
#######################################################
#                                                     #
#                        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   15 (  124),  selected   15 , name T0386TS389_3-D2
# Molecule2: number of CA atoms   81 (  636),  selected   15 , name T0386_D2.pdb
# PARAMETERS: T0386TS389_3-D2.T0386_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:    15       220 - 237         1.86     1.86
  LCS_AVERAGE:     18.52

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    15       220 - 237         1.86     1.86
  LCS_AVERAGE:     18.52

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    11       224 - 234         0.53     2.04
  LCS_AVERAGE:     10.70

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:   81
LCS_GDT     P     220     P     220      0   15   15     0    0    0    0    3    3   13   14   15   15   15   15   15   15   15   15   15   15   15   15 
LCS_GDT     R     224     R     224     11   15   15     8   12   12   12   13   14   14   14   15   15   15   15   15   15   15   15   15   15   15   15 
LCS_GDT     L     225     L     225     11   15   15     8   12   12   12   13   14   14   14   15   15   15   15   15   15   15   15   15   15   15   15 
LCS_GDT     L     226     L     226     11   15   15     8   12   12   12   13   14   14   14   15   15   15   15   15   15   15   15   15   15   15   15 
LCS_GDT     K     227     K     227     11   15   15     8   12   12   12   13   14   14   14   15   15   15   15   15   15   15   15   15   15   15   15 
LCS_GDT     E     228     E     228     11   15   15     8   12   12   12   13   14   14   14   15   15   15   15   15   15   15   15   15   15   15   15 
LCS_GDT     F     229     F     229     11   15   15     8   12   12   12   13   14   14   14   15   15   15   15   15   15   15   15   15   15   15   15 
LCS_GDT     M     230     M     230     11   15   15     8   12   12   12   13   14   14   14   15   15   15   15   15   15   15   15   15   15   15   15 
LCS_GDT     H     231     H     231     11   15   15     8   12   12   12   13   14   14   14   15   15   15   15   15   15   15   15   15   15   15   15 
LCS_GDT     T     232     T     232     11   15   15     6   12   12   12   13   14   14   14   15   15   15   15   15   15   15   15   15   15   15   15 
LCS_GDT     M     233     M     233     11   15   15     4   12   12   12   13   14   14   14   15   15   15   15   15   15   15   15   15   15   15   15 
LCS_GDT     K     234     K     234     11   15   15     3   12   12   12   13   14   14   14   15   15   15   15   15   15   15   15   15   15   15   15 
LCS_GDT     N     235     N     235      3   15   15     3    3    4    7   13   14   14   14   15   15   15   15   15   15   15   15   15   15   15   15 
LCS_GDT     T     236     T     236      3   15   15     3   12   12   12   13   14   14   14   15   15   15   15   15   15   15   15   15   15   15   15 
LCS_GDT     G     237     G     237      3   15   15     3    3    4    7   13   14   14   14   15   15   15   15   15   15   15   15   15   15   15   15 
LCS_AVERAGE  LCS_A:  15.91  (  10.70   18.52   18.52 )

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     12     12     12     13     14     14     14     15     15     15     15     15     15     15     15     15     15     15     15 
GDT PERCENT_CA   9.88  14.81  14.81  14.81  16.05  17.28  17.28  17.28  18.52  18.52  18.52  18.52  18.52  18.52  18.52  18.52  18.52  18.52  18.52  18.52
GDT RMS_LOCAL    0.15   0.59   0.59   0.59   1.09   1.39   1.39   1.39   1.86   1.86   1.86   1.86   1.86   1.86   1.86   1.86   1.86   1.86   1.86   1.86
GDT RMS_ALL_CA   2.15   1.98   1.98   1.98   1.92   1.91   1.91   1.91   1.86   1.86   1.86   1.86   1.86   1.86   1.86   1.86   1.86   1.86   1.86   1.86

#      Molecule1      Molecule2       DISTANCE
LGA    P     220      P     220          5.259
LGA    R     224      R     224          0.727
LGA    L     225      L     225          1.253
LGA    L     226      L     226          0.525
LGA    K     227      K     227          0.713
LGA    E     228      E     228          0.971
LGA    F     229      F     229          0.788
LGA    M     230      M     230          0.618
LGA    H     231      H     231          1.137
LGA    T     232      T     232          0.166
LGA    M     233      M     233          0.940
LGA    K     234      K     234          1.368
LGA    N     235      N     235          3.127
LGA    T     236      T     236          0.496
LGA    G     237      G     237          2.871

