
#######################################################
#                                                     #
#                        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   70 (  578),  selected   70 , name one
# Molecule2: number of CA atoms  141 ( 1112),  selected   70 , 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:    50      28_A - 77_A        4.95    13.34
  LONGEST_CONTINUOUS_SEGMENT:    50      29_A - 78_A        4.81    13.13
  LCS_AVERAGE:     31.22

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    20      27_A - 46_A        1.86    15.40
  LONGEST_CONTINUOUS_SEGMENT:    20      28_A - 47_A        2.00    13.69
  LCS_AVERAGE:     12.99

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    17       9_A - 25_A        0.79    22.80
  LCS_AVERAGE:      9.79

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   70
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     S     9_A     S     9_A     17   19   27      6   13   16   17   19   19   19   19   19   20   21   22   23   25   30   34   34   35   37   39 
LCS_GDT     K    10_A     K    10_A     17   19   27     12   15   16   17   19   19   19   19   19   20   21   22   23   25   30   34   34   35   37   39 
LCS_GDT     A    11_A     A    11_A     17   19   27     12   15   16   17   19   19   19   19   19   20   21   22   23   25   30   34   34   35   37   39 
LCS_GDT     K    12_A     K    12_A     17   19   27     12   15   16   17   19   19   19   19   19   20   21   22   23   25   30   34   34   35   37   39 
LCS_GDT     V    13_A     V    13_A     17   19   27     12   15   16   17   19   19   19   19   19   20   21   22   23   25   30   34   34   35   37   39 
LCS_GDT     N    14_A     N    14_A     17   19   27     12   15   16   17   19   19   19   19   19   20   21   22   23   25   30   34   34   35   37   39 
LCS_GDT     D    15_A     D    15_A     17   19   27     12   15   16   17   19   19   19   19   19   20   21   22   23   25   30   34   34   35   37   39 
LCS_GDT     F    16_A     F    16_A     17   19   27     12   15   16   17   19   19   19   19   19   20   21   22   23   24   28   34   34   35   36   39 
LCS_GDT     L    17_A     L    17_A     17   19   27     12   15   16   17   19   19   19   19   19   20   21   22   23   25   30   34   34   35   37   39 
LCS_GDT     A    18_A     A    18_A     17   19   27     12   15   16   17   19   19   19   19   19   20   21   22   23   25   30   34   34   35   37   39 
LCS_GDT     E    19_A     E    19_A     17   19   27     12   15   16   17   19   19   19   19   19   20   21   22   23   25   30   34   34   35   37   39 
LCS_GDT     I    20_A     I    20_A     17   19   27     12   15   16   17   19   19   19   19   19   19   21   22   23   24   30   34   34   35   37   39 
LCS_GDT     F    21_A     F    21_A     17   19   27     12   15   16   17   19   19   19   19   19   20   21   22   23   25   30   34   34   35   37   39 
LCS_GDT     K    22_A     K    22_A     17   19   27     11   15   16   17   19   19   19   19   19   20   21   22   23   25   30   34   34   35   37   39 
LCS_GDT     K    23_A     K    23_A     17   19   27      7   15   16   17   19   19   19   19   19   19   20   22   23   23   26   34   34   35   37   39 
LCS_GDT     I    24_A     I    24_A     17   19   29      4   10   16   17   19   19   19   19   19   19   20   22   23   25   30   34   34   35   37   39 
LCS_GDT     G    25_A     G    25_A     17   19   31      7   15   16   17   19   19   19   19   19   23   24   26   27   29   32   34   35   39   40   45 
LCS_GDT     S    26_A     S    26_A      4   19   32      3    4    5   16   19   19   19   19   22   23   26   30   31   33   35   38   38   42   43   46 
