
#######################################################
#                                                     #
#                        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_3_2-D2
# Molecule2: number of CA atoms   81 (  636),  selected    6 , name T0386_D2.pdb
# PARAMETERS: T0386TS074_3_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         0.38     0.38
  LCS_AVERAGE:      7.41

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6       219 - 224         0.38     0.38
  LCS_AVERAGE:      7.41

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6       219 - 224         0.38     0.38
  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     5    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     5    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     5    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     5    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     5    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     3    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      5      6      6      6      6      6      6      6      6      6      6      6      6      6      6      6      6      6      6      6 
GDT PERCENT_CA   6.17   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    0.18   0.38   0.38   0.38   0.38   0.38   0.38   0.38   0.38   0.38   0.38   0.38   0.38   0.38   0.38   0.38   0.38   0.38   0.38   0.38
GDT RMS_ALL_CA   0.52   0.38   0.38   0.38   0.38   0.38   0.38   0.38   0.38   0.38   0.38   0.38   0.38   0.38   0.38   0.38   0.38   0.38   0.38   0.38

#      Molecule1      Molecule2       DISTANCE
LGA    N     219      N     219          0.210
LGA    P     220      P     220          0.151
LGA    E     221      E     221          0.523
LGA    K     222      K     222          0.346
LGA    I     223      I     223          0.247
LGA    R     224      R     224          0.585

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)    6   81    4.0      6    0.38     7.407     7.407     1.252

LGA_LOCAL      RMSD =  0.379  Number of atoms =    6  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  0.379  Number of atoms =    6 
Std_ALL_ATOMS  RMSD =  0.379  (standard rmsd on all 6 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.201838 * X  +   0.971635 * Y  +   0.123235 * Z  + -62.434959
  Y_new =  -0.819690 * X  +  -0.098711 * Y  +  -0.564237 * Z  +  50.280830
  Z_new =  -0.536068 * X  +  -0.214899 * Y  +   0.816364 * Z  +  91.388237 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.257400    2.884193  [ DEG:   -14.7479    165.2521 ]
  Theta =   0.565772    2.575820  [ DEG:    32.4164    147.5836 ]
  Phi   =  -1.812230    1.329362  [ DEG:  -103.8332     76.1668 ]
 
# 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-D2                             
REMARK     2: T0386_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0386TS074_3_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   0.38   7.407     0.38
REMARK  ---------------------------------------------------------- 
MOLECULE T0386TS074_3_2-D2
REMARK PARENT number 2
PFRMAT TS
TARGET T0386
PARENT 2g03_A
ATOM   1470  N   ASN   219       2.180  54.931  75.754  1.00  0.50
ATOM   1471  CA  ASN   219       2.728  55.785  74.705  1.00  0.50
ATOM   1472  C   ASN   219       2.661  57.282  75.029  1.00  0.50
ATOM   1473  O   ASN   219       3.599  58.007  74.732  1.00  0.50
ATOM   1474  CB  ASN   219       2.075  55.531  73.366  1.00  0.50
ATOM   1475  CG  ASN   219       2.330  54.146  72.793  1.00  0.60
ATOM   1476  OD1 ASN   219       3.482  53.945  72.310  1.00  0.60
ATOM   1477  ND2 ASN   219       1.348  53.313  72.741  1.00  0.80
ATOM   1478  N   PRO   220       1.559  57.735  75.617  1.00  0.50
ATOM   1479  CA  PRO   220       1.409  59.149  75.940  1.00  0.50
ATOM   1480  C   PRO   220       2.342  59.518  77.091  1.00  0.50
ATOM   1481  O   PRO   220       3.022  60.526  77.033  1.00  0.50
ATOM   1482  CB  PRO   220      -0.055  59.488  76.262  1.00  0.50
ATOM   1483  CG  PRO   220      -1.029  58.317  76.181  1.00  0.60
ATOM   1484  CD  PRO   220       0.228  57.088  76.443  1.00  0.60
ATOM   1485  N   GLU   221       2.383  58.683  78.129  1.00  0.50
ATOM   1486  CA  GLU   221       3.284  58.851  79.255  1.00  0.50
ATOM   1487  C   GLU   221       4.745  59.037  78.836  1.00  0.50
ATOM   1488  O   GLU   221       5.451  59.909  79.369  1.00  0.50
ATOM   1489  CB  GLU   221       3.174  57.633  80.175  1.00  0.50
ATOM   1490  CG  GLU   221       1.886  57.546  80.756  1.00  0.60
ATOM   1491  CD  GLU   221       1.428  58.735  81.787  1.00  0.60
ATOM   1492  OE1 GLU   221       2.185  59.213  82.588  1.00  0.80
ATOM   1493  OE2 GLU   221       0.256  59.143  81.715  1.00  0.80
ATOM   1494  N   LYS   222       5.201  58.206  77.902  1.00  0.50
ATOM   1495  CA  LYS   222       6.577  58.256  77.387  1.00  0.50
ATOM   1496  C   LYS   222       6.830  59.485  76.512  1.00  0.50
ATOM   1497  O   LYS   222       7.978  59.948  76.377  1.00  0.50
ATOM   1498  CB  LYS   222       6.974  56.934  76.663  1.00  0.50
ATOM   1499  CG  LYS   222       8.414  56.963  76.201  1.00  0.60
ATOM   1500  CD  LYS   222       8.726  55.637  75.503  1.00  0.60
ATOM   1501  CE  LYS   222       8.062  55.353  74.211  1.00  0.80
ATOM   1502  NZ  LYS   222       8.480  56.307  73.116  1.00  0.80
ATOM   1503  N   ILE   223       5.758  60.005  75.921  1.00  0.50
ATOM   1504  CA  ILE   223       5.812  61.245  75.140  1.00  0.50
ATOM   1505  C   ILE   223       6.009  62.509  76.031  1.00  0.50
ATOM   1506  O   ILE   223       6.670  63.464  75.624  1.00  0.50
ATOM   1507  CB  ILE   223       4.529  61.320  74.317  1.00  0.50
ATOM   1508  CG1 ILE   223       4.314  60.268  73.252  1.00  0.60
ATOM   1509  CG2 ILE   223       4.432  62.740  73.741  1.00  0.60
ATOM   1510  CD1 ILE   223       3.026  60.171  72.604  1.00  0.80
ATOM   1511  N   ARG   224       4.619  62.419  77.557  1.00  0.50
ATOM   1512  CA  ARG   224       4.535  63.657  78.321  1.00  0.50
ATOM   1513  C   ARG   224       5.912  64.165  78.675  1.00  0.50
ATOM   1514  O   ARG   224       6.133  65.375  78.750  1.00  0.50
ATOM   1515  CB  ARG   224       3.725  63.496  79.599  1.00  0.50
ATOM   1516  CG  ARG   224       2.233  63.261  79.434  1.00  0.60
ATOM   1517  CD  ARG   224       1.711  63.050  80.830  1.00  0.60
ATOM   1518  NE  ARG   224       0.278  62.816  80.698  1.00  0.80
ATOM   1519  CZ  ARG   224      -0.536  62.645  81.738  1.00  0.80
ATOM   1520  NH1 ARG   224      -0.028  62.602  82.970  1.00  1.10
ATOM   1521  NH2 ARG   224      -1.831  62.462  81.503  1.00  1.10
TER
END
