
#######################################################
#                                                     #
#                        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    3 (   21),  selected    3 , name T0356TS389_3-D1
# Molecule2: number of CA atoms  124 (  963),  selected    3 , name T0356_D1.pdb
# PARAMETERS: T0356TS389_3-D1.T0356_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
# WARNING! The change of the parameter DIST cutoff may give you better result.

  LONGEST_CONTINUOUS_SEGMENT:     3       314 - 316         0.51     0.51
  LCS_AVERAGE:      2.42

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     3       314 - 316         0.51     0.51
  LCS_AVERAGE:      2.42

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     3       314 - 316         0.51     0.51
  LCS_AVERAGE:      2.42

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:  124
LCS_GDT     D     314     D     314      3    3    3     0    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3 
LCS_GDT     A     315     A     315      3    3    3     1    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3 
LCS_GDT     I     316     I     316      3    3    3     0    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3    3 
LCS_AVERAGE  LCS_A:   2.42  (   2.42    2.42    2.42 )

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      1      3      3      3      3      3      3      3      3      3      3      3      3      3      3      3      3      3      3      3 
GDT PERCENT_CA   0.81   2.42   2.42   2.42   2.42   2.42   2.42   2.42   2.42   2.42   2.42   2.42   2.42   2.42   2.42   2.42   2.42   2.42   2.42   2.42
GDT RMS_LOCAL   31.63   0.51   0.51   0.51   0.51   0.51   0.51   0.51   0.51   0.51   0.51   0.51   0.51   0.51   0.51   0.51   0.51   0.51   0.51   0.51
GDT RMS_ALL_CA   0.51   0.51   0.51   0.51   0.51   0.51   0.51   0.51   0.51   0.51   0.51   0.51   0.51   0.51   0.51   0.51   0.51   0.51   0.51   0.51

#      Molecule1      Molecule2       DISTANCE
LGA    D     314      D     314          0.538
LGA    A     315      A     315          0.439
LGA    I     316      I     316          0.539

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)    3  124    4.0      3    0.51     2.419     2.419     0.494

LGA_LOCAL      RMSD =  0.508  Number of atoms =    3  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  0.508  Number of atoms =    3 
Std_ALL_ATOMS  RMSD =  0.508  (standard rmsd on all 3 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.152193 * X  +  -0.632514 * Y  +  -0.759450 * Z  +  80.057152
  Y_new =   0.286613 * X  +   0.707137 * Y  +  -0.646382 * Z  +  74.552818
  Z_new =   0.945881 * X  +  -0.316043 * Y  +   0.073666 * Z  +  77.859673 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.341798    1.799795  [ DEG:   -76.8794    103.1206 ]
  Theta =  -1.240297   -1.901295  [ DEG:   -71.0638   -108.9362 ]
  Phi   =   2.058939   -1.082654  [ DEG:   117.9685    -62.0315 ]
 
# 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: T0356TS389_3-D1                               
REMARK     2: T0356_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0356TS389_3-D1.T0356_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:    3  124   4.0    3   0.51   2.419     0.51
REMARK  ---------------------------------------------------------- 
MOLECULE T0356TS389_3-D1
PFRMAT TS
TARGET T0356
MODEL  3
PARENT N/A
ATOM    964  N   ASP   314      76.775  74.083  97.866  1.00  0.00
ATOM    965  CA  ASP   314      76.580  75.187  96.945  1.00  0.00
ATOM    966  CB  ASP   314      77.719  76.201  97.074  1.00  0.00
ATOM    967  CG  ASP   314      77.673  76.964  98.385  1.00  0.00
ATOM    968  OD1 ASP   314      76.619  76.933  99.053  1.00  0.00
ATOM    969  OD2 ASP   314      78.691  77.590  98.742  1.00  0.00
ATOM    970  O   ASP   314      76.397  75.665  94.614  1.00  0.00
ATOM    971  C   ASP   314      76.531  74.802  95.477  1.00  0.00
ATOM    972  N   ALA   315      76.626  73.511  95.179  1.00  0.00
ATOM    973  CA  ALA   315      76.607  73.072  93.787  1.00  0.00
ATOM    974  CB  ALA   315      77.375  71.767  93.635  1.00  0.00
ATOM    975  O   ALA   315      75.012  72.591  92.064  1.00  0.00
ATOM    976  C   ALA   315      75.201  72.829  93.258  1.00  0.00
ATOM    977  N   ILE   316      74.214  72.895  94.146  1.00  0.00
ATOM    978  CA  ILE   316      72.827  72.681  93.757  1.00  0.00
ATOM    979  CB  ILE   316      72.172  71.565  94.594  1.00  0.00
ATOM    980  CG1 ILE   316      72.299  71.873  96.086  1.00  0.00
ATOM    981  CG2 ILE   316      72.846  70.228  94.319  1.00  0.00
ATOM    982  CD1 ILE   316      71.444  70.990  96.968  1.00  0.00
ATOM    983  O   ILE   316      71.899  74.510  95.012  1.00  0.00
ATOM    984  C   ILE   316      71.953  73.919  93.933  1.00  0.00
TER
END
