
#######################################################
#                                                     #
#                        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_1_2-D1
# Molecule2: number of CA atoms   61 (  477),  selected    7 , name T0381_D1.pdb
# PARAMETERS: T0381TS268_1_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          1.38     1.38
  LCS_AVERAGE:     11.48

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     7        71 - 77          1.38     1.38
  LCS_AVERAGE:     11.48

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5        73 - 77          0.76     2.75
  LCS_AVERAGE:      7.26

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      3    7    7     3    5    6    6    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7 
LCS_GDT     A      72     A      72      3    7    7     3    5    6    6    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7 
LCS_GDT     F      73     F      73      5    7    7     3    5    6    6    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7 
LCS_GDT     W      74     W      74      5    7    7     3    4    5    6    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7 
LCS_GDT     L      75     L      75      5    7    7     3    4    6    6    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7 
LCS_GDT     T      76     T      76      5    7    7     3    5    6    6    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7 
LCS_GDT     P      77     P      77      5    7    7     3    5    6    6    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7 
LCS_AVERAGE  LCS_A:  10.07  (   7.26   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      5      6      6      7      7      7      7      7      7      7      7      7      7      7      7      7      7      7      7 
GDT PERCENT_CA   4.92   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  11.48
GDT RMS_LOCAL    0.07   0.65   0.98   0.98   1.38   1.38   1.38   1.38   1.38   1.38   1.38   1.38   1.38   1.38   1.38   1.38   1.38   1.38   1.38   1.38
GDT RMS_ALL_CA   2.83   1.57   1.45   1.45   1.38   1.38   1.38   1.38   1.38   1.38   1.38   1.38   1.38   1.38   1.38   1.38   1.38   1.38   1.38   1.38

#      Molecule1      Molecule2       DISTANCE
LGA    S      71      S      71          1.203
LGA    A      72      A      72          1.196
LGA    F      73      F      73          0.791
LGA    W      74      W      74          2.552
LGA    L      75      L      75          1.407
LGA    T      76      T      76          0.330
LGA    P      77      P      77          1.133

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)    7   61    4.0      7    1.38    10.246    10.979     0.472

LGA_LOCAL      RMSD =  1.383  Number of atoms =    7  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  1.383  Number of atoms =    7 
Std_ALL_ATOMS  RMSD =  1.383  (standard rmsd on all 7 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.461879 * X  +   0.489149 * Y  +   0.739866 * Z  +  66.117638
  Y_new =  -0.465074 * X  +  -0.843867 * Y  +   0.267573 * Z  +  48.409969
  Z_new =   0.755231 * X  +  -0.220506 * Y  +   0.617254 * Z  +  24.230143 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.343107    2.798486  [ DEG:   -19.6586    160.3414 ]
  Theta =  -0.856007   -2.285586  [ DEG:   -49.0456   -130.9544 ]
  Phi   =  -2.352748    0.788845  [ DEG:  -134.8025     45.1975 ]
 