LCS_GDT     K    27_A     K    27_A      4   20   34      3    4   11   16   19   19   19   20   22   24   26   28   29   32   35   36   38   40   44   46 
LCS_GDT     E    28_A     E    28_A      4   20   50      5   11   14   16   18   19   20   23   25   28   31   35   39   41   44   48   50   51   51   51 
LCS_GDT     N    29_A     N    29_A     16   20   50      7   12   15   17   18   21   23   25   27   29   31   37   39   43   46   48   50   51   51   51 
LCS_GDT     T    30_A     T    30_A     16   20   50      7   12   15   17   18   21   23   24   27   30   35   38   41   45   47   48   50   51   51   51 
LCS_GDT     K    31_A     K    31_A     16   20   50      8   12   15   17   18   21   23   25   28   35   40   42   43   47   48   48   50   51   51   51 
LCS_GDT     E    32_A     E    32_A     16   20   50      8   12   15   17   18   21   23   25   28   34   39   42   43   47   48   48   50   51   51   51 
LCS_GDT     G    33_A     G    33_A     16   20   50      8   12   15   17   18   21   23   25   27   30   35   40   43   45   48   48   50   51   51   51 
LCS_GDT     L    34_A     L    34_A     16   20   50      8   12   15   17   18   21   23   25   27   34   40   42   43   47   48   48   50   51   51   51 
LCS_GDT     A    35_A     A    35_A     16   20   50      8   12   15   17   18   21   23   26   33   37   40   42   44   47   48   48   50   51   51   51 
LCS_GDT     E    36_A     E    36_A     16   20   50      8   12   15   17   18   21   23   26   30   37   40   42   44   47   48   48   50   51   51   51 
LCS_GDT     L    37_A     L    37_A     16   20   50      8   12   15   17   18   21   23   26   28   35   40   42   44   47   48   48   50   51   51   51 
LCS_GDT     Y    38_A     Y    38_A     16   20   50      8   12   15   17   18   21   24   28   33   37   40   42   44   47   48   48   50   51   51   51 
LCS_GDT     E    39_A     E    39_A     16   20   50      7   12   15   17   18   22   25   28   33   37   40   42   44   47   48   48   50   51   51   51 
LCS_GDT     Y    40_A     Y    40_A     16   20   50      5   12   15   17   18   22   25   28   33   37   40   42   44   47   48   48   50   51   51   51 
LCS_GDT     K    41_A     K    41_A     16   20   50      4   12   15   17   18   22   25   28   33   37   40   42   44   47   48   48   50   51   51   51 
LCS_GDT     K    42_A     K    42_A     16   20   50      6   12   15   17   18   22   25   28   33   37   40   42   44   47   48   48   50   51   51   51 
LCS_GDT     K    43_A     K    43_A     16   20   50      5   12   15   17   18   22   25   28   33   37   40   42   44   47   48   48   50   51   51   51 
LCS_GDT     Y    44_A     Y    44_A     16   20   50      3    7   15   16   18   22   25   28   33   37   40   42   44   47   48   48   50   51   51   51 
LCS_GDT     S    45_A     S    45_A      3   20   50      3   12   15   17   18   21   23   26   29   33   37   41   44   47   48   48   50   51   51   51 
LCS_GDT     D    46_A     D    46_A     11   20   50      5    8   11   16   18   20   24   28   33   37   40   42   44   47   48   48   50   51   51   51 
LCS_GDT     A    47_A     A    47_A     11   20   50      5    8   11   13   17   20   24   28   33   37   40   42   44   47   48   48   50   51   51   51 
LCS_GDT     D    48_A     D    48_A     11   15   50      5    5   10   13   17   22   25   28   33   37   40   42   44   47   48   48   50   51   51   51 
LCS_GDT     I    49_A     I    49_A     11   15   50      5    9   11   13   16   22   25   28   33   37   40   42   44   47   48   48   50   51   51   51 
