
#######################################################
#                                                     #
#                        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    5 (   42),  selected    5 , name T0386TS494_1-D2
# Molecule2: number of CA atoms   81 (  636),  selected    5 , name T0386_D2.pdb
# PARAMETERS: T0386TS494_1-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:     5       219 - 223         0.23     0.23
  LCS_AVERAGE:      6.17

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5       219 - 223         0.23     0.23
  LCS_AVERAGE:      6.17

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5       219 - 223         0.23     0.23
  LCS_AVERAGE:      6.17

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      5    5    5     5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5 
LCS_GDT     P     220     P     220      5    5    5     5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5 
LCS_GDT     E     221     E     221      5    5    5     5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5 
LCS_GDT     K     222     K     222      5    5    5     5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5 
LCS_GDT     I     223     I     223      5    5    5     5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5 
LCS_AVERAGE  LCS_A:   6.17  (   6.17    6.17    6.17 )

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      5      5      5      5      5      5      5      5      5      5      5      5      5      5      5      5      5      5      5 
GDT PERCENT_CA   6.17   6.17   6.17   6.17   6.17   6.17   6.17   6.17   6.17   6.17   6.17   6.17   6.17   6.17   6.17   6.17   6.17   6.17   6.17   6.17
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          0.183
LGA    P     220      P     220          0.185
LGA    E     221      E     221          0.264
LGA    K     222      K     222          0.163
LGA    I     223      I     223          0.324

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)    5   81    4.0      5    0.23     6.173     6.173     1.505

LGA_LOCAL      RMSD =  0.232  Number of atoms =    5  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  0.232  Number of atoms =    5 
Std_ALL_ATOMS  RMSD =  0.232  (standard rmsd on all 5 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.925195 * X  +  -0.308297 * Y  +  -0.221287 * Z  +  17.475258
  Y_new =  -0.334162 * X  +   0.938208 * Y  +   0.090011 * Z  +   3.934331
  Z_new =   0.179863 * X  +   0.157223 * Y  +  -0.971046 * Z  +  64.341553 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.981075   -0.160518  [ DEG:   170.8030     -9.1970 ]
  Theta =  -0.180847   -2.960745  [ DEG:   -10.3618   -169.6382 ]
  Phi   =  -2.794992    0.346600  [ DEG:  -160.1413     19.8587 ]
 
# 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: T0386TS494_1-D2                               
REMARK     2: T0386_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0386TS494_1-D2.T0386_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:    5   81   4.0    5   0.23   6.173     0.23
REMARK  ---------------------------------------------------------- 
MOLECULE T0386TS494_1-D2
PFRMAT     TS
TARGET     T0386
MODEL      1
PARENT     2g03_A
ATOM   1444  N   ASN   219       3.160  55.633  73.141  1.00  0.02
ATOM   1446  CA  ASN   219       2.747  55.672  74.547  1.00  0.00
ATOM   1447  CB  ASN   219       3.747  54.851  75.351  1.00  0.02
ATOM   1448  CG  ASN   219       3.262  54.635  76.781  1.00  0.02
ATOM   1449  OD1 ASN   219       3.168  55.580  77.576  1.00  0.02
ATOM   1450  ND2 ASN   219       2.986  53.383  77.095  1.00  0.02
ATOM   1453  C   ASN   219       2.705  57.103  75.071  1.00  0.02
ATOM   1454  O   ASN   219       3.757  57.730  75.256  1.00  0.02
ATOM   1455  N   PRO   220       1.535  57.510  75.541  1.00  0.02
ATOM   1456  CA  PRO   220       1.320  58.903  75.954  1.00  0.00
ATOM   1457  CB  PRO   220      -0.156  59.015  76.179  1.00  0.00
ATOM   1458  CG  PRO   220      -0.796  57.645  76.021  1.00  0.00
ATOM   1459  CD  PRO   220       0.321  56.696  75.625  1.00  0.02
ATOM   1460  C   PRO   220       2.088  59.307  77.222  1.00  0.00
ATOM   1461  O   PRO   220       2.617  60.425  77.264  1.00  0.02
ATOM   1462  N   GLU   221       2.426  58.340  78.062  1.00  0.02
ATOM   1464  CA  GLU   221       3.152  58.630  79.303  1.00  0.02
ATOM   1465  CB  GLU   221       2.824  57.530  80.310  1.00  0.02
ATOM   1466  CG  GLU   221       3.329  57.851  81.717  1.00  0.02
ATOM   1467  CD  GLU   221       2.610  59.080  82.273  1.00  0.03
ATOM   1468  OE1 GLU   221       1.442  59.239  81.942  1.00  0.02
ATOM   1469  OE2 GLU   221       3.185  59.745  83.122  1.00  0.02
ATOM   1470  C   GLU   221       4.662  58.687  79.055  1.00  0.00
ATOM   1471  O   GLU   221       5.416  59.170  79.908  1.00  0.03
ATOM   1472  N   LYS   222       5.082  58.269  77.870  1.00  0.03
ATOM   1474  CA  LYS   222       6.484  58.400  77.466  1.00  0.02
ATOM   1475  CB  LYS   222       6.871  57.198  76.606  1.00  0.02
ATOM   1476  CG  LYS   222       6.599  55.865  77.297  1.00  0.94
ATOM   1477  CD  LYS   222       7.410  55.700  78.574  1.00  1.59
ATOM   1478  CE  LYS   222       7.123  54.362  79.242  1.00  1.96
ATOM   1479  NZ  LYS   222       7.926  54.203  80.463  1.00  1.94
ATOM   1480  C   LYS   222       6.682  59.670  76.638  1.00  0.03
ATOM   1481  O   LYS   222       7.819  60.043  76.325  1.00  0.00
ATOM   1482  N   ILE   223       5.579  60.303  76.271  1.00  0.00
ATOM   1484  CA  ILE   223       5.629  61.516  75.452  1.00  0.02
ATOM   1485  CB  ILE   223       4.714  61.332  74.242  1.00  0.03
ATOM   1486  CG2 ILE   223       4.841  62.515  73.285  1.00  0.02
ATOM   1487  CG1 ILE   223       5.040  60.043  73.498  1.00  0.02
ATOM   1488  CD1 ILE   223       4.068  59.814  72.346  1.00  0.00
ATOM   1489  C   ILE   223       5.174  62.724  76.271  1.00  0.02
ATOM   1490  O   ILE   223       6.049  63.382  76.819  1.00  0.00
ATOM   1491  OXT ILE   223       3.997  63.050  76.220  1.00  0.00
TER  
END
