
#######################################################
#                                                     #
#                        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   82 (  674),  selected   67 , name one
# Molecule2: number of CA atoms   76 (  627),  selected   67 , 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:    31      38_A - 68_A        4.99    13.13
  LCS_AVERAGE:     35.94

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    16      58_A - 73_A        1.91    22.68
  LCS_AVERAGE:     12.55

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    10      64_A - 73_A        0.95    21.78
  LCS_AVERAGE:      8.27

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   67
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    10_A     L    10_A      6    7   17      4    5    6    6    6    7    8    8    9   16   16   16   17   21   26   27   27   29   33   34 
LCS_GDT     F    11_A     F    11_A      6    7   21      4    5    6    6    6    7   16   18   20   22   23   25   25   26   26   28   30   31   33   37 
LCS_GDT     G    12_A     G    12_A      6    7   21      4    5    6    6    6    7    8   10   13   15   17   18   23   25   26   28   30   31   33   34 
LCS_GDT     E    13_A     E    13_A      6    7   21      4    5    6    6    6    6    8    8   10   11   21   21   23   25   26   28   30   31   33   34 
LCS_GDT     H    14_A     H    14_A      6    7   21      4    5    6    6    6    7    9   18   20   22   23   25   25   25   26   28   30   31   33   34 
LCS_GDT     Y    15_A     Y    15_A      6    7   21      4    5    6   11   15   16   16   19   20   22   23   25   25   26   26   29   33   34   36   37 
LCS_GDT     S    16_A     S    16_A      5    7   21      4    5    5    6    7   10   16   18   19   20   21   25   25   26   28   31   33   34   36   37 
LCS_GDT     A    17_A     A    17_A      5    6   21      4    5    5    6    7   10   11   13   14   15   17   19   20   26   30   31   33   34   36   37 
LCS_GDT     N    18_A     N    18_A      5    8   21      4    5    5    6    7   10   11   13   14   15   18   21   24   27   30   32   34   35   37   38 
LCS_GDT     Q    19_A     Q    19_A      6    8   21      4    6    7    7    7   10   11   13   14   15   17   21   24   27   30   32   34   35   37   38 
LCS_GDT     F    20_A     F    20_A      6    8   21      4    6    7    7    7   10   11   13   14   15   20   22   24   27   30   32   34   37   39   42 
LCS_GDT     A    21_A     A    21_A      6    8   21      4    6    7    7    7    9   11   13   14   19   22   24   29   31   32   35   38   41   44   46 
LCS_GDT     K    22_A     K    22_A      6    8   21      4    6    7    7    7   10   11   13   14   15   17   20   26   29   32   35   38   41   44   46 
LCS_GDT     I    23_A     I    23_A      6    8   25      4    6    7    7    7   10   11   13   14   15   17   18   19   22   24   30   36   41   44   46 
LCS_GDT     L    24_A     L    24_A      6    8   26      4    6    7    7    7   10   11   13   15   19   21   24   28   31   34   37   39   43   44   46 
LCS_GDT     I    25_A     I    25_A      3    8   26      0    3    3    6    7    9   11   15   19   20   22   24   28   31   34   37   39   43   44   46 
LCS_GDT     N    26_A     N    26_A      4    5   26      3    3    4    4    5    6   12   15   19   20   22   22   28   30   34   36   39   43   43   46 
LCS_GDT     K    27_A     K    27_A      4    5   26      3    3    4    4    4    8   12   15   19   20   22   22   28   30   34   36   39   43   43   45 
LCS_GDT     D    28_A     D    28_A      4    5   26      3    3    4    4    4    6    8   10   12   15   17   21   23   24   28   30   36   43   43   45 
