
#######################################################
#                                                     #
#                        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_1_2
# Molecule2: number of CA atoms  291 ( 2337),  selected   16 , name T0386.pdb
# PARAMETERS: T0386TS074_1_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         3.30     3.30
  LCS_AVERAGE:      5.50

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    12       209 - 220         1.11     4.15
  LCS_AVERAGE:      3.61

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    10       209 - 218         0.90     4.10
  LONGEST_CONTINUOUS_SEGMENT:    10       210 - 219         0.92     4.01
  LONGEST_CONTINUOUS_SEGMENT:    10       211 - 220         0.99     4.13
  LCS_AVERAGE:      3.09

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     10   12   16     3    5   11   12   12   12   12   13   14   14   15   16   16   16   16   16   16   16   16   16 
LCS_GDT     M     210     M     210     10   12   16     3    8   11   12   12   12   12   13   14   14   15   16   16   16   16   16   16   16   16   16 
LCS_GDT     Q     211     Q     211     10   12   16     5    8   11   12   12   12   12   13   14   14   15   16   16   16   16   16   16   16   16   16 
LCS_GDT     H     212     H     212     10   12   16     5    8   11   12   12   12   12   13   14   14   15   16   16   16   16   16   16   16   16   16 
LCS_GDT     L     213     L     213     10   12   16     5    8   11   12   12   12   12   13   14   14   15   16   16   16   16   16   16   16   16   16 
LCS_GDT     F     214     F     214     10   12   16     5    8   11   12   12   12   12   13   14   14   15   16   16   16   16   16   16   16   16   16 
LCS_GDT     E     215     E     215     10   12   16     5    8   11   12   12   12   12   13   14   14   15   16   16   16   16   16   16   16   16   16 
LCS_GDT     D     216     D     216     10   12   16     4    8   11   12   12   12   12   13   14   14   15   16   16   16   16   16   16   16   16   16 
LCS_GDT     I     217     I     217     10   12   16     4    8   11   12   12   12   12   13   14   14   15   16   16   16   16   16   16   16   16   16 
LCS_GDT     S     218     S     218     10   12   16     2    8   11   12   12   12   12   13   14   14   15   16   16   16   16   16   16   16   16   16 
LCS_GDT     N     219     N     219     10   12   16     6    6    7   12   12   12   12   13   14   14   15   16   16   16   16   16   16   16   16   16 
LCS_GDT     P     220     P     220     10   12   16     6    8   11   12   12   12   12   13   14   14   15   16   16   16   16   16   16   16   16   16 
LCS_GDT     E     221     E     221      6    6   16     6    6    6    6    6    9   10   12   14   14   15   16   16   16   16   16   16   16   16   16 
LCS_GDT     K     222     K     222      6    6   16     6    6    6    6    6    6    6    6    8   12   15   16   16   16   16   16   16   16   16   16 
LCS_GDT     I     223     I     223      6    6   16     6    6    6    6    6    6    6    6    8   12   15   16   16   16   16   16   16   16   16   16 
LCS_GDT     R     224     R     224      6    6   16     6    6    6    6    9   12   12   13   14   14   15   16   16   16   16   16   16   16   16   16 
LCS_AVERAGE  LCS_A:   4.07  (   3.09    3.61    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      6      8     11     12     12     12     12     13     14     14     15     16     16     16     16     16     16     16     16     16 
GDT PERCENT_CA   2.06   2.75   3.78   4.12   4.12   4.12   4.12   4.47   4.81   4.81   5.15   5.50   5.50   5.50   5.50   5.50   5.50   5.50   5.50   5.50
GDT RMS_LOCAL    0.23   0.65   1.01   1.11   1.11   1.11   1.11   1.88   2.41   2.41   2.90   3.30   3.30   3.30   3.30   3.30   3.30   3.30   3.30   3.30
GDT RMS_ALL_CA  14.75   3.92   4.23   4.15   4.15   4.15   4.15   3.57   3.48   3.48   3.36   3.30   3.30   3.30   3.30   3.30   3.30   3.30   3.30   3.30

#      Molecule1      Molecule2       DISTANCE
LGA    P     209      P     209          2.093
LGA    M     210      M     210          1.995
LGA    Q     211      Q     211          0.627
LGA    H     212      H     212          0.781
LGA    L     213      L     213          0.902
LGA    F     214      F     214          0.880
LGA    E     215      E     215          0.812
LGA    D     216      D     216          1.999
LGA    I     217      I     217          2.300
LGA    S     218      S     218          1.463
LGA    N     219      N     219          1.784
LGA    P     220      P     220          3.569
LGA    E     221      E     221          5.925
LGA    K     222      K     222          7.365
LGA    I     223      I     223          6.292
LGA    R     224      R     224          3.566

