
#######################################################
#                                                     #
#                        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    6 (   30),  selected    6 , name T0372TS103_1_2-D1
# Molecule2: number of CA atoms  126 ( 1027),  selected    6 , name T0372_D1.pdb
# PARAMETERS: T0372TS103_1_2-D1.T0372_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:     6       290 - 295         4.03     4.03
  LCS_AVERAGE:      4.76

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
# WARNING! The change of the parameter DIST cutoff may give you better result.

  LONGEST_CONTINUOUS_SEGMENT:     3       290 - 292         1.22     7.53
  LONGEST_CONTINUOUS_SEGMENT:     3       291 - 293         0.28     6.76
  LONGEST_CONTINUOUS_SEGMENT:     3       292 - 294         0.51     6.99
  LONGEST_CONTINUOUS_SEGMENT:     3       293 - 295         0.60     6.34
  LCS_AVERAGE:      2.38

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     3       291 - 293         0.28     6.76
  LONGEST_CONTINUOUS_SEGMENT:     3       292 - 294         0.51     6.99
  LONGEST_CONTINUOUS_SEGMENT:     3       293 - 295         0.60     6.34
  LCS_AVERAGE:      1.98

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:  126
LCS_GDT     K     290     K     290      0    3    6     0    0    2    3    3    3    4    4    6    6    6    6    6    6    6    6    6    6    6    6 
LCS_GDT     Y     291     Y     291      3    3    6     3    3    3    3    3    3    4    5    6    6    6    6    6    6    6    6    6    6    6    6 
LCS_GDT     M     292     M     292      3    3    6     3    3    3    3    3    3    4    5    6    6    6    6    6    6    6    6    6    6    6    6 
LCS_GDT     A     293     A     293      3    3    6     3    3    3    3    3    3    4    5    6    6    6    6    6    6    6    6    6    6    6    6 
LCS_GDT     C     294     C     294      3    3    6     0    3    3    3    3    3    4    5    6    6    6    6    6    6    6    6    6    6    6    6 
LCS_GDT     L     295     L     295      3    3    6     0    3    3    3    3    3    4    5    6    6    6    6    6    6    6    6    6    6    6    6 
LCS_AVERAGE  LCS_A:   3.04  (   1.98    2.38    4.76 )

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      3      3      3      3      3      4      5      6      6      6      6      6      6      6      6      6      6      6      6 
GDT PERCENT_CA   2.38   2.38   2.38   2.38   2.38   2.38   3.17   3.97   4.76   4.76   4.76   4.76   4.76   4.76   4.76   4.76   4.76   4.76   4.76   4.76
GDT RMS_LOCAL    0.28   0.28   0.28   0.28   0.28   0.28   2.47   3.32   4.03   4.03   4.03   4.03   4.03   4.03   4.03   4.03   4.03   4.03   4.03   4.03
GDT RMS_ALL_CA   6.76   6.76   6.76   6.76   6.76   6.76   6.03   5.21   4.03   4.03   4.03   4.03   4.03   4.03   4.03   4.03   4.03   4.03   4.03   4.03

#      Molecule1      Molecule2       DISTANCE
LGA    K     290      K     290         10.369
LGA    Y     291      Y     291          3.665
LGA    M     292      M     292          3.010
LGA    A     293      A     293          3.663
LGA    C     294      C     294          2.001
LGA    L     295      L     295          3.905

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)    6  126    4.0      5    3.32     3.373     3.199     0.146

LGA_LOCAL      RMSD =  3.321  Number of atoms =    5  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  5.207  Number of atoms =    6 
Std_ALL_ATOMS  RMSD =  4.028  (standard rmsd on all 6 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.472601 * X  +   0.189709 * Y  +  -0.860615 * Z  +  -5.093486
  Y_new =   0.768398 * X  +  -0.566883 * Y  +   0.297000 * Z  +  92.694267
  Z_new =  -0.431524 * X  +  -0.801657 * Y  +  -0.413682 * Z  +  93.036667 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.047188    1.094405  [ DEG:  -117.2952     62.7048 ]
  Theta =   0.446182    2.695411  [ DEG:    25.5643    154.4357 ]
  Phi   =   1.019386   -2.122207  [ DEG:    58.4065   -121.5935 ]
 
# 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: T0372TS103_1_2-D1                             
REMARK     2: T0372_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0372TS103_1_2-D1.T0372_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:    6  126   4.0    5   3.32   3.199     4.03
REMARK  ---------------------------------------------------------- 
MOLECULE T0372TS103_1_2-D1
REMARK PARENT number 2
PFRMAT TS
TARGET T0372
PARENT 1z5x_U
ATOM    825  N   LYS   290      24.819  40.261  -2.114  1.00  1.00
ATOM    826  CA  LYS   290      26.003  40.904  -1.561  1.00  1.00
ATOM    827  C   LYS   290      25.581  41.870  -0.459  1.00  1.00
ATOM    828  O   LYS   290      24.532  41.681   0.159  1.00  1.00
ATOM    829  CB  LYS   290      26.736  41.699  -2.644  1.00  1.00
ATOM    830  N   TYR   291      24.794  45.957   0.646  1.00  1.00
ATOM    831  CA  TYR   291      24.305  47.148  -0.040  1.00  1.00
ATOM    832  C   TYR   291      25.481  47.832  -0.719  1.00  1.00
ATOM    833  O   TYR   291      25.420  48.129  -1.916  1.00  1.00
ATOM    834  CB  TYR   291      23.647  48.187   0.925  1.00  1.00
ATOM    835  N   MET   292      26.560  48.055   0.037  1.00  1.00
ATOM    836  CA  MET   292      27.747  48.749  -0.482  1.00  1.00
ATOM    837  C   MET   292      28.418  48.049  -1.640  1.00  1.00
ATOM    838  O   MET   292      28.814  48.687  -2.604  1.00  1.00
ATOM    839  CB  MET   292      28.763  48.981   0.633  1.00  1.00
ATOM    840  N   ALA   293      28.556  46.737  -1.559  1.00  1.00
ATOM    841  CA  ALA   293      29.178  46.033  -2.655  1.00  1.00
ATOM    842  C   ALA   293      28.323  46.134  -3.924  1.00  1.00
ATOM    843  O   ALA   293      28.851  46.258  -5.040  1.00  1.00
ATOM    844  CB  ALA   293      29.376  44.582  -2.291  1.00  1.00
ATOM    845  N   CYS   294      27.004  46.075  -3.741  1.00  1.00
ATOM    846  CA  CYS   294      26.041  46.167  -4.840  1.00  1.00
ATOM    847  C   CYS   294      26.106  47.545  -5.489  1.00  1.00
ATOM    848  O   CYS   294      26.161  47.672  -6.713  1.00  1.00
ATOM    849  CB  CYS   294      24.616  45.922  -4.334  1.00  1.00
ATOM    850  N   LEU   295      26.074  48.578  -4.652  1.00  1.00
ATOM    851  CA  LEU   295      26.140  49.955  -5.115  1.00  1.00
ATOM    852  C   LEU   295      27.437  50.217  -5.856  1.00  1.00
ATOM    853  O   LEU   295      27.456  50.675  -6.992  1.00  1.00
ATOM    854  CB  LEU   295      26.054  50.906  -3.925  1.00  1.00
TER
END
