
#######################################################
#                                                     #
#                        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    4 (   27),  selected    4 , name T0316TS186_5-D3
# Molecule2: number of CA atoms   90 (  711),  selected    4 , name T0316_D3.pdb
# PARAMETERS: T0316TS186_5-D3.T0316_D3.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
# WARNING! The change of the parameter DIST cutoff may give you better result.

  LCS_AVERAGE:      0.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LCS_AVERAGE:      0.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LCS_AVERAGE:      0.00

# WARNING! The change of the distance cutoff DIST may give you better result.

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:   90
LCS_GDT     M     284     M     284      0    0    0     0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    2    2    2    2 
LCS_GDT     S     285     S     285      0    0    0     0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    2    2    2    2 
LCS_GDT     T     286     T     286      0    0    0     0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    2    2    2    2 
LCS_GDT     S     287     S     287      0    0    0     0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    1    2    2    2    2 
LCS_AVERAGE  LCS_A:   0.00  (   0.00    0.00    0.00 )

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      0      0      0      0      0      0      0      0      0      0      0      0      0      0      0      1      2      2      2      2 
GDT PERCENT_CA   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   0.00   1.11   2.22   2.22   2.22   2.22
GDT RMS_LOCAL  1000.00 1000.00 1000.00 1000.00 1000.00 1000.00 1000.00 1000.00 1000.00 1000.00 1000.00 1000.00 1000.00 1000.00 1000.00  32.58  23.76  23.76  23.76  23.76
GDT RMS_ALL_CA 1000.00 1000.00 1000.00 1000.00 1000.00 1000.00 1000.00 1000.00 1000.00 1000.00 1000.00 1000.00 1000.00 1000.00 1000.00  12.94  12.94  12.94  12.94  12.94

#      Molecule1      Molecule2       DISTANCE
LGA    M     284      M     284         15.344
LGA    S     285      S     285         18.242
LGA    T     286      T     286         45.388
LGA    S     287      S     287         47.007

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)    4   90    4.0      0  1000.00     0.278     0.000     0.000

LGA_LOCAL      RMSD =999.999  Number of atoms =    0  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 34.778  Number of atoms =    4 
Std_ALL_ATOMS  RMSD = 12.229  (standard rmsd on all 4 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.000000 * X  +   0.000000 * Y  +   0.000000 * Z  +   0.000000
  Y_new =   0.000000 * X  +   0.000000 * Y  +   0.000000 * Z  +   0.000000
  Z_new =   0.000000 * X  +   0.000000 * Y  +   0.000000 * Z  +   0.000000 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.000000   -3.141593  [ DEG:     0.0000   -180.0000 ]
  Theta =  -0.000000    3.141593  [ DEG:    -0.0000    180.0000 ]
  Phi   =   0.000000   -3.141593  [ DEG:     0.0000   -180.0000 ]
 
# NOTE! The number N = 0 of calculated residues is smaller then cutoff lN:n = 1 

# 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: no coordinates  
REMARK     1: T0316TS186_5-D3                               
REMARK     2: T0316_D3.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0316TS186_5-D3.T0316_D3.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:    4   90   4.0    0 1000.00   0.000    12.23
REMARK  ---------------------------------------------------------- 
