
#######################################################
#                                                     #
#                        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_3_2-D1
# Molecule2: number of CA atoms   61 (  477),  selected    7 , name T0381_D1.pdb
# PARAMETERS: T0381TS268_3_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          1.09     1.09
  LCS_AVERAGE:     11.48

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     7        71 - 77          1.09     1.09
  LCS_AVERAGE:     11.48

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6        71 - 76          0.86     1.35
  LCS_AVERAGE:      9.60

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    6    7    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     3    5    6    7    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     3    5    6    7    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     3    5    6    7    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     3    5    6    7    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    6    7    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    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7 
LCS_AVERAGE  LCS_A:  10.85  (   9.60   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      7      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  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  11.48
GDT RMS_LOCAL    0.10   0.71   0.86   1.09   1.09   1.09   1.09   1.09   1.09   1.09   1.09   1.09   1.09   1.09   1.09   1.09   1.09   1.09   1.09   1.09
GDT RMS_ALL_CA   2.85   1.32   1.35   1.09   1.09   1.09   1.09   1.09   1.09   1.09   1.09   1.09   1.09   1.09   1.09   1.09   1.09   1.09   1.09   1.09

#      Molecule1      Molecule2       DISTANCE
LGA    S      71      S      71          0.820
LGA    A      72      A      72          0.961
LGA    F      73      F      73          0.879
LGA    W      74      W      74          1.013
LGA    L      75      L      75          0.746
LGA    T      76      T      76          1.589
LGA    P      77      P      77          1.362

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)    7   61    4.0      7    1.09    10.656    11.094     0.588

LGA_LOCAL      RMSD =  1.091  Number of atoms =    7  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  1.091  Number of atoms =    7 
Std_ALL_ATOMS  RMSD =  1.091  (standard rmsd on all 7 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.078491 * X  +   0.474542 * Y  +   0.876727 * Z  +  62.934139
  Y_new =   0.883939 * X  +  -0.439775 * Y  +   0.158898 * Z  +  36.150211
  Z_new =   0.460966 * X  +   0.762501 * Y  +  -0.453985 * Z  +   3.958061 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.107818   -1.033774  [ DEG:   120.7691    -59.2309 ]
  Theta =  -0.479084   -2.662509  [ DEG:   -27.4495   -152.5505 ]
  Phi   =   1.482231   -1.659361  [ DEG:    84.9256    -95.0744 ]
 
