
#######################################################
#                                                     #
#                        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   22 (  107),  selected    7 , name T0291TS261_1_2-D2
# Molecule2: number of CA atoms  181 ( 1450),  selected    7 , name T0291_D2.pdb
# PARAMETERS: T0291TS261_1_2-D2.T0291_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:     7       173 - 195         3.82     3.82
  LCS_AVERAGE:      3.87

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4       173 - 176         1.62    20.31
  LCS_AVERAGE:      1.97

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
# WARNING! The change of the parameter DIST cutoff may give you better result.

  LONGEST_CONTINUOUS_SEGMENT:     3       173 - 175         0.89    20.50
  LONGEST_CONTINUOUS_SEGMENT:     3       174 - 176         0.48    19.58
  LONGEST_CONTINUOUS_SEGMENT:     3       193 - 195         0.01    11.97
  LCS_AVERAGE:      1.66

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:  181
LCS_GDT     L     173     L     173      3    4    7     0    3    3    3    4    4    5    5    6    6    7    7    7    7    7    7    7    7    7    7 
LCS_GDT     G     174     G     174      3    4    7     2    3    3    3    4    4    5    5    6    6    7    7    7    7    7    7    7    7    7    7 
LCS_GDT     R     175     R     175      3    4    7     0    3    3    3    4    4    4    5    6    6    7    7    7    7    7    7    7    7    7    7 
LCS_GDT     V     176     V     176      3    4    7     2    3    3    3    4    4    4    4    5    6    7    7    7    7    7    7    7    7    7    7 
LCS_GDT     P     193     P     193      3    3    7     3    3    3    3    3    4    5    5    6    6    7    7    7    7    7    7    7    7    7    7 
LCS_GDT     I     194     I     194      3    3    7     3    3    3    3    3    4    5    5    6    6    7    7    7    7    7    7    7    7    7    7 
LCS_GDT     R     195     R     195      3    3    7     3    3    3    3    3    4    5    5    6    6    7    7    7    7    7    7    7    7    7    7 
LCS_AVERAGE  LCS_A:   2.50  (   1.66    1.97    3.87 )

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      3      3      3      4      4      5      5      6      6      7      7      7      7      7      7      7      7      7      7 
GDT PERCENT_CA   1.66   1.66   1.66   1.66   2.21   2.21   2.76   2.76   3.31   3.31   3.87   3.87   3.87   3.87   3.87   3.87   3.87   3.87   3.87   3.87
GDT RMS_LOCAL    0.01   0.01   0.01   0.01   1.62   1.62   2.51   2.51   3.09   3.09   3.82   3.82   3.82   3.82   3.82   3.82   3.82   3.82   3.82   3.82
GDT RMS_ALL_CA  11.97  11.97  11.97  11.97  20.31  20.31   6.02   6.02   4.50   4.50   3.82   3.82   3.82   3.82   3.82   3.82   3.82   3.82   3.82   3.82

#      Molecule1      Molecule2       DISTANCE
LGA    L     173      L     173          3.292
LGA    G     174      G     174          2.253
LGA    R     175      R     175          6.718
LGA    V     176      V     176         13.313
LGA    P     193      P     193          1.728
LGA    I     194      I     194          2.813
LGA    R     195      R     195          2.139

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   22  181    4.0      5    2.51     2.486     2.517     0.192

LGA_LOCAL      RMSD =  2.505  Number of atoms =    5  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  6.021  Number of atoms =    7 
Std_ALL_ATOMS  RMSD =  3.821  (standard rmsd on all 7 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.800684 * X  +  -0.568340 * Y  +  -0.189460 * Z  +   0.129601
  Y_new =  -0.535521 * X  +  -0.820760 * Y  +   0.198924 * Z  +  56.109814
  Z_new =  -0.268558 * X  +  -0.057815 * Y  +  -0.961527 * Z  + 109.427246 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -3.081536    0.060056  [ DEG:  -176.5590      3.4410 ]
  Theta =   0.271895    2.869697  [ DEG:    15.5784    164.4216 ]
  Phi   =  -0.589499    2.552094  [ DEG:   -33.7758    146.2242 ]
 