LCS_GDT     E    50_A     E    50_A     11   15   50      7    9   11   13   16   19   24   28   33   37   40   42   44   47   48   48   50   51   51   51 
LCS_GDT     P    51_A     P    51_A     11   15   50      7    9   11   13   16   19   24   28   32   37   40   42   44   47   48   48   50   51   51   51 
LCS_GDT     F    52_A     F    52_A     11   15   50      7    9   11   13   16   22   25   28   33   37   40   42   44   47   48   48   50   51   51   51 
LCS_GDT     L    53_A     L    53_A     11   15   50      7    9   11   13   16   22   25   28   33   37   40   42   44   47   48   48   50   51   51   51 
LCS_GDT     K    54_A     K    54_A     11   15   50      7    9   11   13   16   19   24   28   32   37   40   42   44   47   48   48   50   51   51   51 
LCS_GDT     N    55_A     N    55_A     11   15   50      7    9   11   13   16   20   24   28   32   37   40   42   44   47   48   48   50   51   51   51 
LCS_GDT     S    56_A     S    56_A     11   15   50      7    9   11   13   16   22   25   28   33   37   40   42   44   47   48   48   50   51   51   51 
LCS_GDT     S    57_A     S    57_A     10   15   50      6    9   11   15   17   22   25   28   33   37   40   42   44   47   48   48   50   51   51   51 
LCS_GDT     Q    58_A     Q    58_A      7   15   50      5    6    9   14   18   22   23   28   33   37   40   42   44   47   48   48   50   51   51   51 
LCS_GDT     F    59_A     F    59_A      7   14   50      5    6    7    7    7    7   13   18   33   37   40   42   44   47   48   48   50   51   51   51 
LCS_GDT     F    60_A     F    60_A      7   17   50      5    6    7    7    7   20   25   28   32   37   40   41   44   47   48   48   50   51   51   51 
LCS_GDT     Q    61_A     Q    61_A      7   18   50      5    6    7    7   15   18   18   21   26   31   38   41   44   47   48   48   50   51   51   51 
LCS_GDT     S    62_A     S    62_A      7   18   50      3    6    7   14   14   19   19   26   30   37   40   42   44   47   48   48   50   51   51   51 
LCS_GDT     Y    63_A     Y    63_A     15   18   50      4   13   15   17   18   22   25   28   33   37   40   42   44   47   48   48   50   51   51   51 
LCS_GDT     V    64_A     V    64_A     15   18   50      5   13   15   17   18   22   25   28   33   37   40   42   44   47   48   48   50   51   51   51 
LCS_GDT     E    65_A     E    65_A     15   18   50      5   13   15   17   18   22   25   28   33   37   40   42   44   47   48   48   50   51   51   51 
LCS_GDT     R    66_A     R    66_A     15   18   50      5   13   15   17   18   22   25   28   33   37   40   42   44   47   48   48   50   51   51   51 
LCS_GDT     G    67_A     G    67_A     15   18   50      9   13   15   17   18   22   25   28   33   37   40   42   44   47   48   48   50   51   51   51 
LCS_GDT     L    68_A     L    68_A     15   18   50      9   13   15   17   18   22   25   28   33   37   40   42   44   47   48   48   50   51   51   51 
LCS_GDT     R    69_A     R    69_A     15   18   50      9   13   15   17   18   22   25   28   33   37   40   42   44   47   48   48   50   51   51   51 
LCS_GDT     V    70_A     V    70_A     15   18   50      9   13   15   17   18   22   25   28   33   37   40   42   44   47   48   48   50   51   51   51 
LCS_GDT     I    71_A     I    71_A     15   18   50      9   13   15   17   18   22   25   28   33   37   40   42   44   47   48   48   50   51   51   51 
LCS_GDT     E    72_A     E    72_A     15   18   50      8   13   15   17   18   22   25   28   33   37   40   42   44   47   48   48   50   51   51   51 
