
#######################################################
#                                                     #
#                        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   19 (  157),  selected   19 , name one
# Molecule2: number of CA atoms  376 ( 2937),  selected   19 , name two
# PARAMETERS: input.pdb  -ie  -3  -d:4  -sda  -swap  -ch1:A  -ch2:A  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    13     232_A - 244_A       4.90     6.15
  LCS_AVERAGE:      3.30

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5     240_A - 244_A       1.95    24.77
  LCS_AVERAGE:      1.11

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     4     240_A - 243_A       0.90    28.87
  LCS_AVERAGE:      0.85

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   19
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     Q   227_A     Q   227_A      3    4   11      0    3    3    3    3    5    6    8   10   11   11   15   16   16   18   19   19   19   19   19 
LCS_GDT     P   228_A     P   228_A      3    4   11      0    3    3    4    5    7    7    8   10   11   11   15   16   16   18   19   19   19   19   19 
LCS_GDT     F   229_A     F   229_A      3    4   11      0    3    3    4    5    7    7    8   10   11   11   15   16   16   18   19   19   19   19   19 
LCS_GDT     T   230_A     T   230_A      3    4   11      3    3    4    4    5    7    7    8   10   11   11   15   16   16   18   19   19   19   19   19 
LCS_GDT     K   231_A     K   231_A      3    4   11      3    3    4    4    4    5    6    7    8    9   10   12   14   15   18   19   19   19   19   19 
LCS_GDT     G   232_A     G   232_A      3    4   13      3    3    4    4    4    5    6    7    8   11   11   15   16   16   18   19   19   19   19   19 
LCS_GDT     A   233_A     A   233_A      3    4   13      0    3    3    4    5    7    7    8   10   11   11   15   16   16   18   19   19   19   19   19 
LCS_GDT     Y   234_A     Y   234_A      3    3   13      0    3    3    3    4    7    7    8   10   11   11   15   16   16   18   19   19   19   19   19 
LCS_GDT     Y   235_A     Y   235_A      3    4   13      1    3    3    3    4    7    7    8   10   11   11   15   16   16   18   19   19   19   19   19 
LCS_GDT     I   236_A     I   236_A      3    4   13      0    3    3    3    4    5    6    7    8    9   11   15   16   16   18   19   19   19   19   19 
LCS_GDT     G   237_A     G   237_A      3    4   13      3    3    3    4    4    5    6    7    8    9   11   12   16   16   18   19   19   19   19   19 
LCS_GDT     K   238_A     K   238_A      3    4   13      3    3    3    3    4    5    7    8    8    9   11   15   16   16   18   19   19   19   19   19 
LCS_GDT     M   239_A     M   239_A      3    4   13      3    3    3    4    5    7    7    8    8    9   10   12   13   15   18   19   19   19   19   19 
LCS_GDT     V   240_A     V   240_A      4    5   13      3    3    4    4    5    7    7    8    8    9   10   12   14   16   18   19   19   19   19   19 
LCS_GDT     W   241_A     W   241_A      4    5   13      3    3    4    4    5    7    7    8    8    9   11   15   16   16   18   19   19   19   19   19 
LCS_GDT     S   242_A     S   242_A      4    5   13      3    3    4    4    5    7    7    8    8    9   11   15   16   16   18   19   19   19   19   19 
LCS_GDT     K   243_A     K   243_A      4    5   13      3    3    4    4    5    7    7    8   10   11   11   15   16   16   18   19   19   19   19   19 
LCS_GDT     G   244_A     G   244_A      3    5   13      3    3    4    4    5    7    7    8   10   11   11   15   16   16   18   19   19   19   19   19 
LCS_GDT     Y   245_A     Y   245_A      3    3   12      0    3    3    4    5    7    7    8   10   11   11   15   16   16   18   19   19   19   19   19 
LCS_AVERAGE  LCS_A:   1.75  (   0.85    1.11    3.30 )

