
#######################################################
#                                                     #
#                        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    6 (   52),  selected    6 , name T0386TS074_1_2-D2
# Molecule2: number of CA atoms   81 (  636),  selected    6 , name T0386_D2.pdb
# PARAMETERS: T0386TS074_1_2-D2.T0386_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:     6       219 - 224         0.23     0.23
  LCS_AVERAGE:      7.41

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6       219 - 224         0.23     0.23
  LCS_AVERAGE:      7.41

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6       219 - 224         0.23     0.23
  LCS_AVERAGE:      7.41

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:   81
LCS_GDT     N     219     N     219      6    6    6     6    6    6    6    6    6    6    6    6    6    6    6    6    6    6    6    6    6    6    6 
LCS_GDT     P     220     P     220      6    6    6     6    6    6    6    6    6    6    6    6    6    6    6    6    6    6    6    6    6    6    6 
LCS_GDT     E     221     E     221      6    6    6     6    6    6    6    6    6    6    6    6    6    6    6    6    6    6    6    6    6    6    6 
LCS_GDT     K     222     K     222      6    6    6     6    6    6    6    6    6    6    6    6    6    6    6    6    6    6    6    6    6    6    6 
LCS_GDT     I     223     I     223      6    6    6     6    6    6    6    6    6    6    6    6    6    6    6    6    6    6    6    6    6    6    6 
LCS_GDT     R     224     R     224      6    6    6     6    6    6    6    6    6    6    6    6    6    6    6    6    6    6    6    6    6    6    6 
LCS_AVERAGE  LCS_A:   7.41  (   7.41    7.41    7.41 )

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      6      6      6      6      6      6      6      6      6      6      6      6      6      6      6      6      6      6      6 
GDT PERCENT_CA   7.41   7.41   7.41   7.41   7.41   7.41   7.41   7.41   7.41   7.41   7.41   7.41   7.41   7.41   7.41   7.41   7.41   7.41   7.41   7.41
GDT RMS_LOCAL    0.23   0.23   0.23   0.23   0.23   0.23   0.23   0.23   0.23   0.23   0.23   0.23   0.23   0.23   0.23   0.23   0.23   0.23   0.23   0.23
GDT RMS_ALL_CA   0.23   0.23   0.23   0.23   0.23   0.23   0.23   0.23   0.23   0.23   0.23   0.23   0.23   0.23   0.23   0.23   0.23   0.23   0.23   0.23

#      Molecule1      Molecule2       DISTANCE
LGA    N     219      N     219          0.164
LGA    P     220      P     220          0.189
LGA    E     221      E     221          0.382
LGA    K     222      K     222          0.165
LGA    I     223      I     223          0.079
LGA    R     224      R     224          0.258

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)    6   81    4.0      6    0.23     7.407     7.407     1.836

LGA_LOCAL      RMSD =  0.227  Number of atoms =    6  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  0.227  Number of atoms =    6 
Std_ALL_ATOMS  RMSD =  0.227  (standard rmsd on all 6 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.224974 * X  +   0.949993 * Y  +   0.216564 * Z  + -59.980419
  Y_new =  -0.759280 * X  +  -0.031635 * Y  +  -0.649994 * Z  +  46.063747
  Z_new =  -0.610639 * X  +  -0.310665 * Y  +   0.728428 * Z  +  95.516273 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.403129    2.738464  [ DEG:   -23.0976    156.9024 ]
  Theta =   0.656867    2.484725  [ DEG:    37.6357    142.3643 ]
  Phi   =  -1.858855    1.282738  [ DEG:  -106.5045     73.4955 ]
 
