
#######################################################
#                                                     #
#                        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_2_2
# Molecule2: number of CA atoms  291 ( 2337),  selected   16 , name T0386.pdb
# PARAMETERS: T0386TS074_2_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:    16       209 - 224         3.08     3.08
  LCS_AVERAGE:      5.50

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    13       209 - 221         1.96     3.54
  LCS_AVERAGE:      4.02

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    11       209 - 219         0.96     3.65
  LCS_AVERAGE:      3.29

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     11   13   16     3    6   10   12   12   12   12   13   14   14   16   16   16   16   16   16   16   16   16   16 
LCS_GDT     M     210     M     210     11   13   16     3    7   10   12   12   12   12   13   14   15   16   16   16   16   16   16   16   16   16   16 
LCS_GDT     Q     211     Q     211     11   13   16     5    8   10   12   12   12   12   13   14   15   16   16   16   16   16   16   16   16   16   16 
LCS_GDT     H     212     H     212     11   13   16     5    8   10   12   12   12   12   13   14   15   16   16   16   16   16   16   16   16   16   16 
LCS_GDT     L     213     L     213     11   13   16     5    8   10   12   12   12   12   13   14   15   16   16   16   16   16   16   16   16   16   16 
LCS_GDT     F     214     F     214     11   13   16     5    8   10   12   12   12   12   13   14   15   16   16   16   16   16   16   16   16   16   16 
LCS_GDT     E     215     E     215     11   13   16     5    8   10   12   12   12   12   13   14   15   16   16   16   16   16   16   16   16   16   16 
LCS_GDT     D     216     D     216     11   13   16     5    8   10   12   12   12   12   13   14   15   16   16   16   16   16   16   16   16   16   16 
LCS_GDT     I     217     I     217     11   13   16     5    8   10   12   12   12   12   13   14   15   16   16   16   16   16   16   16   16   16   16 
LCS_GDT     S     218     S     218     11   13   16     5    8   10   12   12   12   12   13   14   15   16   16   16   16   16   16   16   16   16   16 
LCS_GDT     N     219     N     219     11   13   16     5    6   10   12   12   12   12   13   14   15   16   16   16   16   16   16   16   16   16   16 
LCS_GDT     P     220     P     220      8   13   16     5    6    8   12   12   12   12   13   14   15   16   16   16   16   16   16   16   16   16   16 
LCS_GDT     E     221     E     221      6   13   16     4    6    6    6    9    9   11   13   14   15   16   16   16   16   16   16   16   16   16   16 
LCS_GDT     K     222     K     222      6    6   16     5    6    6    6    6    6    6    6   11   15   16   16   16   16   16   16   16   16   16   16 
LCS_GDT     I     223     I     223      6    6   16     5    6    6    6    6    6    6    6    9   15   16   16   16   16   16   16   16   16   16   16 
LCS_GDT     R     224     R     224      6    6   16     5    6    6    9    9   12   12   13   14   15   16   16   16   16   16   16   16   16   16   16 
LCS_AVERAGE  LCS_A:   4.27  (   3.29    4.02    5.50 )

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      5      8     10     12     12     12     12     13     14     15     16     16     16     16     16     16     16     16     16     16 
GDT PERCENT_CA   1.72   2.75   3.44   4.12   4.12   4.12   4.12   4.47   4.81   5.15   5.50   5.50   5.50   5.50   5.50   5.50   5.50   5.50   5.50   5.50
GDT RMS_LOCAL    0.18   0.51   0.85   1.08   1.08   1.08   1.08   1.77   2.24   3.09   3.08   3.08   3.08   3.08   3.08   3.08   3.08   3.08   3.08   3.08
GDT RMS_ALL_CA   3.63   3.36   3.54   3.87   3.87   3.87   3.87   3.34   3.26   3.11   3.08   3.08   3.08   3.08   3.08   3.08   3.08   3.08   3.08   3.08

#      Molecule1      Molecule2       DISTANCE
LGA    P     209      P     209          1.772
LGA    M     210      M     210          1.885
LGA    Q     211      Q     211          0.331
LGA    H     212      H     212          0.396
LGA    L     213      L     213          0.536
LGA    F     214      F     214          0.667
LGA    E     215      E     215          0.779
LGA    D     216      D     216          1.450
LGA    I     217      I     217          1.722
LGA    S     218      S     218          1.348
LGA    N     219      N     219          2.161
LGA    P     220      P     220          3.870
LGA    E     221      E     221          5.451
LGA    K     222      K     222          6.914
LGA    I     223      I     223          5.845
LGA    R     224      R     224          3.298

