
#######################################################
#                                                     #
#                        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   19 (  146),  selected   19 , name T0386TS009_1_3-D1
# Molecule2: number of CA atoms  206 ( 1668),  selected   19 , name T0386_D1.pdb
# PARAMETERS: T0386TS009_1_3-D1.T0386_D1.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:    19       163 - 181         3.23     3.23
  LCS_AVERAGE:      9.22

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     8       167 - 174         1.87     3.83
  LCS_AVERAGE:      3.35

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5       169 - 173         0.98     4.21
  LONGEST_CONTINUOUS_SEGMENT:     5       170 - 174         0.69     3.47
  LCS_AVERAGE:      2.04

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:  206
LCS_GDT     E     163     E     163      3    6   19     3    6    6    8   11   12   13   16   18   18   18   19   19   19   19   19   19   19   19   19 
LCS_GDT     G     164     G     164      3    6   19     3    3    5    7    8   11   13   16   18   18   18   19   19   19   19   19   19   19   19   19 
LCS_GDT     N     165     N     165      4    6   19     3    4    8    8   11   12   13   16   18   18   18   19   19   19   19   19   19   19   19   19 
LCS_GDT     G     166     G     166      4    6   19     3    4    5    5    7   11   13   16   18   18   18   19   19   19   19   19   19   19   19   19 
LCS_GDT     R     167     R     167      4    8   19     3    4    8    8   11   12   13   16   18   18   18   19   19   19   19   19   19   19   19   19 
LCS_GDT     T     168     T     168      4    8   19     3    4    5    5    5    9   10   15   18   18   18   19   19   19   19   19   19   19   19   19 
LCS_GDT     Q     169     Q     169      5    8   19     4    4    7    7   11   12   13   16   18   18   18   19   19   19   19   19   19   19   19   19 
LCS_GDT     R     170     R     170      5    8   19     4    6    8    8   11   12   13   16   18   18   18   19   19   19   19   19   19   19   19   19 
LCS_GDT     L     171     L     171      5    8   19     4    6    8    8   11   12   13   16   18   18   18   19   19   19   19   19   19   19   19   19 
LCS_GDT     F     172     F     172      5    8   19     4    6    8    8   11   12   13   16   18   18   18   19   19   19   19   19   19   19   19   19 
LCS_GDT     F     173     F     173      5    8   19     4    6    8    8   11   12   13   16   18   18   18   19   19   19   19   19   19   19   19   19 
LCS_GDT     E     174     E     174      5    8   19     4    6    8    8   11   12   13   16   18   18   18   19   19   19   19   19   19   19   19   19 
LCS_GDT     N     175     N     175      4    7   19     3    3    7    7   11   12   13   16   18   18   18   19   19   19   19   19   19   19   19   19 
LCS_GDT     L     176     L     176      4    6   19     3    4    4    5    6    6    9   15   18   18   18   19   19   19   19   19   19   19   19   19 
LCS_GDT     A     177     A     177      4    6   19     3    4    4    6    8   11   13   16   18   18   18   19   19   19   19   19   19   19   19   19 
LCS_GDT     K     178     K     178      4    6   19     3    4    4    6    8   12   13   16   18   18   18   19   19   19   19   19   19   19   19   19 
LCS_GDT     A     179     A     179      4    6   19     3    4    5    6   11   12   13   16   18   18   18   19   19   19   19   19   19   19   19   19 
LCS_GDT     A     180     A     180      4    6   19     3    4    8    8   10   12   13   16   18   18   18   19   19   19   19   19   19   19   19   19 
