
#######################################################
#                                                     #
#                        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   42 (  348),  selected   41 , name one
# Molecule2: number of CA atoms   41 (  336),  selected   41 , 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:    35       2_B - 36_B        4.71     9.07
  LCS_AVERAGE:     81.14

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    23       6_B - 28_B        1.88    10.73
  LONGEST_CONTINUOUS_SEGMENT:    23       7_B - 29_B        1.89    10.79
  LCS_AVERAGE:     46.76

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    19       9_B - 27_B        0.99    12.18
  LCS_AVERAGE:     36.59

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   41
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     A     2_B     A     2_B      5    6   35      3    4    5    5    7    9   11   12   14   14   26   28   30   31   32   33   34   34   35   35 
LCS_GDT     S     3_B     S     3_B      5    6   35      3    4    5    5    7    9   11   16   21   22   25   28   29   31   32   34   34   34   35   35 
LCS_GDT     Q     4_B     Q     4_B      5    6   35      3    4    5    5    7   11   18   20   21   24   26   28   30   31   32   34   34   34   35   35 
LCS_GDT     R     5_B     R     5_B      9   21   35      5    5   11   14   15   18   21   24   25   26   28   28   30   31   32   34   34   34   35   35 
LCS_GDT     L     6_B     L     6_B     10   23   35      5    6   11   16   18   21   22   24   25   26   28   28   30   31   32   34   34   34   35   35 
LCS_GDT     F     7_B     F     7_B     14   23   35      5    6   11   16   19   21   22   24   25   26   28   28   30   31   32   34   34   34   35   35 
LCS_GDT     V     8_B     V     8_B     18   23   35      5    9   18   19   19   21   22   24   25   26   28   28   30   31   32   34   34   34   35   35 
LCS_GDT     L     9_B     L     9_B     19   23   35      5   17   18   19   19   21   22   24   25   26   28   28   30   31   32   34   34   34   35   35 
LCS_GDT     D    10_B     D    10_B     19   23   35     15   17   18   19   19   21   22   24   25   26   28   28   30   31   32   34   34   34   35   35 
LCS_GDT     N    11_B     N    11_B     19   23   35     15   17   18   19   19   21   22   24   25   26   28   28   30   31   32   34   34   34   35   35 
LCS_GDT     E    12_B     E    12_B     19   23   35     15   17   18   19   19   21   22   24   25   26   28   28   30   31   32   34   34   34   35   35 
LCS_GDT     R    13_B     R    13_B     19   23   35     15   17   18   19   19   21   22   24   25   26   28   28   30   31   32   34   34   34   35   35 
LCS_GDT     Y    14_B     Y    14_B     19   23   35     15   17   18   19   19   21   22   24   25   26   28   28   30   31   32   34   34   34   35   35 
LCS_GDT     D    15_B     D    15_B     19   23   35     15   17   18   19   19   21   22   24   25   26   28   28   30   31   32   34   34   34   35   35 
LCS_GDT     S    16_B     S    16_B     19   23   35     15   17   18   19   19   21   22   24   25   26   28   28   30   31   32   34   34   34   35   35 
LCS_GDT     F    17_B     F    17_B     19   23   35     15   17   18   19   19   21   22   24   25   26   28   28   30   31   32   34   34   34   35   35 
LCS_GDT     I    18_B     I    18_B     19   23   35     15   17   18   19   19   21   22   24   25   26   28   28   30   31   32   34   34   34   35   35 
LCS_GDT     T    19_B     T    19_B     19   23   35     15   17   18   19   19   21   22   24   25   26   28   28   30   31   32   34   34   34   35   35 