LCS_GDT     G    29_A     G    29_A      4    5   26      3    3    7    7    7   10   11   15   18   20   22   22   26   29   29   30   36   43   43   45 
LCS_GDT     S    30_A     S    30_A      3    8   26      3    3    5    7    8    9   13   15   19   20   22   22   26   29   32   34   39   43   43   45 
LCS_GDT     N    31_A     N    31_A      7    8   26      3    5    7    7    8    9   13   15   19   20   22   24   28   31   34   37   39   43   44   46 
LCS_GDT     V    32_A     V    32_A      7    8   26      5    6    7    7    8    9   13   15   19   20   22   24   28   30   34   37   39   43   44   46 
LCS_GDT     D    33_A     D    33_A      7    8   26      5    6    7    7    8    9   13   15   19   20   22   24   28   31   34   37   39   43   44   46 
LCS_GDT     R    34_A     R    34_A      7    8   26      5    6    7    7    8    9   13   15   19   20   22   24   28   31   34   37   39   43   44   46 
LCS_GDT     K    35_A     K    35_A      7    8   26      5    6    7    7    8    9   11   15   19   20   22   24   28   31   34   37   39   43   44   46 
LCS_GDT     T    36_A     T    36_A      7    8   26      5    6    7    7    8    9   13   15   19   20   22   24   28   31   34   37   39   43   44   46 
LCS_GDT     I    37_A     I    37_A      7    8   26      4    6    7    7    8    9   13   15   19   20   22   24   28   31   34   37   39   43   44   46 
LCS_GDT     Q    38_A     Q    38_A      3    8   31      3    3    3    5    8    9   13   15   19   22   25   26   29   31   34   37   39   43   44   46 
LCS_GDT     N    39_A     N    39_A      6    7   31      5    6    6    6    8    9   13   15   19   22   25   25   29   31   34   37   39   43   44   46 
LCS_GDT     W    40_A     W    40_A      6    7   31      5    6    6    6    8    9   11   14   19   20   25   25   29   31   34   37   39   43   44   46 
LCS_GDT     I    41_A     I    41_A      6    7   31      5    6    6    6    6    6   10   14   19   22   25   26   29   31   34   37   39   43   44   46 
LCS_GDT     N    42_A     N    42_A      6    7   31      5    6    6    6    6    9   11   15   18   22   25   26   29   31   34   37   39   43   44   46 
LCS_GDT     R    43_A     R    43_A      6    7   31      5    6    6    6    6    7   11   13   16   19   22   26   29   31   34   37   39   43   44   46 
LCS_GDT     D    44_A     D    44_A      6    7   31      5    6    6    6    8    9   13   15   19   22   25   26   29   31   34   37   39   43   44   46 
LCS_GDT     Q    45_A     Q    45_A      3    3   31      3    4    4    5    7    9   13   15   19   22   25   26   29   31   34   37   39   43   44   46 
LCS_GDT     D    46_A     D    46_A      3    3   31      3    4    6    7    8    9   13   15   19   20   22   24   29   31   34   37   39   43   44   46 
LCS_GDT     L    47_A     L    47_A      3    3   31      3    3    4    6    6    9   13   15   19   22   25   26   29   31   34   37   39   43   44   46 
LCS_GDT     N    48_A     N    48_A      7    8   31      6    6    6    7    8    9   11   14   18   22   25   26   29   31   34   37   39   43   44   46 
LCS_GDT     D    49_A     D    49_A      7    8   31      6    6    6    7    8    9   11   14   18   22   25   26   29   31   34   37   39   43   44   46 
LCS_GDT     W    50_A     W    50_A      7    8   31      6    6    6    7    8    9   11   14   18   22   25   26   29   31   34   37   39   43   44   46 
LCS_GDT     V    51_A     V    51_A      7    8   31      6    6    6    7    7    7   11   14   18   22   25   26   29   31   33   37   39   43   44   46 
LCS_GDT     I    52_A     I    52_A      7    8   31      6    6    6    7    7    9   14   17   18   22   25   26   29   31   34   37   39   43   44   46 