LCS_GDT     G     181     G     181      4    6   19     3    4    4    5    6    6    6    6    6    7   18   19   19   19   19   19   19   19   19   19 
LCS_AVERAGE  LCS_A:   4.87  (   2.04    3.35    9.22 )

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      4      6      8      8     11     12     13     16     18     18     18     19     19     19     19     19     19     19     19     19 
GDT PERCENT_CA   1.94   2.91   3.88   3.88   5.34   5.83   6.31   7.77   8.74   8.74   8.74   9.22   9.22   9.22   9.22   9.22   9.22   9.22   9.22   9.22
GDT RMS_LOCAL    0.23   0.76   1.14   1.14   1.75   1.90   2.05   2.61   2.95   2.95   2.95   3.23   3.23   3.23   3.23   3.23   3.23   3.23   3.23   3.23
GDT RMS_ALL_CA   4.45   3.58   3.60   3.60   3.41   3.41   3.37   3.27   3.27   3.27   3.27   3.23   3.23   3.23   3.23   3.23   3.23   3.23   3.23   3.23

#      Molecule1      Molecule2       DISTANCE
LGA    E     163      E     163          2.498
LGA    G     164      G     164          3.153
LGA    N     165      N     165          1.852
LGA    G     166      G     166          3.995
LGA    R     167      R     167          2.237
LGA    T     168      T     168          4.678
LGA    Q     169      Q     169          2.526
LGA    R     170      R     170          0.704
LGA    L     171      L     171          0.720
LGA    F     172      F     172          0.992
LGA    F     173      F     173          1.048
LGA    E     174      E     174          1.651
LGA    N     175      N     175          3.451
LGA    L     176      L     176          4.731
LGA    A     177      A     177          3.955
LGA    K     178      K     178          3.463
LGA    A     179      A     179          2.717
LGA    A     180      A     180          3.551
LGA    G     181      G     181          6.809

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   19  206    4.0     16    2.61     5.947     5.712     0.590

LGA_LOCAL      RMSD =  2.611  Number of atoms =   16  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  3.268  Number of atoms =   19 
Std_ALL_ATOMS  RMSD =  3.235  (standard rmsd on all 19 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.267920 * X  +   0.920358 * Y  +   0.284886 * Z  + -21.116243
  Y_new =  -0.909809 * X  +   0.144411 * Y  +   0.389092 * Z  + 190.069534
  Z_new =   0.316963 * X  +  -0.363438 * Y  +   0.876041 * Z  + -26.481281 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.393254    2.748339  [ DEG:   -22.5318    157.4682 ]
  Theta =  -0.322525   -2.819067  [ DEG:   -18.4793   -161.5206 ]
  Phi   =  -1.284412    1.857181  [ DEG:   -73.5914    106.4086 ]
 
# 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: T0386TS009_1_3-D1                             
REMARK     2: T0386_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0386TS009_1_3-D1.T0386_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   19  206   4.0   16   2.61   5.712     3.23
REMARK  ---------------------------------------------------------- 
MOLECULE T0386TS009_1_3-D1
REMARK PARENT number 3
PFRMAT TS                                                                       
TARGET T0386                                                                    
PARENT N/A                          
ATOM   1323  N   GLU   163      17.902  64.152  48.296  1.00  0.00             
ATOM   1324  CA  GLU   163      16.902  64.595  49.260  1.00  0.00             
ATOM   1325  C   GLU   163      15.837  63.526  49.481  1.00  0.00             
ATOM   1326  O   GLU   163      15.060  63.597  50.433  1.00  0.00             
ATOM   1327  CB  GLU   163      17.564  64.961  50.590  1.00  0.00             
ATOM   1328  CG  GLU   163      17.668  66.456  50.841  1.00  0.00             
ATOM   1329  CD  GLU   163      18.050  66.782  52.272  1.00  0.00             
