
#######################################################
#                                                     #
#                        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_4_2-D1
# Molecule2: number of CA atoms   61 (  477),  selected    7 , name T0381_D1.pdb
# PARAMETERS: T0381TS268_4_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          1.52     1.52
  LCS_AVERAGE:     11.48

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     7        71 - 77          1.52     1.52
  LCS_AVERAGE:     11.48

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6        71 - 76          0.97     1.90
  LCS_AVERAGE:      9.37

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      6    7    7     3    5    5    6    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7 
LCS_GDT     A      72     A      72      6    7    7     4    5    5    6    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7 
LCS_GDT     F      73     F      73      6    7    7     4    5    5    6    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7 
LCS_GDT     W      74     W      74      6    7    7     4    5    5    6    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7 
LCS_GDT     L      75     L      75      6    7    7     4    5    5    6    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7 
LCS_GDT     T      76     T      76      6    7    7     3    5    5    6    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7 
LCS_GDT     P      77     P      77      4    7    7     3    3    5    6    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7 
LCS_AVERAGE  LCS_A:  10.77  (   9.37   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      4      5      5      6      7      7      7      7      7      7      7      7      7      7      7      7      7      7      7      7 
GDT PERCENT_CA   6.56   8.20   8.20   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    0.32   0.62   0.62   0.97   1.52   1.52   1.52   1.52   1.52   1.52   1.52   1.52   1.52   1.52   1.52   1.52   1.52   1.52   1.52   1.52
GDT RMS_ALL_CA   1.96   1.79   1.79   1.90   1.52   1.52   1.52   1.52   1.52   1.52   1.52   1.52   1.52   1.52   1.52   1.52   1.52   1.52   1.52   1.52

#      Molecule1      Molecule2       DISTANCE
LGA    S      71      S      71          2.257
LGA    A      72      A      72          0.749
LGA    F      73      F      73          0.741
LGA    W      74      W      74          1.040
LGA    L      75      L      75          0.957
LGA    T      76      T      76          1.413
LGA    P      77      P      77          2.460

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)    7   61    4.0      7    1.52    10.246    10.857     0.431

LGA_LOCAL      RMSD =  1.524  Number of atoms =    7  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  1.524  Number of atoms =    7 
Std_ALL_ATOMS  RMSD =  1.524  (standard rmsd on all 7 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.151520 * X  +   0.364523 * Y  +  -0.918784 * Z  +  -7.268046
  Y_new =  -0.778066 * X  +  -0.529300 * Y  +  -0.338311 * Z  +  82.221672
  Z_new =  -0.609635 * X  +   0.766136 * Y  +   0.203423 * Z  +  37.872059 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.311266   -1.830327  [ DEG:    75.1300   -104.8700 ]
  Theta =   0.655600    2.485993  [ DEG:    37.5631    142.4369 ]
  Phi   =  -1.378465    1.763128  [ DEG:   -78.9802    101.0198 ]
 