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   15   81    4.0     14    1.39    16.358    17.316     0.938

LGA_LOCAL      RMSD =  1.393  Number of atoms =   14  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  1.912  Number of atoms =   15 
Std_ALL_ATOMS  RMSD =  1.863  (standard rmsd on all 15 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.670040 * X  +   0.437653 * Y  +   0.599589 * Z  +  20.661371
  Y_new =  -0.678672 * X  +   0.033917 * Y  +   0.733658 * Z  +  69.738228
  Z_new =   0.300752 * X  +  -0.898504 * Y  +   0.319749 * Z  +  76.767136 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.228904    1.912689  [ DEG:   -70.4110    109.5890 ]
  Theta =  -0.305481   -2.836112  [ DEG:   -17.5028   -162.4973 ]
  Phi   =  -0.791798    2.349794  [ DEG:   -45.3667    134.6333 ]
 
# 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: T0386TS389_3-D2                               
REMARK     2: T0386_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0386TS389_3-D2.T0386_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   15   81   4.0   14   1.39  17.316     1.86
REMARK  ---------------------------------------------------------- 
MOLECULE T0386TS389_3-D2
PFRMAT TS
TARGET T0386
MODEL  3
PARENT N/A
ATOM   1175  N   PRO   220       6.218  60.510  76.883  1.00  0.00
ATOM   1176  CA  PRO   220       6.053  61.462  75.765  1.00  0.00
ATOM   1177  CB  PRO   220       4.678  61.121  75.187  1.00  0.00
ATOM   1178  CG  PRO   220       4.503  59.667  75.476  1.00  0.00
ATOM   1179  CD  PRO   220       5.071  59.443  76.848  1.00  0.00
ATOM   1180  O   PRO   220       6.880  63.745  75.772  1.00  0.00
ATOM   1181  C   PRO   220       6.109  62.915  76.281  1.00  0.00
ATOM   1182  N   ARG   224       5.302  63.200  77.305  1.00  0.00
ATOM   1183  CA  ARG   224       5.279  64.496  77.975  1.00  0.00
ATOM   1184  CB  ARG   224       4.336  64.459  79.180  1.00  0.00
ATOM   1185  CG  ARG   224       2.863  64.388  78.815  1.00  0.00
ATOM   1186  CD  ARG   224       1.990  64.281  80.054  1.00  0.00
ATOM   1187  NE  ARG   224       0.572  64.181  79.718  1.00  0.00
ATOM   1188  CZ  ARG   224      -0.396  64.004  80.612  1.00  0.00
ATOM   1189  NH1 ARG   224      -1.658  63.927  80.213  1.00  0.00
ATOM   1190  NH2 ARG   224      -0.100  63.906  81.900  1.00  0.00
ATOM   1191  O   ARG   224       7.095  66.037  78.323  1.00  0.00
ATOM   1192  C   ARG   224       6.674  64.895  78.478  1.00  0.00
ATOM   1193  N   LEU   225       7.381  63.931  79.058  1.00  0.00
ATOM   1194  CA  LEU   225       8.692  64.168  79.626  1.00  0.00
ATOM   1195  CB  LEU   225       9.172  62.938  80.399  1.00  0.00
ATOM   1196  CG  LEU   225       8.422  62.613  81.690  1.00  0.00
ATOM   1197  CD1 LEU   225       8.878  61.279  82.257  1.00  0.00
ATOM   1198  CD2 LEU   225       8.671  63.686  82.740  1.00  0.00
ATOM   1199  O   LEU   225      10.538  65.386  78.694  1.00  0.00
ATOM   1200  C   LEU   225       9.725  64.476  78.541  1.00  0.00
ATOM   1201  N   LEU   226       9.671  63.737  77.439  1.00  0.00
ATOM   1202  CA  LEU   226      10.579  63.954  76.318  1.00  0.00
ATOM   1203  CB  LEU   226      10.394  62.869  75.257  1.00  0.00
