
#######################################################
#                                                     #
#                        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   16 (  136),  selected   16 , name T0386TS074_4_2
# Molecule2: number of CA atoms  291 ( 2337),  selected   16 , name T0386.pdb
# PARAMETERS: T0386TS074_4_2.T0386.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       210 - 224         3.39     8.86
  LCS_AVERAGE:      4.83

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    11       210 - 220         1.30     9.35
  LCS_AVERAGE:      3.11

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     9       210 - 218         0.91     9.21
  LCS_AVERAGE:      2.51

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:  291
LCS_GDT     P     209     P     209      0    0    0     0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
LCS_GDT     M     210     M     210      9   11   15     0    6    9   11   11   11   11   11   12   13   15   15   15   15   15   15   15   15   15   15 
LCS_GDT     Q     211     Q     211      9   11   15     6    7    9   11   11   11   11   11   12   13   15   15   15   15   15   15   15   15   15   15 
LCS_GDT     H     212     H     212      9   11   15     6    7    9   11   11   11   11   11   12   13   15   15   15   15   15   15   15   15   15   15 
LCS_GDT     L     213     L     213      9   11   15     6    7    9   11   11   11   11   11   12   13   15   15   15   15   15   15   15   15   15   15 
LCS_GDT     F     214     F     214      9   11   15     6    7    9   11   11   11   11   11   12   13   15   15   15   15   15   15   15   15   15   15 
LCS_GDT     E     215     E     215      9   11   15     6    7    9   11   11   11   11   11   12   13   15   15   15   15   15   15   15   15   15   15 
LCS_GDT     D     216     D     216      9   11   15     3    7    9   11   11   11   11   11   12   13   15   15   15   15   15   15   15   15   15   15 
LCS_GDT     I     217     I     217      9   11   15     6    7    9   11   11   11   11   11   12   13   15   15   15   15   15   15   15   15   15   15 
LCS_GDT     S     218     S     218      9   11   15     3    5    9   11   11   11   11   11   12   13   15   15   15   15   15   15   15   15   15   15 
LCS_GDT     N     219     N     219      6   11   15     5    6    9   11   11   11   11   11   12   13   15   15   15   15   15   15   15   15   15   15 
LCS_GDT     P     220     P     220      6   11   15     5    6    7   11   11   11   11   11   12   13   15   15   15   15   15   15   15   15   15   15 
LCS_GDT     E     221     E     221      6    6   15     5    6    6    6    6    6    6    8   12   13   15   15   15   15   15   15   15   15   15   15 
LCS_GDT     K     222     K     222      6    6   15     5    6    6    6    6    6    6    8   12   12   15   15   15   15   15   15   15   15   15   15 
LCS_GDT     I     223     I     223      6    6   15     5    6    6    6    6    6    6    7   12   13   15   15   15   15   15   15   15   15   15   15 
LCS_GDT     R     224     R     224      6    6   15     5    6    6    6    6   10   11   11   12   13   15   15   15   15   15   15   15   15   15   15 
LCS_AVERAGE  LCS_A:   3.49  (   2.51    3.11    4.83 )

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      6      7      9     11     11     11     11     11     12     13     15     15     15     15     15     15     15     15     15     15 
GDT PERCENT_CA   2.06   2.41   3.09   3.78   3.78   3.78   3.78   3.78   4.12   4.47   5.15   5.15   5.15   5.15   5.15   5.15   5.15   5.15   5.15   5.15
GDT RMS_LOCAL    0.40   0.44   0.91   1.30   1.30   1.30   1.30   1.30   2.13   2.64   3.39   3.39   3.39   3.39   3.39   3.39   3.39   3.39   3.39   3.39
GDT RMS_ALL_CA   9.03   9.10   9.21   9.35   9.35   9.35   9.35   9.35   8.82   8.85   8.86   8.86   8.86   8.86   8.86   8.86   8.86   8.86   8.86   8.86

#      Molecule1      Molecule2       DISTANCE
LGA    P     209      P     209         33.384
LGA    M     210      M     210          1.141
LGA    Q     211      Q     211          1.209
LGA    H     212      H     212          0.593
LGA    L     213      L     213          0.640
LGA    F     214      F     214          0.631
LGA    E     215      E     215          1.309
LGA    D     216      D     216          1.777
LGA    I     217      I     217          1.318
LGA    S     218      S     218          1.417
LGA    N     219      N     219          1.446
LGA    P     220      P     220          2.001
LGA    E     221      E     221          7.814
LGA    K     222      K     222          9.559
LGA    I     223      I     223          7.559
LGA    R     224      R     224          7.552

