
#######################################################
#                                                     #
#                        LGA                          #
#                  ---------------                    #
#                                                     #
#               Local-Global Alignment                #
#        A Method for Finding 3-D Similarities        #
#               in Protein Structures                 #
#                                                     #
#                  ------------ 10/2009               #
#                                                     #
#      Adam Zemla (adamz@llnl.gov)                    #
#      Lawrence Livermore National Laboratory, CA     #
#                                                     #
#######################################################

!!!   License for LGA program has expired  !!!
#   For updated version of the LGA program   #
# please contact Adam Zemla:  adamz@llnl.gov #

# Molecule1: number of CA atoms   45 (  355),  selected    7 , name one
# Molecule2: number of CA atoms    7 (   56),  selected    7 , name two
# PARAMETERS: input.pdb  -ie  -3  -d:4  -sda  -swap  -ch1:B  -ch2:B  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     7       5_B - 11_B        1.78     1.78
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     7       5_B - 11_B        1.78     1.78
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5       6_B - 10_B        0.95     2.67
  LCS_AVERAGE:     65.31

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:    7
LCS_GDT     RESIDUE       RESIDUE       SEGMENT_SIZE    GLOBAL DISTANCE TEST COLUMNS: number of residues under the threshold assigned to each residue pair
LCS_GDT   NAME NUMBER   NAME NUMBER    1.0  2.0  5.0    0.5  1.0  1.5  2.0  2.5  3.0  3.5  4.0  4.5  5.0  5.5  6.0  6.5  7.0  7.5  8.0  8.5  9.0  9.5 10.0
LCS_GDT     E     5_B     E     5_B      3    7    7      3    3    3    4    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7 
LCS_GDT     M     6_B     M     6_B      5    7    7      3    5    5    6    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7 
LCS_GDT     T     7_B     T     7_B      5    7    7      3    5    5    6    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7 
LCS_GDT     L     8_B     L     8_B      5    7    7      3    4    5    6    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7 
LCS_GDT     K     9_B     K     9_B      5    7    7      3    5    5    6    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7 
LCS_GDT     F    10_B     F    10_B      5    7    7      3    5    5    6    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7 
LCS_GDT     G    11_B     G    11_B      4    7    7      3    5    5    6    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7    7 
LCS_AVERAGE  LCS_A:  88.44  (  65.31  100.00  100.00 )

GLOBAL_DISTANCE_TEST (summary information about detected largest sets of residues (represented by selected AToms) that can fit under specified thresholds)
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_AT      3      5      5      6      7      7      7      7      7      7      7      7      7      7      7      7      7      7      7      7 
GDT PERCENT_AT  42.86  71.43  71.43  85.71 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.12   0.72   0.72   1.12   1.78   1.78   1.78   1.78   1.78   1.78   1.78   1.78   1.78   1.78   1.78   1.78   1.78   1.78   1.78   1.78
GDT RMS_ALL_AT   6.81   2.43   2.43   2.49   1.78   1.78   1.78   1.78   1.78   1.78   1.78   1.78   1.78   1.78   1.78   1.78   1.78   1.78   1.78   1.78

# Checking swapping

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    E     5_B      E     5_B     2.395     0    0.627   1.024     9.151   69.048   40.370
LGA    M     6_B      M     6_B     1.692     0    0.632   1.193     8.358   77.381   48.274
LGA    T     7_B      T     7_B     2.148     0    0.139   0.185     6.308   69.048   50.136
LGA    L     8_B      L     8_B     1.995     0    0.160   0.438     8.717   82.024   48.333
LGA    K     9_B      K     9_B     1.673     0    0.159   0.215     9.951   79.405   45.926
LGA    F    10_B      F    10_B     1.356     0    0.033   1.360     8.595   85.952   45.974
LGA    G    11_B      G    11_B     0.516     0    0.648   0.648     2.143   84.048   84.048

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:        7      28     28  100.00      56     56  100.00                 7
SUMMARY(RMSD_GDC):     1.777          1.576                  3.859           78.129   51.866

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   45    7    4.0      7    1.78    89.286    94.612     0.373

LGA_LOCAL      RMSD:   1.777  Number of atoms:    7  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   1.777  Number of assigned atoms:    7 
Std_ASGN_ATOMS RMSD:   1.777  Standard rmsd on all 7 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.044305 * X  +   0.266268 * Y  +   0.962880 * Z  +   1.363517
  Y_new =  -0.947494 * X  +  -0.316733 * Y  +   0.043990 * Z  +  38.146328
  Z_new =   0.316689 * X  +  -0.910374 * Y  +   0.266320 * Z  + -32.561504 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -1.617522 -0.322237 -1.286199   [DEG:  -92.6772  -18.4628  -73.6938 ]
ZXZ:  1.616451  1.301224  2.806819   [DEG:   92.6158   74.5546  160.8189 ]
 
# END of job
