
#######################################################
#                                                     #
#                        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 (   30),  selected    6 , name T0372TS103_1_1-D1
# Molecule2: number of CA atoms  126 ( 1027),  selected    6 , name T0372_D1.pdb
# PARAMETERS: T0372TS103_1_1-D1.T0372_D1.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       112 - 117         3.95     3.95
  LCS_AVERAGE:      4.76

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
# WARNING! The change of the parameter DIST cutoff may give you better result.

  LONGEST_CONTINUOUS_SEGMENT:     3       112 - 114         0.39     7.52
  LONGEST_CONTINUOUS_SEGMENT:     3       113 - 115         0.61     6.29
  LONGEST_CONTINUOUS_SEGMENT:     3       114 - 116         0.74     5.79
  LONGEST_CONTINUOUS_SEGMENT:     3       115 - 117         0.72     7.41
  LCS_AVERAGE:      2.38

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     3       112 - 114         0.39     7.52
  LONGEST_CONTINUOUS_SEGMENT:     3       114 - 116         0.74     5.79
  LONGEST_CONTINUOUS_SEGMENT:     3       115 - 117         0.72     7.41
  LCS_AVERAGE:      2.38

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:  126
LCS_GDT     F     112     F     112      3    3    6     3    3    3    3    3    3    4    5    5    5    6    6    6    6    6    6    6    6    6    6 
LCS_GDT     I     113     I     113      3    3    6     3    3    3    3    3    3    4    5    5    5    6    6    6    6    6    6    6    6    6    6 
LCS_GDT     F     114     F     114      3    3    6     3    3    3    3    3    3    4    5    5    5    6    6    6    6    6    6    6    6    6    6 
LCS_GDT     T     115     T     115      3    3    6     0    3    3    3    3    3    4    5    5    5    6    6    6    6    6    6    6    6    6    6 
LCS_GDT     E     116     E     116      3    3    6     0    3    3    3    3    3    4    5    5    5    6    6    6    6    6    6    6    6    6    6 
LCS_GDT     D     117     D     117      3    3    6     0    3    3    3    3    3    4    4    5    5    6    6    6    6    6    6    6    6    6    6 
LCS_AVERAGE  LCS_A:   3.17  (   2.38    2.38    4.76 )

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      3      3      3      3      3      3      4      5      5      5      6      6      6      6      6      6      6      6      6      6 
GDT PERCENT_CA   2.38   2.38   2.38   2.38   2.38   2.38   3.17   3.97   3.97   3.97   4.76   4.76   4.76   4.76   4.76   4.76   4.76   4.76   4.76   4.76
GDT RMS_LOCAL    0.39   0.39   0.39   0.39   0.39   0.39   2.50   3.29   3.29   3.29   3.95   3.95   3.95   3.95   3.95   3.95   3.95   3.95   3.95   3.95
GDT RMS_ALL_CA   7.52   7.52   7.52   7.52   7.52   7.52   5.24   4.45   4.45   4.45   3.95   3.95   3.95   3.95   3.95   3.95   3.95   3.95   3.95   3.95

#      Molecule1      Molecule2       DISTANCE
LGA    F     112      F     112          3.609
LGA    I     113      I     113          3.322
LGA    F     114      F     114          3.198
LGA    T     115      T     115          2.078
LGA    E     116      E     116          3.939
LGA    D     117      D     117          8.052

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)    6  126    4.0      5    3.29     3.373     3.126     0.147

LGA_LOCAL      RMSD =  3.290  Number of atoms =    5  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  4.453  Number of atoms =    6 
Std_ALL_ATOMS  RMSD =  3.947  (standard rmsd on all 6 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.580098 * X  +  -0.760627 * Y  +   0.291433 * Z  +  19.606207
  Y_new =   0.739176 * X  +  -0.341260 * Y  +   0.580656 * Z  +   5.552999
  Z_new =  -0.342208 * X  +   0.552257 * Y  +   0.760201 * Z  + -36.243332 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.628265   -2.513327  [ DEG:    35.9970   -144.0031 ]
  Theta =   0.349266    2.792327  [ DEG:    20.0115    159.9886 ]
  Phi   =   2.236194   -0.905399  [ DEG:   128.1245    -51.8755 ]
 
# 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: T0372TS103_1_1-D1                             
REMARK     2: T0372_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0372TS103_1_1-D1.T0372_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:    6  126   4.0    5   3.29   3.126     3.95
REMARK  ---------------------------------------------------------- 
MOLECULE T0372TS103_1_1-D1
REMARK PARENT number 1
PFRMAT TS
TARGET T0372
PARENT 1h1y_A
ATOM    398  N   PHE   112      24.344  48.220  -5.411  1.00  1.00
ATOM    399  CA  PHE   112      24.587  48.457  -3.989  1.00  1.00
ATOM    400  C   PHE   112      23.360  48.130  -3.124  1.00  1.00
ATOM    401  O   PHE   112      23.482  47.470  -2.093  1.00  1.00
ATOM    402  CB  PHE   112      25.049  49.904  -3.765  1.00  1.00
ATOM    403  N   ILE   113      22.165  48.587  -3.528  1.00  1.00
ATOM    404  CA  ILE   113      20.967  48.285  -2.731  1.00  1.00
ATOM    405  C   ILE   113      20.718  46.776  -2.575  1.00  1.00
ATOM    406  O   ILE   113      20.221  46.322  -1.542  1.00  1.00
ATOM    407  CB  ILE   113      19.848  48.958  -3.516  1.00  1.00
ATOM    408  N   PHE   114      21.057  46.003  -3.606  1.00  1.00
ATOM    409  CA  PHE   114      20.854  44.555  -3.565  1.00  1.00
ATOM    410  C   PHE   114      21.807  43.856  -2.608  1.00  1.00
ATOM    411  O   PHE   114      21.467  42.829  -2.024  1.00  1.00
ATOM    412  CB  PHE   114      20.987  43.944  -4.976  1.00  1.00
ATOM    413  N   THR   115      23.009  44.410  -2.456  1.00  1.00
ATOM    414  CA  THR   115      24.004  43.846  -1.555  1.00  1.00
ATOM    415  C   THR   115      23.668  44.246  -0.112  1.00  1.00
ATOM    416  O   THR   115      23.901  43.487   0.824  1.00  1.00
ATOM    417  CB  THR   115      25.429  44.379  -1.892  1.00  1.00
ATOM    418  N   GLU   116      23.106  45.435   0.046  1.00  1.00
ATOM    419  CA  GLU   116      22.786  45.962   1.372  1.00  1.00
ATOM    420  C   GLU   116      21.385  45.668   1.911  1.00  1.00
ATOM    421  O   GLU   116      21.063  46.052   3.035  1.00  1.00
ATOM    422  CB  GLU   116      23.024  47.477   1.363  1.00  1.00
ATOM    423  N   ASP   117      20.567  44.982   1.121  1.00  1.00
ATOM    424  CA  ASP   117      19.193  44.659   1.518  1.00  1.00
ATOM    425  C   ASP   117      19.093  43.704   2.707  1.00  1.00
ATOM    426  O   ASP   117      20.034  42.975   3.002  1.00  1.00
ATOM    427  CB  ASP   117      18.446  44.066   0.325  1.00  1.00
TER
END