# 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_3_2-D1                             
REMARK     2: T0381_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0381TS268_3_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   1.09  11.094     1.09
REMARK  ---------------------------------------------------------- 
MOLECULE T0381TS268_3_2-D1
REMARK PARENT number 2
PFRMAT TS
TARGET T0381
PARENT 1tf1_C
ATOM    549  N   SER    71      10.859  64.848   9.351  1.00  0.00
ATOM    550  CA  SER    71       9.561  64.153   9.200  1.00  0.00
ATOM    551  C   SER    71       9.601  62.845   9.913  1.00  0.00
ATOM    552  O   SER    71      10.018  62.768  11.067  1.00  0.00
ATOM    553  CB  SER    71       9.258  63.900   7.722  1.00  0.00
ATOM    554  OG  SER    71      10.200  63.006   7.154  1.00  0.00
ATOM    555  N   ALA    72       9.158  61.772   9.232  1.00  0.00
ATOM    556  CA  ALA    72       9.179  60.488   9.863  1.00  0.00
ATOM    557  C   ALA    72      10.611  60.137  10.063  1.00  0.00
ATOM    558  O   ALA    72      11.466  60.472   9.245  1.00  0.00
ATOM    559  CB  ALA    72       8.495  59.454   8.982  1.00  0.00
ATOM    560  N   PHE    73      10.915  59.463  11.186  1.00  0.00
ATOM    561  CA  PHE    73      12.275  59.111  11.443  1.00  0.00
ATOM    562  C   PHE    73      12.318  57.627  11.581  1.00  0.00
ATOM    563  O   PHE    73      11.446  57.022  12.204  1.00  0.00
ATOM    564  CB  PHE    73      12.768  59.778  12.729  1.00  0.00
ATOM    565  CG  PHE    73      14.168  59.393  13.114  1.00  0.00
ATOM    566  CD1 PHE    73      15.257  59.967  12.482  1.00  0.00
ATOM    567  CD2 PHE    73      14.395  58.457  14.108  1.00  0.00
ATOM    568  CE1 PHE    73      16.545  59.613  12.836  1.00  0.00
ATOM    569  CE2 PHE    73      15.683  58.103  14.461  1.00  0.00
ATOM    570  CZ  PHE    73      16.756  58.677  13.830  1.00  0.00
ATOM    571  N   TRP    74      13.339  56.996  10.974  1.00  0.00
ATOM    572  CA  TRP    74      13.466  55.573  11.057  1.00  0.00
ATOM    573  C   TRP    74      14.481  55.326  12.118  1.00  0.00
ATOM    574  O   TRP    74      15.474  56.046  12.209  1.00  0.00
ATOM    575  CB  TRP    74      13.924  54.996   9.717  1.00  0.00
ATOM    576  CG  TRP    74      12.913  55.146   8.622  1.00  0.00
ATOM    577  CD1 TRP    74      12.854  56.142   7.690  1.00  0.00
ATOM    578  CD2 TRP    74      11.811  54.271   8.345  1.00  0.00
ATOM    579  NE1 TRP    74      11.786  55.943   6.849  1.00  0.00
ATOM    580  CE2 TRP    74      11.129  54.800   7.231  1.00  0.00
ATOM    581  CE3 TRP    74      11.336  53.094   8.929  1.00  0.00
ATOM    582  CZ2 TRP    74       9.998  54.192   6.690  1.00  0.00
ATOM    583  CZ3 TRP    74      10.214  52.495   8.389  1.00  0.00
ATOM    584  CH2 TRP    74       9.555  53.041   7.282  1.00  0.00
ATOM    585  N   LEU    75      14.252  54.315  12.975  1.00  0.00
ATOM    586  CA  LEU    75      15.227  54.100  13.998  1.00  0.00
ATOM    587  C   LEU    75      15.966  52.857  13.626  1.00  0.00
ATOM    588  O   LEU    75      15.414  51.758  13.662  1.00  0.00
ATOM    589  CB  LEU    75      14.548  53.931  15.358  1.00  0.00
ATOM    590  CG  LEU    75      15.470  53.657  16.548  1.00  0.00
ATOM    591  CD1 LEU    75      16.421  54.823  16.771  1.00  0.00
ATOM    592  CD2 LEU    75      14.661  53.452  17.820  1.00  0.00
ATOM    593  N   THR    76      17.246  53.010  13.243  1.00  0.00
ATOM    594  CA  THR    76      18.041  51.866  12.919  1.00  0.00
ATOM    595  C   THR    76      19.259  51.962  13.772  1.00  0.00
ATOM    596  O   THR    76      19.778  53.052  14.010  1.00  0.00
ATOM    597  CB  THR    76      18.431  51.853  11.430  1.00  0.00
ATOM    598  OG1 THR    76      17.247  51.834  10.623  1.00  0.00
ATOM    599  CG2 THR    76      19.265  50.621  11.108  1.00  0.00
ATOM    600  N   PRO    77      19.717  50.851  14.267  1.00  0.00
ATOM    601  CA  PRO    77      20.872  50.917  15.110  1.00  0.00
ATOM    602  C   PRO    77      22.107  51.243  14.342  1.00  0.00
ATOM    603  O   PRO    77      22.278  50.741  13.231  1.00  0.00
ATOM    604  CB  PRO    77      20.962  49.520  15.726  1.00  0.00
ATOM    605  CG  PRO    77      20.271  48.634  14.744  1.00  0.00
ATOM    606  CD  PRO    77      19.176  49.462  14.134  1.00  0.00
TER
END