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   16  291    4.0     13    1.88     4.210     4.200     0.657

LGA_LOCAL      RMSD =  1.878  Number of atoms =   13  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  3.360  Number of atoms =   16 
Std_ALL_ATOMS  RMSD =  3.300  (standard rmsd on all 16 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.131487 * X  +  -0.941588 * Y  +  -0.310038 * Z  +  63.564754
  Y_new =  -0.991166 * X  +  -0.119396 * Y  +  -0.057748 * Z  +  55.127712
  Z_new =   0.017357 * X  +   0.314892 * Y  +  -0.948969 * Z  +  48.181889 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.821200   -0.320393  [ DEG:   161.6429    -18.3572 ]
  Theta =  -0.017358   -3.124234  [ DEG:    -0.9946   -179.0054 ]
  Phi   =  -1.438907    1.702685  [ DEG:   -82.4433     97.5567 ]
 
# 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_1_2                                
REMARK     2: T0386.pdb                                     
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0386TS074_1_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   1.88   4.200     3.30
REMARK  ---------------------------------------------------------- 
MOLECULE T0386TS074_1_2
REMARK PARENT number 2
PFRMAT TS
TARGET T0386
PARENT 2g03_A
ATOM   1386  N   PRO   209      16.008  48.254  67.371  1.00  1.05
ATOM   1387  CA  PRO   209      15.932  49.591  66.802  1.00  1.05
ATOM   1388  C   PRO   209      14.477  49.801  66.504  1.00  1.05
ATOM   1389  O   PRO   209      13.872  50.689  67.092  1.00  1.05
ATOM   1390  CB  PRO   209      16.673  49.747  65.461  1.00  1.05
ATOM   1391  CG  PRO   209      17.363  48.482  64.950  1.00  1.15
ATOM   1392  CD  PRO   209      16.312  47.385  65.863  1.00  1.15
ATOM   1393  N   MET   210      13.937  48.919  65.645  1.00  0.90
ATOM   1394  CA  MET   210      12.590  49.025  65.153  1.00  0.90
ATOM   1395  C   MET   210      11.530  49.205  66.204  1.00  0.90
ATOM   1396  O   MET   210      10.820  50.198  66.145  1.00  0.90
ATOM   1397  CB  MET   210      12.279  47.799  64.295  1.00  0.90
ATOM   1398  CG  MET   210      10.896  47.802  63.637  1.00  1.00
ATOM   1399  SD  MET   210      10.711  49.153  62.406  1.00  1.00
ATOM   1400  CE  MET   210       9.061  48.884  61.852  1.00  1.20
ATOM   1401  N   GLN   211      11.542  48.627  67.210  1.00  0.90
ATOM   1402  CA  GLN   211      10.396  48.547  68.117  1.00  0.90
ATOM   1403  C   GLN   211      10.537  49.438  69.369  1.00  0.90
ATOM   1404  O   GLN   211       9.578  50.085  69.775  1.00  0.90
ATOM   1405  CB  GLN   211      10.095  47.088  68.498  1.00  0.90
ATOM   1406  CG  GLN   211       8.888  46.896  69.373  1.00  1.00
ATOM   1407  CD  GLN   211       7.603  47.249  68.777  1.00  1.00
ATOM   1408  OE1 GLN   211       7.228  46.658  67.749  1.00  1.20
ATOM   1409  NE2 GLN   211       6.852  48.169  69.378  1.00  1.20
ATOM   1410  N   HIS   212      11.728  49.492  69.957  1.00  0.90
ATOM   1411  CA  HIS   212      11.935  50.260  71.173  1.00  0.90
ATOM   1412  C   HIS   212      11.849  51.772  70.926  1.00  0.90
ATOM   1413  O   HIS   212      11.227  52.513  71.708  1.00  0.90
ATOM   1414  CB  HIS   212      13.270  49.895  71.807  1.00  0.90
ATOM   1415  CG  HIS   212      13.559  50.597  73.140  1.00  1.00
ATOM   1416  ND1 HIS   212      14.031  51.921  73.168  1.00  1.00
ATOM   1417  CD2 HIS   212      13.330  50.164  74.366  1.00  1.20
ATOM   1418  CE1 HIS   212      14.119  52.307  74.483  1.00  1.20
