
#######################################################
#                                                     #
#                        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_3_2
# Molecule2: number of CA atoms  291 ( 2337),  selected   16 , name T0386.pdb
# PARAMETERS: T0386TS074_3_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         3.36     3.36
  LCS_AVERAGE:      5.50

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    12       209 - 220         1.31     4.29
  LCS_AVERAGE:      3.61

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    10       209 - 218         0.83     4.53
  LONGEST_CONTINUOUS_SEGMENT:    10       210 - 219         0.89     4.35
  LCS_AVERAGE:      3.03

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    6   10   11   12   12   12   13   13   13   14   16   16   16   16   16   16   16   16   16 
LCS_GDT     M     210     M     210     10   12   16     6    9   10   11   12   12   12   13   13   13   15   16   16   16   16   16   16   16   16   16 
LCS_GDT     Q     211     Q     211     10   12   16     5    9   10   11   12   12   12   13   13   13   15   16   16   16   16   16   16   16   16   16 
LCS_GDT     H     212     H     212     10   12   16     5    9   10   11   12   12   12   13   13   13   15   16   16   16   16   16   16   16   16   16 
LCS_GDT     L     213     L     213     10   12   16     5    9   10   11   12   12   12   13   13   13   15   16   16   16   16   16   16   16   16   16 
LCS_GDT     F     214     F     214     10   12   16     6    9   10   11   12   12   12   13   13   13   15   16   16   16   16   16   16   16   16   16 
LCS_GDT     E     215     E     215     10   12   16     6    9   10   11   12   12   12   13   13   13   15   16   16   16   16   16   16   16   16   16 
LCS_GDT     D     216     D     216     10   12   16     6    9   10   11   12   12   12   13   13   13   15   16   16   16   16   16   16   16   16   16 
LCS_GDT     I     217     I     217     10   12   16     6    9   10   11   12   12   12   13   13   13   15   16   16   16   16   16   16   16   16   16 
LCS_GDT     S     218     S     218     10   12   16     6    9   10   11   12   12   12   13   13   13   15   16   16   16   16   16   16   16   16   16 
LCS_GDT     N     219     N     219     10   12   16     5    6    9   11   12   12   12   13   13   13   15   16   16   16   16   16   16   16   16   16 
LCS_GDT     P     220     P     220      7   12   16     5    6    7   11   12   12   12   13   13   13   15   16   16   16   16   16   16   16   16   16 
LCS_GDT     E     221     E     221      6    6   16     5    6    6    6    6    6    6   11   13   13   15   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    8   11   12   15   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    7    7   12   15   16   16   16   16   16   16   16   16   16 
LCS_GDT     R     224     R     224      6    6   16     3    6    6    6    8   12   12   13   13   13   15   16   16   16   16   16   16   16   16   16 
LCS_AVERAGE  LCS_A:   4.04  (   3.03    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      9     10     11     12     12     12     13     13     13     15     16     16     16     16     16     16     16     16     16 
GDT PERCENT_CA   2.06   3.09   3.44   3.78   4.12   4.12   4.12   4.47   4.47   4.47   5.15   5.50   5.50   5.50   5.50   5.50   5.50   5.50   5.50   5.50
GDT RMS_LOCAL    0.22   0.61   0.83   1.07   1.31   1.31   1.31   1.98   1.98   1.98   3.37   3.36   3.36   3.36   3.36   3.36   3.36   3.36   3.36   3.36
GDT RMS_ALL_CA   4.76   4.41   4.53   4.35   4.29   4.29   4.29   3.65   3.65   3.65   3.41   3.36   3.36   3.36   3.36   3.36   3.36   3.36   3.36   3.36

#      Molecule1      Molecule2       DISTANCE
LGA    P     209      P     209          1.621
LGA    M     210      M     210          1.079
LGA    Q     211      Q     211          0.764
LGA    H     212      H     212          0.907
LGA    L     213      L     213          0.956
LGA    F     214      F     214          0.697
LGA    E     215      E     215          1.041
LGA    D     216      D     216          2.364
LGA    I     217      I     217          2.361
LGA    S     218      S     218          1.446
LGA    N     219      N     219          2.020
LGA    P     220      P     220          3.848
LGA    E     221      E     221          7.064
LGA    K     222      K     222          7.782
LGA    I     223      I     223          6.021
LGA    R     224      R     224          3.814

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   16  291    4.0     13    1.98     4.210     4.146     0.624