# 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-D2                             
REMARK     2: T0386_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0386TS074_1_2-D2.T0386_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:    6   81   4.0    6   0.23   7.407     0.23
REMARK  ---------------------------------------------------------- 
MOLECULE T0386TS074_1_2-D2
REMARK PARENT number 2
PFRMAT TS
TARGET T0386
PARENT 2g03_A
ATOM   1470  N   ASN   219       2.379  54.811  75.685  1.00  0.90
ATOM   1471  CA  ASN   219       2.878  55.719  74.658  1.00  0.90
ATOM   1472  C   ASN   219       2.695  57.201  75.001  1.00  0.90
ATOM   1473  O   ASN   219       3.580  58.000  74.731  1.00  0.90
ATOM   1474  CB  ASN   219       2.269  55.437  73.304  1.00  0.90
ATOM   1475  CG  ASN   219       2.635  54.084  72.716  1.00  1.00
ATOM   1476  OD1 ASN   219       1.670  53.300  72.478  1.00  1.00
ATOM   1477  ND2 ASN   219       3.882  53.783  72.593  1.00  1.20
ATOM   1478  N   PRO   220       1.551  57.563  75.575  1.00  0.90
ATOM   1479  CA  PRO   220       1.291  58.956  75.915  1.00  0.90
ATOM   1480  C   PRO   220       2.175  59.377  77.087  1.00  0.90
ATOM   1481  O   PRO   220       2.778  60.433  77.055  1.00  0.90
ATOM   1482  CB  PRO   220      -0.199  59.180  76.215  1.00  0.90
ATOM   1483  CG  PRO   220      -1.081  57.941  76.100  1.00  1.00
ATOM   1484  CD  PRO   220       0.259  56.806  76.368  1.00  1.00
ATOM   1485  N   GLU   221       2.260  58.532  78.113  1.00  0.90
ATOM   1486  CA  GLU   221       3.127  58.749  79.258  1.00  0.90
ATOM   1487  C   GLU   221       4.578  59.051  78.867  1.00  0.90
ATOM   1488  O   GLU   221       5.207  59.964  79.425  1.00  0.90
ATOM   1489  CB  GLU   221       3.093  57.513  80.159  1.00  0.90
ATOM   1490  CG  GLU   221       1.806  57.321  80.716  1.00  1.00
ATOM   1491  CD  GLU   221       1.243  58.457  81.755  1.00  1.00
ATOM   1492  OE1 GLU   221       1.950  58.979  82.575  1.00  1.20
ATOM   1493  OE2 GLU   221       0.044  58.776  81.668  1.00  1.20
ATOM   1494  N   LYS   222       5.109  58.269  77.931  1.00  0.90
ATOM   1495  CA  LYS   222       6.486  58.429  77.442  1.00  0.90
ATOM   1496  C   LYS   222       6.662  59.687  76.588  1.00  0.90
ATOM   1497  O   LYS   222       7.773  60.236  76.479  1.00  0.90
ATOM   1498  CB  LYS   222       6.993  57.151  76.707  1.00  0.90
ATOM   1499  CG  LYS   222       8.434  57.295  76.271  1.00  1.00
ATOM   1500  CD  LYS   222       8.856  56.007  75.560  1.00  1.00
ATOM   1501  CE  LYS   222       8.237  55.694  74.253  1.00  1.20
ATOM   1502  NZ  LYS   222       8.601  56.691  73.179  1.00  1.20
ATOM   1503  N   ILE   223       5.563  60.134  75.984  1.00  0.90
ATOM   1504  CA  ILE   223       5.538  61.387  75.222  1.00  0.90
ATOM   1505  C   ILE   223       5.625  62.648  76.133  1.00  0.90
ATOM   1506  O   ILE   223       6.219  63.656  75.751  1.00  0.90
ATOM   1507  CB  ILE   223       4.267  61.378  74.377  1.00  0.90
ATOM   1508  CG1 ILE   223       4.149  60.329  73.295  1.00  1.00
ATOM   1509  CG2 ILE   223       4.074  62.796  73.820  1.00  1.00
ATOM   1510  CD1 ILE   223       2.884  60.147  72.622  1.00  1.20
ATOM   1511  N   ARG   224       5.075  62.567  77.342  1.00  0.90
ATOM   1512  CA  ARG   224       5.023  63.703  78.254  1.00  0.90
ATOM   1513  C   ARG   224       6.411  64.224  78.543  1.00  0.90
ATOM   1514  O   ARG   224       6.600  65.425  78.743  1.00  0.90
ATOM   1515  CB  ARG   224       4.341  63.360  79.570  1.00  0.90
ATOM   1516  CG  ARG   224       2.849  63.083  79.512  1.00  1.00
ATOM   1517  CD  ARG   224       2.467  62.688  80.913  1.00  1.00
ATOM   1518  NE  ARG   224       1.036  62.410  80.882  1.00  1.20
ATOM   1519  CZ  ARG   224       0.328  62.084  81.962  1.00  1.20
ATOM   1520  NH1 ARG   224       0.950  61.920  83.129  1.00  1.50
ATOM   1521  NH2 ARG   224      -0.977  61.876  81.822  1.00  1.50
TER
END
