
#######################################################
#                                                     #
#                        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_2_2-D2
# Molecule2: number of CA atoms   81 (  636),  selected    6 , name T0386_D2.pdb
# PARAMETERS: T0386TS074_2_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     4    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    0.26   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   0.42   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          0.245
LGA    P     220      P     220          0.251
LGA    E     221      E     221          0.628
LGA    K     222      K     222          0.314
LGA    I     223      I     223          0.352
LGA    R     224      R     224          0.347

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)    6   81    4.0      6    0.38     7.407     7.407     1.253

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 =  -0.244872 * X  +   0.955881 * Y  +   0.162263 * Z  + -61.323704
  Y_new =  -0.780439 * X  +  -0.095026 * Y  +  -0.617969 * Z  +  50.221210
  Z_new =  -0.575286 * X  +  -0.277959 * Y  +   0.769276 * Z  +  94.453979 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.346729    2.794864  [ DEG:   -19.8661    160.1339 ]
  Theta =   0.612953    2.528639  [ DEG:    35.1196    144.8804 ]
  Phi   =  -1.874830    1.266763  [ DEG:  -107.4198     72.5802 ]
 
# 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_2_2-D2                             
REMARK     2: T0386_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0386TS074_2_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_2_2-D2
REMARK PARENT number 2
PFRMAT TS
TARGET T0386
PARENT 2g03_A
ATOM   1470  N   ASN   219       2.341  54.824  75.806  1.00  0.80
ATOM   1471  CA  ASN   219       2.841  55.662  74.719  1.00  0.80
ATOM   1472  C   ASN   219       2.690  57.163  74.979  1.00  0.80
ATOM   1473  O   ASN   219       3.585  57.928  74.648  1.00  0.80
ATOM   1474  CB  ASN   219       2.204  55.312  73.394  1.00  0.80
ATOM   1475  CG  ASN   219       2.536  53.921  72.881  1.00  0.90
ATOM   1476  OD1 ASN   219       3.698  53.764  72.404  1.00  0.90
ATOM   1477  ND2 ASN   219       1.603  53.032  72.867  1.00  1.10
ATOM   1478  N   PRO   220       1.563  57.581  75.547  1.00  0.80
ATOM   1479  CA  PRO   220       1.333  58.996  75.810  1.00  0.80
ATOM   1480  C   PRO   220       2.244  59.466  76.942  1.00  0.80
ATOM   1481  O   PRO   220       2.866  60.507  76.838  1.00  0.80
ATOM   1482  CB  PRO   220      -0.148  59.265  76.119  1.00  0.80
ATOM   1483  CG  PRO   220      -1.054  58.039  76.091  1.00  0.90
ATOM   1484  CD  PRO   220       0.270  56.895  76.403  1.00  0.90
ATOM   1485  N   GLU   221       2.331  58.681  78.014  1.00  0.80
ATOM   1486  CA  GLU   221       3.220  58.948  79.130  1.00  0.80
ATOM   1487  C   GLU   221       4.669  59.198  78.701  1.00  0.80
ATOM   1488  O   GLU   221       5.325  60.130  79.194  1.00  0.80
ATOM   1489  CB  GLU   221       3.178  57.767  80.102  1.00  0.80
ATOM   1490  CG  GLU   221       1.897  57.633  80.690  1.00  0.90
ATOM   1491  CD  GLU   221       1.372  58.837  81.670  1.00  0.90
ATOM   1492  OE1 GLU   221       2.101  59.392  82.446  1.00  1.10
ATOM   1493  OE2 GLU   221       0.178  59.173  81.581  1.00  1.10
ATOM   1494  N   LYS   222       5.171  58.353  77.803  1.00  0.80
ATOM   1495  CA  LYS   222       6.543  58.458  77.285  1.00  0.80
ATOM   1496  C   LYS   222       6.727  59.661  76.356  1.00  0.80
ATOM   1497  O   LYS   222       7.846  60.182  76.198  1.00  0.80
ATOM   1498  CB  LYS   222       7.014  57.130  76.618  1.00  0.80
ATOM   1499  CG  LYS   222       8.449  57.220  76.152  1.00  0.90
ATOM   1500  CD  LYS   222       8.836  55.886  75.512  1.00  0.90
ATOM   1501  CE  LYS   222       8.191  55.509  74.235  1.00  1.10
ATOM   1502  NZ  LYS   222       8.555  56.436  73.099  1.00  1.10
ATOM   1503  N   ILE   223       5.387  59.980  76.290  1.00  0.80
ATOM   1504  CA  ILE   223       5.447  61.188  75.460  1.00  0.80
ATOM   1505  C   ILE   223       5.570  62.492  76.303  1.00  0.80
ATOM   1506  O   ILE   223       6.225  63.447  75.886  1.00  0.80
ATOM   1507  CB  ILE   223       4.202  61.193  74.577  1.00  0.80
ATOM   1508  CG1 ILE   223       4.064  60.093  73.550  1.00  0.90
ATOM   1509  CG2 ILE   223       4.097  62.585  73.938  1.00  0.90
ATOM   1510  CD1 ILE   223       2.811  59.934  72.849  1.00  1.10
ATOM   1511  N   ARG   224       4.982  62.506  77.497  1.00  0.80
ATOM   1512  CA  ARG   224       4.961  63.692  78.344  1.00  0.80
ATOM   1513  C   ARG   224       6.364  64.160  78.648  1.00  0.80
ATOM   1514  O   ARG   224       6.607  65.360  78.788  1.00  0.80
ATOM   1515  CB  ARG   224       4.224  63.456  79.654  1.00  0.80
ATOM   1516  CG  ARG   224       2.722  63.249  79.563  1.00  0.90
ATOM   1517  CD  ARG   224       2.280  62.952  80.971  1.00  0.90
ATOM   1518  NE  ARG   224       0.838  62.743  80.909  1.00  1.10
ATOM   1519  CZ  ARG   224       0.084  62.513  81.982  1.00  1.10
ATOM   1520  NH1 ARG   224       0.662  62.384  83.176  1.00  1.40
ATOM   1521  NH2 ARG   224      -1.226  62.361  81.812  1.00  1.40
TER
END
