
#######################################################
#                                                     #
#                        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 (   53),  selected    6 , name T0372TS022_1_1-D2
# Molecule2: number of CA atoms  172 ( 1400),  selected    6 , name T0372_D2.pdb
# PARAMETERS: T0372TS022_1_1-D2.T0372_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       118 - 123         0.67     0.67
  LCS_AVERAGE:      3.49

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6       118 - 123         0.67     0.67
  LCS_AVERAGE:      3.49

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6       118 - 123         0.67     0.67
  LCS_AVERAGE:      3.49

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:  172
LCS_GDT     R     118     R     118      6    6    6     4    5    6    6    6    6    6    6    6    6    6    6    6    6    6    6    6    6    6    6 
LCS_GDT     A     119     A     119      6    6    6     4    5    6    6    6    6    6    6    6    6    6    6    6    6    6    6    6    6    6    6 
LCS_GDT     Y     120     Y     120      6    6    6     4    5    6    6    6    6    6    6    6    6    6    6    6    6    6    6    6    6    6    6 
LCS_GDT     A     121     A     121      6    6    6     3    5    6    6    6    6    6    6    6    6    6    6    6    6    6    6    6    6    6    6 
LCS_GDT     D     122     D     122      6    6    6     4    5    6    6    6    6    6    6    6    6    6    6    6    6    6    6    6    6    6    6 
LCS_GDT     Y     123     Y     123      6    6    6     3    3    6    6    6    6    6    6    6    6    6    6    6    6    6    6    6    6    6    6 
LCS_AVERAGE  LCS_A:   3.49  (   3.49    3.49    3.49 )

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      4      5      6      6      6      6      6      6      6      6      6      6      6      6      6      6      6      6      6      6 
GDT PERCENT_CA   2.33   2.91   3.49   3.49   3.49   3.49   3.49   3.49   3.49   3.49   3.49   3.49   3.49   3.49   3.49   3.49   3.49   3.49   3.49   3.49
GDT RMS_LOCAL    0.25   0.45   0.67   0.67   0.67   0.67   0.67   0.67   0.67   0.67   0.67   0.67   0.67   0.67   0.67   0.67   0.67   0.67   0.67   0.67
GDT RMS_ALL_CA   0.77   0.81   0.67   0.67   0.67   0.67   0.67   0.67   0.67   0.67   0.67   0.67   0.67   0.67   0.67   0.67   0.67   0.67   0.67   0.67

#      Molecule1      Molecule2       DISTANCE
LGA    R     118      R     118          0.578
LGA    A     119      A     119          0.080
LGA    Y     120      Y     120          0.305
LGA    A     121      A     121          0.931
LGA    D     122      D     122          0.564
LGA    Y     123      Y     123          1.023

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)    6  172    4.0      6    0.67     3.343     3.442     0.783

LGA_LOCAL      RMSD =  0.666  Number of atoms =    6  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  0.666  Number of atoms =    6 
Std_ALL_ATOMS  RMSD =  0.666  (standard rmsd on all 6 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.112720 * X  +  -0.190536 * Y  +  -0.975187 * Z  +  30.786345
  Y_new =   0.575854 * X  +   0.787288 * Y  +  -0.220385 * Z  +  -3.207102
  Z_new =   0.809745 * X  +  -0.586407 * Y  +   0.020977 * Z  +   2.226959 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.535039    1.606554  [ DEG:   -87.9513     92.0487 ]
  Theta =  -0.943717   -2.197875  [ DEG:   -54.0710   -125.9290 ]
  Phi   =   1.764097   -1.377496  [ DEG:   101.0753    -78.9247 ]
 