ATOM   1330  OE1 GLU   163      19.256  66.730  52.590  1.00  0.00             
ATOM   1331  OE2 GLU   163      17.143  67.087  53.074  1.00  0.00             
ATOM   1332  N   GLY   164      15.808  62.535  48.596  1.00  0.00             
ATOM   1333  CA  GLY   164      14.834  61.467  48.715  1.00  0.00             
ATOM   1334  C   GLY   164      14.562  61.087  50.157  1.00  0.00             
ATOM   1335  O   GLY   164      13.496  61.381  50.697  1.00  0.00             
ATOM   1336  N   ASN   165      15.531  60.429  50.787  1.00  0.00             
ATOM   1337  CA  ASN   165      15.393  60.007  52.175  1.00  0.00             
ATOM   1338  C   ASN   165      15.153  61.201  53.093  1.00  0.00             
ATOM   1339  O   ASN   165      14.433  61.099  54.086  1.00  0.00             
ATOM   1340  CB  ASN   165      14.253  58.996  52.318  1.00  0.00             
ATOM   1341  CG  ASN   165      14.615  57.832  53.219  1.00  0.00             
ATOM   1342  OD1 ASN   165      14.092  56.728  53.064  1.00  0.00             
ATOM   1343  ND2 ASN   165      15.514  58.076  54.166  1.00  0.00             
ATOM   1344  N   GLY   166      15.760  62.334  52.754  1.00  0.00             
ATOM   1345  CA  GLY   166      15.597  63.529  53.559  1.00  0.00             
ATOM   1346  C   GLY   166      14.372  63.468  54.448  1.00  0.00             
ATOM   1347  O   GLY   166      13.256  63.741  54.005  1.00  0.00             
ATOM   1348  N   ARG   167      14.574  63.107  55.712  1.00  0.00             
ATOM   1349  CA  ARG   167      13.477  63.009  56.667  1.00  0.00             
ATOM   1350  C   ARG   167      12.645  61.754  56.425  1.00  0.00             
ATOM   1351  O   ARG   167      11.665  61.502  57.126  1.00  0.00             
ATOM   1352  CB  ARG   167      14.012  63.018  58.099  1.00  0.00             
ATOM   1353  CG  ARG   167      13.454  64.138  58.964  1.00  0.00             
ATOM   1354  CD  ARG   167      13.306  63.698  60.410  1.00  0.00             
ATOM   1355  NE  ARG   167      13.281  64.833  61.328  1.00  0.00             
ATOM   1356  CZ  ARG   167      12.193  65.256  61.964  1.00  0.00             
ATOM   1357  NH1 ARG   167      11.036  64.634  61.782  1.00  0.00             
ATOM   1358  NH2 ARG   167      12.264  66.298  62.780  1.00  0.00             
ATOM   1359  N   THR   168      13.043  60.969  55.429  1.00  0.00             
ATOM   1360  CA  THR   168      12.319  59.711  55.086  1.00  0.00             
ATOM   1361  C   THR   168      10.809  59.920  55.107  1.00  0.00             
ATOM   1362  O   THR   168      10.052  59.015  55.457  1.00  0.00             
ATOM   1363  CB  THR   168      12.735  59.182  53.701  1.00  0.00             
ATOM   1364  OG1 THR   168      13.133  60.277  52.867  1.00  0.00             
ATOM   1365  CG2 THR   168      13.891  58.202  53.829  1.00  0.00             
ATOM   1366  N   GLN   169      10.377  61.120  54.732  1.00  0.00             
ATOM   1367  CA  GLN   169       8.957  61.450  54.708  1.00  0.00             
ATOM   1368  C   GLN   169       8.337  61.319  56.096  1.00  0.00             
ATOM   1369  O   GLN   169       7.193  61.716  56.314  1.00  0.00             
ATOM   1370  CB  GLN   169       8.745  62.866  54.169  1.00  0.00             
ATOM   1371  CG  GLN   169       8.029  62.918  52.829  1.00  0.00             
ATOM   1372  CD  GLN   169       8.403  64.142  52.016  1.00  0.00             
ATOM   1373  OE1 GLN   169       8.055  64.248  50.840  1.00  0.00             
ATOM   1374  NE2 GLN   169       9.114  65.073  52.643  1.00  0.00             
ATOM   1375  N   ARG   170       9.101  60.761  57.029  1.00  0.00             