LGA_LOCAL      RMSD =  1.983  Number of atoms =   13  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  3.545  Number of atoms =   16 
Std_ALL_ATOMS  RMSD =  3.361  (standard rmsd on all 16 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.114510 * X  +  -0.982173 * Y  +  -0.149078 * Z  +  68.057747
  Y_new =  -0.992969 * X  +  -0.108631 * Y  +  -0.047029 * Z  +  55.484169
  Z_new =   0.029997 * X  +   0.153415 * Y  +  -0.987706 * Z  +  57.319221 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.987499   -0.154093  [ DEG:   171.1711     -8.8289 ]
  Theta =  -0.030001   -3.111592  [ DEG:    -1.7189   -178.2811 ]
  Phi   =  -1.455982    1.685610  [ DEG:   -83.4216     96.5784 ]
 
# 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_3_2                                
REMARK     2: T0386.pdb                                     
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0386TS074_3_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   1.98   4.146     3.36
REMARK  ---------------------------------------------------------- 
MOLECULE T0386TS074_3_2
REMARK PARENT number 2
PFRMAT TS
TARGET T0386
PARENT 2g03_A
ATOM   1386  N   PRO   209      15.769  48.962  67.805  1.00  0.57
ATOM   1387  CA  PRO   209      15.766  50.372  67.447  1.00  0.57
ATOM   1388  C   PRO   209      14.347  50.666  67.049  1.00  0.57
ATOM   1389  O   PRO   209      13.686  51.433  67.739  1.00  0.57
ATOM   1390  CB  PRO   209      16.634  50.713  66.222  1.00  0.57
ATOM   1391  CG  PRO   209      17.354  49.523  65.586  1.00  0.67
ATOM   1392  CD  PRO   209      16.206  48.328  66.213  1.00  0.67
ATOM   1393  N   MET   210      13.901  49.980  65.984  1.00  0.50
ATOM   1394  CA  MET   210      12.610  50.209  65.389  1.00  0.50
ATOM   1395  C   MET   210      11.438  50.104  66.326  1.00  0.50
ATOM   1396  O   MET   210      10.690  51.065  66.425  1.00  0.50
ATOM   1397  CB  MET   210      12.434  49.252  64.212  1.00  0.50
ATOM   1398  CG  MET   210      13.397  49.474  63.043  1.00  0.60
ATOM   1399  SD  MET   210      13.137  51.097  62.223  1.00  0.60
ATOM   1400  CE  MET   210      11.582  50.834  61.438  1.00  0.80
ATOM   1401  N   GLN   211      11.424  49.067  67.133  1.00  0.50
ATOM   1402  CA  GLN   211      10.180  48.905  67.887  1.00  0.50
ATOM   1403  C   GLN   211      10.189  49.627  69.251  1.00  0.50
ATOM   1404  O   GLN   211       9.198  50.246  69.627  1.00  0.50
ATOM   1405  CB  GLN   211       9.818  47.419  68.043  1.00  0.50
ATOM   1406  CG  GLN   211       8.515  47.153  68.745  1.00  0.60
ATOM   1407  CD  GLN   211       7.313  47.614  68.060  1.00  0.60
ATOM   1408  OE1 GLN   211       7.050  47.167  66.928  1.00  0.80
ATOM   1409  NE2 GLN   211       6.510  48.471  68.685  1.00  0.80
ATOM   1410  N   HIS   212      11.304  49.574  69.971  1.00  0.50
ATOM   1411  CA  HIS   212      11.381  50.177  71.291  1.00  0.50
ATOM   1412  C   HIS   212      11.344  51.711  71.231  1.00  0.50
ATOM   1413  O   HIS   212      10.647  52.364  72.026  1.00  0.50
ATOM   1414  CB  HIS   212      12.630  49.698  72.018  1.00  0.50
ATOM   1415  CG  HIS   212      12.773  50.219  73.454  1.00  0.60
ATOM   1416  ND1 HIS   212      13.257  51.515  73.704  1.00  0.60
ATOM   1417  CD2 HIS   212      12.400  49.643  74.581  1.00  0.80
ATOM   1418  CE1 HIS   212      13.200  51.730  75.059  1.00  0.80
ATOM   1419  NE2 HIS   212      12.673  50.569  75.616  1.00  1.10