LCS_GDT     V    53_A     V    53_A      7    8   31      6    6    6    7    7    7   10   14   18   22   25   26   29   31   34   37   39   43   44   46 
LCS_GDT     Q    54_A     Q    54_A      7    8   31      3    4    4    7    7    7   15   17   18   20   22   26   29   31   32   35   37   39   41   44 
LCS_GDT     L    55_A     L    55_A      3    8   31      3    4    4    8   14   15   17   19   20   22   23   26   29   31   32   35   37   41   44   46 
LCS_GDT     K    56_A     K    56_A      3    4   31      3    4    6   11   15   16   17   19   20   22   25   26   29   31   34   37   39   43   44   46 
LCS_GDT     E    57_A     E    57_A      3    8   31      0    4    4    5   10   15   17   19   20   22   25   26   29   31   32   35   38   41   44   46 
LCS_GDT     E    58_A     E    58_A      8   16   31      6    7    9   12   16   18   19   19   20   22   23   25   27   28   31   33   34   37   38   40 
LCS_GDT     L    59_A     L    59_A      8   16   31      6    7    9   12   16   18   19   19   19   19   21   23   27   29   32   33   34   37   41   43 
LCS_GDT     L    60_A     L    60_A      8   16   31      6    7    9   12   16   18   19   19   19   21   23   25   29   31   32   34   38   41   43   46 
LCS_GDT     K    61_A     K    61_A      8   16   31      6    7    9   12   16   18   19   19   20   22   25   26   29   31   34   37   39   43   44   46 
LCS_GDT     R    62_A     R    62_A      8   16   31      6    7    9   12   16   18   19   19   20   22   25   26   29   31   34   37   39   43   44   46 
LCS_GDT     E    63_A     E    63_A      8   16   31      6    7    9   12   16   18   19   19   20   22   25   26   29   31   34   37   39   43   44   46 
LCS_GDT     V    64_A     V    64_A     10   16   31      3    7    9   12   16   18   19   19   20   22   25   26   29   31   34   37   39   43   44   46 
LCS_GDT     I    65_A     I    65_A     10   16   31      3    8    9   12   16   18   19   19   20   22   25   26   29   31   34   37   39   43   44   46 
LCS_GDT     L    66_A     L    66_A     10   16   31      7    8    9   12   16   18   19   19   20   22   25   26   29   31   34   37   39   43   44   46 
LCS_GDT     K    67_A     K    67_A     10   16   31      7    8    9   12   16   18   19   19   20   22   25   26   29   31   34   37   39   43   44   46 
LCS_GDT     N    68_A     N    68_A     10   16   31      7    8    9   11   16   18   19   19   20   22   25   26   29   31   34   37   39   43   44   46 
LCS_GDT     L    69_A     L    69_A     10   16   29      7    8    9   11   16   18   19   19   20   22   25   26   29   31   34   37   39   43   44   46 
LCS_GDT     L    70_A     L    70_A     10   16   26      7    8    9   12   16   18   19   19   20   22   23   25   26   31   33   37   38   43   44   46 
LCS_GDT     T    71_A     T    71_A     10   16   26      7    8    9   12   16   18   19   19   20   22   23   25   25   29   33   35   38   43   44   46 
LCS_GDT     N    72_A     N    72_A     10   16   26      7    8    9   11   16   18   19   19   20   22   23   25   28   31   33   37   39   43   44   46 
LCS_GDT     L    73_A     L    73_A     10   16   26      7    8    9   11   16   18   19   19   20   22   23   25   25   29   32   35   38   41   44   46 
LCS_GDT     S    74_A     S    74_A      3   15   26      3    3    4   10   15   18   19   19   20   22   23   25   25   27   30   33   34   35   37   40 
LCS_GDT     Q    75_A     Q    75_A      3   15   26      3    8    9   11   15   17   19   19   20   22   23   25   25   26   26   28   30   33   36   38 
LCS_GDT     A    76_A     A    76_A      3   15   26      3    3    3   10   15   18   19   19   20   22   23   25   25   26   26   28   32   35   37   39 
LCS_AVERAGE  LCS_A:  18.92  (   8.27   12.55   35.94 )