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   16  291    4.0     13    1.77     4.210     4.305     0.695

LGA_LOCAL      RMSD =  1.769  Number of atoms =   13  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  3.136  Number of atoms =   16 
Std_ALL_ATOMS  RMSD =  3.076  (standard rmsd on all 16 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.221123 * X  +  -0.889882 * Y  +  -0.399017 * Z  +  60.994865
  Y_new =  -0.974757 * X  +  -0.188710 * Y  +  -0.119321 * Z  +  59.176823
  Z_new =   0.030883 * X  +   0.415329 * Y  +  -0.909147 * Z  +  41.967514 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.713070   -0.428523  [ DEG:   155.4474    -24.5526 ]
  Theta =  -0.030888   -3.110705  [ DEG:    -1.7697   -178.2303 ]
  Phi   =  -1.347723    1.793870  [ DEG:   -77.2188    102.7812 ]
 
# 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_2_2                                
REMARK     2: T0386.pdb                                     
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0386TS074_2_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   13   1.77   4.305     3.08
REMARK  ---------------------------------------------------------- 
MOLECULE T0386TS074_2_2
REMARK PARENT number 2
PFRMAT TS
TARGET T0386
PARENT 2g03_A
ATOM   1386  N   PRO   209      15.874  48.438  67.772  1.00  0.92
ATOM   1387  CA  PRO   209      15.780  49.731  67.111  1.00  0.92
ATOM   1388  C   PRO   209      14.326  49.887  66.774  1.00  0.92
ATOM   1389  O   PRO   209      13.691  50.798  67.290  1.00  0.92
ATOM   1390  CB  PRO   209      16.542  49.814  65.776  1.00  0.92
ATOM   1391  CG  PRO   209      17.270  48.533  65.364  1.00  1.02
ATOM   1392  CD  PRO   209      16.226  47.476  66.331  1.00  1.02
ATOM   1393  N   MET   210      13.823  48.936  65.968  1.00  0.80
ATOM   1394  CA  MET   210      12.483  48.977  65.448  1.00  0.80
ATOM   1395  C   MET   210      11.398  49.204  66.465  1.00  0.80
ATOM   1396  O   MET   210      10.669  50.174  66.326  1.00  0.80
ATOM   1397  CB  MET   210      12.215  47.689  64.669  1.00  0.80
ATOM   1398  CG  MET   210      10.845  47.615  63.988  1.00  0.90
ATOM   1399  SD  MET   210      10.653  48.875  62.666  1.00  0.90
ATOM   1400  CE  MET   210       9.021  48.530  62.103  1.00  1.10
ATOM   1401  N   GLN   211      11.406  48.696  67.508  1.00  0.80
ATOM   1402  CA  GLN   211      10.244  48.650  68.397  1.00  0.80
ATOM   1403  C   GLN   211      10.342  49.626  69.589  1.00  0.80
ATOM   1404  O   GLN   211       9.361  50.277  69.932  1.00  0.80
ATOM   1405  CB  GLN   211       9.969  47.213  68.872  1.00  0.80
ATOM   1406  CG  GLN   211       8.749  47.054  69.737  1.00  0.90
ATOM   1407  CD  GLN   211       7.469  47.336  69.097  1.00  0.90
ATOM   1408  OE1 GLN   211       7.127  46.667  68.105  1.00  1.10
ATOM   1409  NE2 GLN   211       6.687  48.276  69.620  1.00  1.10
ATOM   1410  N   HIS   212      11.520  49.748  70.192  1.00  0.80
ATOM   1411  CA  HIS   212      11.687  50.602  71.357  1.00  0.80
ATOM   1412  C   HIS   212      11.571  52.091  71.006  1.00  0.80
ATOM   1413  O   HIS   212      10.920  52.869  71.724  1.00  0.80
ATOM   1414  CB  HIS   212      13.017  50.312  72.037  1.00  0.80
ATOM   1415  CG  HIS   212      13.265  51.108  73.323  1.00  0.90
ATOM   1416  ND1 HIS   212      13.707  52.442  73.270  1.00  0.90
ATOM   1417  CD2 HIS   212      13.023  50.755  74.572  1.00  1.10
ATOM   1418  CE1 HIS   212      13.763  52.918  74.556  1.00  1.10