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   16  291    4.0     11    1.30     3.780     3.772     0.785

LGA_LOCAL      RMSD =  1.302  Number of atoms =   11  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  9.353  Number of atoms =   16 
Std_ALL_ATOMS  RMSD =  7.446  (standard rmsd on all 16 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.506144 * X  +  -0.834275 * Y  +  -0.218641 * Z  +  59.967937
  Y_new =  -0.849475 * X  +  -0.438437 * Y  +  -0.293539 * Z  +  75.815170
  Z_new =   0.149032 * X  +   0.334303 * Y  +  -0.930608 * Z  +  47.038940 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.796718   -0.344874  [ DEG:   160.2402    -19.7598 ]
  Theta =  -0.149590   -2.992003  [ DEG:    -8.5709   -171.4291 ]
  Phi   =  -1.033448    2.108145  [ DEG:   -59.2122    120.7878 ]
 
# 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: T0386TS074_4_2                                
REMARK     2: T0386.pdb                                     
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0386TS074_4_2.T0386.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   16  291   4.0   11   1.30   3.772     7.45
REMARK  ---------------------------------------------------------- 
MOLECULE T0386TS074_4_2
REMARK PARENT number 2
PFRMAT TS
TARGET T0386
PARENT 2g03_A
ATOM   1386  N   PRO   209      12.848  81.682  56.555  1.00  0.22
ATOM   1387  CA  PRO   209      13.729  80.521  56.400  1.00  0.22
ATOM   1388  C   PRO   209      15.195  80.843  56.693  1.00  0.22
ATOM   1389  O   PRO   209      15.819  80.224  57.551  1.00  0.22
ATOM   1390  CB  PRO   209      13.500  80.117  54.946  1.00  0.22
ATOM   1391  CG  PRO   209      12.503  81.127  54.483  1.00  0.32
ATOM   1392  CD  PRO   209      12.718  82.389  55.225  1.00  0.32
ATOM   1393  N   MET   210      14.867  50.590  66.238  1.00  0.20
ATOM   1394  CA  MET   210      13.607  50.219  65.653  1.00  0.20
ATOM   1395  C   MET   210      12.457  50.097  66.616  1.00  0.20
ATOM   1396  O   MET   210      11.472  50.795  66.429  1.00  0.20
ATOM   1397  CB  MET   210      13.787  48.914  64.878  1.00  0.20
ATOM   1398  CG  MET   210      12.541  48.424  64.133  1.00  0.30
ATOM   1399  SD  MET   210      12.036  49.569  62.788  1.00  0.30
ATOM   1400  CE  MET   210      13.255  49.217  61.567  1.00  0.50
ATOM   1401  N   GLN   211      12.569  49.612  67.662  1.00  0.20
ATOM   1402  CA  GLN   211      11.436  49.207  68.495  1.00  0.20
ATOM   1403  C   GLN   211      11.170  50.162  69.679  1.00  0.20
ATOM   1404  O   GLN   211      10.020  50.478  69.968  1.00  0.20
ATOM   1405  CB  GLN   211      11.592  47.753  68.973  1.00  0.20
ATOM   1406  CG  GLN   211      10.441  47.223  69.781  1.00  0.30
ATOM   1407  CD  GLN   211       9.169  47.099  69.077  1.00  0.30
ATOM   1408  OE1 GLN   211       9.097  46.362  68.077  1.00  0.50
ATOM   1409  NE2 GLN   211       8.110  47.751  69.551  1.00  0.50
ATOM   1410  N   HIS   212      12.222  50.637  70.338  1.00  0.20
ATOM   1411  CA  HIS   212      12.061  51.496  71.499  1.00  0.20
ATOM   1412  C   HIS   212      11.510  52.880  71.126  1.00  0.20
ATOM   1413  O   HIS   212      10.616  53.416  71.803  1.00  0.20
ATOM   1414  CB  HIS   212      13.381  51.628  72.245  1.00  0.20
ATOM   1415  CG  HIS   212      13.308  52.457  73.533  1.00  0.30
ATOM   1416  ND1 HIS   212      13.321  53.863  73.485  1.00  0.30
ATOM   1417  CD2 HIS   212      13.127  52.041  74.772  1.00  0.50
