
#######################################################
#                                                     #
#                        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   34 (  315),  selected   26 , name one
# Molecule2: number of CA atoms   26 (  234),  selected   26 , name two
# PARAMETERS: input.pdb  -ie  -3  -d:4  -sda  -swap  -ch1:D  -ch2:F  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    22      12_F - 33_F        4.71     6.96
  LCS_AVERAGE:     82.99

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    13      21_F - 33_F        1.76    11.45
  LCS_AVERAGE:     44.38

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    12      22_F - 33_F        0.65    11.93
  LCS_AVERAGE:     37.87

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   26
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     L     8_D     L     8_F      3    3   19      0    3    3    3    3    3    4    7   14   15   16   17   18   19   20   22   24   25   25   26 
LCS_GDT     Q     9_D     Q     9_F      3    4   19      3    3    4    6    6    9   11   13   14   15   16   17   19   21   23   24   24   25   25   26 
LCS_GDT     K    10_D     K    10_F      3    4   19      3    4    5    6    6    6    7   10   11   12   15   17   17   20   23   24   24   25   25   26 
LCS_GDT     L    11_D     L    11_F      3   12   20      3    4    5    6    8   11   12   13   14   15   16   17   19   21   23   24   24   25   25   26 
LCS_GDT     N    12_D     N    12_F     10   12   22      8    8   10   11   11   11   12   13   14   16   17   20   20   21   23   24   24   25   25   26 
LCS_GDT     S    13_D     S    13_F     10   12   22      8    8   10   11   11   11   12   13   14   16   18   20   20   21   23   24   24   25   25   26 
LCS_GDT     W    14_D     W    14_F     10   12   22      8    8   10   11   11   11   12   13   14   15   16   17   18   21   23   24   24   25   25   26 
LCS_GDT     D    15_D     D    15_F     10   12   22      8    8   10   11   11   11   12   13   14   16   17   20   20   21   23   24   24   25   25   26 
LCS_GDT     V    16_D     V    16_F     10   12   22      8    8   10   11   11   14   14   15   16   16   18   20   20   21   23   24   24   25   25   26 
LCS_GDT     F    17_D     F    17_F     10   12   22      8    8   10   11   11   11   12   13   14   16   18   20   20   21   23   24   24   25   25   26 
LCS_GDT     G    18_D     G    18_F     10   12   22      8    8   10   11   11   11   12   13   16   16   18   20   20   21   23   24   24   25   25   26 
LCS_GDT     N    19_D     N    19_F     10   12   22      8    8   10   12   13   14   14   15   16   16   18   20   20   21   23   24   24   25   25   26 
LCS_GDT     W    20_D     W    20_F     10   12   22      3    8   10   11   11   11   12   13   15   15   16   18   18   19   20   22   22   23   24   26 
LCS_GDT     F    21_D     F    21_F     10   13   22      3    4   10   11   11   11   13   15   16   16   18   20   20   21   23   24   24   25   25   26 
LCS_GDT     D    22_D     D    22_F     12   13   22      9   11   11   12   13   14   14   15   16   16   18   20   20   21   23   24   24   25   25   26 
LCS_GDT     L    23_D     L    23_F     12   13   22      9   11   11   12   13   14   14   15   16   16   18   20   20   21   23   24   24   25   25   26 
LCS_GDT     A    24_D     A    24_F     12   13   22      9   11   11   12   13   14   14   15   16   16   18   20   20   21   23   24   24   25   25   26 
LCS_GDT     S    25_D     S    25_F     12   13   22      9   11   11   12   13   14   14   15   16   16   18   20   20   21   23   24   24   25   25   26 
LCS_GDT     W    26_D     W    26_F     12   13   22      9   11   11   12   13   14   14   15   16   16   18   20   20   21   23   24   24   25   25   26 
LCS_GDT     I    27_D     I    27_F     12   13   22      9   11   11   12   13   14   14   15   16   16   18   20   20   21   23   24   24   25   25   26 
LCS_GDT     K    28_D     K    28_F     12   13   22      9   11   11   12   13   14   14   15   16   16   18   20   20   21   23   24   24   25   25   26 
LCS_GDT     Y    29_D     Y    29_F     12   13   22      9   11   11   12   13   14   14   15   16   16   18   20   20   21   23   24   24   25   25   26 
LCS_GDT     I    30_D     I    30_F     12   13   22      9   11   11   12   13   14   14   15   16   16   18   20   20   21   23   24   24   25   25   26 
LCS_GDT     Q    31_D     Q    31_F     12   13   22      5   11   11   12   13   14   14   15   16   16   18   20   20   21   23   24   24   25   25   26 
LCS_GDT     R    32_D     R    32_F     12   13   22      5   11   11   12   13   14   14   15   16   16   18   20   20   21   23   24   24   25   25   26 
LCS_GDT     R    33_D     R    33_F     12   13   22      3    3   11   12   13   14   14   15   16   16   18   20   20   21   23   24   24   25   25   26 
LCS_AVERAGE  LCS_A:  55.08  (  37.87   44.38   82.99 )