# 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_4_2-D1                             
REMARK     2: T0381_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0381TS268_4_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   1.52  10.857     1.52
REMARK  ---------------------------------------------------------- 
MOLECULE T0381TS268_4_2-D1
REMARK PARENT number 2
PFRMAT TS
TARGET T0381
PARENT 1tf1_A
ATOM    549  N   SER    71      11.446  65.098   9.227  1.00  0.00
ATOM    550  CA  SER    71      11.307  63.836   8.460  1.00  0.00
ATOM    551  C   SER    71      10.454  62.885   9.235  1.00  0.00
ATOM    552  O   SER    71       9.586  63.301  10.000  1.00  0.00
ATOM    553  CB  SER    71      12.677  63.200   8.221  1.00  0.00
ATOM    554  OG  SER    71      13.270  62.791   9.442  1.00  0.00
ATOM    555  N   ALA    72      10.674  61.570   9.042  1.00  0.00
ATOM    556  CA  ALA    72       9.926  60.575   9.750  1.00  0.00
ATOM    557  C   ALA    72      10.911  59.832  10.581  1.00  0.00
ATOM    558  O   ALA    72      12.049  59.624  10.163  1.00  0.00
ATOM    559  CB  ALA    72       9.232  59.639   8.773  1.00  0.00
ATOM    560  N   PHE    73      10.508  59.406  11.792  1.00  0.00
ATOM    561  CA  PHE    73      11.484  58.735  12.590  1.00  0.00
ATOM    562  C   PHE    73      11.181  57.276  12.605  1.00  0.00
ATOM    563  O   PHE    73      10.107  56.848  13.025  1.00  0.00
ATOM    564  CB  PHE    73      11.461  59.268  14.023  1.00  0.00
ATOM    565  CG  PHE    73      11.915  60.695  14.148  1.00  0.00
ATOM    566  CD1 PHE    73      11.008  61.736  14.049  1.00  0.00
ATOM    567  CD2 PHE    73      13.248  60.996  14.364  1.00  0.00
ATOM    568  CE1 PHE    73      11.426  63.048  14.162  1.00  0.00
ATOM    569  CE2 PHE    73      13.665  62.308  14.478  1.00  0.00
ATOM    570  CZ  PHE    73      12.761  63.332  14.377  1.00  0.00
ATOM    571  N   TRP    74      12.149  56.478  12.127  1.00  0.00
ATOM    572  CA  TRP    74      12.057  55.053  12.189  1.00  0.00
ATOM    573  C   TRP    74      13.320  54.573  12.806  1.00  0.00
ATOM    574  O   TRP    74      14.255  55.344  13.013  1.00  0.00
ATOM    575  CB  TRP    74      11.892  54.465  10.785  1.00  0.00
ATOM    576  CG  TRP    74      13.024  54.794   9.861  1.00  0.00
ATOM    577  CD1 TRP    74      13.156  55.915   9.094  1.00  0.00
ATOM    578  CD2 TRP    74      14.184  53.993   9.605  1.00  0.00
ATOM    579  NE1 TRP    74      14.327  55.864   8.376  1.00  0.00
ATOM    580  CE2 TRP    74      14.976  54.692   8.672  1.00  0.00
ATOM    581  CE3 TRP    74      14.631  52.753  10.072  1.00  0.00
ATOM    582  CZ2 TRP    74      16.188  54.193   8.200  1.00  0.00
ATOM    583  CZ3 TRP    74      15.834  52.263   9.601  1.00  0.00
ATOM    584  CH2 TRP    74      16.600  52.978   8.674  1.00  0.00
ATOM    585  N   LEU    75      13.361  53.277  13.150  1.00  0.00
ATOM    586  CA  LEU    75      14.503  52.750  13.829  1.00  0.00
ATOM    587  C   LEU    75      15.639  52.654  12.862  1.00  0.00
ATOM    588  O   LEU    75      15.472  52.199  11.730  1.00  0.00
ATOM    589  CB  LEU    75      14.199  51.359  14.390  1.00  0.00
ATOM    590  CG  LEU    75      15.304  50.708  15.223  1.00  0.00
ATOM    591  CD1 LEU    75      15.546  51.492  16.503  1.00  0.00
ATOM    592  CD2 LEU    75      14.924  49.284  15.601  1.00  0.00
ATOM    593  N   THR    76      16.826  53.115  13.302  1.00  0.00
ATOM    594  CA  THR    76      18.047  52.997  12.557  1.00  0.00
ATOM    595  C   THR    76      19.112  52.818  13.591  1.00  0.00
ATOM    596  O   THR    76      18.866  53.049  14.771  1.00  0.00
ATOM    597  CB  THR    76      18.315  54.255  11.709  1.00  0.00
ATOM    598  OG1 THR    76      19.452  54.032  10.865  1.00  0.00
ATOM    599  CG2 THR    76      18.593  55.452  12.605  1.00  0.00
ATOM    600  N   PRO    77      20.280  52.386  13.209  1.00  0.00
ATOM    601  CA  PRO    77      21.298  52.261  14.216  1.00  0.00
ATOM    602  C   PRO    77      21.818  53.608  14.589  1.00  0.00
ATOM    603  O   PRO    77      21.923  54.461  13.711  1.00  0.00
ATOM    604  CB  PRO    77      22.372  51.399  13.551  1.00  0.00
ATOM    605  CG  PRO    77      21.651  50.675  12.464  1.00  0.00
ATOM    606  CD  PRO    77      20.615  51.631  11.944  1.00  0.00
TER
END
