SG1210
ATOM   1210  CA  THR   156      27.489  26.881  12.890  1.00455.85       1SG1211
ATOM   1211  CB  THR   156      28.512  26.760  11.803  1.00455.85       1SG1212
ATOM   1212  OG1 THR   156      28.214  27.674  10.758  1.00455.85       1SG1213
ATOM   1213  CG2 THR   156      28.515  25.311  11.283  1.00455.85       1SG1214
ATOM   1214  C   THR   156      27.508  28.284  13.392  1.00455.85       1SG1215
ATOM   1215  O   THR   156      26.479  28.835  13.777  1.00455.85       1SG1216
ATOM   1216  N   ASN   157      28.708  28.885  13.423  1.00424.17       1SG1217
ATOM   1217  CA  ASN   157      28.857  30.206  13.953  1.00424.17       1SG1218
ATOM   1218  CB  ASN   157      30.313  30.701  13.961  1.00424.17       1SG1219
ATOM   1219  CG  ASN   157      30.320  32.103  14.564  1.00424.17       1SG1220
ATOM   1220  OD1 ASN   157      30.875  33.032  13.980  1.00424.17       1SG1221
ATOM   1221  ND2 ASN   157      29.694  32.262  15.762  1.00424.17       1SG1222
ATOM   1222  C   ASN   157      28.067  31.161  13.132  1.00424.17       1SG1223
ATOM   1223  O   ASN   157      27.442  32.071  13.671  1.00424.17       1SG1224
ATOM   1224  N   GLU   158      28.063  30.989  11.801  1.00302.10       1SG1225
ATOM   1225  CA  GLU   158      27.332  31.932  11.009  1.00302.10       1SG1226
ATOM   1226  CB  GLU   158      27.595  31.761   9.506  1.00302.10       1SG1227
ATOM   1227  CG  GLU   158      29.079  31.694   9.127  1.00302.10       1SG1228
ATOM   1228  CD  GLU   158      29.806  32.919   9.663  1.00302.10       1SG1229
ATOM   1229  OE1 GLU   158      29.138  33.833  10.213  1.00302.10       1SG1230
ATOM   1230  OE2 GLU   158      31.057  32.948   9.523  1.00302.10       1SG1231
ATOM   1231  C   GLU   158      25.885  31.603  11.219  1.00302.10       1SG1232
ATOM   1232  O   GLU   158      25.429  30.559  10.762  1.00302.10       1SG1233
ATOM   1233  N   ASP   159      25.124  32.480  11.912  1.00219.23       1SG1234
ATOM   1234  CA  ASP   159      23.741  32.176  12.163  1.00219.23       1SG1235
ATOM   1235  CB  ASP   159      23.126  32.955  13.343  1.00219.23       1SG1236
ATOM   1236  CG  ASP   159      21.755  32.421  13.732  1.00219.23       1SG1237
ATOM   1237  OD1 ASP   159      21.004  31.933  12.847  1.00219.23       1SG1238
ATOM   1238  OD2 ASP   159      21.441  32.512  14.948  1.00219.23       1SG1239
ATOM   1239  C   ASP   159      22.977  32.478  10.921  1.00219.23       1SG1240
ATOM   1240  O   ASP   159      23.102  33.551  10.333  1.00219.23       1SG1241
ATOM   1241  N   ALA   160      22.125  31.523  10.520  1.00129.94       1SG1242
ATOM   1242  CA  ALA   160      21.363  31.659   9.324  1.00129.94       1SG1243
ATOM   1243  CB  ALA   160      20.415  30.478   9.080  1.00129.94       1SG1244
ATOM   1244  C   ALA   160      20.521  32.883   9.465  1.00129.94       1SG1245
ATOM   1245  O   ALA   160      20.348  33.617   8.495  1.00129.94       1SG1246
ATOM   1246  N   VAL   161      20.002  33.146  10.682  1.00236.05       1SG1247
ATOM   1247  CA  VAL   161      19.128  34.261  10.935  1.00236.05       1SG1248
ATOM   1248  CB  VAL   161      18.117  33.965  12.002  1.00236.05       1SG1249
