
#######################################################
#                                                     #
#                        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_5_2-D1
# Molecule2: number of CA atoms   61 (  477),  selected    7 , name T0381_D1.pdb
# PARAMETERS: T0381TS268_5_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          1.84     1.84
  LCS_AVERAGE:     11.48

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     7        71 - 77          1.84     1.84
  LCS_AVERAGE:     11.48

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4        71 - 74          0.47     4.86
  LONGEST_CONTINUOUS_SEGMENT:     4        72 - 75          0.88     3.07
  LONGEST_CONTINUOUS_SEGMENT:     4        73 - 76          0.86     3.12
  LCS_AVERAGE:      6.32

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    4    5    7    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    4    5    7    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    4    5    7    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    4    5    7    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    4    5    7    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    4    5    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7 
LCS_GDT     P      77     P      77      3    7    7     3    3    4    5    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7 
LCS_AVERAGE  LCS_A:   9.76  (   6.32   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      4      5      7      7      7      7      7      7      7      7      7      7      7      7      7      7      7      7 
GDT PERCENT_CA   4.92   6.56   6.56   8.20  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    0.08   0.43   0.43   1.04   1.84   1.84   1.84   1.84   1.84   1.84   1.84   1.84   1.84   1.84   1.84   1.84   1.84   1.84   1.84   1.84
GDT RMS_ALL_CA   4.32   2.33   2.33   2.43   1.84   1.84   1.84   1.84   1.84   1.84   1.84   1.84   1.84   1.84   1.84   1.84   1.84   1.84   1.84   1.84

#      Molecule1      Molecule2       DISTANCE
LGA    S      71      S      71          2.029
LGA    A      72      A      72          1.902
LGA    F      73      F      73          0.137
LGA    W      74      W      74          2.297
LGA    L      75      L      75          0.793
LGA    T      76      T      76          2.164
LGA    P      77      P      77          2.290

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)    7   61    4.0      7    1.84     9.426    10.490     0.362

LGA_LOCAL      RMSD =  1.836  Number of atoms =    7  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  1.836  Number of atoms =    7 
Std_ALL_ATOMS  RMSD =  1.836  (standard rmsd on all 7 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.909640 * X  +   0.169668 * Y  +  -0.379168 * Z  + -21.454557
  Y_new =   0.061111 * X  +  -0.957510 * Y  +  -0.281853 * Z  +  49.701847
  Z_new =  -0.410879 * X  +   0.233213 * Y  +  -0.881357 * Z  +   5.632679 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.882914   -0.258678  [ DEG:   165.1788    -14.8212 ]
  Theta =   0.423418    2.718175  [ DEG:    24.2600    155.7400 ]
  Phi   =   0.067080   -3.074512  [ DEG:     3.8434   -176.1566 ]
 
