
#######################################################
#                                                     #
#                        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   33 (  231),  selected   33 , name one
# Molecule2: number of CA atoms   33 (  231),  selected   33 , 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:    16      18_A - 33_A        4.78    22.03
  LCS_AVERAGE:     42.98

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    10      14_A - 23_A        2.00    19.53
  LCS_AVERAGE:     24.89

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6      26_A - 31_A        0.66    23.47
  LONGEST_CONTINUOUS_SEGMENT:     6      27_A - 32_A        0.96    22.43
  LCS_AVERAGE:     14.51

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   33
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     Y     1_A     Y     1_A      5    8   11      4    5    5    5    8    8    8    9    9    9    9    9   10   10   10   11   11   12   12   12 
LCS_GDT     R     2_A     R     2_A      5    8   11      4    5    5    5    8    8    8    9    9    9    9    9   10   10   10   11   11   12   12   12 
LCS_GDT     Q     3_A     Q     3_A      5    8   11      4    5    5    5    8    8    8    9    9    9    9    9   10   10   10   11   11   12   12   12 
LCS_GDT     S     4_A     S     4_A      5    8   11      4    5    5    5    8    8    8    9    9    9    9    9   10   10   10   11   11   12   12   12 
LCS_GDT     S     5_A     S     5_A      5    8   11      3    5    5    5    8    8    8    9    9    9    9    9   10   10   11   11   11   12   12   13 
LCS_GDT     A     6_A     A     6_A      4    8   12      3    4    4    5    8    8    8    9    9    9    9   11   11   11   11   12   12   12   12   13 
LCS_GDT     T     7_A     T     7_A      4    8   12      3    4    5    5    8    8    8    9    9    9   10   11   11   11   11   13   13   13   13   14 
LCS_GDT     S     8_A     S     8_A      4    8   12      3    4    4    5    8    8    8    9   10   10   10   11   11   11   11   13   13   14   14   15 
LCS_GDT     S     9_A     S     9_A      5    6   12      3    4    5    5    5    6    8    9   10   10   10   11   11   11   11   13   13   13   13   15 
LCS_GDT     F    10_A     F    10_A      5    6   12      3    4    5    5    5    6    8    9   10   10   10   11   11   11   11   13   13   15   16   17 
LCS_GDT     G    11_A     G    11_A      5    6   13      3    4    5    5    5    6    8    9   10   10   10   11   12   13   14   15   16   17   20   21 
LCS_GDT     G    12_A     G    12_A      5    6   14      0    4    5    5    5    6    8    9   10   10   10   11   13   14   14   17   18   20   20   22 
LCS_GDT     L    13_A     L    13_A      5    6   14      3    4    5    5    5    6    8   10   10   10   11   12   13   14   14   17   19   20   20   22 
LCS_GDT     G    14_A     G    14_A      4   10   14      3    4    4    6    8   10   10   11   12   12   12   12   13   15   17   18   19   20   20   22 