ATOM   1419  NE2 HIS   212      13.692  51.219  75.238  1.00  1.50
ATOM   1420  N   LEU   213      12.458  52.231  69.834  1.00  0.90
ATOM   1421  CA  LEU   213      12.379  53.629  69.429  1.00  0.90
ATOM   1422  C   LEU   213      10.940  54.001  69.105  1.00  0.90
ATOM   1423  O   LEU   213      10.464  55.052  69.538  1.00  0.90
ATOM   1424  CB  LEU   213      13.337  53.933  68.239  1.00  0.90
ATOM   1425  CG  LEU   213      13.268  55.423  67.908  1.00  1.00
ATOM   1426  CD1 LEU   213      13.780  56.233  69.014  1.00  1.00
ATOM   1427  CD2 LEU   213      14.416  55.642  66.739  1.00  1.20
ATOM   1428  N   PHE   214      10.237  53.155  68.356  1.00  0.90
ATOM   1429  CA  PHE   214       8.837  53.445  68.034  1.00  0.90
ATOM   1430  C   PHE   214       7.976  53.516  69.326  1.00  0.90
ATOM   1431  O   PHE   214       7.358  54.535  69.617  1.00  0.90
ATOM   1432  CB  PHE   214       8.243  52.421  67.031  1.00  0.90
ATOM   1433  CG  PHE   214       8.956  52.524  65.671  1.00  1.00
ATOM   1434  CD1 PHE   214       9.465  53.778  65.306  1.00  1.00
ATOM   1435  CD2 PHE   214       8.683  51.610  64.682  1.00  1.20
ATOM   1436  CE1 PHE   214       9.887  53.971  64.006  1.00  1.20
ATOM   1437  CE2 PHE   214       9.110  51.766  63.389  1.00  1.50
ATOM   1438  CZ  PHE   214       9.753  52.985  63.048  1.00  1.50
ATOM   1439  N   GLU   215       7.980  52.463  70.123  1.00  0.90
ATOM   1440  CA  GLU   215       7.077  52.404  71.264  1.00  0.90
ATOM   1441  C   GLU   215       7.418  53.307  72.464  1.00  0.90
ATOM   1442  O   GLU   215       6.510  53.884  73.043  1.00  0.90
ATOM   1443  CB  GLU   215       6.776  50.945  71.646  1.00  0.90
ATOM   1444  CG  GLU   215       6.019  50.222  70.564  1.00  1.00
ATOM   1445  CD  GLU   215       4.592  50.819  70.334  1.00  1.00
ATOM   1446  OE1 GLU   215       3.884  51.186  71.285  1.00  1.20
ATOM   1447  OE2 GLU   215       4.184  50.865  69.142  1.00  1.20
ATOM   1448  N   ASP   216       8.697  53.433  72.820  1.00  0.90
ATOM   1449  CA  ASP   216       9.106  54.391  73.849  1.00  0.90
ATOM   1450  C   ASP   216       8.877  55.817  73.366  1.00  0.90
ATOM   1451  O   ASP   216       8.613  56.711  74.174  1.00  0.90
ATOM   1452  CB  ASP   216      10.562  54.198  74.269  1.00  0.90
ATOM   1453  CG  ASP   216      10.813  52.934  75.056  1.00  1.00
ATOM   1454  OD1 ASP   216       9.868  52.280  75.562  1.00  1.00
ATOM   1455  OD2 ASP   216      11.959  52.550  75.305  1.00  1.20
ATOM   1456  N   ILE   217       8.970  56.023  72.050  1.00  0.90
ATOM   1457  CA  ILE   217       8.690  57.301  71.426  1.00  0.90
ATOM   1458  C   ILE   217       7.231  57.702  71.499  1.00  0.90
ATOM   1459  O   ILE   217       6.918  58.845  71.812  1.00  0.90
ATOM   1460  CB  ILE   217       8.692  57.903  72.832  1.00  0.90
ATOM   1461  CG1 ILE   217       8.354  59.394  72.898  1.00  1.00
ATOM   1462  CG2 ILE   217      10.038  57.554  73.479  1.00  1.00
ATOM   1463  CD1 ILE   217       8.012  59.899  74.263  1.00  1.20
ATOM   1464  N   SER   218       5.099  57.297  71.854  1.00  0.90
ATOM   1465  CA  SER   218       3.646  57.462  71.898  1.00  0.90
ATOM   1466  C   SER   218       3.183  57.788  73.323  1.00  0.90
ATOM   1467  O   SER   218       2.375  58.686  73.518  1.00  0.90
ATOM   1468  CB  SER   218       2.914  56.183  71.392  1.00  0.90
ATOM   1469  OG  SER   218       1.399  56.389  71.370  1.00  1.00