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      9     11     11     12     13     14     14     15     16     16     18     20     20     21     23     24     24     25     25     26 
GDT PERCENT_AT  34.62  42.31  42.31  46.15  50.00  53.85  53.85  57.69  61.54  61.54  69.23  76.92  76.92  80.77  88.46  92.31  92.31  96.15  96.15 100.00
GDT RMS_LOCAL    0.24   0.42   0.42   0.65   1.04   1.75   1.75   2.18   2.65   2.65   3.53   4.16   4.16   4.71   5.04   5.25   5.25   5.61   5.61   5.89
GDT RMS_ALL_AT  11.66  11.97  11.97  11.93  10.96   9.59   9.59   9.76   9.04   9.04   8.14   6.95   6.95   6.22   6.07   5.99   5.99   5.91   5.91   5.89

# Checking swapping
#   possible swapping detected:  D    15_D      D    15_F
#   possible swapping detected:  F    17_D      F    17_F

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    L     8_D      L     8_F    24.748     0    0.270   0.297    27.343    0.000    0.000
LGA    Q     9_D      Q     9_F    18.312     0    0.574   0.562    20.817    0.000    0.000
LGA    K    10_D      K    10_F    18.997     0    0.060   0.337    23.064    0.000    0.000
LGA    L    11_D      L    11_F    16.603     0    0.591   0.635    18.077    0.000    0.000
LGA    N    12_D      N    12_F    13.330     0    0.585   1.388    14.556    0.357    0.179
LGA    S    13_D      S    13_F    12.090     0    0.049   0.697    14.763    0.000    0.000
LGA    W    14_D      W    14_F    14.676     0    0.042   1.157    23.001    0.000    0.000
LGA    D    15_D      D    15_F    10.408     0    0.045   0.960    13.865    6.786    3.393
LGA    V    16_D      V    16_F     4.054     0    0.023   0.042     6.363   29.405   35.578
LGA    F    17_D      F    17_F     9.129     0    0.038   1.318    17.876    5.714    2.078
LGA    G    18_D      G    18_F     7.015     0    0.200   0.200     7.689   26.071   26.071
LGA    N    19_D      N    19_F     1.812     0    0.234   1.102     7.297   54.643   42.262
LGA    W    20_D      W    20_F     6.318     0    0.150   1.191    16.376   20.595    6.224
LGA    F    21_D      F    21_F     4.746     0    0.612   1.211    11.891   42.500   18.615
LGA    D    22_D      D    22_F     2.539     0    0.565   0.988     7.907   64.881   40.179
LGA    L    23_D      L    23_F     2.216     0    0.095   1.043     4.899   66.786   60.655
LGA    A    24_D      A    24_F     1.923     0    0.024   0.023     2.199   72.976   71.333
LGA    S    25_D      S    25_F     1.631     0    0.149   0.725     2.245   79.405   77.302
LGA    W    26_D      W    26_F     1.313     0    0.025   0.485     2.932   83.690   73.163
LGA    I    27_D      I    27_F     0.573     0    0.036   0.106     1.196   95.238   91.786
LGA    K    28_D      K    28_F     0.546     0    0.111   0.246     1.811   95.238   88.624
LGA    Y    29_D      Y    29_F     0.325     0    0.040   0.374     1.741   97.619   88.452
LGA    I    30_D      I    30_F     1.018     0    0.051   0.680     3.078   83.690   76.488
LGA    Q    31_D      Q    31_F     1.837     0    0.015   1.269     7.022   72.976   50.688
LGA    R    32_D      R    32_F     1.424     0    0.442   0.925     2.946   79.286   74.545
LGA    R    33_D      R    33_F     1.536     0    0.609   0.606     7.724   75.000   48.225

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       26     104    104  100.00     234    234  100.00                26
SUMMARY(RMSD_GDC):     5.886          5.718                  7.855           44.341   37.532

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   34   26    4.0     15    2.18    59.615    55.157     0.658

LGA_LOCAL      RMSD:   2.179  Number of atoms:   15  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   9.758  Number of assigned atoms:   26 
Std_ASGN_ATOMS RMSD:   5.886  Standard rmsd on all 26 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.038919 * X  +   0.316961 * Y  +  -0.947640 * Z  +  39.233654
  Y_new =   0.079282 * X  +  -0.946348 * Y  +  -0.313273 * Z  + -68.436974
  Z_new =  -0.996092 * X  +  -0.062938 * Y  +  -0.061960 * Z  +  -6.704505 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  1.114460  1.482362 -2.348362   [DEG:   63.8539   84.9331 -134.5512 ]
ZXZ: -1.251524  1.632796 -1.633898   [DEG:  -71.7070   93.5523  -93.6154 ]
 
# END of job