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      3      4      4      5      7      7      8     10     11     11     15     16     16     18     19     19     19     19     19 
GDT PERCENT_AT   0.80   0.80   1.06   1.06   1.33   1.86   1.86   2.13   2.66   2.93   2.93   3.99   4.26   4.26   4.79   5.05   5.05   5.05   5.05   5.05
GDT RMS_LOCAL    0.03   0.03   0.90   0.90   1.64   2.37   2.35   2.62   3.32   3.54   3.54   4.75   4.97   4.97   5.42   5.59   5.59   5.59   5.59   5.59
GDT RMS_ALL_AT  27.71  27.71  28.87  28.87   6.77  22.68   6.60   6.54   6.46   6.42   6.42   5.75   5.68   5.68   5.62   5.59   5.59   5.59   5.59   5.59

# Checking swapping
#   possible swapping detected:  F   229_A      F   229_A
#   possible swapping detected:  Y   234_A      Y   234_A
#   possible swapping detected:  Y   235_A      Y   235_A
#   possible swapping detected:  Y   245_A      Y   245_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    Q   227_A      Q   227_A     5.872     0    0.151   1.207     8.668   35.238   19.312
LGA    P   228_A      P   228_A     2.996     0    0.673   0.533     6.531   55.595   40.476
LGA    F   229_A      F   229_A     2.500     0    0.608   1.535     8.135   49.524   34.372
LGA    T   230_A      T   230_A     2.280     0    0.624   0.793     3.213   59.405   67.619
LGA    K   231_A      K   231_A     7.309     0    0.452   1.056    14.850   11.190    5.026
LGA    G   232_A      G   232_A     6.665     0    0.599   0.599     6.665   26.190   26.190
LGA    A   233_A      A   233_A     1.701     0    0.604   0.590     3.597   71.429   65.810
LGA    Y   234_A      Y   234_A     2.907     0    0.556   1.452    11.529   51.905   29.167
LGA    Y   235_A      Y   235_A     3.731     0    0.612   1.475     7.437   48.452   27.579
LGA    I   236_A      I   236_A     6.710     0    0.626   0.840    11.103   15.476    8.274
LGA    G   237_A      G   237_A    10.286     0    0.610   0.610    10.286    1.190    1.190
LGA    K   238_A      K   238_A     9.279     0    0.611   1.109    10.279    4.167    2.434
LGA    M   239_A      M   239_A     9.936     0    0.498   0.718    12.257    0.238    0.119
LGA    V   240_A      V   240_A    11.815     0    0.588   1.452    15.351    1.905    1.088
LGA    W   241_A      W   241_A     7.837     0    0.084   1.051     9.607   14.048   19.048
LGA    S   242_A      S   242_A     6.949     0    0.674   0.820     9.432   19.524   13.730
LGA    K   243_A      K   243_A     2.240     0    0.257   1.210    11.132   65.119   38.413
LGA    G   244_A      G   244_A     2.045     0    0.095   0.095     5.741   53.452   53.452
LGA    Y   245_A      Y   245_A     6.421     0    0.084   0.316    10.045   16.429   10.278

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       19      76     76  100.00     157    157  100.00               376
SUMMARY(RMSD_GDC):     5.591          5.448                  6.910            1.597    1.233

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   19  376    4.0      8    2.62     2.261     1.995     0.294

LGA_LOCAL      RMSD:   2.619  Number of atoms:    8  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   6.543  Number of assigned atoms:   19 
Std_ASGN_ATOMS RMSD:   5.591  Standard rmsd on all 19 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.463265 * X  +   0.865690 * Y  +  -0.189648 * Z  +   1.110885
  Y_new =  -0.204300 * X  +   0.103911 * Y  +   0.973378 * Z  +  18.468323
  Z_new =   0.862350 * X  +   0.489677 * Y  +   0.128722 * Z  +  30.636639 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -2.726248 -1.039893  1.313740   [DEG: -156.2025  -59.5815   75.2717 ]
ZXZ: -2.949168  1.441716  1.054360   [DEG: -168.9749   82.6042   60.4104 ]
 
# END of job