LCS_GDT     G    15_A     G    15_A      4   10   14      3    4    4    4    7   10   10   11   12   12   12   12   13   15   17   18   19   20   20   22 
LCS_GDT     G    16_A     G    16_A      4   10   14      3    4    4    6    8   10   10   11   12   12   12   12   13   15   17   18   19   20   20   22 
LCS_GDT     S    17_A     S    17_A      5   10   14      3    4    5    5    8   10   10   11   12   12   12   12   13   15   17   18   19   20   20   22 
LCS_GDT     V    18_A     V    18_A      5   10   16      4    4    5    6    8   10   10   11   12   12   13   13   13   15   17   18   19   20   20   22 
LCS_GDT     R    19_A     R    19_A      5   10   16      4    4    5    5    8   10   10   11   12   12   14   14   14   15   17   18   19   20   20   22 
LCS_GDT     F    20_A     F    20_A      5   10   16      4    4    5    5    8   10   10   11   12   12   14   14   14   15   17   18   19   20   20   22 
LCS_GDT     G    21_A     G    21_A      5   10   16      4    4    5    6    8   10   10   12   12   12   14   14   14   15   17   18   19   20   20   22 
LCS_GDT     P    22_A     P    22_A      4   10   16      3    4    4    6    8   10   10   12   12   12   14   14   14   15   17   18   19   20   20   22 
LCS_GDT     G    23_A     G    23_A      4   10   16      3    4    4    6    8   10   10   12   12   12   14   14   14   15   17   18   19   20   20   22 
LCS_GDT     V    24_A     V    24_A      3    5   16      3    3    4    5    6    8   10   12   12   12   14   14   14   15   17   18   19   20   20   22 
LCS_GDT     A    25_A     A    25_A      3    8   16      3    3    4    6    6    8   10   12   12   12   14   14   14   15   16   18   19   20   20   22 
LCS_GDT     F    26_A     F    26_A      6    8   16      4    6    6    8    8    8   10   12   12   12   14   14   14   15   15   17   19   20   20   22 
LCS_GDT     R    27_A     R    27_A      6    8   16      4    6    6    8    8    8   10   12   12   12   14   14   14   15   17   18   19   20   20   22 
LCS_GDT     A    28_A     A    28_A      6    8   16      4    6    6    8    8    8   10   12   12   12   14   14   14   15   17   18   19   20   20   22 
LCS_GDT     P    29_A     P    29_A      6    8   16      4    6    6    8    8    8   10   12   12   12   14   14   14   15   17   18   19   20   20   22 
LCS_GDT     S    30_A     S    30_A      6    8   16      4    6    6    8    8    8   10   12   12   12   14   14   14   15   17   18   19   20   20   22 
LCS_GDT     I    31_A     I    31_A      6    8   16      4    6    6    8    8    8   10   12   12   12   14   14   14   15   17   18   19   20   20   22 
LCS_GDT     H    32_A     H    32_A      6    8   16      3    4    6    8    8    8   10   12   12   12   14   14   14   15   17   18   19   20   20   22 
LCS_GDT     G    33_A     G    33_A      3    8   16      3    3    5    8    8    8    8    9    9    9   12   13   13   15   15   15   16   17   20   22 
LCS_AVERAGE  LCS_A:  27.46  (  14.51   24.89   42.98 )