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      7      8      9     12     16     18     19     19     20     22     25     26     29     31     34     37     39     43     44     46 
GDT PERCENT_AT   9.21  10.53  11.84  15.79  21.05  23.68  25.00  25.00  26.32  28.95  32.89  34.21  38.16  40.79  44.74  48.68  51.32  56.58  57.89  60.53
GDT RMS_LOCAL    0.28   0.37   0.65   1.62   1.91   2.15   2.22   2.22   2.47   2.87   4.18   4.39   4.65   4.84   5.53   5.75   5.95   6.34   6.56   6.74
GDT RMS_ALL_AT  23.11  22.58  21.78  24.55  22.68  22.31  22.62  22.62  21.15  22.78  12.92  12.86  12.92  12.81  13.29  12.93  13.28  13.53  12.55  12.58

# Checking swapping
#   possible swapping detected:  F    11_A      F    11_A
#   possible swapping detected:  Y    15_A      Y    15_A
#   possible swapping detected:  D    33_A      D    33_A
#   possible swapping detected:  D    44_A      D    44_A
#   possible swapping detected:  D    46_A      D    46_A
#   possible swapping detected:  D    49_A      D    49_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    L    10_A      L    10_A    18.113     0    0.129   0.167    20.433    0.000    0.000
LGA    F    11_A      F    11_A    14.563     0    0.105   1.327    16.295    0.000    0.000
LGA    G    12_A      G    12_A    20.042     0    0.136   0.136    20.720    0.000    0.000
LGA    E    13_A      E    13_A    23.009     0    0.033   0.659    30.980    0.000    0.000
LGA    H    14_A      H    14_A    16.872     0    0.397   1.415    18.933    0.000    0.000
LGA    Y    15_A      Y    15_A    14.060     0    0.643   1.449    16.210    0.000    0.000
LGA    S    16_A      S    16_A    17.465     0    0.028   0.132    18.168    0.000    0.000
LGA    A    17_A      A    17_A    21.658     0    0.247   0.264    24.188    0.000    0.000
LGA    N    18_A      N    18_A    19.506     0    0.174   0.864    21.713    0.000    0.000
LGA    Q    19_A      Q    19_A    16.214     0    0.363   1.329    18.304    0.000    0.000
LGA    F    20_A      F    20_A    17.781     0    0.063   1.276    20.538    0.000    0.000
LGA    A    21_A      A    21_A    20.073     0    0.124   0.144    22.993    0.000    0.000
LGA    K    22_A      K    22_A    21.697     0    0.170   1.055    24.293    0.000    0.000
LGA    I    23_A      I    23_A    24.775     0    0.198   1.341    28.230    0.000    0.000
LGA    L    24_A      L    24_A    26.862     0    0.594   1.506    29.340    0.000    0.000
LGA    I    25_A      I    25_A    32.280     0    0.617   1.708    36.212    0.000    0.000
LGA    N    26_A      N    26_A    37.812     0    0.571   1.215    40.311    0.000    0.000
LGA    K    27_A      K    27_A    40.872     0    0.037   0.797    43.374    0.000    0.000
LGA    D    28_A      D    28_A    43.157     0    0.659   0.783    44.169    0.000    0.000
LGA    G    29_A      G    29_A    43.296     0    0.586   0.586    43.486    0.000    0.000
LGA    S    30_A      S    30_A    44.292     0    0.711   0.614    45.647    0.000    0.000
LGA    N    31_A      N    31_A    38.445     0    0.657   1.560    40.171    0.000    0.000
LGA    V    32_A      V    32_A    38.001     0    0.055   0.965    38.443    0.000    0.000
LGA    D    33_A      D    33_A    39.753     0    0.065   1.054    41.630    0.000    0.000
LGA    R    34_A      R    34_A    37.009     0    0.150   0.925    38.282    0.000    0.000
LGA    K    35_A      K    35_A    38.815     0    0.223   0.324    46.700    0.000    0.000
LGA    T    36_A      T    36_A    36.906     0    0.307   1.017    39.396    0.000    0.000
LGA    I    37_A      I    37_A    32.457     0    0.624   1.185    34.407    0.000    0.000
LGA    Q    38_A      Q    38_A    27.940     0    0.579   1.397    29.401    0.000    0.000
LGA    N    39_A      N    39_A    30.537     0    0.599   1.237    34.755    0.000    0.000
LGA    W    40_A      W    40_A    27.647     0    0.035   1.578    29.676    0.000    0.000
LGA    I    41_A      I    41_A    21.694     0    0.022   0.259    24.223    0.000    0.000
LGA    N    42_A      N    42_A    21.447     0    0.050   0.202    25.002    0.000    0.000