ATOM   1204  CG  LEU   226      11.274  62.979  74.011  1.00  0.00
ATOM   1205  CD1 LEU   226      12.745  62.896  74.385  1.00  0.00
ATOM   1206  CD2 LEU   226      10.966  61.854  73.034  1.00  0.00
ATOM   1207  O   LEU   226      11.275  66.050  75.380  1.00  0.00
ATOM   1208  C   LEU   226      10.327  65.318  75.655  1.00  0.00
ATOM   1209  N   LYS   227       9.061  65.655  75.420  1.00  0.00
ATOM   1210  CA  LYS   227       8.700  66.990  74.944  1.00  0.00
ATOM   1211  CB  LYS   227       7.179  67.151  74.898  1.00  0.00
ATOM   1212  CG  LYS   227       6.503  66.349  73.796  1.00  0.00
ATOM   1213  CD  LYS   227       5.001  66.573  73.793  1.00  0.00
ATOM   1214  CE  LYS   227       4.325  65.768  72.694  1.00  0.00
ATOM   1215  NZ  LYS   227       2.846  65.940  72.711  1.00  0.00
ATOM   1216  O   LYS   227       9.773  69.096  75.376  1.00  0.00
ATOM   1217  C   LYS   227       9.255  68.083  75.852  1.00  0.00
ATOM   1218  N   GLU   228       9.164  67.854  77.159  1.00  0.00
ATOM   1219  CA  GLU   228       9.702  68.752  78.147  1.00  0.00
ATOM   1220  CB  GLU   228       9.425  68.228  79.556  1.00  0.00
ATOM   1221  CG  GLU   228       7.965  68.309  79.972  1.00  0.00
ATOM   1222  CD  GLU   228       7.706  67.657  81.316  1.00  0.00
ATOM   1223  OE1 GLU   228       8.650  67.071  81.885  1.00  0.00
ATOM   1224  OE2 GLU   228       6.556  67.731  81.802  1.00  0.00
ATOM   1225  O   GLU   228      11.706  70.071  78.012  1.00  0.00
ATOM   1226  C   GLU   228      11.204  68.933  78.025  1.00  0.00
ATOM   1227  N   PHE   229      11.931  67.826  77.930  1.00  0.00
ATOM   1228  CA  PHE   229      13.385  67.896  77.895  1.00  0.00
ATOM   1229  CB  PHE   229      13.993  66.502  78.066  1.00  0.00
ATOM   1230  CG  PHE   229      13.932  65.983  79.475  1.00  0.00
ATOM   1231  CD1 PHE   229      12.987  65.040  79.840  1.00  0.00
ATOM   1232  CD2 PHE   229      14.822  66.435  80.435  1.00  0.00
ATOM   1233  CE1 PHE   229      12.930  64.561  81.135  1.00  0.00
ATOM   1234  CE2 PHE   229      14.764  65.957  81.731  1.00  0.00
ATOM   1235  CZ  PHE   229      13.824  65.025  82.081  1.00  0.00
ATOM   1236  O   PHE   229      14.864  69.179  76.554  1.00  0.00
ATOM   1237  C   PHE   229      13.878  68.466  76.577  1.00  0.00
ATOM   1238  N   MET   230      13.178  68.171  75.482  1.00  0.00
ATOM   1239  CA  MET   230      13.500  68.749  74.189  1.00  0.00
ATOM   1240  CB  MET   230      12.523  68.253  73.121  1.00  0.00
ATOM   1241  CG  MET   230      12.802  68.791  71.728  1.00  0.00
ATOM   1242  SD  MET   230      11.618  68.195  70.503  1.00  0.00
ATOM   1243  CE  MET   230      10.164  69.141  70.949  1.00  0.00
ATOM   1244  O   MET   230      14.244  70.984  73.732  1.00  0.00
ATOM   1245  C   MET   230      13.410  70.278  74.280  1.00  0.00
ATOM   1246  N   HIS   231      12.409  70.789  74.985  1.00  0.00
ATOM   1247  CA  HIS   231      12.242  72.225  75.112  1.00  0.00
ATOM   1248  CB  HIS   231      10.888  72.553  75.748  1.00  0.00
ATOM   1249  CG  HIS   231      10.613  74.019  75.856  1.00  0.00
ATOM   1250  CD2 HIS   231      10.076  75.043  74.972  1.00  0.00
ATOM   1251  ND1 HIS   231      10.866  74.742  77.003  1.00  0.00