LCS_GDT     M    73_A     M    73_A     15   18   50      9   13   15   17   18   22   25   28   33   37   40   42   44   47   48   48   50   51   51   51 
LCS_GDT     E    74_A     E    74_A     15   18   50      9   13   15   17   18   22   25   28   33   37   40   42   44   47   48   48   50   51   51   51 
LCS_GDT     R    75_A     R    75_A     15   18   50      9   13   15   17   18   22   25   28   33   37   40   42   44   47   48   48   50   51   51   51 
LCS_GDT     E    76_A     E    76_A     15   18   50      9   13   15   17   18   22   25   28   33   37   40   42   44   47   48   48   50   51   51   51 
LCS_GDT     G    77_A     G    77_A     15   18   50      4    9   15   17   18   22   23   26   31   36   40   42   44   47   48   48   50   51   51   51 
LCS_GDT     K    78_A     K    78_A     15   18   50      4    5    6   17   17   19   21   25   28   31   37   41   44   47   48   48   50   51   51   51 
LCS_AVERAGE  LCS_A:  18.00  (   9.79   12.99   31.22 )

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     12     15     16     17     19     22     25     28     33     37     40     42     44     47     48     48     50     51     51     51 
GDT PERCENT_AT   8.51  10.64  11.35  12.06  13.48  15.60  17.73  19.86  23.40  26.24  28.37  29.79  31.21  33.33  34.04  34.04  35.46  36.17  36.17  36.17
GDT RMS_LOCAL    0.27   0.56   0.69   0.79   1.27   1.95   2.27   2.65   3.14   3.35   3.60   3.92   3.96   4.32   4.45   4.45   4.81   5.02   5.02   5.02
GDT RMS_ALL_AT  21.70  22.19  22.65  22.80  23.07  12.52  14.06  14.37  13.37  13.79  13.63  13.48  13.28  13.20  13.16  13.16  13.13  13.24  13.24  13.24

# Checking swapping
#   possible swapping detected:  E    19_A      E    19_A
#   possible swapping detected:  E    32_A      E    32_A
#   possible swapping detected:  Y    38_A      Y    38_A
#   possible swapping detected:  E    39_A      E    39_A
#   possible swapping detected:  Y    44_A      Y    44_A
#   possible swapping detected:  F    52_A      F    52_A
#   possible swapping detected:  F    59_A      F    59_A
#   possible swapping detected:  E    72_A      E    72_A
#   possible swapping detected:  E    74_A      E    74_A
#   possible swapping detected:  E    76_A      E    76_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    S     9_A      S     9_A    35.676     0    0.589   0.703    38.960    0.000    0.000
LGA    K    10_A      K    10_A    31.054     0    0.123   0.596    32.828    0.000    0.000
LGA    A    11_A      A    11_A    31.195     0    0.017   0.022    32.761    0.000    0.000
LGA    K    12_A      K    12_A    30.873     0    0.015   0.058    37.895    0.000    0.000
LGA    V    13_A      V    13_A    28.192     0    0.084   0.840    29.361    0.000    0.000
LGA    N    14_A      N    14_A    25.912     0    0.091   1.114    26.852    0.000    0.000
LGA    D    15_A      D    15_A    26.191     0    0.053   1.004    27.380    0.000    0.000
LGA    F    16_A      F    16_A    25.045     0    0.019   0.101    25.920    0.000    0.000
LGA    L    17_A      L    17_A    23.006     0    0.022   0.047    24.092    0.000    0.000
LGA    A    18_A      A    18_A    22.417     0    0.055   0.061    23.147    0.000    0.000
LGA    E    19_A      E    19_A    22.042     0    0.008   1.198    25.089    0.000    0.000
LGA    I    20_A      I    20_A    21.312     0    0.028   0.046    22.835    0.000    0.000
LGA    F    21_A      F    21_A    20.880     0    0.054   1.242    22.855    0.000    0.000
LGA    K    22_A      K    22_A    21.331     0    0.045   0.791    21.752    0.000    0.000
LGA    K    23_A      K    23_A    21.454     0    0.058   0.891    23.614    0.000    0.000
