
#######################################################
#                                                     #
#                        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 T0386TS046_2-D2
# Molecule2: number of CA atoms   81 (  636),  selected    6 , name T0386_D2.pdb
# PARAMETERS: T0386TS046_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         0.27     0.27
  LCS_AVERAGE:      7.41

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6       219 - 224         0.27     0.27
  LCS_AVERAGE:      7.41

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6       219 - 224         0.27     0.27
  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    0.27   0.27   0.27   0.27   0.27   0.27   0.27   0.27   0.27   0.27   0.27   0.27   0.27   0.27   0.27   0.27   0.27   0.27   0.27   0.27
GDT RMS_ALL_CA   0.27   0.27   0.27   0.27   0.27   0.27   0.27   0.27   0.27   0.27   0.27   0.27   0.27   0.27   0.27   0.27   0.27   0.27   0.27   0.27

#      Molecule1      Molecule2       DISTANCE
LGA    N     219      N     219          0.229
LGA    P     220      P     220          0.264
LGA    E     221      E     221          0.174
LGA    K     222      K     222          0.450
LGA    I     223      I     223          0.244
LGA    R     224      R     224          0.197

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)    6   81    4.0      6    0.27     7.407     7.407     1.603

LGA_LOCAL      RMSD =  0.274  Number of atoms =    6  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  0.275  Number of atoms =    6 
Std_ALL_ATOMS  RMSD =  0.274  (standard rmsd on all 6 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.004892 * X  +   0.900731 * Y  +   0.434350 * Z  + -51.431011
  Y_new =  -0.929267 * X  +   0.164538 * Y  +  -0.330742 * Z  +  32.240017
  Z_new =  -0.369376 * X  +  -0.402009 * Y  +   0.837824 * Z  + 103.406502 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.447378    2.694215  [ DEG:   -25.6329    154.3671 ]
  Theta =   0.378338    2.763255  [ DEG:    21.6772    158.3228 ]
  Phi   =  -1.565532    1.576061  [ DEG:   -89.6984     90.3016 ]
 
# 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: T0386TS046_2-D2                               
REMARK     2: T0386_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0386TS046_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   0.27   7.407     0.27
REMARK  ---------------------------------------------------------- 
MOLECULE T0386TS046_2-D2
PFRMAT TS
TARGET T0386
MODEL 2
PARENT 2G03_A
ATOM   1462  N   ASN   219       2.313  54.889  75.757  1.00  5.02
ATOM   1463  CA  ASN   219       2.867  55.755  74.753  1.00  5.02
ATOM   1464  C   ASN   219       2.734  57.208  75.153  1.00  5.02
ATOM   1465  O   ASN   219       3.755  57.888  75.211  1.00  5.02
ATOM   1466  CB  ASN   219       2.144  55.560  73.419  1.00  5.02
ATOM   1467  CG  ASN   219       2.719  56.424  72.314  1.00  5.02
ATOM   1468  OD1 ASN   219       3.865  56.243  71.902  1.00  5.02
ATOM   1469  ND2 ASN   219       1.921  57.370  71.830  1.00  5.02
ATOM   1470  N   PRO   220       1.576  57.757  75.449  1.00  5.69
ATOM   1471  CA  PRO   220       1.612  59.114  75.923  1.00  5.69
ATOM   1472  C   PRO   220       2.305  59.347  77.222  1.00  5.69
ATOM   1473  O   PRO   220       2.748  60.471  77.453  1.00  5.69
ATOM   1474  CB  PRO   220       0.138  59.494  76.069  1.00  5.69
ATOM   1475  CG  PRO   220      -0.578  58.583  75.129  1.00  5.69
ATOM   1476  CD  PRO   220       0.169  57.279  75.163  1.00  5.69
ATOM   1477  N   GLU   221       2.402  58.332  78.092  1.00  5.62
ATOM   1478  CA  GLU   221       3.144  58.526  79.301  1.00  5.62
ATOM   1479  C   GLU   221       4.523  58.854  78.832  1.00  5.62
ATOM   1480  O   GLU   221       5.156  59.795  79.306  1.00  5.62
ATOM   1481  CB  GLU   221       3.123  57.255  80.152  1.00  5.62
ATOM   1482  CG  GLU   221       3.836  57.391  81.487  1.00  5.62
ATOM   1483  CD  GLU   221       3.746  56.132  82.327  1.00  5.62
ATOM   1484  OE1 GLU   221       3.109  55.159  81.872  1.00  5.62
ATOM   1485  OE2 GLU   221       4.312  56.119  83.440  1.00  5.62
ATOM   1486  N   LYS   222       4.986  58.093  77.821  1.00  5.81
ATOM   1487  CA  LYS   222       6.301  58.216  77.267  1.00  5.81
ATOM   1488  C   LYS   222       6.441  59.557  76.624  1.00  5.81
ATOM   1489  O   LYS   222       7.507  60.168  76.670  1.00  5.81
ATOM   1490  CB  LYS   222       6.544  57.131  76.216  1.00  5.81
ATOM   1491  CG  LYS   222       7.935  57.157  75.605  1.00  5.81
ATOM   1492  CD  LYS   222       8.133  56.008  74.630  1.00  5.81
ATOM   1493  CE  LYS   222       9.515  56.051  73.998  1.00  5.81
ATOM   1494  NZ  LYS   222       9.716  54.939  73.029  1.00  5.81
ATOM   1495  N   ILE   223       5.379  60.060  75.974  1.00  5.54
ATOM   1496  CA  ILE   223       5.528  61.368  75.415  1.00  5.54
ATOM   1497  C   ILE   223       4.761  62.328  76.276  1.00  5.54
ATOM   1498  O   ILE   223       3.550  62.493  76.145  1.00  5.54
ATOM   1499  CB  ILE   223       4.984  61.431  73.975  1.00  5.54
ATOM   1500  CG1 ILE   223       5.718  60.428  73.083  1.00  5.54
ATOM   1501  CG2 ILE   223       5.175  62.823  73.394  1.00  5.54
ATOM   1502  CD1 ILE   223       5.107  60.271  71.709  1.00  5.54
ATOM   1503  N   ARG   224       5.480  63.010  77.192  1.00  5.84
ATOM   1504  CA  ARG   224       4.892  63.964  78.089  1.00  5.84
ATOM   1505  C   ARG   224       4.268  65.071  77.252  1.00  5.84
ATOM   1506  O   ARG   224       5.028  65.962  76.785  1.00  5.84
ATOM   1507  CB  ARG   224       5.956  64.554  79.017  1.00  5.84
ATOM   1508  CG  ARG   224       6.537  63.559  80.008  1.00  5.84
ATOM   1509  CD  ARG   224       7.604  64.204  80.877  1.00  5.84
ATOM   1510  NE  ARG   224       8.193  63.253  81.817  1.00  5.84
ATOM   1511  CZ  ARG   224       9.190  63.542  82.646  1.00  5.84
ATOM   1512  NH1 ARG   224       9.662  62.613  83.466  1.00  5.84
ATOM   1513  NH2 ARG   224       9.714  64.761  82.654  1.00  5.84
TER
END