ATOM   1252  CE1 HIS   231      10.516  76.025  76.797  1.00  0.00
ATOM   1253  NE2 HIS   231      10.041  76.214  75.582  1.00  0.00
ATOM   1254  O   HIS   231      13.892  73.875  75.685  1.00  0.00
ATOM   1255  C   HIS   231      13.345  72.806  75.989  1.00  0.00
ATOM   1256  N   THR   232      13.687  72.088  77.062  1.00  0.00
ATOM   1257  CA  THR   232      14.767  72.496  77.933  1.00  0.00
ATOM   1258  CB  THR   232      15.056  71.434  79.010  1.00  0.00
ATOM   1259  CG2 THR   232      16.208  71.876  79.899  1.00  0.00
ATOM   1260  OG1 THR   232      13.891  71.243  79.822  1.00  0.00
ATOM   1261  O   THR   232      16.740  73.715  77.289  1.00  0.00
ATOM   1262  C   THR   232      16.050  72.709  77.115  1.00  0.00
ATOM   1263  N   MET   233      16.358  71.766  76.224  1.00  0.00
ATOM   1264  CA  MET   233      17.540  71.872  75.357  1.00  0.00
ATOM   1265  CB  MET   233      17.773  70.558  74.609  1.00  0.00
ATOM   1266  CG  MET   233      19.066  70.522  73.808  1.00  0.00
ATOM   1267  SD  MET   233      20.530  70.694  74.846  1.00  0.00
ATOM   1268  CE  MET   233      20.561  69.097  75.655  1.00  0.00
ATOM   1269  O   MET   233      18.371  73.617  73.924  1.00  0.00
ATOM   1270  C   MET   233      17.388  72.978  74.318  1.00  0.00
ATOM   1271  N   LYS   234      16.147  73.210  73.901  1.00  0.00
ATOM   1272  CA  LYS   234      15.853  74.299  73.006  1.00  0.00
ATOM   1273  CB  LYS   234      14.374  74.287  72.616  1.00  0.00
ATOM   1274  CG  LYS   234      13.980  73.136  71.705  1.00  0.00
ATOM   1275  CD  LYS   234      12.499  73.182  71.365  1.00  0.00
ATOM   1276  CE  LYS   234      12.105  72.027  70.459  1.00  0.00
ATOM   1277  NZ  LYS   234      10.650  72.043  70.141  1.00  0.00
ATOM   1278  O   LYS   234      16.528  76.593  72.915  1.00  0.00
ATOM   1279  C   LYS   234      16.155  75.658  73.632  1.00  0.00
ATOM   1280  N   ASN   235      15.993  75.762  74.961  1.00  0.00
ATOM   1281  CA  ASN   235      16.234  77.003  75.690  1.00  0.00
ATOM   1282  CB  ASN   235      15.904  76.826  77.173  1.00  0.00
ATOM   1283  CG  ASN   235      14.411  76.824  77.440  1.00  0.00
ATOM   1284  ND2 ASN   235      13.902  75.700  77.932  1.00  0.00
ATOM   1285  OD1 ASN   235      13.726  77.820  77.206  1.00  0.00
ATOM   1286  O   ASN   235      18.037  78.580  75.640  1.00  0.00
ATOM   1287  C   ASN   235      17.706  77.406  75.557  1.00  0.00
ATOM   1288  N   THR   236      18.570  76.403  75.385  1.00  0.00
ATOM   1289  CA  THR   236      19.999  76.594  75.260  1.00  0.00
ATOM   1290  CB  THR   236      20.779  75.387  75.815  1.00  0.00
ATOM   1291  CG2 THR   236      20.446  75.168  77.283  1.00  0.00
ATOM   1292  OG1 THR   236      20.429  74.208  75.079  1.00  0.00
ATOM   1293  O   THR   236      21.636  76.848  73.522  1.00  0.00
ATOM   1294  C   THR   236      20.437  76.775  73.800  1.00  0.00
ATOM   1295  N   GLY   237      19.474  76.838  72.870  1.00  0.00
ATOM   1296  CA  GLY   237      19.768  77.056  71.450  1.00  0.00
ATOM   1297  O   GLY   237      20.307  75.914  69.410  1.00  0.00
ATOM   1298  C   GLY   237      19.848  75.825  70.552  1.00  0.00
TER
END