LCS_GDT     Q    20_B     Q    20_B     19   23   35     15   17   18   19   19   21   22   24   25   26   28   28   30   31   32   34   34   34   35   35 
LCS_GDT     L    21_B     L    21_B     19   23   35     15   17   18   19   19   21   22   24   25   26   28   28   30   31   32   34   34   34   35   35 
LCS_GDT     E    22_B     E    22_B     19   23   35     15   17   18   19   19   21   22   24   25   26   28   28   30   31   32   34   34   34   35   35 
LCS_GDT     A    23_B     A    23_B     19   23   35     15   17   18   19   19   21   22   24   25   26   28   28   30   31   32   34   34   34   35   35 
LCS_GDT     P    24_B     P    24_B     19   23   35     15   17   18   19   19   21   22   24   25   26   28   28   30   31   32   34   34   34   35   35 
LCS_GDT     V    25_B     V    25_B     19   23   35      3   17   17   19   19   21   22   24   25   26   28   28   30   31   32   34   34   34   35   35 
LCS_GDT     Q    26_B     Q    26_B     19   23   35      3   10   11   14   19   21   21   22   24   25   28   28   30   31   32   34   34   34   35   35 
LCS_GDT     N    27_B     N    27_B     19   23   35      3    8   16   18   19   21   21   23   24   26   28   28   30   31   32   34   34   34   35   35 
LCS_GDT     A    28_B     A    28_B     14   23   35     11   17   18   19   19   21   22   24   25   26   28   28   30   31   32   34   34   34   35   35 
LCS_GDT     E    29_B     E    29_B     14   23   35     11   11   12   14   15   21   22   24   25   26   28   28   30   31   32   34   34   34   35   35 
LCS_GDT     G    30_B     G    30_B     14   16   35     11   11   12   14   15   15   16   16   16   17   28   28   30   31   32   34   34   34   35   35 
LCS_GDT     R    31_B     R    31_B     14   16   35     11   11   12   14   15   15   16   24   25   26   28   28   30   31   32   34   34   34   35   35 
LCS_GDT     E    32_B     E    32_B     14   16   35     11   11   12   14   15   15   16   24   25   26   28   28   30   31   32   34   34   34   35   35 
LCS_GDT     R    33_B     R    33_B     14   16   35     11   11   12   14   15   15   16   16   16   17   21   28   30   30   32   34   34   34   35   35 
LCS_GDT     L    34_B     L    34_B     14   16   35     11   11   12   14   15   15   16   16   16   17   17   18   28   30   32   34   34   34   35   35 
LCS_GDT     M    35_B     M    35_B     14   16   35     11   11   12   14   15   15   16   16   16   18   27   28   30   31   32   34   34   34   35   35 
LCS_GDT     A    36_B     A    36_B     14   16   35     11   11   12   14   15   15   16   16   16   17   17   18   22   30   32   34   34   34   35   35 
LCS_GDT     V    37_B     V    37_B     14   16   34     11   11   12   14   15   15   16   16   16   17   17   17   18   19   22   24   26   33   35   35 
LCS_GDT     K    38_B     K    38_B     14   16   21     11   11   12   14   15   15   16   16   16   17   17   17   18   19   20   22   24   27   32   34 
LCS_GDT     P    39_B     P    39_B     14   16   21      3    9   12   14   15   15   16   16   16   17   17   17   18   18   19   20   21   22   24   25 
LCS_GDT     E    40_B     E    40_B     14   16   21      3    5   12   14   15   15   16   16   16   17   17   17   18   18   19   20   21   22   22   25 
LCS_GDT     W    41_B     W    41_B      3   16   21      3    3    3    3    3    4    4    9   13   16   16   17   18   18   19   19   20   20   22   23 
LCS_GDT     K    42_B     K    42_B      3    3   21      3    3    3    3    3    4    4    5    5    5    8    9   13   17   17   18   18   18   19   19 
LCS_AVERAGE  LCS_A:  54.83  (  36.59   46.76   81.14 )