LGA    R    43_A      R    43_A    23.596     0    0.228   1.064    33.502    0.000    0.000
LGA    D    44_A      D    44_A    19.746     0    0.470   0.444    21.105    0.000    0.000
LGA    Q    45_A      Q    45_A    20.902     0    0.557   0.997    26.617    0.000    0.000
LGA    D    46_A      D    46_A    23.457     0    0.619   1.176    27.440    0.000    0.000
LGA    L    47_A      L    47_A    22.120     0    0.596   1.442    22.738    0.000    0.000
LGA    N    48_A      N    48_A    22.499     0    0.616   1.482    26.794    0.000    0.000
LGA    D    49_A      D    49_A    24.227     0    0.034   0.986    28.925    0.000    0.000
LGA    W    50_A      W    50_A    22.921     0    0.029   0.259    24.718    0.000    0.000
LGA    V    51_A      V    51_A    17.136     0    0.068   0.163    19.492    0.000    0.000
LGA    I    52_A      I    52_A    15.396     0    0.145   1.078    18.086    0.000    0.000
LGA    V    53_A      V    53_A    17.694     0    0.605   0.527    21.745    0.000    0.000
LGA    Q    54_A      Q    54_A    12.269     0    0.271   0.851    14.191    0.357    0.159
LGA    L    55_A      L    55_A     9.051     0    0.604   1.401    10.298    2.262    1.369
LGA    K    56_A      K    56_A     8.524     0    0.592   1.414    14.823    2.976    1.693
LGA    E    57_A      E    57_A     7.482     0    0.580   0.909    14.000   18.690    8.466
LGA    E    58_A      E    58_A     1.396     0    0.593   1.298     5.809   77.619   55.185
LGA    L    59_A      L    59_A     2.731     0    0.055   1.470     8.430   64.881   41.786
LGA    L    60_A      L    60_A     3.239     0    0.047   1.402     9.073   55.357   34.643
LGA    K    61_A      K    61_A     2.492     0    0.022   0.834     9.111   66.786   39.788
LGA    R    62_A      R    62_A     2.013     0    0.047   1.082     9.182   70.952   36.926
LGA    E    63_A      E    63_A     1.561     0    0.042   0.374     6.721   83.810   55.608
LGA    V    64_A      V    64_A     1.757     0    0.582   0.890     4.972   64.048   64.626
LGA    I    65_A      I    65_A     0.950     0    0.253   1.408     4.329   83.810   68.929
LGA    L    66_A      L    66_A     1.399     0    0.070   0.541     3.634   77.143   70.298
LGA    K    67_A      K    67_A     2.046     0    0.084   0.827     2.962   68.810   67.619
LGA    N    68_A      N    68_A     2.143     0    0.030   1.109     4.672   70.833   61.726
LGA    L    69_A      L    69_A     1.377     0    0.035   0.090     2.302   81.429   76.190
LGA    L    70_A      L    70_A     1.340     0    0.079   1.354     3.444   79.286   73.274
LGA    T    71_A      T    71_A     2.741     0    0.044   0.202     4.106   57.262   49.524
LGA    N    72_A      N    72_A     2.806     0    0.042   0.107     4.106   59.167   53.869
LGA    L    73_A      L    73_A     1.536     0    0.531   0.451     2.957   68.929   74.107
LGA    S    74_A      S    74_A     2.703     0    0.122   0.190     5.647   62.976   50.794
LGA    Q    75_A      Q    75_A     2.794     0    0.545   1.255     9.421   57.500   35.503
LGA    A    76_A      A    76_A     3.131     0    0.261   0.268     5.290   61.071   54.095

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       67     268    268  100.00     555    555  100.00                76
SUMMARY(RMSD_GDC):    12.037         11.901                 12.602           17.578   14.160

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   82   76    4.0     19    2.22    25.000    22.083     0.819

LGA_LOCAL      RMSD:   2.220  Number of atoms:   19  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  22.619  Number of assigned atoms:   67 
Std_ASGN_ATOMS RMSD:  12.037  Standard rmsd on all 67 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.230971 * X  +   0.368208 * Y  +  -0.900597 * Z  +   9.658493
  Y_new =   0.729132 * X  +   0.547374 * Y  +   0.410790 * Z  + -74.880394
  Z_new =   0.644219 * X  +  -0.751535 * Y  +  -0.142045 * Z  +  43.529327 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  1.264021 -0.700002 -1.757599   [DEG:   72.4231  -40.1072 -100.7030 ]
ZXZ: -1.998737  1.713323  2.432930   [DEG: -114.5192   98.1662  139.3967 ]
 
# END of job