ATOM   1376  CA  ARG   170       8.627  60.576  58.396  1.00  0.00             
ATOM   1377  C   ARG   170       7.113  60.730  58.481  1.00  0.00             
ATOM   1378  O   ARG   170       6.402  59.788  58.828  1.00  0.00             
ATOM   1379  CB  ARG   170       9.047  59.205  58.928  1.00  0.00             
ATOM   1380  CG  ARG   170      10.364  59.210  59.687  1.00  0.00             
ATOM   1381  CD  ARG   170      10.976  57.819  59.740  1.00  0.00             
ATOM   1382  NE  ARG   170      11.912  57.676  60.852  1.00  0.00             
ATOM   1383  CZ  ARG   170      11.547  57.462  62.112  1.00  0.00             
ATOM   1384  NH1 ARG   170      10.262  57.365  62.423  1.00  0.00             
ATOM   1385  NH2 ARG   170      12.470  57.344  63.058  1.00  0.00             
ATOM   1386  N   LEU   171       6.626  61.925  58.164  1.00  0.00             
ATOM   1387  CA  LEU   171       5.196  62.206  58.204  1.00  0.00             
ATOM   1388  C   LEU   171       4.391  61.048  57.621  1.00  0.00             
ATOM   1389  O   LEU   171       3.216  60.872  57.946  1.00  0.00             
ATOM   1390  CB  LEU   171       4.746  62.491  59.638  1.00  0.00             
ATOM   1391  CG  LEU   171       4.656  63.964  60.040  1.00  0.00             
ATOM   1392  CD1 LEU   171       3.503  64.189  61.006  1.00  0.00             
ATOM   1393  CD2 LEU   171       4.513  64.849  58.811  1.00  0.00             
ATOM   1394  N   PHE   172       5.031  60.263  56.761  1.00  0.00             
ATOM   1395  CA  PHE   172       4.376  59.123  56.132  1.00  0.00             
ATOM   1396  C   PHE   172       3.464  58.398  57.117  1.00  0.00             
ATOM   1397  O   PHE   172       2.242  58.416  56.976  1.00  0.00             
ATOM   1398  CB  PHE   172       3.576  59.572  54.908  1.00  0.00             
ATOM   1399  CG  PHE   172       3.972  58.877  53.636  1.00  0.00             
ATOM   1400  CD1 PHE   172       4.561  57.624  53.669  1.00  0.00             
ATOM   1401  CD2 PHE   172       3.758  59.477  52.408  1.00  0.00             
ATOM   1402  CE1 PHE   172       4.926  56.986  52.500  1.00  0.00             
ATOM   1403  CE2 PHE   172       4.123  58.838  51.238  1.00  0.00             
ATOM   1404  CZ  PHE   172       4.705  57.598  51.281  1.00  0.00             
ATOM   1405  N   PHE   173       4.068  57.760  58.115  1.00  0.00             
ATOM   1406  CA  PHE   173       3.312  57.029  59.125  1.00  0.00             
ATOM   1407  C   PHE   173       2.338  57.946  59.856  1.00  0.00             
ATOM   1408  O   PHE   173       1.264  57.517  60.278  1.00  0.00             
ATOM   1409  CB  PHE   173       2.557  55.861  58.488  1.00  0.00             
ATOM   1410  CG  PHE   173       2.553  54.612  59.324  1.00  0.00             
ATOM   1411  CD1 PHE   173       3.569  54.368  60.233  1.00  0.00             
ATOM   1412  CD2 PHE   173       1.535  53.683  59.203  1.00  0.00             
ATOM   1413  CE1 PHE   173       3.565  53.220  61.002  1.00  0.00             
ATOM   1414  CE2 PHE   173       1.531  52.535  59.972  1.00  0.00             
ATOM   1415  CZ  PHE   173       2.540  52.302  60.869  1.00  0.00             
ATOM   1416  N   GLU   174       2.721  59.210  60.004  1.00  0.00             
ATOM   1417  CA  GLU   174       1.882  60.190  60.685  1.00  0.00             
ATOM   1418  C   GLU   174       0.431  59.725  60.746  1.00  0.00             
ATOM   1419  O   GLU   174      -0.417  60.386  61.346  1.00  0.00             
ATOM   1420  CB  GLU   174       2.408  60.457  62.096  1.00  0.00             
ATOM   1421  CG  GLU   174       2.796  61.905  62.350  1.00  0.00             
ATOM   1422  CD  GLU   174       3.803  62.050  63.475  1.00  0.00             