# 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: T0291TS261_1_2-D2                             
REMARK     2: T0291_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0291TS261_1_2-D2.T0291_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   22  181   4.0    5   2.51   2.517     3.82
REMARK  ---------------------------------------------------------- 
MOLECULE T0291TS261_1_2-D2
REMARK PARENT number 2
PFRMAT TS
TARGET T0291
PARENT 1t46_A
ATOM   1328  N   LEU   173      -7.036  22.151  61.933  1.00  3.03
ATOM   1329  CA  LEU   173      -8.010  21.576  60.999  1.00  3.03
ATOM   1330  C   LEU   173      -7.424  21.275  59.615  1.00  3.03
ATOM   1331  O   LEU   173      -7.965  20.451  58.870  1.00  3.03
ATOM   1332  CB  LEU   173      -9.211  22.518  60.833  1.00  3.03
ATOM   1333  N   GLY   174      -6.323  21.943  59.282  1.00  5.08
ATOM   1334  CA  GLY   174      -5.751  21.861  57.943  1.00  5.08
ATOM   1335  C   GLY   174      -4.606  20.856  57.789  1.00  5.08
ATOM   1336  O   GLY   174      -3.883  20.900  56.803  1.00  5.08
ATOM   1337  N   ARG   175      -4.446  19.944  58.743  1.00  3.25
ATOM   1338  CA  ARG   175      -3.545  18.817  58.511  1.00  3.25
ATOM   1339  C   ARG   175      -4.294  17.503  58.422  1.00  3.25
ATOM   1340  O   ARG   175      -5.225  17.264  59.189  1.00  3.25
ATOM   1341  CB  ARG   175      -2.437  18.714  59.556  1.00  3.25
ATOM   1342  N   VAL   176      -3.863  16.670  57.476  1.00  4.40
ATOM   1343  CA  VAL   176      -4.443  15.360  57.220  1.00  4.40
ATOM   1344  C   VAL   176      -3.833  14.337  58.178  1.00  4.40
ATOM   1345  O   VAL   176      -3.019  13.499  57.772  1.00  4.40
ATOM   1346  CB  VAL   176      -4.184  14.961  55.760  1.00  4.40
ATOM   1347  N   LEU   177      -4.233  14.419  59.447  1.00  3.71
ATOM   1348  CA  LEU   177      -3.665  13.581  60.505  1.00  3.71
ATOM   1349  C   LEU   177      -3.980  12.097  60.310  1.00  3.71
ATOM   1350  O   LEU   177      -3.308  11.234  60.874  1.00  3.71
ATOM   1351  CB  LEU   177      -4.103  14.070  61.915  1.00  3.71
ATOM   1352  N   GLU   178      -4.995  11.816  59.499  1.00  5.14
ATOM   1353  CA  GLU   178      -5.364  10.444  59.161  1.00  5.14
ATOM   1354  C   GLU   178      -4.266   9.746  58.356  1.00  5.14
ATOM   1355  O   GLU   178      -3.988   8.565  58.572  1.00  5.14
ATOM   1356  CB  GLU   178      -6.692  10.427  58.401  1.00  5.14
ATOM   1357  N   ASP   179      -3.628  10.488  57.454  1.00  4.57
ATOM   1358  CA  ASP   179      -2.592   9.930  56.586  1.00  4.57
ATOM   1359  C   ASP   179      -1.177  10.420  56.890  1.00  4.57
ATOM   1360  O   ASP   179      -0.256  10.233  56.088  1.00  4.57
ATOM   1361  CB  ASP   179      -2.951  10.165  55.115  1.00  4.57
ATOM   1362  N   ASP   180      -1.013  11.051  58.050  1.00  4.66
ATOM   1363  CA  ASP   180       0.303  11.426  58.546  1.00  4.66
ATOM   1364  C   ASP   180       0.700  10.406  59.604  1.00  4.66
ATOM   1365  O   ASP   180       0.079  10.338  60.668  1.00  4.66
ATOM   1366  CB  ASP   180       0.286  12.845  59.132  1.00  4.66
ATOM   1367  N   PRO   181       1.726   9.615  59.297  1.00  5.45
ATOM   1368  CA  PRO   181       2.173   8.522  60.166  1.00  5.45
ATOM   1369  C   PRO   181       2.814   9.016  61.466  1.00  5.45
ATOM   1370  O   PRO   181       3.060   8.232  62.390  1.00  5.45
ATOM   1371  CB  PRO   181       3.132   7.591  59.416  1.00  5.45
ATOM   1372  N   ALA   183       3.083  10.319  61.527  1.00  5.08
ATOM   1373  CA  ALA   183       3.552  10.952  62.754  1.00  5.08
ATOM   1374  C   ALA   183       2.421  11.133  63.764  1.00  5.08
ATOM   1375  O   ALA   183       2.659  11.473  64.930  1.00  5.08
ATOM   1376  CB  ALA   183       4.233  12.284  62.439  1.00  5.08
ATOM   1377  N   ALA   184       1.190  10.908  63.312  1.00  5.15
