
#######################################################
#                                                     #
#                        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    7 (   58),  selected    7 , name T0381TS268_2_2-D1
# Molecule2: number of CA atoms   61 (  477),  selected    7 , name T0381_D1.pdb
# PARAMETERS: T0381TS268_2_2-D1.T0381_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:     7        71 - 77          1.71     1.71
  LCS_AVERAGE:     11.48

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     7        71 - 77          1.71     1.71
  LCS_AVERAGE:     11.48

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4        71 - 74          0.46     3.99
  LONGEST_CONTINUOUS_SEGMENT:     4        73 - 76          0.71     2.59
  LONGEST_CONTINUOUS_SEGMENT:     4        74 - 77          0.87     4.06
  LCS_AVERAGE:      6.56

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:   61
LCS_GDT     S      71     S      71      4    7    7     3    4    5    6    6    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7 
LCS_GDT     A      72     A      72      4    7    7     3    4    5    6    6    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7 
LCS_GDT     F      73     F      73      4    7    7     3    4    5    6    6    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7 
LCS_GDT     W      74     W      74      4    7    7     3    4    5    6    6    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7 
LCS_GDT     L      75     L      75      4    7    7     3    4    5    6    6    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7 
LCS_GDT     T      76     T      76      4    7    7     3    4    5    6    6    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7 
LCS_GDT     P      77     P      77      4    7    7     0    3    5    6    6    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7 
LCS_AVERAGE  LCS_A:   9.84  (   6.56   11.48   11.48 )

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      4      5      6      6      7      7      7      7      7      7      7      7      7      7      7      7      7      7      7 
GDT PERCENT_CA   4.92   6.56   8.20   9.84   9.84  11.48  11.48  11.48  11.48  11.48  11.48  11.48  11.48  11.48  11.48  11.48  11.48  11.48  11.48  11.48
GDT RMS_LOCAL    0.26   0.46   1.01   1.31   1.31   1.71   1.71   1.71   1.71   1.71   1.71   1.71   1.71   1.71   1.71   1.71   1.71   1.71   1.71   1.71
GDT RMS_ALL_CA   4.16   3.99   1.87   2.06   2.06   1.71   1.71   1.71   1.71   1.71   1.71   1.71   1.71   1.71   1.71   1.71   1.71   1.71   1.71   1.71

#      Molecule1      Molecule2       DISTANCE
LGA    S      71      S      71          1.697
LGA    A      72      A      72          1.172
LGA    F      73      F      73          0.953
LGA    W      74      W      74          2.744
LGA    L      75      L      75          0.984
LGA    T      76      T      76          1.173
LGA    P      77      P      77          2.307

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)    7   61    4.0      7    1.71     9.836    10.620     0.388

LGA_LOCAL      RMSD =  1.705  Number of atoms =    7  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  1.705  Number of atoms =    7 
Std_ALL_ATOMS  RMSD =  1.705  (standard rmsd on all 7 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.295219 * X  +   0.541332 * Y  +   0.787277 * Z  +  39.279125
  Y_new =  -0.311538 * X  +  -0.724427 * Y  +   0.614939 * Z  +  46.193680
  Z_new =   0.903211 * X  +  -0.426809 * Y  +  -0.045219 * Z  +   4.568487 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.676350    1.465242  [ DEG:   -96.0478     83.9522 ]
  Theta =  -1.127192   -2.014400  [ DEG:   -64.5834   -115.4166 ]
  Phi   =  -0.812286    2.329306  [ DEG:   -46.5406    133.4594 ]
 