# 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_1_2-D1                             
REMARK     2: T0381_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0381TS268_1_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   1.38  10.979     1.38
REMARK  ---------------------------------------------------------- 
MOLECULE T0381TS268_1_2-D1
REMARK PARENT number 2
PFRMAT TS
TARGET T0381
PARENT 1tf1_C
ATOM    549  N   SER    71      10.696  64.237   9.299  1.00  0.00
ATOM    550  CA  SER    71       9.564  63.468   8.733  1.00  0.00
ATOM    551  C   SER    71       9.364  62.230   9.542  1.00  0.00
ATOM    552  O   SER    71       9.063  62.295  10.732  1.00  0.00
ATOM    553  CB  SER    71       9.853  63.080   7.282  1.00  0.00
ATOM    554  OG  SER    71      10.952  62.189   7.202  1.00  0.00
ATOM    555  N   ALA    72       9.529  61.054   8.907  1.00  0.00
ATOM    556  CA  ALA    72       9.357  59.828   9.622  1.00  0.00
ATOM    557  C   ALA    72      10.498  59.714  10.572  1.00  0.00
ATOM    558  O   ALA    72      11.585  60.232  10.320  1.00  0.00
ATOM    559  CB  ALA    72       9.351  58.649   8.661  1.00  0.00
ATOM    560  N   PHE    73      10.267  59.042  11.714  1.00  0.00
ATOM    561  CA  PHE    73      11.320  58.892  12.670  1.00  0.00
ATOM    562  C   PHE    73      12.305  57.955  12.058  1.00  0.00
ATOM    563  O   PHE    73      11.932  56.945  11.465  1.00  0.00
ATOM    564  CB  PHE    73      10.776  58.323  13.982  1.00  0.00
ATOM    565  CG  PHE    73       9.944  59.296  14.766  1.00  0.00
ATOM    566  CD1 PHE    73       8.562  59.220  14.748  1.00  0.00
ATOM    567  CD2 PHE    73      10.542  60.289  15.522  1.00  0.00
ATOM    568  CE1 PHE    73       7.797  60.116  15.470  1.00  0.00
ATOM    569  CE2 PHE    73       9.777  61.185  16.244  1.00  0.00
ATOM    570  CZ  PHE    73       8.409  61.101  16.221  1.00  0.00
ATOM    571  N   TRP    74      13.605  58.285  12.169  1.00  0.00
ATOM    572  CA  TRP    74      14.603  57.443  11.583  1.00  0.00
ATOM    573  C   TRP    74      14.787  56.275  12.490  1.00  0.00
ATOM    574  O   TRP    74      14.792  56.417  13.709  1.00  0.00
ATOM    575  CB  TRP    74      15.924  58.203  11.432  1.00  0.00
ATOM    576  CG  TRP    74      15.876  59.287  10.400  1.00  0.00
ATOM    577  CD1 TRP    74      15.756  60.628  10.627  1.00  0.00
ATOM    578  CD2 TRP    74      15.949  59.124   8.979  1.00  0.00
ATOM    579  NE1 TRP    74      15.749  61.311   9.434  1.00  0.00
ATOM    580  CE2 TRP    74      15.866  60.408   8.407  1.00  0.00
ATOM    581  CE3 TRP    74      16.076  58.017   8.134  1.00  0.00
ATOM    582  CZ2 TRP    74      15.906  60.617   7.029  1.00  0.00
ATOM    583  CZ3 TRP    74      16.114  58.228   6.769  1.00  0.00
ATOM    584  CH2 TRP    74      16.031  59.516   6.228  1.00  0.00
ATOM    585  N   LEU    75      14.930  55.072  11.905  1.00  0.00
ATOM    586  CA  LEU    75      15.127  53.917  12.726  1.00  0.00
ATOM    587  C   LEU    75      16.567  53.554  12.586  1.00  0.00
ATOM    588  O   LEU    75      17.093  53.477  11.477  1.00  0.00
ATOM    589  CB  LEU    75      14.232  52.768  12.257  1.00  0.00
ATOM    590  CG  LEU    75      12.724  53.028  12.286  1.00  0.00
ATOM    591  CD1 LEU    75      11.963  51.841  11.717  1.00  0.00
ATOM    592  CD2 LEU    75      12.246  53.261  13.711  1.00  0.00
ATOM    593  N   THR    76      17.252  53.343  13.725  1.00  0.00
ATOM    594  CA  THR    76      18.637  52.987  13.657  1.00  0.00
ATOM    595  C   THR    76      18.810  51.713  14.413  1.00  0.00
ATOM    596  O   THR    76      18.113  51.440  15.389  1.00  0.00
ATOM    597  CB  THR    76      19.531  54.077  14.277  1.00  0.00
ATOM    598  OG1 THR    76      19.198  54.243  15.660  1.00  0.00
ATOM    599  CG2 THR    76      19.329  55.402  13.559  1.00  0.00
ATOM    600  N   PRO    77      19.719  50.912  13.939  1.00  0.00
ATOM    601  CA  PRO    77      20.013  49.673  14.599  1.00  0.00
ATOM    602  C   PRO    77      20.891  49.936  15.775  1.00  0.00
ATOM    603  O   PRO    77      21.528  50.988  15.820  1.00  0.00
ATOM    604  CB  PRO    77      20.718  48.840  13.527  1.00  0.00
ATOM    605  CG  PRO    77      21.421  49.844  12.676  1.00  0.00
ATOM    606  CD  PRO    77      20.509  51.037  12.601  1.00  0.00
TER
END