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      4      6      6      8      8     10     10     12     12     12     14     14     14     15     17     18     19     20     20     22 
GDT PERCENT_AT  12.12  18.18  18.18  24.24  24.24  30.30  30.30  36.36  36.36  36.36  42.42  42.42  42.42  45.45  51.52  54.55  57.58  60.61  60.61  66.67
GDT RMS_LOCAL    0.17   0.66   0.66   1.40   1.40   2.00   2.00   2.85   2.85   2.76   3.78   3.78   3.78   4.19   5.62   5.84   6.00   6.24   6.24   6.85
GDT RMS_ALL_AT  24.90  23.47  23.47  27.29  27.29  19.53  19.53  30.65  30.65  20.09  24.91  24.91  24.91  24.57  19.24  19.33  19.54  19.12  19.12  18.57

# Checking swapping
#   possible swapping detected:  F    10_A      F    10_A
#   possible swapping detected:  F    26_A      F    26_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    Y     1_A      Y     1_A    52.941     0    0.022   0.429    53.837    0.000    0.000
LGA    R     2_A      R     2_A    53.493     0    0.034   0.926    59.921    0.000    0.000
LGA    Q     3_A      Q     3_A    49.452     0    0.083   1.264    51.179    0.000    0.000
LGA    S     4_A      S     4_A    49.276     0    0.108   0.538    49.744    0.000    0.000
LGA    S     5_A      S     5_A    46.852     0    0.523   0.557    47.920    0.000    0.000
LGA    A     6_A      A     6_A    44.307     0    0.648   0.618    44.968    0.000    0.000
LGA    T     7_A      T     7_A    46.864     0    0.086   0.162    49.512    0.000    0.000
LGA    S     8_A      S     8_A    44.929     0    0.623   0.835    47.289    0.000    0.000
LGA    S     9_A      S     9_A    38.704     0    0.668   0.763    40.638    0.000    0.000
LGA    F    10_A      F    10_A    35.913     0    0.117   1.220    40.713    0.000    0.000
LGA    G    11_A      G    11_A    38.452     0    0.433   0.433    39.456    0.000    0.000
LGA    G    12_A      G    12_A    40.913     0    0.243   0.243    40.913    0.000    0.000
LGA    L    13_A      L    13_A    38.470     0    0.642   0.570    39.412    0.000    0.000
LGA    G    14_A      G    14_A    37.287     0    0.275   0.275    37.855    0.000    0.000
LGA    G    15_A      G    15_A    33.066     0    0.588   0.588    34.715    0.000    0.000
LGA    G    16_A      G    16_A    28.788     0    0.559   0.559    30.739    0.000    0.000
LGA    S    17_A      S    17_A    23.152     0    0.231   0.661    25.179    0.000    0.000
LGA    V    18_A      V    18_A    19.880     0    0.121   1.097    22.172    0.000    0.000
LGA    R    19_A      R    19_A    12.778     0    0.060   1.133    15.616    0.000    0.000
LGA    F    20_A      F    20_A     9.254     0    0.029   0.247    18.790   12.619    4.589
LGA    G    21_A      G    21_A     3.199     0    0.026   0.026     5.727   46.548   46.548
LGA    P    22_A      P    22_A     4.164     0    0.622   0.601     6.124   48.810   41.565
LGA    G    23_A      G    23_A     1.741     0    0.244   0.244     3.437   63.095   63.095
LGA    V    24_A      V    24_A     3.319     0    0.501   0.994     6.213   57.262   44.218
LGA    A    25_A      A    25_A     2.501     0    0.600   0.540     4.287   54.048   54.667
LGA    F    26_A      F    26_A     1.202     0    0.649   1.302     9.893   79.881   40.216
LGA    R    27_A      R    27_A     3.632     0    0.036   1.157    15.680   61.548   24.892
LGA    A    28_A      A    28_A     2.971     0    0.018   0.022     5.752   65.119   56.381
LGA    P    29_A      P    29_A     2.532     0    0.051   0.345     6.527   69.286   49.728
LGA    S    30_A      S    30_A     2.351     0    0.049   0.063     5.337   71.190   57.063
LGA    I    31_A      I    31_A     2.945     0    0.594   0.751     6.402   61.190   40.298
LGA    H    32_A      H    32_A     2.280     0    0.551   0.970     8.317   47.738   29.524
LGA    G    33_A      G    33_A     8.613     0    0.528   0.528    11.198    6.071    6.071

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       33     132    132  100.00     231    231  100.00                33
SUMMARY(RMSD_GDC):    15.062         14.946                 15.563           22.558   16.935

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   33   33    4.0     12    2.85    33.333    30.464     0.407

LGA_LOCAL      RMSD:   2.845  Number of atoms:   12  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  30.647  Number of assigned atoms:   33 
Std_ASGN_ATOMS RMSD:  15.062  Standard rmsd on all 33 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.881527 * X  +   0.272626 * Y  +  -0.385468 * Z  +  51.676460
  Y_new =  -0.464890 * X  +  -0.358747 * Y  +   0.809431 * Z  +   9.976661
  Z_new =   0.082386 * X  +   0.892735 * Y  +   0.442986 * Z  +  -3.717910 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -2.656291 -0.082480  1.110184   [DEG: -152.1942   -4.7257   63.6088 ]
ZXZ: -2.697149  1.111870  0.092025   [DEG: -154.5352   63.7054    5.2726 ]
 
# END of job
