
#######################################################
#                                                     #
#                        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:    24       4_A - 27_A        4.84    11.91
  LCS_AVERAGE:     67.13

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    17       8_A - 24_A        1.97    13.28
  LCS_AVERAGE:     36.36

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     8      11_A - 18_A        0.77    12.88
  LONGEST_CONTINUOUS_SEGMENT:     8      12_A - 19_A        0.97    13.04
  LCS_AVERAGE:     15.98

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      3    4   12      2    3    3    4    6    6    6    6    6   11   11   15   16   18   21   22   24   24   26   26 
LCS_GDT     R     2_A     R     2_A      3    4   12      0    3    4    5    6    6    6   11   12   13   15   17   18   18   20   22   24   24   26   26 
LCS_GDT     Q     3_A     Q     3_A      3    4   23      2    3    3    4    5    5    6   10   12   13   14   17   18   18   20   22   24   24   26   26 
LCS_GDT     S     4_A     S     4_A      4    4   24      1    3    4    4    7    7   10   12   14   16   16   17   18   19   21   22   24   24   26   26 
LCS_GDT     S     5_A     S     5_A      4    4   24      2    3    4    4    5    7    7   12   13   16   16   17   19   21   22   23   24   24   26   26 
LCS_GDT     A     6_A     A     6_A      4    4   24      2    3    5    6    7    9   13   16   18   18   20   20   20   21   22   23   24   24   26   26 
LCS_GDT     T     7_A     T     7_A      4    4   24      3    3    4    4    6   12   14   17   18   19   20   20   20   21   22   23   24   24   26   26 
LCS_GDT     S     8_A     S     8_A      3   17   24      3    3    3    4   12   16   17   17   18   19   20   20   20   21   22   23   24   24   26   26 
LCS_GDT     S     9_A     S     9_A      3   17   24      3    3    7   11   12   16   17   17   18   19   20   20   20   21   22   23   24   24   26   26 
LCS_GDT     F    10_A     F    10_A      6   17   24      3    4    8   11   13   16   17   17   18   19   20   20   20   21   22   23   24   24   26   26 
LCS_GDT     G    11_A     G    11_A      8   17   24      5    9   11   12   14   16   17   17   18   19   20   20   20   21   22   23   24   24   26   26 
LCS_GDT     G    12_A     G    12_A      8   17   24      4    8   11   12   14   16   17   17   18   19   20   20   20   21   22   23   24   24   26   26 
LCS_GDT     L    13_A     L    13_A      8   17   24      4    9   11   12   14   16   17   17   18   19   20   20   20   21   22   23   24   24   26   26 
LCS_GDT     G    14_A     G    14_A      8   17   24      5    9   11   12   14   16   17   17   18   19   20   20   20   21   22   23   24   24   26   26 
LCS_GDT     G    15_A     G    15_A      8   17   24      5    9   11   12   14   16   17   17   18   19   20   20   20   21   22   23   24   24   26   26 
LCS_GDT     G    16_A     G    16_A      8   17   24      4    9   11   12   14   16   17   17   18   19   20   20   20   21   22   23   24   24   26   26 
LCS_GDT     S    17_A     S    17_A      8   17   24      5    9   11   12   14   16   17   17   18   19   20   20   20   21   22   23   24   24   26   26 
LCS_GDT     V    18_A     V    18_A      8   17   24      5    9   11   12   14   16   17   17   18   19   20   20   20   21   22   23   24   24   26   26 
LCS_GDT     R    19_A     R    19_A      8   17   24      3    3    8   11   14   16   17   17   18   19   20   20   20   21   22   23   24   24   26   26 
LCS_GDT     F    20_A     F    20_A      5   17   24      4    9   11   12   14   16   17   17   18   19   20   20   20   21   22   23   24   24   26   26 
LCS_GDT     G    21_A     G    21_A      5   17   24      5    9   11   12   14   16   17   17   18   19   20   20   20   21   22   23   24   24   26   26 
LCS_GDT     P    22_A     P    22_A      5   17   24      3    4    5   10   14   16   17   17   18   19   20   20   20   21   22   23   24   24   26   26 
LCS_GDT     G    23_A     G    23_A      5   17   24      3    4    9   12   14   16   17   17   18   19   20   20   20   21   22   23   24   24   26   26 
LCS_GDT     V    24_A     V    24_A      5   17   24      3    6   11   12   14   16   17   17   18   19   20   20   20   21   22   23   24   24   26   26 
LCS_GDT     A    25_A     A    25_A      4    9   24      3    4    7    8    8    9   10   12   14   19   20   20   20   21   22   23   24   24   26   26 
LCS_GDT     F    26_A     F    26_A      4    9   24      3    4    4    6    8    9   10   12   14   16   16   17   18   21   22   23   24   24   26   26 
LCS_GDT     R    27_A     R    27_A      4    9   24      3    4    7    8    8    9   10   12   14   15   16   17   18   18   22   23   23   24   25   25 
LCS_GDT     A    28_A     A    28_A      5    9   23      3    5    7    8    8    9   10   12   14   16   16   17   18   18   18   20   20   21   23   25 
LCS_GDT     P    29_A     P    29_A      5    9   17      4    5    7    8    8    9   10   12   14   16   16   17   18   18   18   20   20   21   22   25 
LCS_GDT     S    30_A     S    30_A      5    9   17      4    5    7    8    8    9   10   12   14   16   16   17   18   18   18   20   20   21   21   21 
LCS_GDT     I    31_A     I    31_A      5    9   17      4    5    6    8    8    9   10   12   13   16   16   17   18   18   18   20   20   21   21   21 
LCS_GDT     H    32_A     H    32_A      5    9   17      4    5    7    8    8    9   10   12   14   16   16   17   18   18   18   20   20   21   21   21 
LCS_GDT     G    33_A     G    33_A      3    7   17      3    3    3    5    7    9   10   12   13   16   16   17   18   18   18   20   20   21   21   21 
LCS_AVERAGE  LCS_A:  39.82  (  15.98   36.36   67.13 )