ATOM   1249  CG1 VAL   161      18.876  33.869  13.332  1.00236.05       1SG1250
ATOM   1250  CG2 VAL   161      16.990  35.015  11.977  1.00236.05       1SG1251
ATOM   1251  C   VAL   161      19.981  35.402  11.389  1.00236.05       1SG1252
ATOM   1252  O   VAL   161      21.205  35.299  11.365  1.00236.05       1SG1253
ATOM   1253  N   PHE   162      19.347  36.538  11.761  1.00310.55       1SG1254
ATOM   1254  CA  PHE   162      20.059  37.718  12.155  1.00310.55       1SG1255
ATOM   1255  CB  PHE   162      19.145  38.805  12.747  1.00310.55       1SG1256
ATOM   1256  CG  PHE   162      19.972  39.985  13.126  1.00310.55       1SG1257
ATOM   1257  CD1 PHE   162      20.278  40.958  12.206  1.00310.55       1SG1258
ATOM   1258  CD2 PHE   162      20.442  40.120  14.413  1.00310.55       1SG1259
ATOM   1259  CE1 PHE   162      21.038  42.048  12.557  1.00310.55       1SG1260
ATOM   1260  CE2 PHE   162      21.203  41.208  14.770  1.00310.55       1SG1261
ATOM   1261  CZ  PHE   162      21.507  42.175  13.842  1.00310.55       1SG1262
ATOM   1262  C   PHE   162      21.058  37.327  13.187  1.00310.55       1SG1263
ATOM   1263  O   PHE   162      20.728  36.757  14.226  1.00310.55       1SG1264
ATOM   1264  N   LEU   163      22.323  37.623  12.852  1.00466.95       1SG1265
ATOM   1265  CA  LEU   163      23.525  37.356  13.578  1.00466.95       1SG1266
ATOM   1266  CB  LEU   163      23.360  36.691  14.956  1.00466.95       1SG1267
ATOM   1267  CG  LEU   163      24.710  36.418  15.651  1.00466.95       1SG1268
ATOM   1268  CD1 LEU   163      25.497  37.716  15.891  1.00466.95       1SG1269
ATOM   1269  CD2 LEU   163      24.520  35.594  16.934  1.00466.95       1SG1270
ATOM   1270  C   LEU   163      24.290  36.427  12.710  1.00466.95       1SG1271
ATOM   1271  O   LEU   163      24.508  35.271  13.064  1.00466.95       1SG1272
ATOM   1272  N   THR   164      24.743  36.943  11.556  1.00279.18       1SG1273
ATOM   1273  CA  THR   164      25.444  36.158  10.589  1.00279.18       1SG1274
ATOM   1274  CB  THR   164      24.692  35.989   9.301  1.00279.18       1SG1275
ATOM   1275  OG1 THR   164      25.334  35.036   8.468  1.00279.18       1SG1276
ATOM   1276  CG2 THR   164      24.640  37.352   8.588  1.00279.18       1SG1277
ATOM   1277  C   THR   164      26.683  36.909  10.262  1.00279.18       1SG1278
ATOM   1278  O   THR   164      26.931  37.981  10.814  1.00279.18       1SG1279
ATOM   1279  N   ASP   165      27.516  36.351   9.370  1.00 94.17       1SG1280
ATOM   1280  CA  ASP   165      28.712  37.057   9.047  1.00 94.17       1SG1281
ATOM   1281  CB  ASP   165      29.745  36.225   8.272  1.00 94.17       1SG1282
ATOM   1282  CG  ASP   165      31.064  36.977   8.357  1.00 94.17       1SG1283
ATOM   1283  OD1 ASP   165      31.079  38.079   8.968  1.00 94.17       1SG1284
ATOM   1284  OD2 ASP   165      32.078  36.458   7.817  1.00 94.17       1SG1285
ATOM   1285  C   ASP   165      28.308  38.243   8.177  1.00 94.17       1SG1286
ATOM   1286  O   ASP   165      28.257  38.080   6.929  1.00 94.17       1SG1287
ATOM   1287  OXT ASP   165      28.040  39.331   8.755  1.00 94.17       1SG1288
TER
END
