
#######################################################
#                                                     #
#                        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 (   32),  selected    4 , name T0298TS671_2-D1
# Molecule2: number of CA atoms  148 ( 1074),  selected    4 , name T0298_D1.pdb
# PARAMETERS: T0298TS671_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         0.34     0.34
  LCS_AVERAGE:      2.70

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4       316 - 319         0.34     0.34
  LCS_AVERAGE:      2.70

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4       316 - 319         0.34     0.34
  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     4    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     4    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     4    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     4    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      4      4      4      4      4      4      4      4      4      4      4      4      4      4      4      4      4      4      4      4 
GDT PERCENT_CA   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   2.70
GDT RMS_LOCAL    0.34   0.34   0.34   0.34   0.34   0.34   0.34   0.34   0.34   0.34   0.34   0.34   0.34   0.34   0.34   0.34   0.34   0.34   0.34   0.34
GDT RMS_ALL_CA   0.34   0.34   0.34   0.34   0.34   0.34   0.34   0.34   0.34   0.34   0.34   0.34   0.34   0.34   0.34   0.34   0.34   0.34   0.34   0.34

#      Molecule1      Molecule2       DISTANCE
LGA    V     316      V     316          0.234
LGA    R     317      R     317          0.306
LGA    K     318      K     318          0.407
LGA    G     319      G     319          0.374

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)    4  148    4.0      4    0.34     2.703     2.703     0.915

LGA_LOCAL      RMSD =  0.337  Number of atoms =    4  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  0.337  Number of atoms =    4 
Std_ALL_ATOMS  RMSD =  0.337  (standard rmsd on all 4 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.635434 * X  +   0.297891 * Y  +   0.712379 * Z  + -32.556324
  Y_new =  -0.467221 * X  +  -0.882860 * Y  +  -0.047576 * Z  + 109.682159
  Z_new =   0.614759 * X  +  -0.363070 * Y  +   0.700180 * Z  +   5.026735 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.478368    2.663225  [ DEG:   -27.4085    152.5916 ]
  Theta =  -0.662080   -2.479513  [ DEG:   -37.9344   -142.0656 ]
  Phi   =  -2.507580    0.634012  [ DEG:  -143.6738     36.3262 ]
 
# 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: T0298TS671_2-D1                               
REMARK     2: T0298_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0298TS671_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   0.34   2.703     0.34
REMARK  ---------------------------------------------------------- 
MOLECULE T0298TS671_2-D1
PFRMAT TS
TARGET T0298
MODEL  2  REFINED
PARENT 1GL3_A 1BRM_C 1MB4_B 1PQU_D
ATOM   1395  N   VAL   316     -13.381  65.702   4.009  1.00  0.00
ATOM   1396  CA  VAL   316     -14.117  65.250   2.819  1.00  0.00
ATOM   1397  C   VAL   316     -15.649  65.596   2.915  1.00  0.00
ATOM   1398  O   VAL   316     -16.176  66.021   1.897  1.00  0.00
ATOM   1399  CB  VAL   316     -13.953  63.720   2.654  1.00  0.00
ATOM   1400  CG1 VAL   316     -14.756  63.234   1.387  1.00  0.00
ATOM   1401  CG2 VAL   316     -12.505  63.224   2.428  1.00  0.00
ATOM   1402  N   ARG   317     -16.298  65.281   4.044  1.00  0.00
ATOM   1403  CA  ARG   317     -17.757  65.474   4.209  1.00  0.00
ATOM   1404  C   ARG   317     -18.241  66.903   4.253  1.00  0.00
ATOM   1405  O   ARG   317     -18.785  67.356   3.234  1.00  0.00
ATOM   1406  CB  ARG   317     -18.123  64.806   5.492  1.00  0.00
ATOM   1407  CG  ARG   317     -17.926  63.350   5.639  1.00  0.00
ATOM   1408  CD  ARG   317     -18.922  62.539   4.858  1.00  0.00
ATOM   1409  NE  ARG   317     -18.749  61.100   4.937  1.00  0.00
ATOM   1410  CZ  ARG   317     -17.749  60.398   4.352  1.00  0.00
ATOM   1411  NH1 ARG   317     -16.759  60.992   3.627  1.00  0.00
ATOM   1412  NH2 ARG   317     -17.766  59.060   4.493  1.00  0.00
ATOM   1413  N   LYS   318     -17.941  67.676   5.274  1.00  0.00
ATOM   1414  CA  LYS   318     -18.519  69.037   5.332  1.00  0.00
ATOM   1415  C   LYS   318     -17.604  70.053   4.589  1.00  0.00
ATOM   1416  O   LYS   318     -18.163  70.981   3.978  1.00  0.00
ATOM   1417  CB  LYS   318     -18.734  69.343   6.816  1.00  0.00
ATOM   1418  CG  LYS   318     -19.936  68.794   7.562  1.00  0.00
ATOM   1419  CD  LYS   318     -20.971  69.863   7.792  1.00  0.00
ATOM   1420  CE  LYS   318     -22.441  69.625   7.775  1.00  0.00
ATOM   1421  NZ  LYS   318     -23.248  70.850   7.419  1.00  0.00
ATOM   1422  N   GLY   319     -16.281  70.016   4.793  1.00  0.00
ATOM   1423  CA  GLY   319     -15.297  70.858   4.128  1.00  0.00
ATOM   1424  C   GLY   319     -14.954  70.227   2.751  1.00  0.00
ATOM   1425  O   GLY   319     -14.319  70.890   1.921  1.00  0.00
ATOM   1426  OXT GLY   319     -15.579  69.196   2.426  1.00  0.00
TER
END
