
#######################################################
#                                                     #
#                        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_4_2-D2
# Molecule2: number of CA atoms   81 (  636),  selected    6 , name T0386_D2.pdb
# PARAMETERS: T0386TS074_4_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         0.36     0.36
  LCS_AVERAGE:      7.41

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6       219 - 224         0.36     0.36
  LCS_AVERAGE:      7.41

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6       219 - 224         0.36     0.36
  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     5    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    0.25   0.36   0.36   0.36   0.36   0.36   0.36   0.36   0.36   0.36   0.36   0.36   0.36   0.36   0.36   0.36   0.36   0.36   0.36   0.36
GDT RMS_ALL_CA   0.40   0.36   0.36   0.36   0.36   0.36   0.36   0.36   0.36   0.36   0.36   0.36   0.36   0.36   0.36   0.36   0.36   0.36   0.36   0.36

#      Molecule1      Molecule2       DISTANCE
LGA    N     219      N     219          0.175
LGA    P     220      P     220          0.201
LGA    E     221      E     221          0.567
LGA    K     222      K     222          0.258
LGA    I     223      I     223          0.259
LGA    R     224      R     224          0.483

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)    6   81    4.0      6    0.36     7.407     7.407     1.317

LGA_LOCAL      RMSD =  0.356  Number of atoms =    6  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  0.356  Number of atoms =    6 
Std_ALL_ATOMS  RMSD =  0.356  (standard rmsd on all 6 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.244730 * X  +   0.952498 * Y  +   0.181262 * Z  + -60.873806
  Y_new =  -0.744333 * X  +  -0.064759 * Y  +  -0.664661 * Z  +  48.129898
  Z_new =  -0.621350 * X  +  -0.297582 * Y  +   0.724824 * Z  +  94.500587 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.389574    2.752019  [ DEG:   -22.3209    157.6790 ]
  Theta =   0.670464    2.471128  [ DEG:    38.4148    141.5852 ]
  Phi   =  -1.888453    1.253140  [ DEG:  -108.2004     71.7996 ]
 
# 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_4_2-D2                             
REMARK     2: T0386_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0386TS074_4_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   0.36   7.407     0.36
REMARK  ---------------------------------------------------------- 
MOLECULE T0386TS074_4_2-D2
REMARK PARENT number 2
PFRMAT TS
TARGET T0386
PARENT 2g03_A
ATOM   1470  N   ASN   219       2.462  54.886  75.736  1.00  0.20
ATOM   1471  CA  ASN   219       2.930  55.781  74.683  1.00  0.20
ATOM   1472  C   ASN   219       2.717  57.265  74.993  1.00  0.20
ATOM   1473  O   ASN   219       3.582  58.076  74.694  1.00  0.20
ATOM   1474  CB  ASN   219       2.313  55.453  73.343  1.00  0.20
ATOM   1475  CG  ASN   219       2.702  54.094  72.783  1.00  0.30
ATOM   1476  OD1 ASN   219       3.872  54.002  72.307  1.00  0.30
ATOM   1477  ND2 ASN   219       1.808  53.169  72.735  1.00  0.50
ATOM   1478  N   PRO   220       1.573  57.615  75.571  1.00  0.20
ATOM   1479  CA  PRO   220       1.285  59.010  75.882  1.00  0.20
ATOM   1480  C   PRO   220       2.172  59.478  77.034  1.00  0.20
ATOM   1481  O   PRO   220       2.752  60.546  76.970  1.00  0.20
ATOM   1482  CB  PRO   220      -0.206  59.208  76.195  1.00  0.20
ATOM   1483  CG  PRO   220      -1.062  57.947  76.119  1.00  0.30
ATOM   1484  CD  PRO   220       0.307  56.849  76.397  1.00  0.30
ATOM   1485  N   GLU   221       2.288  58.659  78.078  1.00  0.20
ATOM   1486  CA  GLU   221       3.163  58.924  79.207  1.00  0.20
ATOM   1487  C   GLU   221       4.602  59.248  78.792  1.00  0.20
ATOM   1488  O   GLU   221       5.217  60.188  79.321  1.00  0.20
ATOM   1489  CB  GLU   221       3.167  57.708  80.137  1.00  0.20
ATOM   1490  CG  GLU   221       1.891  57.500  80.714  1.00  0.30
ATOM   1491  CD  GLU   221       1.315  58.649  81.733  1.00  0.30
ATOM   1492  OE1 GLU   221       2.018  59.205  82.531  1.00  0.50
ATOM   1493  OE2 GLU   221       0.108  58.938  81.653  1.00  0.50
ATOM   1494  N   LYS   222       5.140  58.456  77.868  1.00  0.20
ATOM   1495  CA  LYS   222       6.508  58.635  77.359  1.00  0.20
ATOM   1496  C   LYS   222       6.646  59.875  76.474  1.00  0.20
ATOM   1497  O   LYS   222       7.743  60.446  76.340  1.00  0.20
ATOM   1498  CB  LYS   222       7.035  57.351  76.649  1.00  0.20
ATOM   1499  CG  LYS   222       8.468  57.516  76.193  1.00  0.30
ATOM   1500  CD  LYS   222       8.910  56.221  75.507  1.00  0.30
ATOM   1501  CE  LYS   222       8.282  55.864  74.215  1.00  0.50
ATOM   1502  NZ  LYS   222       8.611  56.845  73.114  1.00  0.50
ATOM   1503  N   ILE   223       5.431  59.884  76.034  1.00  0.20
ATOM   1504  CA  ILE   223       5.464  61.144  75.285  1.00  0.20
ATOM   1505  C   ILE   223       5.586  62.392  76.209  1.00  0.20
ATOM   1506  O   ILE   223       6.223  63.381  75.846  1.00  0.20
ATOM   1507  CB  ILE   223       4.205  61.192  74.422  1.00  0.20
ATOM   1508  CG1 ILE   223       4.064  60.159  73.328  1.00  0.30
ATOM   1509  CG2 ILE   223       4.074  62.621  73.876  1.00  0.30
ATOM   1510  CD1 ILE   223       2.803  60.031  72.636  1.00  0.50
ATOM   1511  N   ARG   224       5.015  62.321  77.410  1.00  0.20
ATOM   1512  CA  ARG   224       4.994  63.449  78.332  1.00  0.20
ATOM   1513  C   ARG   224       6.396  63.914  78.645  1.00  0.20
ATOM   1514  O   ARG   224       6.627  65.106  78.861  1.00  0.20
ATOM   1515  CB  ARG   224       4.280  63.120  79.635  1.00  0.20
ATOM   1516  CG  ARG   224       2.779  62.900  79.553  1.00  0.30
ATOM   1517  CD  ARG   224       2.362  62.507  80.945  1.00  0.30
ATOM   1518  NE  ARG   224       0.922  62.284  80.891  1.00  0.50
ATOM   1519  CZ  ARG   224       0.188  61.975  81.957  1.00  0.50
ATOM   1520  NH1 ARG   224       0.786  61.776  83.132  1.00  0.80
ATOM   1521  NH2 ARG   224      -1.122  61.818  81.797  1.00  0.80
TER
END