# 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: T0372TS022_1_1-D2                             
REMARK     2: T0372_D2.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0372TS022_1_1-D2.T0372_D2.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:    6  172   4.0    6   0.67   3.442     0.67
REMARK  ---------------------------------------------------------- 
MOLECULE T0372TS022_1_1-D2
REMARK PARENT number 1
PFRMAT TS
TARGET T0372
PARENT 1qst_A
ATOM    945  N   ARG   118      21.818  38.426   9.274  1.00  0.00
ATOM    946  CA  ARG   118      22.740  39.425   9.743  1.00  0.00
ATOM    947  C   ARG   118      23.969  38.864  10.389  1.00  0.00
ATOM    948  O   ARG   118      24.280  39.151  11.544  1.00  0.00
ATOM    949  CB  ARG   118      22.071  40.325  10.784  1.00  0.00
ATOM    950  CG  ARG   118      20.814  41.022  10.287  1.00  0.00
ATOM    951  CD  ARG   118      21.112  41.903   9.083  1.00  0.00
ATOM    952  NE  ARG   118      22.061  42.966   9.405  1.00  0.00
ATOM    953  CZ  ARG   118      22.621  43.764   8.502  1.00  0.00
ATOM    954  NH1 ARG   118      23.474  44.704   8.887  1.00  0.00
ATOM    955  NH2 ARG   118      22.328  43.620   7.217  1.00  0.00
ATOM    956  N   ALA   119      24.706  38.041   9.618  1.00  0.00
ATOM    957  CA  ALA   119      25.957  37.494  10.050  1.00  0.00
ATOM    958  C   ALA   119      26.912  38.629  10.260  1.00  0.00
ATOM    959  O   ALA   119      27.679  38.635  11.221  1.00  0.00
ATOM    960  CB  ALA   119      26.511  36.544   9.000  1.00  0.00
ATOM    961  N   TYR   120      26.889  39.636   9.364  1.00  0.00
ATOM    962  CA  TYR   120      27.812  40.720   9.533  1.00  0.00
ATOM    963  C   TYR   120      27.074  41.911  10.049  1.00  0.00
ATOM    964  O   TYR   120      26.144  42.422   9.429  1.00  0.00
ATOM    965  CB  TYR   120      28.470  41.077   8.198  1.00  0.00
ATOM    966  CG  TYR   120      29.375  39.995   7.653  1.00  0.00
ATOM    967  CD1 TYR   120      28.880  39.014   6.804  1.00  0.00
ATOM    968  CD2 TYR   120      30.722  39.958   7.990  1.00  0.00
ATOM    969  CE1 TYR   120      29.700  38.022   6.301  1.00  0.00
ATOM    970  CE2 TYR   120      31.557  38.974   7.498  1.00  0.00
ATOM    971  CZ  TYR   120      31.033  38.001   6.647  1.00  0.00
ATOM    972  OH  TYR   120      31.852  37.014   6.148  1.00  0.00
ATOM    973  N   ALA   121      27.462  42.365  11.253  1.00  0.00
ATOM    974  CA  ALA   121      26.867  43.535  11.816  1.00  0.00
ATOM    975  C   ALA   121      27.482  43.700  13.161  1.00  0.00
ATOM    976  O   ALA   121      27.961  42.733  13.755  1.00  0.00
ATOM    977  CB  ALA   121      25.360  43.361  11.930  1.00  0.00
ATOM    978  N   ASP   122      27.487  44.940  13.683  1.00  0.00
ATOM    979  CA  ASP   122      28.069  45.136  14.975  1.00  0.00
ATOM    980  C   ASP   122      26.967  45.022  15.969  1.00  0.00
ATOM    981  O   ASP   122      26.139  45.922  16.092  1.00  0.00
ATOM    982  CB  ASP   122      28.722  46.516  15.064  1.00  0.00
ATOM    983  CG  ASP   122      29.394  46.758  16.401  1.00  0.00
ATOM    984  OD1 ASP   122      29.254  45.901  17.299  1.00  0.00
ATOM    985  OD2 ASP   122      30.060  47.803  16.552  1.00  0.00
ATOM    986  N   TYR   123      26.915  43.896  16.705  1.00  0.00
ATOM    987  CA  TYR   123      25.885  43.787  17.688  1.00  0.00
ATOM    988  C   TYR   123      26.544  43.888  19.051  1.00  0.00
ATOM    989  O   TYR   123      26.278  44.901  19.751  1.00  0.00
ATOM    990  CB  TYR   123      25.159  42.447  17.557  1.00  0.00
ATOM    991  CG  TYR   123      24.492  42.240  16.216  1.00  0.00
ATOM    992  CD1 TYR   123      25.064  41.415  15.257  1.00  0.00
ATOM    993  CD2 TYR   123      23.292  42.872  15.913  1.00  0.00
ATOM    994  CE1 TYR   123      24.462  41.221  14.028  1.00  0.00
ATOM    995  CE2 TYR   123      22.676  42.689  14.691  1.00  0.00
ATOM    996  CZ  TYR   123      23.272  41.855  13.745  1.00  0.00
ATOM    997  OH  TYR   123      22.669  41.663  12.524  1.00  0.00
TER
END