ATOM   1420  N   LEU   213      12.082  52.286  70.282  1.00  0.50
ATOM   1421  CA  LEU   213      12.069  53.726  70.053  1.00  0.50
ATOM   1422  C   LEU   213      10.681  54.175  69.621  1.00  0.50
ATOM   1423  O   LEU   213      10.172  55.176  70.129  1.00  0.50
ATOM   1424  CB  LEU   213      13.161  54.149  69.027  1.00  0.50
ATOM   1425  CG  LEU   213      13.235  55.675  68.976  1.00  0.60
ATOM   1426  CD1 LEU   213      14.607  56.129  68.761  1.00  0.60
ATOM   1427  CD2 LEU   213      12.495  56.078  67.553  1.00  0.80
ATOM   1428  N   PHE   214      10.057  53.449  68.694  1.00  0.50
ATOM   1429  CA  PHE   214       8.707  53.817  68.257  1.00  0.50
ATOM   1430  C   PHE   214       7.705  53.750  69.444  1.00  0.50
ATOM   1431  O   PHE   214       7.072  54.742  69.792  1.00  0.50
ATOM   1432  CB  PHE   214       8.218  52.944  67.071  1.00  0.50
ATOM   1433  CG  PHE   214       9.084  53.197  65.826  1.00  0.60
ATOM   1434  CD1 PHE   214       9.648  54.471  65.682  1.00  0.60
ATOM   1435  CD2 PHE   214       8.914  52.422  64.702  1.00  0.80
ATOM   1436  CE1 PHE   214      10.219  54.816  64.473  1.00  0.80
ATOM   1437  CE2 PHE   214       9.488  52.727  63.496  1.00  1.10
ATOM   1438  CZ  PHE   214      10.181  53.962  63.388  1.00  1.10
ATOM   1439  N   GLU   215       7.604  52.605  70.094  1.00  0.50
ATOM   1440  CA  GLU   215       6.575  52.428  71.111  1.00  0.50
ATOM   1441  C   GLU   215       6.787  53.165  72.446  1.00  0.50
ATOM   1442  O   GLU   215       5.828  53.689  72.990  1.00  0.50
ATOM   1443  CB  GLU   215       6.211  50.943  71.266  1.00  0.50
ATOM   1444  CG  GLU   215       5.100  50.731  72.258  1.00  0.60
ATOM   1445  CD  GLU   215       3.751  51.366  71.784  1.00  0.60
ATOM   1446  OE1 GLU   215       3.611  51.803  70.632  1.00  0.80
ATOM   1447  OE2 GLU   215       2.833  51.451  72.645  1.00  0.80
ATOM   1448  N   ASP   216       8.019  53.208  72.957  1.00  0.50
ATOM   1449  CA  ASP   216       8.320  54.018  74.138  1.00  0.50
ATOM   1450  C   ASP   216       8.168  55.499  73.821  1.00  0.50
ATOM   1451  O   ASP   216       7.825  56.292  74.701  1.00  0.50
ATOM   1452  CB  ASP   216       9.717  53.733  74.691  1.00  0.50
ATOM   1453  CG  ASP   216       9.858  52.373  75.333  1.00  0.60
ATOM   1454  OD1 ASP   216       8.852  51.687  75.642  1.00  0.60
ATOM   1455  OD2 ASP   216      10.962  51.929  75.657  1.00  0.80
ATOM   1456  N   ILE   217       8.413  55.866  72.559  1.00  0.50
ATOM   1457  CA  ILE   217       8.225  57.220  72.077  1.00  0.50
ATOM   1458  C   ILE   217       6.772  57.649  72.037  1.00  0.50
ATOM   1459  O   ILE   217       6.442  58.752  72.456  1.00  0.50
ATOM   1460  CB  ILE   217       8.074  57.640  73.540  1.00  0.50
ATOM   1461  CG1 ILE   217       9.304  57.392  74.415  1.00  0.60
ATOM   1462  CG2 ILE   217       6.800  56.975  74.078  1.00  0.60
ATOM   1463  CD1 ILE   217      10.153  58.599  74.656  1.00  0.80
ATOM   1464  N   SER   218       5.906  56.799  71.490  1.00  0.50
ATOM   1465  CA  SER   218       4.459  57.009  71.512  1.00  0.50
ATOM   1466  C   SER   218       3.956  57.157  72.954  1.00  0.50
ATOM   1467  O   SER   218       3.170  58.048  73.244  1.00  0.50
ATOM   1468  CB  SER   218       3.703  55.838  70.813  1.00  0.50
ATOM   1469  OG  SER   218       3.951  54.515  71.539  1.00  0.60
ATOM   1470  N   ASN   219       3.682  57.112  74.475  1.00  0.50