# 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_5_2-D1                             
REMARK     2: T0381_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0381TS268_5_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   1.84  10.490     1.84
REMARK  ---------------------------------------------------------- 
MOLECULE T0381TS268_5_2-D1
REMARK PARENT number 2
PFRMAT TS
TARGET T0381
PARENT 1tf1_A
ATOM    549  N   SER    71       6.880  62.553   8.884  1.00  0.00
ATOM    550  CA  SER    71       8.181  62.886   8.264  1.00  0.00
ATOM    551  C   SER    71       9.203  61.864   8.622  1.00  0.00
ATOM    552  O   SER    71       8.899  60.678   8.730  1.00  0.00
ATOM    553  CB  SER    71       8.670  64.252   8.748  1.00  0.00
ATOM    554  OG  SER    71       9.928  64.574   8.180  1.00  0.00
ATOM    555  N   ALA    72      10.461  62.305   8.801  1.00  0.00
ATOM    556  CA  ALA    72      11.488  61.367   9.123  1.00  0.00
ATOM    557  C   ALA    72      11.311  60.921  10.535  1.00  0.00
ATOM    558  O   ALA    72      10.951  61.698  11.418  1.00  0.00
ATOM    559  CB  ALA    72      12.859  62.007   8.967  1.00  0.00
ATOM    560  N   PHE    73      11.543  59.617  10.760  1.00  0.00
ATOM    561  CA  PHE    73      11.527  59.033  12.063  1.00  0.00
ATOM    562  C   PHE    73      12.668  58.074  12.046  1.00  0.00
ATOM    563  O   PHE    73      13.103  57.654  10.975  1.00  0.00
ATOM    564  CB  PHE    73      10.197  58.322  12.316  1.00  0.00
ATOM    565  CG  PHE    73       9.957  57.145  11.412  1.00  0.00
ATOM    566  CD1 PHE    73      10.354  55.874  11.789  1.00  0.00
ATOM    567  CD2 PHE    73       9.335  57.310  10.187  1.00  0.00
ATOM    568  CE1 PHE    73      10.134  54.791  10.958  1.00  0.00
ATOM    569  CE2 PHE    73       9.114  56.228   9.356  1.00  0.00
ATOM    570  CZ  PHE    73       9.511  54.973   9.737  1.00  0.00
ATOM    571  N   TRP    74      13.214  57.706  13.219  1.00  0.00
ATOM    572  CA  TRP    74      14.371  56.869  13.125  1.00  0.00
ATOM    573  C   TRP    74      14.111  55.507  13.664  1.00  0.00
ATOM    574  O   TRP    74      13.347  55.309  14.607  1.00  0.00
ATOM    575  CB  TRP    74      15.532  57.471  13.919  1.00  0.00
ATOM    576  CG  TRP    74      15.994  58.796  13.395  1.00  0.00
ATOM    577  CD1 TRP    74      15.549  60.030  13.777  1.00  0.00
ATOM    578  CD2 TRP    74      16.992  59.023  12.391  1.00  0.00
ATOM    579  NE1 TRP    74      16.207  61.010  13.074  1.00  0.00
ATOM    580  CE2 TRP    74      17.098  60.417  12.216  1.00  0.00
ATOM    581  CE3 TRP    74      17.804  58.183  11.622  1.00  0.00
ATOM    582  CZ2 TRP    74      17.985  60.989  11.305  1.00  0.00
ATOM    583  CZ3 TRP    74      18.682  58.756  10.721  1.00  0.00
ATOM    584  CH2 TRP    74      18.767  60.144  10.567  1.00  0.00
ATOM    585  N   LEU    75      14.760  54.526  13.010  1.00  0.00
ATOM    586  CA  LEU    75      14.753  53.151  13.406  1.00  0.00
ATOM    587  C   LEU    75      16.168  52.903  13.791  1.00  0.00
ATOM    588  O   LEU    75      17.068  53.579  13.296  1.00  0.00
ATOM    589  CB  LEU    75      14.308  52.261  12.244  1.00  0.00
ATOM    590  CG  LEU    75      12.921  52.547  11.664  1.00  0.00
ATOM    591  CD1 LEU    75      12.642  51.648  10.468  1.00  0.00
ATOM    592  CD2 LEU    75      11.841  52.299  12.706  1.00  0.00
ATOM    593  N   THR    76      16.425  51.949  14.701  1.00  0.00
ATOM    594  CA  THR    76      17.803  51.774  15.033  1.00  0.00
ATOM    595  C   THR    76      18.468  51.083  13.892  1.00  0.00
ATOM    596  O   THR    76      17.930  50.172  13.260  1.00  0.00
ATOM    597  CB  THR    76      17.974  50.926  16.307  1.00  0.00
ATOM    598  OG1 THR    76      17.319  51.573  17.406  1.00  0.00
ATOM    599  CG2 THR    76      19.448  50.758  16.642  1.00  0.00
ATOM    600  N   PRO    77      19.677  51.533  13.686  1.00  0.00
ATOM    601  CA  PRO    77      20.496  51.128  12.577  1.00  0.00
ATOM    602  C   PRO    77      20.564  49.644  12.536  1.00  0.00
ATOM    603  O   PRO    77      20.306  49.007  13.555  1.00  0.00
ATOM    604  CB  PRO    77      21.858  51.761  12.871  1.00  0.00
ATOM    605  CG  PRO    77      21.542  52.944  13.725  1.00  0.00
ATOM    606  CD  PRO    77      20.404  52.526  14.613  1.00  0.00
TER
END