ATOM   1419  NE2 HIS   212      13.344  51.875  75.376  1.00  1.40
ATOM   1420  N   LEU   213      12.192  52.489  69.895  1.00  0.80
ATOM   1421  CA  LEU   213      12.090  53.855  69.394  1.00  0.80
ATOM   1422  C   LEU   213      10.649  54.169  69.022  1.00  0.80
ATOM   1423  O   LEU   213      10.141  55.236  69.374  1.00  0.80
ATOM   1424  CB  LEU   213      13.064  54.099  68.203  1.00  0.80
ATOM   1425  CG  LEU   213      12.967  55.561  67.771  1.00  0.90
ATOM   1426  CD1 LEU   213      13.440  56.456  68.827  1.00  0.90
ATOM   1427  CD2 LEU   213      14.132  55.727  66.609  1.00  1.10
ATOM   1428  N   PHE   214       9.979  53.258  68.319  1.00  0.80
ATOM   1429  CA  PHE   214       8.579  53.494  67.953  1.00  0.80
ATOM   1430  C   PHE   214       7.693  53.632  69.223  1.00  0.80
ATOM   1431  O   PHE   214       7.047  54.654  69.434  1.00  0.80
ATOM   1432  CB  PHE   214       8.027  52.390  67.013  1.00  0.80
ATOM   1433  CG  PHE   214       8.763  52.417  65.663  1.00  0.90
ATOM   1434  CD1 PHE   214       9.252  53.655  65.220  1.00  0.90
ATOM   1435  CD2 PHE   214       8.529  51.432  64.733  1.00  1.10
ATOM   1436  CE1 PHE   214       9.694  53.770  63.918  1.00  1.10
ATOM   1437  CE2 PHE   214       8.976  51.510  63.439  1.00  1.40
ATOM   1438  CZ  PHE   214       9.599  52.718  63.027  1.00  1.40
ATOM   1439  N   GLU   215       7.705  52.636  70.090  1.00  0.80
ATOM   1440  CA  GLU   215       6.782  52.633  71.218  1.00  0.80
ATOM   1441  C   GLU   215       7.080  53.623  72.358  1.00  0.80
ATOM   1442  O   GLU   215       6.150  54.217  72.881  1.00  0.80
ATOM   1443  CB  GLU   215       6.506  51.198  71.691  1.00  0.80
ATOM   1444  CG  GLU   215       5.499  51.153  72.809  1.00  0.90
ATOM   1445  CD  GLU   215       4.085  51.643  72.356  1.00  0.90
ATOM   1446  OE1 GLU   215       3.820  51.841  71.161  1.00  1.10
ATOM   1447  OE2 GLU   215       3.246  51.868  73.270  1.00  1.10
ATOM   1448  N   ASP   216       8.348  53.803  72.727  1.00  0.80
ATOM   1449  CA  ASP   216       8.717  54.837  73.694  1.00  0.80
ATOM   1450  C   ASP   216       8.466  56.223  73.111  1.00  0.80
ATOM   1451  O   ASP   216       8.167  57.162  73.853  1.00  0.80
ATOM   1452  CB  ASP   216      10.169  54.708  74.152  1.00  0.80
ATOM   1453  CG  ASP   216      10.433  53.506  75.028  1.00  0.90
ATOM   1454  OD1 ASP   216       9.493  52.866  75.561  1.00  0.90
ATOM   1455  OD2 ASP   216      11.583  53.167  75.322  1.00  1.10
ATOM   1456  N   ILE   217       8.579  56.340  71.786  1.00  0.80
ATOM   1457  CA  ILE   217       8.284  57.566  71.071  1.00  0.80
ATOM   1458  C   ILE   217       6.814  57.937  71.093  1.00  0.80
ATOM   1459  O   ILE   217       6.470  59.091  71.321  1.00  0.80
ATOM   1460  CB  ILE   217       8.245  58.261  72.434  1.00  0.80
ATOM   1461  CG1 ILE   217       7.873  59.745  72.392  1.00  0.90
ATOM   1462  CG2 ILE   217       9.586  57.989  73.126  1.00  0.90
ATOM   1463  CD1 ILE   217       7.494  60.334  73.713  1.00  1.10
ATOM   1464  N   SER   218       5.943  56.973  70.808  1.00  0.80
ATOM   1465  CA  SER   218       4.496  57.140  70.930  1.00  0.80
ATOM   1466  C   SER   218       4.119  57.554  72.358  1.00  0.80
ATOM   1467  O   SER   218       3.322  58.461  72.547  1.00  0.80
ATOM   1468  CB  SER   218       3.737  55.833  70.549  1.00  0.80
ATOM   1469  OG  SER   218       4.111  54.686  71.488  1.00  0.90
