
#######################################################
#                                                     #
#                        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    5 (   36),  selected    5 , name T0316TS464_3-D1
# Molecule2: number of CA atoms  188 ( 1493),  selected    5 , name T0316_D1.pdb
# PARAMETERS: T0316TS464_3-D1.T0316_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:     5       189 - 193         2.30     2.30
  LCS_AVERAGE:      2.66

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4       189 - 192         1.27     3.55
  LONGEST_CONTINUOUS_SEGMENT:     4       190 - 193         1.53     3.40
  LCS_AVERAGE:      2.13

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
# WARNING! The change of the parameter DIST cutoff may give you better result.

  LONGEST_CONTINUOUS_SEGMENT:     3       190 - 192         0.73     3.56
  LONGEST_CONTINUOUS_SEGMENT:     3       191 - 193         0.51     5.60
  LCS_AVERAGE:      1.28

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:  188
LCS_GDT     S     189     S     189      0    4    5     0    0    4    4    4    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5 
LCS_GDT     T     190     T     190      3    4    5     0    3    4    4    4    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5 
LCS_GDT     A     191     A     191      3    4    5     0    3    4    4    4    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5 
LCS_GDT     K     192     K     192      3    4    5     1    3    4    4    4    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5 
LCS_GDT     K     193     K     193      3    4    5     0    3    3    4    4    5    5    5    5    5    5    5    5    5    5    5    5    5    5    5 
LCS_AVERAGE  LCS_A:   2.02  (   1.28    2.13    2.66 )

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      4      4      4      5      5      5      5      5      5      5      5      5      5      5      5      5      5      5 
GDT PERCENT_CA   0.53   1.60   2.13   2.13   2.13   2.66   2.66   2.66   2.66   2.66   2.66   2.66   2.66   2.66   2.66   2.66   2.66   2.66   2.66   2.66
GDT RMS_LOCAL   31.62   0.51   1.27   1.27   1.27   2.30   2.30   2.30   2.30   2.30   2.30   2.30   2.30   2.30   2.30   2.30   2.30   2.30   2.30   2.30
GDT RMS_ALL_CA   5.60   5.60   3.55   3.55   3.55   2.30   2.30   2.30   2.30   2.30   2.30   2.30   2.30   2.30   2.30   2.30   2.30   2.30   2.30   2.30

#      Molecule1      Molecule2       DISTANCE
LGA    S     189      S     189          2.363
LGA    T     190      T     190          2.719
LGA    A     191      A     191          1.772
LGA    K     192      K     192          2.861
LGA    K     193      K     193          1.435

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)    5  188    4.0      5    2.30     2.261     2.331     0.209

LGA_LOCAL      RMSD =  2.296  Number of atoms =    5  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  2.296  Number of atoms =    5 
Std_ALL_ATOMS  RMSD =  2.296  (standard rmsd on all 5 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.302180 * X  +   0.791178 * Y  +   0.531719 * Z  + -23.756126
  Y_new =  -0.953225 * X  +   0.246663 * Y  +   0.174699 * Z  +  56.446331
  Z_new =   0.007063 * X  +  -0.559638 * Y  +   0.828707 * Z  +  20.266481 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.593966    2.547627  [ DEG:   -34.0317    145.9683 ]
  Theta =  -0.007063   -3.134530  [ DEG:    -0.4047   -179.5953 ]
  Phi   =  -1.263810    1.877783  [ DEG:   -72.4110    107.5890 ]
 
# 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: T0316TS464_3-D1                               
REMARK     2: T0316_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0316TS464_3-D1.T0316_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:    5  188   4.0    5   2.30   2.331     2.30
REMARK  ---------------------------------------------------------- 
MOLECULE T0316TS464_3-D1
PFRMAT TS
TARGET T0316
MODEL 3
PARENT N/A
ATOM    753  N   SER   189      26.872  46.961  13.788  1.00  0.00
ATOM    754  CA  SER   189      26.094  47.983  14.413  1.00  0.00
ATOM    755  CB  SER   189      26.528  49.402  14.009  1.00  0.00
ATOM    756  OG  SER   189      27.855  49.647  14.454  1.00  0.00
ATOM    757  C   SER   189      24.668  47.805  14.007  1.00  0.00
ATOM    758  O   SER   189      23.813  47.531  14.848  1.00  0.00
ATOM    759  N   THR   190      24.360  47.938  12.700  1.00  0.00
ATOM    760  CA  THR   190      22.977  47.796  12.348  1.00  0.00
ATOM    761  CB  THR   190      22.173  49.015  12.681  1.00  0.00
ATOM    762  OG1 THR   190      20.795  48.781  12.432  1.00  0.00
ATOM    763  CG2 THR   190      22.682  50.186  11.823  1.00  0.00
ATOM    764  C   THR   190      22.827  47.580  10.876  1.00  0.00
ATOM    765  O   THR   190      23.754  47.797  10.096  1.00  0.00
ATOM    766  N   ALA   191      21.623  47.113  10.481  1.00  0.00
ATOM    767  CA  ALA   191      21.234  46.978   9.107  1.00  0.00
ATOM    768  CB  ALA   191      21.798  48.079   8.191  1.00  0.00
ATOM    769  C   ALA   191      21.667  45.661   8.559  1.00  0.00
ATOM    770  O   ALA   191      22.518  44.980   9.129  1.00  0.00
ATOM    771  N   LYS   192      21.046  45.263   7.427  1.00  0.00
ATOM    772  CA  LYS   192      21.487  44.082   6.752  1.00  0.00
ATOM    773  CB  LYS   192      20.697  43.666   5.508  1.00  0.00
ATOM    774  CG  LYS   192      21.152  42.282   5.039  1.00  0.00
ATOM    775  CD  LYS   192      20.218  41.589   4.050  1.00  0.00
ATOM    776  CE  LYS   192      20.590  40.122   3.823  1.00  0.00
ATOM    777  NZ  LYS   192      21.955  40.026   3.260  1.00  0.00
ATOM    778  C   LYS   192      22.838  44.449   6.297  1.00  0.00
ATOM    779  O   LYS   192      23.711  43.596   6.138  1.00  0.00
ATOM    780  N   LYS   193      22.978  45.770   6.057  1.00  0.00
ATOM    781  CA  LYS   193      24.200  46.413   5.705  1.00  0.00
ATOM    782  CB  LYS   193      24.083  47.923   5.977  1.00  0.00
ATOM    783  CG  LYS   193      25.295  48.796   5.664  1.00  0.00
ATOM    784  CD  LYS   193      24.965  50.282   5.826  1.00  0.00
ATOM    785  CE  LYS   193      24.340  50.594   7.190  1.00  0.00
ATOM    786  NZ  LYS   193      23.877  51.998   7.244  1.00  0.00
ATOM    787  C   LYS   193      25.150  45.838   6.690  1.00  0.00
ATOM    788  O   LYS   193      25.149  46.204   7.864  1.00  0.00
TER
END
