
#######################################################
#                                                     #
#                        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_3_2-D1
# Molecule2: number of CA atoms  148 ( 1074),  selected    4 , name T0298_D1.pdb
# PARAMETERS: T0298TS022_3_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         0.50     0.50
  LCS_AVERAGE:      2.70

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4       316 - 319         0.50     0.50
  LCS_AVERAGE:      2.70

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4       316 - 319         0.50     0.50
  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    0.12   0.50   0.50   0.50   0.50   0.50   0.50   0.50   0.50   0.50   0.50   0.50   0.50   0.50   0.50   0.50   0.50   0.50   0.50   0.50
GDT RMS_ALL_CA   0.62   0.50   0.50   0.50   0.50   0.50   0.50   0.50   0.50   0.50   0.50   0.50   0.50   0.50   0.50   0.50   0.50   0.50   0.50   0.50

#      Molecule1      Molecule2       DISTANCE
LGA    V     316      V     316          0.373
LGA    R     317      R     317          0.329
LGA    K     318      K     318          0.334
LGA    G     319      G     319          0.791

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)    4  148    4.0      4    0.50     2.703     2.703     0.671

LGA_LOCAL      RMSD =  0.496  Number of atoms =    4  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  0.496  Number of atoms =    4 
Std_ALL_ATOMS  RMSD =  0.496  (standard rmsd on all 4 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.714517 * X  +  -0.362839 * Y  +   0.598175 * Z  + -44.028606
  Y_new =   0.552841 * X  +   0.816806 * Y  +  -0.164911 * Z  +  16.485445
  Z_new =  -0.428756 * X  +   0.448527 * Y  +   0.784214 * Z  + -73.944153 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.519535   -2.622057  [ DEG:    29.7672   -150.2328 ]
  Theta =   0.443116    2.698477  [ DEG:    25.3887    154.6113 ]
  Phi   =   0.658514   -2.483079  [ DEG:    37.7300   -142.2700 ]
 
# 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_3_2-D1                             
REMARK     2: T0298_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0298TS022_3_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   0.50   2.703     0.50
REMARK  ---------------------------------------------------------- 
MOLECULE T0298TS022_3_2-D1
REMARK PARENT number 2
PFRMAT TS
TARGET T0298
PARENT 1nwc_A
ATOM   2317  N   VAL   316     -13.468  65.942   4.172  1.00  0.00
ATOM   2318  CA  VAL   316     -14.171  65.589   2.978  1.00  0.00
ATOM   2319  C   VAL   316     -15.637  65.897   3.053  1.00  0.00
ATOM   2320  O   VAL   316     -16.170  66.573   2.173  1.00  0.00
ATOM   2321  CB  VAL   316     -14.052  64.082   2.678  1.00  0.00
ATOM   2322  CG1 VAL   316     -14.956  63.698   1.516  1.00  0.00
ATOM   2323  CG2 VAL   316     -12.620  63.724   2.311  1.00  0.00
ATOM   2324  N   ARG   317     -16.343  65.414   4.098  1.00  0.00
ATOM   2325  CA  ARG   317     -17.769  65.583   4.060  1.00  0.00
ATOM   2326  C   ARG   317     -18.212  67.010   4.153  1.00  0.00
ATOM   2327  O   ARG   317     -18.745  67.563   3.192  1.00  0.00
ATOM   2328  CB  ARG   317     -18.428  64.841   5.225  1.00  0.00
ATOM   2329  CG  ARG   317     -19.945  64.921   5.234  1.00  0.00
ATOM   2330  CD  ARG   317     -20.544  64.191   4.042  1.00  0.00
ATOM   2331  NE  ARG   317     -22.004  64.196   4.075  1.00  0.00
ATOM   2332  CZ  ARG   317     -22.775  63.812   3.062  1.00  0.00
ATOM   2333  NH1 ARG   317     -24.095  63.851   3.182  1.00  0.00
ATOM   2334  NH2 ARG   317     -22.224  63.390   1.933  1.00  0.00
ATOM   2335  N   LYS   318     -17.975  67.658   5.311  1.00  0.00
ATOM   2336  CA  LYS   318     -18.430  69.008   5.472  1.00  0.00
ATOM   2337  C   LYS   318     -17.564  69.898   4.658  1.00  0.00
ATOM   2338  O   LYS   318     -18.036  70.826   4.004  1.00  0.00
ATOM   2339  CB  LYS   318     -18.353  69.428   6.941  1.00  0.00
ATOM   2340  CG  LYS   318     -19.358  68.725   7.841  1.00  0.00
ATOM   2341  CD  LYS   318     -20.781  69.151   7.519  1.00  0.00
ATOM   2342  CE  LYS   318     -21.784  68.454   8.423  1.00  0.00
ATOM   2343  NZ  LYS   318     -23.183  68.868   8.123  1.00  0.00
ATOM   2344  N   GLY   319     -16.250  69.616   4.681  1.00  0.00
ATOM   2345  CA  GLY   319     -15.320  70.440   3.977  1.00  0.00
ATOM   2346  C   GLY   319     -15.471  70.155   2.492  1.00  0.00
ATOM   2347  O   GLY   319     -14.742  70.806   1.698  1.00  0.00
TER
END