ATOM   1470  N   ASN   219       3.173  56.220  74.829  1.00  0.90
ATOM   1471  CA  ASN   219       2.811  56.373  76.235  1.00  0.90
ATOM   1472  C   ASN   219       3.183  57.738  76.823  1.00  0.90
ATOM   1473  O   ASN   219       2.414  58.296  77.593  1.00  0.90
ATOM   1474  CB  ASN   219       3.396  55.277  77.095  1.00  0.90
ATOM   1475  CG  ASN   219       2.863  53.886  76.795  1.00  1.00
ATOM   1476  OD1 ASN   219       3.720  53.027  76.433  1.00  1.00
ATOM   1477  ND2 ASN   219       1.590  53.694  76.826  1.00  1.20
ATOM   1478  N   PRO   220       4.356  58.258  76.477  1.00  0.90
ATOM   1479  CA  PRO   220       4.793  59.543  77.008  1.00  0.90
ATOM   1480  C   PRO   220       3.956  60.667  76.400  1.00  0.90
ATOM   1481  O   PRO   220       3.497  61.544  77.107  1.00  0.90
ATOM   1482  CB  PRO   220       6.295  59.757  76.768  1.00  0.90
ATOM   1483  CG  PRO   220       7.008  58.619  76.045  1.00  1.00
ATOM   1484  CD  PRO   220       5.527  58.008  75.277  1.00  1.00
ATOM   1485  N   GLU   221       3.747  60.620  75.086  1.00  0.90
ATOM   1486  CA  GLU   221       2.900  61.564  74.377  1.00  0.90
ATOM   1487  C   GLU   221       1.507  61.710  74.998  1.00  0.90
ATOM   1488  O   GLU   221       0.996  62.831  75.151  1.00  0.90
ATOM   1489  CB  GLU   221       2.759  61.120  72.919  1.00  0.90
ATOM   1490  CG  GLU   221       4.002  61.177  72.244  1.00  1.00
ATOM   1491  CD  GLU   221       4.695  62.649  72.038  1.00  1.00
ATOM   1492  OE1 GLU   221       4.052  63.623  71.755  1.00  1.20
ATOM   1493  OE2 GLU   221       5.927  62.733  72.189  1.00  1.20
ATOM   1494  N   LYS   222       0.890  60.578  75.331  1.00  0.90
ATOM   1495  CA  LYS   222      -0.447  60.546  75.941  1.00  0.90
ATOM   1496  C   LYS   222      -0.444  61.049  77.386  1.00  0.90
ATOM   1497  O   LYS   222      -1.472  61.528  77.899  1.00  0.90
ATOM   1498  CB  LYS   222      -1.107  59.139  75.815  1.00  0.90
ATOM   1499  CG  LYS   222      -2.511  59.131  76.379  1.00  1.00
ATOM   1500  CD  LYS   222      -3.089  57.723  76.220  1.00  1.00
ATOM   1501  CE  LYS   222      -2.498  56.630  77.024  1.00  1.20
ATOM   1502  NZ  LYS   222      -2.713  56.812  78.508  1.00  1.20
ATOM   1503  N   ILE   223       0.712  60.935  78.036  1.00  0.90
ATOM   1504  CA  ILE   223       0.912  61.469  79.387  1.00  0.90
ATOM   1505  C   ILE   223       0.979  63.025  79.415  1.00  0.90
ATOM   1506  O   ILE   223       0.528  63.654  80.372  1.00  0.90
ATOM   1507  CB  ILE   223       2.183  60.831  79.943  1.00  0.90
ATOM   1508  CG1 ILE   223       2.176  59.338  80.175  1.00  1.00
ATOM   1509  CG2 ILE   223       2.568  61.604  81.213  1.00  1.00
ATOM   1510  CD1 ILE   223       3.415  58.667  80.491  1.00  1.20
ATOM   1511  N   ARG   224       1.497  63.634  78.350  1.00  0.90
ATOM   1512  CA  ARG   224       1.685  65.078  78.291  1.00  0.90
ATOM   1513  C   ARG   224       0.375  65.799  78.494  1.00  0.90
ATOM   1514  O   ARG   224       0.343  66.892  79.064  1.00  0.90
ATOM   1515  CB  ARG   224       2.298  65.530  76.973  1.00  0.90
ATOM   1516  CG  ARG   224       3.742  65.130  76.722  1.00  1.00
ATOM   1517  CD  ARG   224       4.050  65.620  75.332  1.00  1.00
ATOM   1518  NE  ARG   224       5.432  65.242  75.064  1.00  1.20
ATOM   1519  CZ  ARG   224       6.076  65.563  73.944  1.00  1.20
ATOM   1520  NH1 ARG   224       5.422  66.194  72.968  1.00  1.50
ATOM   1521  NH2 ARG   224       7.344  65.187  73.815  1.00  1.50
TER
END