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      5      9     11     12     14     16     17     17     18     19     20     20     20     21     22     23     24     24     26     26 
GDT PERCENT_AT  15.15  27.27  33.33  36.36  42.42  48.48  51.52  51.52  54.55  57.58  60.61  60.61  60.61  63.64  66.67  69.70  72.73  72.73  78.79  78.79
GDT RMS_LOCAL    0.37   0.62   0.81   1.13   1.50   1.79   1.97   1.97   2.22   2.52   2.84   2.84   2.84   3.33   3.94   4.31   5.07   5.07   5.74   5.74
GDT RMS_ALL_AT  12.75  12.93  12.80  12.87  12.79  13.29  13.28  13.28  13.23  13.20  12.98  12.98  12.98  12.83  12.43  12.23  11.72  11.72  11.69  11.69

# Checking swapping
#   possible swapping detected:  Y     1_A      Y     1_A
#   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    17.420     0    0.238   1.189    17.575    0.000    0.000
LGA    R     2_A      R     2_A    17.751     0    0.063   1.284    18.397    0.000    0.000
LGA    Q     3_A      Q     3_A    16.768     0    0.106   0.906    17.766    0.000    0.000
LGA    S     4_A      S     4_A    14.287     0    0.612   0.569    15.896    0.000    0.000
LGA    S     5_A      S     5_A    12.346     0    0.260   0.280    13.994    0.000    0.000
LGA    A     6_A      A     6_A     7.022     0    0.628   0.624     8.915    9.286    9.429
LGA    T     7_A      T     7_A     5.076     0    0.582   1.364     5.259   32.976   31.565
LGA    S     8_A      S     8_A     3.570     0    0.146   0.137     6.619   50.595   41.190
LGA    S     9_A      S     9_A     3.366     0    0.720   0.643     5.288   48.095   41.667
LGA    F    10_A      F    10_A     2.178     0    0.592   1.307     8.125   61.071   42.338
LGA    G    11_A      G    11_A     1.310     0    0.189   0.189     3.461   69.286   69.286
LGA    G    12_A      G    12_A     2.023     0    0.242   0.242     2.494   68.810   68.810
LGA    L    13_A      L    13_A     0.954     0    0.140   0.159     2.675   88.333   77.679
LGA    G    14_A      G    14_A     0.394     0    0.265   0.265     0.494  100.000  100.000
LGA    G    15_A      G    15_A     1.031     0    0.144   0.144     2.309   79.524   79.524
LGA    G    16_A      G    16_A     0.610     0    0.560   0.560     2.217   86.429   86.429
LGA    S    17_A      S    17_A     0.805     0    0.333   0.354     1.327   85.952   87.460
LGA    V    18_A      V    18_A     0.506     0    0.165   1.092     3.592   81.786   70.748
LGA    R    19_A      R    19_A     2.679     0    0.085   1.178    12.184   67.143   28.355
LGA    F    20_A      F    20_A     1.749     0    0.223   1.090    11.212   81.548   35.584
LGA    G    21_A      G    21_A     0.894     0    0.603   0.603     2.357   79.643   79.643
LGA    P    22_A      P    22_A     2.570     0    0.156   0.541     3.989   59.762   53.673
LGA    G    23_A      G    23_A     1.519     0    0.538   0.538     2.016   77.381   77.381
LGA    V    24_A      V    24_A     2.799     0    0.096   0.097     5.455   46.310   41.565
LGA    A    25_A      A    25_A     5.843     0    0.246   0.283     6.618   23.810   21.714
LGA    F    26_A      F    26_A     9.209     0    0.592   1.430    15.005    1.548    0.693
LGA    R    27_A      R    27_A    10.405     0    0.389   1.141    11.701    0.119    0.952
LGA    A    28_A      A    28_A    16.056     0    0.079   0.081    18.256    0.000    0.000
LGA    P    29_A      P    29_A    19.067     0    0.146   0.656    21.522    0.000    0.000
LGA    S    30_A      S    30_A    23.855     0    0.078   0.090    26.411    0.000    0.000
LGA    I    31_A      I    31_A    30.560     0    0.625   0.595    35.384    0.000    0.000
LGA    H    32_A      H    32_A    30.436     0    0.626   0.968    31.058    0.000    0.000
LGA    G    33_A      G    33_A    33.837     0    0.462   0.462    37.123    0.000    0.000

# 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):     9.149          9.154                  9.421           39.376   34.718

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   33   33    4.0     17    1.97    46.212    45.534     0.822

LGA_LOCAL      RMSD:   1.968  Number of atoms:   17  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  13.280  Number of assigned atoms:   33 
Std_ASGN_ATOMS RMSD:   9.149  Standard rmsd on all 33 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.366647 * X  +   0.860969 * Y  +   0.352566 * Z  + -228.817123
  Y_new =   0.170894 * X  +  -0.434833 * Y  +   0.884147 * Z  + -154.213257
  Z_new =   0.914530 * X  +  -0.263918 * Y  +  -0.306565 * Z  +  82.470650 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  0.436161 -1.154345 -2.430810   [DEG:   24.9902  -66.1391 -139.2752 ]
ZXZ:  2.762152  1.882378  1.851747   [DEG:  158.2597  107.8523  106.0973 ]
 
# END of job