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     15     17     18     19     19     21     22     24     25     26     28     28     30     31     32     34     34     34     35     35 
GDT PERCENT_AT  36.59  41.46  43.90  46.34  46.34  51.22  53.66  58.54  60.98  63.41  68.29  68.29  73.17  75.61  78.05  82.93  82.93  82.93  85.37  85.37
GDT RMS_LOCAL    0.28   0.49   0.68   0.83   0.83   1.25   1.69   2.22   2.46   2.61   2.99   2.99   3.50   3.68   3.92   4.61   4.39   4.39   4.71   4.71
GDT RMS_ALL_AT  11.06  11.60  10.82  11.01  11.01  11.59  10.12   9.79   9.65   9.78   9.82   9.82   9.67   9.58   9.44   8.97   9.23   9.23   9.07   9.07

# Checking swapping
#   possible swapping detected:  F     7_B      F     7_B
#   possible swapping detected:  F    17_B      F    17_B
#   possible swapping detected:  E    22_B      E    22_B
#   possible swapping detected:  E    29_B      E    29_B

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    A     2_B      A     2_B    10.399     0    0.515   0.629    12.736    0.595    0.476
LGA    S     3_B      S     3_B     9.973     0    0.560   0.462     9.973    1.310    2.778
LGA    Q     4_B      Q     4_B     8.083     0    0.032   1.330    13.315    5.952    2.646
LGA    R     5_B      R     5_B     4.704     0    0.655   1.169    10.312   34.286   22.771
LGA    L     6_B      L     6_B     3.189     0    0.135   1.376     5.715   53.810   51.429
LGA    F     7_B      F     7_B     2.480     0    0.149   0.190     4.205   62.857   51.775
LGA    V     8_B      V     8_B     1.535     0    0.035   1.193     4.344   75.000   70.340
LGA    L     9_B      L     9_B     1.574     0    0.641   0.576     4.135   64.048   70.595
LGA    D    10_B      D    10_B     1.280     0    0.032   0.826     2.900   81.429   74.286
LGA    N    11_B      N    11_B     1.388     0    0.056   0.965     4.187   79.286   73.869
LGA    E    12_B      E    12_B     1.088     0    0.013   0.936     3.256   81.429   73.386
LGA    R    13_B      R    13_B     1.033     0    0.019   1.176     4.594   81.429   71.126
LGA    Y    14_B      Y    14_B     1.301     0    0.027   0.162     2.258   81.429   73.730
LGA    D    15_B      D    15_B     1.153     0    0.009   0.458     1.424   83.690   82.560
LGA    S    16_B      S    16_B     0.694     0    0.021   0.166     0.903   90.476   90.476
LGA    F    17_B      F    17_B     1.152     0    0.040   0.284     1.316   81.429   83.896
LGA    I    18_B      I    18_B     1.449     0    0.015   0.103     1.965   81.429   77.143
LGA    T    19_B      T    19_B     0.889     0    0.020   0.249     1.190   88.214   87.891
LGA    Q    20_B      Q    20_B     0.950     0    0.011   1.156     4.190   85.952   75.979
LGA    L    21_B      L    21_B     1.664     0    0.019   1.318     4.076   75.000   71.667
LGA    E    22_B      E    22_B     1.280     0    0.097   0.753     2.857   81.429   70.635
LGA    A    23_B      A    23_B     0.948     0    0.072   0.103     1.572   83.810   83.333
LGA    P    24_B      P    24_B     1.314     0    0.053   0.356     2.767   71.190   76.871
LGA    V    25_B      V    25_B     3.269     0    0.062   1.244     5.509   53.810   49.116
LGA    Q    26_B      Q    26_B     5.700     0    0.702   1.186    10.379   18.690   12.751
LGA    N    27_B      N    27_B     4.989     0    0.178   1.163     5.956   34.405   29.762
LGA    A    28_B      A    28_B     1.321     0    0.046   0.049     2.605   69.048   71.524
LGA    E    29_B      E    29_B     3.599     0    0.062   0.804     6.076   39.167   31.799
LGA    G    30_B      G    30_B     7.049     0    0.066   0.066     8.086   13.571   13.571
LGA    R    31_B      R    31_B     5.331     0    0.089   1.194     7.888   22.738   28.355
LGA    E    32_B      E    32_B     5.913     0    0.053   0.835     8.708   15.714   24.180
LGA    R    33_B      R    33_B     9.454     0    0.048   1.207    11.510    2.143    3.203
LGA    L    34_B      L    34_B    10.511     0    0.026   1.392    13.627    0.119    0.060
LGA    M    35_B      M    35_B     8.984     0    0.056   1.131    11.010    1.071   13.274
LGA    A    36_B      A    36_B    12.122     0    0.045   0.047    14.868    0.000    0.000
LGA    V    37_B      V    37_B    15.160     0    0.027   0.065    16.840    0.000    0.000
LGA    K    38_B      K    38_B    17.927     4    0.206   0.228    21.327    0.000    0.000
LGA    P    39_B      P    39_B    20.539     0    0.622   0.627    23.999    0.000    0.000
LGA    E    40_B      E    40_B    23.634     0    0.412   0.337    25.599    0.000    0.000
LGA    W    41_B      W    41_B    23.911     0    0.605   1.116    27.904    0.000    0.000
LGA    K    42_B      K    42_B    29.433     0    0.622   1.069    30.288    0.000    0.000

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       41     164    164  100.00     336    336  100.00                41
SUMMARY(RMSD_GDC):     8.371          8.542                  8.690           43.804   41.884

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   42   41    4.0     24    2.22    57.317    54.233     1.033

LGA_LOCAL      RMSD:   2.223  Number of atoms:   24  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   9.791  Number of assigned atoms:   41 
Std_ASGN_ATOMS RMSD:   8.371  Standard rmsd on all 41 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.844482 * X  +   0.521517 * Y  +  -0.121943 * Z  +   3.211003
  Y_new =  -0.481837 * X  +   0.839192 * Y  +   0.252171 * Z  + -25.142303
  Z_new =   0.233845 * X  +  -0.154197 * Y  +   0.959969 * Z  +  43.587677 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -0.518499 -0.236030 -0.159267   [DEG:  -29.7078  -13.5235   -9.1253 ]
ZXZ: -2.691173  0.283906  2.153751   [DEG: -154.1929   16.2666  123.4008 ]
 
# END of job
