
#######################################################
#                                                     #
#                        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 (   31),  selected    4 , name T0298TS022_1_2-D1
# Molecule2: number of CA atoms  148 ( 1074),  selected    4 , name T0298_D1.pdb
# PARAMETERS: T0298TS022_1_2-D1.T0298_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:     4       316 - 319         0.47     0.47
  LCS_AVERAGE:      2.70

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4       316 - 319         0.47     0.47
  LCS_AVERAGE:      2.70

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4       316 - 319         0.47     0.47
  LCS_AVERAGE:      2.70

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:  148
LCS_GDT     V     316     V     316      4    4    4     3    4    4    4    4    4    4    4    4    4    4    4    4    4    4    4    4    4    4    4 
LCS_GDT     R     317     R     317      4    4    4     3    4    4    4    4    4    4    4    4    4    4    4    4    4    4    4    4    4    4    4 
LCS_GDT     K     318     K     318      4    4    4     3    4    4    4    4    4    4    4    4    4    4    4    4    4    4    4    4    4    4    4 
LCS_GDT     G     319     G     319      4    4    4     0    4    4    4    4    4    4    4    4    4    4    4    4    4    4    4    4    4    4    4 
LCS_AVERAGE  LCS_A:   2.70  (   2.70    2.70    2.70 )

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      4      4      4      4      4      4      4      4      4      4      4      4      4      4      4      4      4 
GDT PERCENT_CA   2.03   2.70   2.70   2.70   2.70   2.70   2.70   2.70   2.70   2.70   2.70   2.70   2.70   2.70   2.70   2.70   2.70   2.70   2.70   2.70
GDT RMS_LOCAL    0.13   0.47   0.47   0.47   0.47   0.47   0.47   0.47   0.47   0.47   0.47   0.47   0.47   0.47   0.47   0.47   0.47   0.47   0.47   0.47
GDT RMS_ALL_CA   0.58   0.47   0.47   0.47   0.47   0.47   0.47   0.47   0.47   0.47   0.47   0.47   0.47   0.47   0.47   0.47   0.47   0.47   0.47   0.47

#      Molecule1      Molecule2       DISTANCE
LGA    V     316      V     316          0.324
LGA    R     317      R     317          0.334
LGA    K     318      K     318          0.324
LGA    G     319      G     319          0.745

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)    4  148    4.0      4    0.47     2.703     2.703     0.704

LGA_LOCAL      RMSD =  0.468  Number of atoms =    4  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  0.468  Number of atoms =    4 
Std_ALL_ATOMS  RMSD =  0.468  (standard rmsd on all 4 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.935194 * X  +   0.353163 * Y  +  -0.026248 * Z  + -47.144043
  Y_new =  -0.335615 * X  +  -0.860190 * Y  +   0.383974 * Z  + 129.344574
  Z_new =   0.113028 * X  +   0.367899 * Y  +   0.922971 * Z  +  12.953382 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.379302   -2.762291  [ DEG:    21.7324   -158.2676 ]
  Theta =  -0.113270   -3.028323  [ DEG:    -6.4899   -173.5101 ]
  Phi   =  -2.797035    0.344557  [ DEG:  -160.2583     19.7417 ]
 
# 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: T0298TS022_1_2-D1                             
REMARK     2: T0298_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0298TS022_1_2-D1.T0298_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:    4  148   4.0    4   0.47   2.703     0.47
REMARK  ---------------------------------------------------------- 
MOLECULE T0298TS022_1_2-D1
REMARK PARENT number 2
PFRMAT TS
TARGET T0298
PARENT 1t4b_A
ATOM   2304  N   VAL   316     -13.428  65.942   4.142  1.00  0.00
ATOM   2305  CA  VAL   316     -14.166  65.538   2.982  1.00  0.00
ATOM   2306  C   VAL   316     -15.627  65.874   3.074  1.00  0.00
ATOM   2307  O   VAL   316     -16.152  66.576   2.212  1.00  0.00
ATOM   2308  CB  VAL   316     -14.078  64.017   2.757  1.00  0.00
ATOM   2309  CG1 VAL   316     -14.985  63.593   1.613  1.00  0.00
ATOM   2310  CG2 VAL   316     -12.652  63.611   2.416  1.00  0.00
ATOM   2311  N   ARG   317     -16.343  65.390   4.112  1.00  0.00
ATOM   2312  CA  ARG   317     -17.768  65.589   4.042  1.00  0.00
ATOM   2313  C   ARG   317     -18.196  67.020   4.154  1.00  0.00
ATOM   2314  O   ARG   317     -18.721  67.589   3.199  1.00  0.00
ATOM   2315  CB  ARG   317     -18.470  64.837   5.176  1.00  0.00
ATOM   2316  CG  ARG   317     -19.986  64.949   5.149  1.00  0.00
ATOM   2317  CD  ARG   317     -20.569  64.256   3.928  1.00  0.00
ATOM   2318  NE  ARG   317     -22.029  64.292   3.925  1.00  0.00
ATOM   2319  CZ  ARG   317     -22.783  63.944   2.887  1.00  0.00
ATOM   2320  NH1 ARG   317     -24.104  64.008   2.974  1.00  0.00
ATOM   2321  NH2 ARG   317     -22.212  63.534   1.761  1.00  0.00
ATOM   2322  N   LYS   318     -17.964  67.653   5.320  1.00  0.00
ATOM   2323  CA  LYS   318     -18.414  69.007   5.484  1.00  0.00
ATOM   2324  C   LYS   318     -17.557  69.901   4.666  1.00  0.00
ATOM   2325  O   LYS   318     -18.041  70.813   3.998  1.00  0.00
ATOM   2326  CB  LYS   318     -18.325  69.428   6.952  1.00  0.00
ATOM   2327  CG  LYS   318     -19.323  68.728   7.860  1.00  0.00
ATOM   2328  CD  LYS   318     -20.747  69.160   7.550  1.00  0.00
ATOM   2329  CE  LYS   318     -21.745  68.467   8.463  1.00  0.00
ATOM   2330  NZ  LYS   318     -23.145  68.886   8.176  1.00  0.00
ATOM   2331  N   GLY   319     -16.241  69.642   4.695  1.00  0.00
ATOM   2332  CA  GLY   319     -15.341  70.485   3.978  1.00  0.00
ATOM   2333  C   GLY   319     -15.506  70.186   2.498  1.00  0.00
ATOM   2334  O   GLY   319     -14.707  70.744   1.700  1.00  0.00
TER
END