ATOM   1423  OE1 GLU   174       5.012  61.869  63.217  1.00  0.00             
ATOM   1424  OE2 GLU   174       3.382  62.343  64.614  1.00  0.00             
ATOM   1425  N   ASN   175       0.152  58.587  60.121  1.00  0.00             
ATOM   1426  CA  ASN   175      -1.196  58.033  60.103  1.00  0.00             
ATOM   1427  C   ASN   175      -2.175  58.939  60.842  1.00  0.00             
ATOM   1428  O   ASN   175      -3.184  58.477  61.374  1.00  0.00             
ATOM   1429  CB  ASN   175      -1.667  57.813  58.663  1.00  0.00             
ATOM   1430  CG  ASN   175      -2.200  56.413  58.432  1.00  0.00             
ATOM   1431  OD1 ASN   175      -2.322  55.966  57.292  1.00  0.00             
ATOM   1432  ND2 ASN   175      -2.519  55.715  59.516  1.00  0.00             
ATOM   1433  N   LEU   176      -1.870  60.232  60.870  1.00  0.00             
ATOM   1434  CA  LEU   176      -2.721  61.206  61.543  1.00  0.00             
ATOM   1435  C   LEU   176      -3.002  60.790  62.983  1.00  0.00             
ATOM   1436  O   LEU   176      -4.155  60.592  63.368  1.00  0.00             
ATOM   1437  CB  LEU   176      -2.077  62.593  61.512  1.00  0.00             
ATOM   1438  CG  LEU   176      -2.966  63.744  61.037  1.00  0.00             
ATOM   1439  CD1 LEU   176      -2.988  64.866  62.062  1.00  0.00             
ATOM   1440  CD2 LEU   176      -4.375  63.249  60.747  1.00  0.00             
ATOM   1441  N   ALA   177      -1.943  60.659  63.774  1.00  0.00             
ATOM   1442  CA  ALA   177      -2.074  60.267  65.172  1.00  0.00             
ATOM   1443  C   ALA   177      -3.137  59.188  65.344  1.00  0.00             
ATOM   1444  O   ALA   177      -2.823  57.997  65.395  1.00  0.00             
ATOM   1445  CB  ALA   177      -0.738  59.781  65.713  1.00  0.00             
ATOM   1446  N   LYS   178      -4.393  59.610  65.434  1.00  0.00             
ATOM   1447  CA  LYS   178      -5.505  58.680  65.601  1.00  0.00             
ATOM   1448  C   LYS   178      -6.395  58.657  64.364  1.00  0.00             
ATOM   1449  O   LYS   178      -7.067  59.641  64.052  1.00  0.00             
ATOM   1450  CB  LYS   178      -4.985  57.273  65.902  1.00  0.00             
ATOM   1451  CG  LYS   178      -5.688  56.585  67.060  1.00  0.00             
ATOM   1452  CD  LYS   178      -5.482  55.080  67.017  1.00  0.00             
ATOM   1453  CE  LYS   178      -5.801  54.440  68.358  1.00  0.00             
ATOM   1454  NZ  LYS   178      -6.083  52.984  68.227  1.00  0.00             
ATOM   1455  N   ALA   179      -6.395  57.529  63.662  1.00  0.00             
ATOM   1456  CA  ALA   179      -7.203  57.376  62.458  1.00  0.00             
ATOM   1457  C   ALA   179      -6.445  56.609  61.379  1.00  0.00             
ATOM   1458  O   ALA   179      -6.330  55.385  61.439  1.00  0.00             
ATOM   1459  CB  ALA   179      -8.510  56.669  62.782  1.00  0.00             
ATOM   1460  N   ALA   180      -5.928  57.337  60.395  1.00  0.00             
ATOM   1461  CA  ALA   180      -5.180  56.728  59.302  1.00  0.00             
ATOM   1462  C   ALA   180      -3.695  56.630  59.637  1.00  0.00             
ATOM   1463  O   ALA   180      -2.854  57.212  58.951  1.00  0.00             
ATOM   1464  CB  ALA   180      -5.738  55.350  58.982  1.00  0.00             
ATOM   1465  N   GLY   181      -3.381  55.890  60.695  1.00  0.00             
ATOM   1466  CA  GLY   181      -1.996  55.732  61.100  1.00  0.00             
ATOM   1467  C   GLY   181      -1.226  57.037  61.058  1.00  0.00             
ATOM   1468  O   GLY   181      -0.225  57.157  60.351  1.00  0.00             
TER
END