ATOM   1378  CA  ALA   184       0.033  10.907  64.193  1.00  5.15
ATOM   1379  C   ALA   184      -0.459   9.479  64.316  1.00  5.15
ATOM   1380  O   ALA   184      -0.788   8.841  63.315  1.00  5.15
ATOM   1381  CB  ALA   184      -1.074  11.821  63.665  1.00  5.15
ATOM   1382  N   TYR   185      -0.488   8.991  65.549  1.00  4.63
ATOM   1383  CA  TYR   185      -0.808   7.595  65.834  1.00  4.63
ATOM   1384  C   TYR   185      -2.095   7.496  66.647  1.00  4.63
ATOM   1385  O   TYR   185      -2.324   8.289  67.561  1.00  4.63
ATOM   1386  CB  TYR   185       0.362   6.911  66.594  1.00  4.63
ATOM   1387  N   THR   186      -2.935   6.514  66.319  1.00  4.53
ATOM   1388  CA  THR   186      -4.137   6.268  67.106  1.00  4.53
ATOM   1389  C   THR   186      -3.756   5.857  68.528  1.00  4.53
ATOM   1390  O   THR   186      -2.960   4.940  68.735  1.00  4.53
ATOM   1391  CB  THR   186      -5.067   5.194  66.468  1.00  4.53
ATOM   1392  N   THR   187      -4.312   6.574  69.495  1.00  5.18
ATOM   1393  CA  THR   187      -4.191   6.239  70.905  1.00  5.18
ATOM   1394  C   THR   187      -5.541   6.562  71.525  1.00  5.18
ATOM   1395  O   THR   187      -5.939   7.731  71.598  1.00  5.18
ATOM   1396  CB  THR   187      -3.064   7.038  71.567  1.00  5.18
ATOM   1397  N   ARG   188      -6.246   5.516  71.948  1.00  4.72
ATOM   1398  CA  ARG   188      -7.634   5.636  72.350  1.00  4.72
ATOM   1399  C   ARG   188      -8.469   6.022  71.146  1.00  4.72
ATOM   1400  O   ARG   188      -8.343   5.420  70.075  1.00  4.72
ATOM   1401  CB  ARG   188      -7.761   6.667  73.484  1.00  4.72
ATOM   1402  N   GLY   189      -9.306   7.040  71.313  1.00  5.82
ATOM   1403  CA  GLY   189     -10.140   7.533  70.222  1.00  5.82
ATOM   1404  C   GLY   189      -9.632   8.869  69.677  1.00  5.82
ATOM   1405  O   GLY   189     -10.401   9.809  69.456  1.00  5.82
ATOM   1406  N   GLY   190      -8.318   8.936  69.466  1.00  5.51
ATOM   1407  CA  GLY   190      -7.660  10.120  68.917  1.00  5.51
ATOM   1408  C   GLY   190      -6.417   9.730  68.128  1.00  5.51
ATOM   1409  O   GLY   190      -5.811   8.688  68.389  1.00  5.51
ATOM   1410  N   LYS   191      -6.055  10.566  67.157  1.00  4.83
ATOM   1411  CA  LYS   191      -4.803  10.422  66.425  1.00  4.83
ATOM   1412  C   LYS   191      -3.848  11.494  66.939  1.00  4.83
ATOM   1413  O   LYS   191      -4.070  12.689  66.734  1.00  4.83
ATOM   1414  CB  LYS   191      -5.026  10.566  64.919  1.00  4.83
ATOM   1415  N   ILE   192      -2.796  11.054  67.621  1.00  7.89
ATOM   1416  CA  ILE   192      -1.947  11.959  68.388  1.00  7.89
ATOM   1417  C   ILE   192      -0.487  11.919  67.955  1.00  7.89
ATOM   1418  O   ILE   192       0.013  10.875  67.532  1.00  7.89
ATOM   1419  CB  ILE   192      -2.065  11.638  69.881  1.00  7.89
ATOM   1420  N   PRO   193       0.201  13.056  68.071  1.00  3.50
ATOM   1421  CA  PRO   193       1.625  13.133  67.718  1.00  3.50
ATOM   1422  C   PRO   193       2.501  12.511  68.810  1.00  3.50
ATOM   1423  O   PRO   193       3.304  13.188  69.444  1.00  3.50
ATOM   1424  CB  PRO   193       1.871  14.643  67.611  1.00  3.50
ATOM   1425  N   ILE   194       2.328  11.210  69.026  1.00  3.76
ATOM   1426  CA  ILE   194       2.893  10.530  70.187  1.00  3.76
ATOM   1427  C   ILE   194       4.406  10.721  70.368  1.00  3.76
ATOM   1428  O   ILE   194       4.862  10.933  71.494  1.00  3.76
ATOM   1429  CB  ILE   194       2.517   9.028  70.178  1.00  3.76
ATOM   1430  N   ARG   195       5.170  10.647  69.277  1.00  4.72
ATOM   1431  CA  ARG   195       6.633  10.771  69.356  1.00  4.72
ATOM   1432  C   ARG   195       7.116  12.154  69.817  1.00  4.72
ATOM   1433  O   ARG   195       8.277  12.308  70.203  1.00  4.72
ATOM   1434  CB  ARG   195       7.303  10.374  68.040  1.00  4.72
TER
END