ATOM   1418  CE1 HIS   212      13.164  54.328  74.768  1.00  0.50
ATOM   1419  NE2 HIS   212      13.048  53.203  75.578  1.00  0.80
ATOM   1420  N   LEU   213      12.032  53.453  70.041  1.00  0.20
ATOM   1421  CA  LEU   213      11.539  54.723  69.521  1.00  0.20
ATOM   1422  C   LEU   213      10.092  54.581  69.075  1.00  0.20
ATOM   1423  O   LEU   213       9.264  55.439  69.390  1.00  0.20
ATOM   1424  CB  LEU   213      12.448  55.260  68.375  1.00  0.20
ATOM   1425  CG  LEU   213      13.829  55.586  68.943  1.00  0.30
ATOM   1426  CD1 LEU   213      14.755  55.983  67.881  1.00  0.30
ATOM   1427  CD2 LEU   213      13.611  56.996  69.778  1.00  0.50
ATOM   1428  N   PHE   214       9.769  53.510  68.352  1.00  0.20
ATOM   1429  CA  PHE   214       8.384  53.305  67.918  1.00  0.20
ATOM   1430  C   PHE   214       7.438  53.159  69.141  1.00  0.20
ATOM   1431  O   PHE   214       6.500  53.931  69.309  1.00  0.20
ATOM   1432  CB  PHE   214       8.246  52.088  66.964  1.00  0.20
ATOM   1433  CG  PHE   214       9.004  52.346  65.650  1.00  0.30
ATOM   1434  CD1 PHE   214       9.108  53.676  65.218  1.00  0.30
ATOM   1435  CD2 PHE   214       9.130  51.340  64.722  1.00  0.50
ATOM   1436  CE1 PHE   214       9.557  53.926  63.938  1.00  0.50
ATOM   1437  CE2 PHE   214       9.594  51.557  63.451  1.00  0.80
ATOM   1438  CZ  PHE   214       9.834  52.900  63.055  1.00  0.80
ATOM   1439  N   GLU   215       7.714  52.212  70.019  1.00  0.20
ATOM   1440  CA  GLU   215       6.782  51.920  71.101  1.00  0.20
ATOM   1441  C   GLU   215       6.705  52.950  72.243  1.00  0.20
ATOM   1442  O   GLU   215       5.612  53.227  72.715  1.00  0.20
ATOM   1443  CB  GLU   215       6.938  50.467  71.578  1.00  0.20
ATOM   1444  CG  GLU   215       6.555  49.477  70.511  1.00  0.30
ATOM   1445  CD  GLU   215       5.038  49.555  70.143  1.00  0.30
ATOM   1446  OE1 GLU   215       4.168  49.719  71.012  1.00  0.50
ATOM   1447  OE2 GLU   215       4.744  49.399  68.926  1.00  0.50
ATOM   1448  N   ASP   216       7.837  53.510  72.670  1.00  0.20
ATOM   1449  CA  ASP   216       7.821  54.604  73.642  1.00  0.20
ATOM   1450  C   ASP   216       7.185  55.847  73.033  1.00  0.20
ATOM   1451  O   ASP   216       6.575  56.646  73.748  1.00  0.20
ATOM   1452  CB  ASP   216       9.219  54.926  74.170  1.00  0.20
ATOM   1453  CG  ASP   216       9.796  53.860  75.071  1.00  0.30
ATOM   1454  OD1 ASP   216       9.072  52.959  75.566  1.00  0.30
ATOM   1455  OD2 ASP   216      10.979  53.887  75.422  1.00  0.50
ATOM   1456  N   ILE   217       6.767  56.123  71.869  1.00  0.20
ATOM   1457  CA  ILE   217       6.126  57.202  71.141  1.00  0.20
ATOM   1458  C   ILE   217       4.613  57.139  71.177  1.00  0.20
ATOM   1459  O   ILE   217       3.956  58.150  71.394  1.00  0.20
ATOM   1460  CB  ILE   217       5.903  57.881  72.495  1.00  0.20
ATOM   1461  CG1 ILE   217       7.180  58.236  73.258  1.00  0.30
ATOM   1462  CG2 ILE   217       4.940  56.998  73.297  1.00  0.30
ATOM   1463  CD1 ILE   217       7.597  59.669  73.150  1.00  0.50
ATOM   1464  N   SER   218       3.458  57.364  71.272  1.00  0.20
ATOM   1465  CA  SER   218       2.047  56.989  71.355  1.00  0.20
ATOM   1466  C   SER   218       1.542  57.102  72.800  1.00  0.20
ATOM   1467  O   SER   218       0.470  57.640  73.037  1.00  0.20
ATOM   1468  CB  SER   218       1.812  55.539  70.833  1.00  0.20
ATOM   1469  OG  SER   218       0.326  55.181  70.854  1.00  0.30