ATOM   1471  CA  ASN   219       3.182  57.344  75.826  1.00  0.50
ATOM   1472  C   ASN   219       3.388  58.780  76.322  1.00  0.50
ATOM   1473  O   ASN   219       2.509  59.328  76.971  1.00  0.50
ATOM   1474  CB  ASN   219       3.772  56.377  76.826  1.00  0.50
ATOM   1475  CG  ASN   219       3.382  54.925  76.604  1.00  0.60
ATOM   1476  OD1 ASN   219       2.204  54.607  76.938  1.00  0.60
ATOM   1477  ND2 ASN   219       4.285  54.101  76.196  1.00  0.80
ATOM   1478  N   PRO   220       4.542  59.372  76.030  1.00  0.50
ATOM   1479  CA  PRO   220       4.824  60.729  76.482  1.00  0.50
ATOM   1480  C   PRO   220       3.959  61.722  75.709  1.00  0.50
ATOM   1481  O   PRO   220       3.367  62.610  76.294  1.00  0.50
ATOM   1482  CB  PRO   220       6.320  61.054  76.351  1.00  0.50
ATOM   1483  CG  PRO   220       7.185  59.928  75.793  1.00  0.60
ATOM   1484  CD  PRO   220       5.834  59.130  74.961  1.00  0.60
ATOM   1485  N   GLU   221       3.874  61.551  74.390  1.00  0.50
ATOM   1486  CA  GLU   221       3.023  62.357  73.533  1.00  0.50
ATOM   1487  C   GLU   221       1.572  62.429  74.018  1.00  0.50
ATOM   1488  O   GLU   221       0.960  63.509  74.029  1.00  0.50
ATOM   1489  CB  GLU   221       3.052  61.786  72.113  1.00  0.50
ATOM   1490  CG  GLU   221       4.343  61.898  71.543  1.00  0.60
ATOM   1491  CD  GLU   221       4.932  63.403  71.267  1.00  0.60
ATOM   1492  OE1 GLU   221       4.242  64.291  70.846  1.00  0.80
ATOM   1493  OE2 GLU   221       6.132  63.608  71.514  1.00  0.80
ATOM   1494  N   LYS   222       1.020  61.279  74.396  1.00  0.50
ATOM   1495  CA  LYS   222      -0.361  61.178  74.892  1.00  0.50
ATOM   1496  C   LYS   222      -0.530  61.793  76.283  1.00  0.50
ATOM   1497  O   LYS   222      -1.636  62.220  76.662  1.00  0.50
ATOM   1498  CB  LYS   222      -0.892  59.713  74.835  1.00  0.50
ATOM   1499  CG  LYS   222      -2.335  59.627  75.277  1.00  0.60
ATOM   1500  CD  LYS   222      -2.781  58.165  75.194  1.00  0.60
ATOM   1501  CE  LYS   222      -2.181  57.197  76.138  1.00  0.80
ATOM   1502  NZ  LYS   222      -2.545  57.479  77.578  1.00  0.80
ATOM   1503  N   ILE   223       0.566  61.835  77.034  1.00  0.50
ATOM   1504  CA  ILE   223       0.599  62.491  78.346  1.00  0.50
ATOM   1505  C   ILE   223       0.538  64.045  78.242  1.00  0.50
ATOM   1506  O   ILE   223      -0.048  64.706  79.098  1.00  0.50
ATOM   1507  CB  ILE   223       1.861  62.015  79.061  1.00  0.50
ATOM   1508  CG1 ILE   223       1.953  60.550  79.422  1.00  0.60
ATOM   1509  CG2 ILE   223       2.064  62.917  80.286  1.00  0.60
ATOM   1510  CD1 ILE   223       3.208  60.017  79.899  1.00  0.80
ATOM   1511  N   ARG   224       1.957  64.634  76.860  1.00  0.50
ATOM   1512  CA  ARG   224       2.170  66.076  76.846  1.00  0.50
ATOM   1513  C   ARG   224       0.853  66.814  76.835  1.00  0.50
ATOM   1514  O   ARG   224       0.741  67.902  77.402  1.00  0.50
ATOM   1515  CB  ARG   224       2.999  66.528  75.652  1.00  0.50
ATOM   1516  CG  ARG   224       4.459  66.110  75.640  1.00  0.60
ATOM   1517  CD  ARG   224       4.999  66.606  74.325  1.00  0.60
ATOM   1518  NE  ARG   224       6.402  66.210  74.286  1.00  0.80
ATOM   1519  CZ  ARG   224       7.227  66.530  73.291  1.00  0.80
ATOM   1520  NH1 ARG   224       6.752  67.176  72.226  1.00  1.10
ATOM   1521  NH2 ARG   224       8.494  66.138  73.370  1.00  1.10
TER
END
