
#######################################################
#                                                     #
#                        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    5 (   24),  selected    5 , name T0322TS239_4_2-D1
# Molecule2: number of CA atoms  128 (  980),  selected    5 , name T0322_D1.pdb
# PARAMETERS: T0322TS239_4_2-D1.T0322_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:     5        16 - 142         1.73     1.73
  LCS_AVERAGE:      3.91

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5        16 - 142         1.73     1.73
  LCS_AVERAGE:      3.91

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
# WARNING! The change of the parameter DIST cutoff may give you better result.

  LONGEST_CONTINUOUS_SEGMENT:     3        16 - 18          0.08    18.53
  LONGEST_CONTINUOUS_SEGMENT:     3        17 - 19          0.66     5.07
  LONGEST_CONTINUOUS_SEGMENT:     3        18 - 142         0.50     3.55
  LCS_AVERAGE:      2.34

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:  128
LCS_GDT     G      16     G      16      3    5    5     3    3    3    4    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5 
LCS_GDT     F      17     F      17      3    5    5     3    3    3    4    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5 
LCS_GDT     S      18     S      18      3    5    5     3    3    3    4    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5 
LCS_GDT     Q      19     Q      19      3    5    5     2    3    3    4    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5 
LCS_GDT     S     142     S     142      3    5    5     0    3    3    4    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5 
LCS_AVERAGE  LCS_A:   3.39  (   2.34    3.91    3.91 )

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      4      5      5      5      5      5      5      5      5      5      5      5      5      5      5      5      5 
GDT PERCENT_CA   2.34   2.34   2.34   3.12   3.91   3.91   3.91   3.91   3.91   3.91   3.91   3.91   3.91   3.91   3.91   3.91   3.91   3.91   3.91   3.91
GDT RMS_LOCAL    0.08   0.08   0.08   1.14   1.73   1.73   1.73   1.73   1.73   1.73   1.73   1.73   1.73   1.73   1.73   1.73   1.73   1.73   1.73   1.73
GDT RMS_ALL_CA  18.53  18.53  18.53   2.55   1.73   1.73   1.73   1.73   1.73   1.73   1.73   1.73   1.73   1.73   1.73   1.73   1.73   1.73   1.73   1.73

#      Molecule1      Molecule2       DISTANCE
LGA    G      16      G      16          1.949
LGA    F      17      F      17          2.154
LGA    S      18      S      18          1.097
LGA    Q      19      Q      19          1.739
LGA    S     142      S     142          1.510

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)    5  128    4.0      5    1.73     3.320     3.612     0.273

LGA_LOCAL      RMSD =  1.729  Number of atoms =    5  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  1.729  Number of atoms =    5 
Std_ALL_ATOMS  RMSD =  1.729  (standard rmsd on all 5 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.420947 * X  +  -0.002795 * Y  +  -0.907081 * Z  +  10.651008
  Y_new =   0.822564 * X  +  -0.420337 * Y  +   0.383020 * Z  +   6.112420
  Z_new =  -0.382350 * X  +  -0.907364 * Y  +  -0.174641 * Z  +   6.237982 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.760942    1.380651  [ DEG:  -100.8945     79.1055 ]
  Theta =   0.392339    2.749254  [ DEG:    22.4793    157.5207 ]
  Phi   =   1.097793   -2.043799  [ DEG:    62.8989   -117.1011 ]
 
# 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: T0322TS239_4_2-D1                             
REMARK     2: T0322_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0322TS239_4_2-D1.T0322_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:    5  128   4.0    5   1.73   3.612     1.73
REMARK  ---------------------------------------------------------- 
MOLECULE T0322TS239_4_2-D1
REMARK PARENT number 2
PFRMAT TS
TARGET T0322
PARENT 1vh5_A
ATOM     76  N   GLY    16       9.796 -19.284 -10.937  1.00  9.99
ATOM     77  CA  GLY    16      11.064 -19.973 -10.891  1.00  9.99
ATOM     78  C   GLY    16      12.160 -19.217 -10.148  1.00  9.99
ATOM     79  O   GLY    16      13.328 -19.600 -10.229  1.00  9.99
ATOM     80  N   PHE    17      11.786 -18.159  -9.425  1.00  9.99
ATOM     81  CA  PHE    17      12.759 -17.411  -8.599  1.00  9.99
ATOM     82  C   PHE    17      12.150 -17.118  -7.241  1.00  9.99
ATOM     83  O   PHE    17      11.069 -17.591  -6.927  1.00  9.99
ATOM     84  CB  PHE    17      13.333 -16.173  -9.333  1.00  9.99
ATOM     85  N   SER    18      12.830 -16.310  -6.432  1.00  9.99
ATOM     86  CA  SER    18      12.423 -16.174  -5.039  1.00  9.99
ATOM     87  C   SER    18      11.009 -15.595  -4.894  1.00  9.99
ATOM     88  O   SER    18      10.268 -15.988  -3.996  1.00  9.99
ATOM     89  CB  SER    18      13.430 -15.320  -4.260  1.00  9.99
ATOM     90  N   GLN    19      10.668 -14.632  -5.740  1.00  9.99
ATOM     91  CA  GLN    19       9.355 -14.009  -5.656  1.00  9.99
ATOM     92  C   GLN    19       8.259 -15.103  -5.810  1.00  9.99
ATOM     93  O   GLN    19       7.314 -15.151  -5.029  1.00  9.99
ATOM     94  CB  GLN    19       9.181 -12.864  -6.691  1.00  9.99
ATOM    639  N   SER   142      22.868   2.581 -17.328  1.00  9.99
ATOM    640  CA  SER   142      22.549   3.116 -18.636  1.00  9.99
ATOM    641  C   SER   142      22.756   2.040 -19.669  1.00  9.99
ATOM    642  O   SER   142      22.059   2.005 -20.673  1.00  9.99
ATOM    643  CB  SER   142      23.405   4.382 -18.932  1.00  9.99
TER
END