ATOM   1470  N   ASN   219       3.485  55.856  75.190  1.00  0.80
ATOM   1471  CA  ASN   219       3.336  56.023  76.632  1.00  0.80
ATOM   1472  C   ASN   219       3.672  57.432  77.128  1.00  0.80
ATOM   1473  O   ASN   219       2.987  57.947  78.000  1.00  0.80
ATOM   1474  CB  ASN   219       4.145  55.009  77.408  1.00  0.80
ATOM   1475  CG  ASN   219       3.699  53.569  77.222  1.00  0.90
ATOM   1476  OD1 ASN   219       2.637  53.232  77.821  1.00  0.90
ATOM   1477  ND2 ASN   219       4.464  52.767  76.564  1.00  1.10
ATOM   1478  N   PRO   220       4.724  58.041  76.589  1.00  0.80
ATOM   1479  CA  PRO   220       5.123  59.375  77.021  1.00  0.80
ATOM   1480  C   PRO   220       4.103  60.402  76.533  1.00  0.80
ATOM   1481  O   PRO   220       3.684  61.259  77.288  1.00  0.80
ATOM   1482  CB  PRO   220       6.543  59.708  76.539  1.00  0.80
ATOM   1483  CG  PRO   220       7.233  58.613  75.732  1.00  0.90
ATOM   1484  CD  PRO   220       5.710  57.853  75.223  1.00  0.90
ATOM   1485  N   GLU   221       3.693  60.295  75.270  1.00  0.80
ATOM   1486  CA  GLU   221       2.666  61.139  74.689  1.00  0.80
ATOM   1487  C   GLU   221       1.380  61.185  75.522  1.00  0.80
ATOM   1488  O   GLU   221       0.800  62.262  75.734  1.00  0.80
ATOM   1489  CB  GLU   221       2.337  60.637  73.281  1.00  0.80
ATOM   1490  CG  GLU   221       3.448  60.780  72.415  1.00  0.90
ATOM   1491  CD  GLU   221       3.965  62.297  72.072  1.00  0.90
ATOM   1492  OE1 GLU   221       3.201  63.203  71.878  1.00  1.10
ATOM   1493  OE2 GLU   221       5.192  62.490  72.024  1.00  1.10
ATOM   1494  N   LYS   222       0.927  60.016  75.970  1.00  0.80
ATOM   1495  CA  LYS   222      -0.289  59.889  76.785  1.00  0.80
ATOM   1496  C   LYS   222      -0.103  60.436  78.203  1.00  0.80
ATOM   1497  O   LYS   222      -1.077  60.842  78.864  1.00  0.80
ATOM   1498  CB  LYS   222      -0.832  58.427  76.793  1.00  0.80
ATOM   1499  CG  LYS   222      -2.122  58.317  77.573  1.00  0.90
ATOM   1500  CD  LYS   222      -2.589  56.861  77.534  1.00  0.90
ATOM   1501  CE  LYS   222      -1.785  55.848  78.253  1.00  1.10
ATOM   1502  NZ  LYS   222      -1.778  56.060  79.750  1.00  1.10
ATOM   1503  N   ILE   223       1.259  60.622  78.092  1.00  0.80
ATOM   1504  CA  ILE   223       1.547  61.221  79.399  1.00  0.80
ATOM   1505  C   ILE   223       1.476  62.777  79.377  1.00  0.80
ATOM   1506  O   ILE   223       1.071  63.400  80.358  1.00  0.80
ATOM   1507  CB  ILE   223       2.920  60.717  79.836  1.00  0.80
ATOM   1508  CG1 ILE   223       3.071  59.238  80.109  1.00  0.90
ATOM   1509  CG2 ILE   223       3.362  61.566  81.036  1.00  0.90
ATOM   1510  CD1 ILE   223       4.391  58.688  80.311  1.00  1.10
ATOM   1511  N   ARG   224       1.826  63.389  78.247  1.00  0.80
ATOM   1512  CA  ARG   224       1.877  64.840  78.128  1.00  0.80
ATOM   1513  C   ARG   224       0.534  65.453  78.448  1.00  0.80
ATOM   1514  O   ARG   224       0.463  66.558  78.988  1.00  0.80
ATOM   1515  CB  ARG   224       2.309  65.294  76.742  1.00  0.80
ATOM   1516  CG  ARG   224       3.749  65.012  76.351  1.00  0.90
ATOM   1517  CD  ARG   224       3.868  65.476  74.924  1.00  0.90
ATOM   1518  NE  ARG   224       5.244  65.209  74.522  1.00  1.10
ATOM   1519  CZ  ARG   224       5.738  65.543  73.332  1.00  1.10
ATOM   1520  NH1 ARG   224       4.934  66.078  72.413  1.00  1.40
ATOM   1521  NH2 ARG   224       7.015  65.273  73.081  1.00  1.40
TER
END