# 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: T0381TS268_2_2-D1                             
REMARK     2: T0381_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0381TS268_2_2-D1.T0381_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:    7   61   4.0    7   1.71  10.620     1.71
REMARK  ---------------------------------------------------------- 
MOLECULE T0381TS268_2_2-D1
REMARK PARENT number 2
PFRMAT TS
TARGET T0381
PARENT 1tf1_D
ATOM    549  N   SER    71       9.530  64.212   9.123  1.00  0.00
ATOM    550  CA  SER    71       8.440  63.216   9.239  1.00  0.00
ATOM    551  C   SER    71       8.941  61.936   9.813  1.00  0.00
ATOM    552  O   SER    71       8.955  61.745  11.028  1.00  0.00
ATOM    553  CB  SER    71       7.838  62.917   7.864  1.00  0.00
ATOM    554  OG  SER    71       7.227  64.070   7.313  1.00  0.00
ATOM    555  N   ALA    72       9.375  61.018   8.933  1.00  0.00
ATOM    556  CA  ALA    72       9.834  59.748   9.394  1.00  0.00
ATOM    557  C   ALA    72      11.097  59.962  10.150  1.00  0.00
ATOM    558  O   ALA    72      11.901  60.831   9.818  1.00  0.00
ATOM    559  CB  ALA    72      10.090  58.818   8.218  1.00  0.00
ATOM    560  N   PHE    73      11.280  59.174  11.224  1.00  0.00
ATOM    561  CA  PHE    73      12.479  59.263  11.992  1.00  0.00
ATOM    562  C   PHE    73      13.212  57.998  11.713  1.00  0.00
ATOM    563  O   PHE    73      12.665  56.909  11.879  1.00  0.00
ATOM    564  CB  PHE    73      12.153  59.395  13.481  1.00  0.00
ATOM    565  CG  PHE    73      11.484  60.691  13.843  1.00  0.00
ATOM    566  CD1 PHE    73      10.104  60.798  13.841  1.00  0.00
ATOM    567  CD2 PHE    73      12.235  61.802  14.185  1.00  0.00
ATOM    568  CE1 PHE    73       9.490  61.990  14.174  1.00  0.00
ATOM    569  CE2 PHE    73      11.620  62.994  14.517  1.00  0.00
ATOM    570  CZ  PHE    73      10.253  63.091  14.512  1.00  0.00
ATOM    571  N   TRP    74      14.476  58.100  11.267  1.00  0.00
ATOM    572  CA  TRP    74      15.148  56.871  10.990  1.00  0.00
ATOM    573  C   TRP    74      15.421  56.239  12.311  1.00  0.00
ATOM    574  O   TRP    74      15.987  56.861  13.208  1.00  0.00
ATOM    575  CB  TRP    74      16.456  57.133  10.239  1.00  0.00
ATOM    576  CG  TRP    74      16.254  57.621   8.837  1.00  0.00
ATOM    577  CD1 TRP    74      16.429  58.896   8.382  1.00  0.00
ATOM    578  CD2 TRP    74      15.840  56.843   7.709  1.00  0.00
ATOM    579  NE1 TRP    74      16.149  58.961   7.037  1.00  0.00
ATOM    580  CE2 TRP    74      15.785  57.712   6.601  1.00  0.00
ATOM    581  CE3 TRP    74      15.511  55.496   7.524  1.00  0.00
ATOM    582  CZ2 TRP    74      15.414  57.279   5.329  1.00  0.00
ATOM    583  CZ3 TRP    74      15.144  55.071   6.262  1.00  0.00
ATOM    584  CH2 TRP    74      15.098  55.956   5.180  1.00  0.00
ATOM    585  N   LEU    75      14.990  54.974  12.465  1.00  0.00
ATOM    586  CA  LEU    75      15.170  54.289  13.707  1.00  0.00
ATOM    587  C   LEU    75      16.536  53.693  13.657  1.00  0.00
ATOM    588  O   LEU    75      16.956  53.219  12.603  1.00  0.00
ATOM    589  CB  LEU    75      14.110  53.198  13.876  1.00  0.00
ATOM    590  CG  LEU    75      12.654  53.667  13.913  1.00  0.00
ATOM    591  CD1 LEU    75      11.709  52.479  14.004  1.00  0.00
ATOM    592  CD2 LEU    75      12.408  54.565  15.116  1.00  0.00
ATOM    593  N   THR    76      17.283  53.720  14.783  1.00  0.00
ATOM    594  CA  THR    76      18.598  53.150  14.728  1.00  0.00
ATOM    595  C   THR    76      18.438  51.675  14.713  1.00  0.00
ATOM    596  O   THR    76      17.785  51.086  15.572  1.00  0.00
ATOM    597  CB  THR    76      19.443  53.565  15.947  1.00  0.00
ATOM    598  OG1 THR    76      19.557  54.993  15.989  1.00  0.00
ATOM    599  CG2 THR    76      20.837  52.963  15.857  1.00  0.00
ATOM    600  N   PRO    77      19.075  51.083  13.746  1.00  0.00
ATOM    601  CA  PRO    77      18.953  49.672  13.539  1.00  0.00
ATOM    602  C   PRO    77      19.512  48.909  14.684  1.00  0.00
ATOM    603  O   PRO    77      20.299  49.465  15.450  1.00  0.00
ATOM    604  CB  PRO    77      19.747  49.415  12.258  1.00  0.00
ATOM    605  CG  PRO    77      19.779  50.737  11.566  1.00  0.00
ATOM    606  CD  PRO    77      19.840  51.774  12.652  1.00  0.00
TER
END