ATOM   1470  N   ASN   219       2.301  56.584  73.757  1.00  0.20
ATOM   1471  CA  ASN   219       1.930  56.758  75.158  1.00  0.20
ATOM   1472  C   ASN   219       1.801  58.222  75.587  1.00  0.20
ATOM   1473  O   ASN   219       0.896  58.556  76.338  1.00  0.20
ATOM   1474  CB  ASN   219       2.881  56.042  76.090  1.00  0.20
ATOM   1475  CG  ASN   219       2.875  54.528  75.959  1.00  0.30
ATOM   1476  OD1 ASN   219       1.878  53.930  76.460  1.00  0.30
ATOM   1477  ND2 ASN   219       3.907  53.950  75.450  1.00  0.50
ATOM   1478  N   PRO   220       2.706  59.080  75.126  1.00  0.20
ATOM   1479  CA  PRO   220       2.665  60.488  75.502  1.00  0.20
ATOM   1480  C   PRO   220       1.473  61.168  74.831  1.00  0.20
ATOM   1481  O   PRO   220       0.742  61.901  75.471  1.00  0.20
ATOM   1482  CB  PRO   220       3.988  61.189  75.158  1.00  0.20
ATOM   1483  CG  PRO   220       5.048  60.301  74.514  1.00  0.30
ATOM   1484  CD  PRO   220       3.869  59.125  73.894  1.00  0.30
ATOM   1485  N   GLU   221       1.272  60.903  73.542  1.00  0.20
ATOM   1486  CA  GLU   221       0.133  61.402  72.791  1.00  0.20
ATOM   1487  C   GLU   221      -1.210  61.116  73.471  1.00  0.20
ATOM   1488  O   GLU   221      -2.085  61.994  73.539  1.00  0.20
ATOM   1489  CB  GLU   221       0.136  60.774  71.395  1.00  0.20
ATOM   1490  CG  GLU   221       1.266  61.190  70.649  1.00  0.30
ATOM   1491  CD  GLU   221       1.385  62.778  70.259  1.00  0.30
ATOM   1492  OE1 GLU   221       0.433  63.425  69.917  1.00  0.50
ATOM   1493  OE2 GLU   221       2.509  63.307  70.333  1.00  0.50
ATOM   1494  N   LYS   222      -1.377  59.885  73.948  1.00  0.20
ATOM   1495  CA  LYS   222      -2.606  59.452  74.631  1.00  0.20
ATOM   1496  C   LYS   222      -2.759  60.083  76.016  1.00  0.20
ATOM   1497  O   LYS   222      -3.881  60.223  76.534  1.00  0.20
ATOM   1498  CB  LYS   222      -2.723  57.898  74.682  1.00  0.20
ATOM   1499  CG  LYS   222      -4.023  57.460  75.320  1.00  0.30
ATOM   1500  CD  LYS   222      -4.062  55.929  75.335  1.00  0.30
ATOM   1501  CE  LYS   222      -3.107  55.213  76.211  1.00  0.50
ATOM   1502  NZ  LYS   222      -3.349  55.475  77.678  1.00  0.50
ATOM   1503  N   ILE   223      -1.497  60.214  76.264  1.00  0.20
ATOM   1504  CA  ILE   223      -1.584  60.950  77.530  1.00  0.20
ATOM   1505  C   ILE   223      -2.130  62.397  77.349  1.00  0.20
ATOM   1506  O   ILE   223      -2.834  62.914  78.216  1.00  0.20
ATOM   1507  CB  ILE   223      -0.192  60.937  78.158  1.00  0.20
ATOM   1508  CG1 ILE   223       0.372  59.602  78.588  1.00  0.30
ATOM   1509  CG2 ILE   223      -0.198  61.951  79.311  1.00  0.30
ATOM   1510  CD1 ILE   223       1.758  59.516  78.983  1.00  0.50
ATOM   1511  N   ARG   224      -1.840  63.022  76.209  1.00  0.20
ATOM   1512  CA  ARG   224      -2.227  64.403  75.956  1.00  0.20
ATOM   1513  C   ARG   224      -3.723  64.572  76.069  1.00  0.20
ATOM   1514  O   ARG   224      -4.204  65.627  76.488  1.00  0.20
ATOM   1515  CB  ARG   224      -1.778  64.890  74.586  1.00  0.20
ATOM   1516  CG  ARG   224      -0.282  65.060  74.380  1.00  0.30
ATOM   1517  CD  ARG   224      -0.126  65.453  72.936  1.00  0.30
ATOM   1518  NE  ARG   224       1.306  65.617  72.711  1.00  0.50
ATOM   1519  CZ  ARG   224       1.825  66.021  71.554  1.00  0.50
ATOM   1520  NH1 ARG   224       1.023  66.216  70.507  1.00  0.80
ATOM   1521  NH2 ARG   224       3.144  66.159  71.468  1.00  0.80
TER
END