LGA    I    24_A      I    24_A    23.081     0    0.473   1.431    26.599    0.000    0.000
LGA    G    25_A      G    25_A    22.909     0    0.140   0.140    23.077    0.000    0.000
LGA    S    26_A      S    26_A    22.294     0    0.432   0.447    23.370    0.000    0.000
LGA    K    27_A      K    27_A    23.178     0    0.048   0.875    26.775    0.000    0.000
LGA    E    28_A      E    28_A    18.256     0    0.613   1.110    19.692    0.000    0.000
LGA    N    29_A      N    29_A    16.031     0    0.394   1.357    18.289    0.000    0.000
LGA    T    30_A      T    30_A    13.674     0    0.028   0.759    15.385    0.000    0.000
LGA    K    31_A      K    31_A    10.124     0    0.045   0.664    11.475    0.714    2.275
LGA    E    32_A      E    32_A    11.455     0    0.021   0.923    13.837    0.000    0.000
LGA    G    33_A      G    33_A    11.629     0    0.016   0.016    11.726    0.119    0.119
LGA    L    34_A      L    34_A     8.785     0    0.011   0.069     9.964    5.952    3.512
LGA    A    35_A      A    35_A     6.870     0    0.016   0.019     7.683   13.810   12.476
LGA    E    36_A      E    36_A     7.642     0    0.008   0.118    11.388   11.190    5.450
LGA    L    37_A      L    37_A     6.972     0    0.031   1.416    11.603   17.738    9.762
LGA    Y    38_A      Y    38_A     4.153     0    0.108   1.262     9.212   44.524   32.103
LGA    E    39_A      E    39_A     3.511     0    0.019   0.842     8.123   52.143   33.069
LGA    Y    40_A      Y    40_A     2.618     0    0.024   1.306     9.849   67.619   33.571
LGA    K    41_A      K    41_A     2.467     0    0.075   0.946    11.216   64.881   36.667
LGA    K    42_A      K    42_A     1.135     0    0.057   0.616     5.586   73.690   57.249
LGA    K    43_A      K    43_A     2.475     0    0.095   0.610     8.013   63.095   42.751
LGA    Y    44_A      Y    44_A     1.880     0    0.295   1.403     8.746   61.429   40.317
LGA    S    45_A      S    45_A     6.609     0    0.437   0.753    10.156   19.881   13.730
LGA    D    46_A      D    46_A     3.412     0    0.373   0.680     6.749   45.119   32.976
LGA    A    47_A      A    47_A     3.320     0    0.115   0.127     3.823   48.333   50.095
LGA    D    48_A      D    48_A     2.688     0    0.107   0.627     3.853   55.357   55.476
LGA    I    49_A      I    49_A     2.810     0    0.059   0.056     3.814   51.905   55.536
LGA    E    50_A      E    50_A     3.981     0    0.070   1.455     7.584   45.000   27.302
LGA    P    51_A      P    51_A     4.041     0    0.020   0.056     4.861   45.119   40.884
LGA    F    52_A      F    52_A     1.900     0    0.046   0.235     2.633   71.071   73.810
LGA    L    53_A      L    53_A     2.206     0    0.058   1.298     4.120   64.881   55.000
LGA    K    54_A      K    54_A     3.612     0    0.013   0.621     6.373   48.333   35.185
LGA    N    55_A      N    55_A     2.883     0    0.004   0.115     4.544   60.952   53.214
LGA    S    56_A      S    56_A     0.993     0    0.205   0.288     2.448   79.524   81.667
LGA    S    57_A      S    57_A     0.716     0    0.627   0.617     2.891   77.619   72.063
LGA    Q    58_A      Q    58_A     6.652     0    0.042   0.923    13.576   18.810    8.519
LGA    F    59_A      F    59_A     6.338     0    0.015   1.292    14.128   31.310   11.818
LGA    F    60_A      F    60_A     2.559     0    0.093   1.457    11.677   57.500   25.887
LGA    Q    61_A      Q    61_A     5.926     0    0.039   1.207    11.204   23.333   11.481
LGA    S    62_A      S    62_A     6.501     0    0.243   0.738     8.548   21.905   16.270
LGA    Y    63_A      Y    63_A     2.044     0    0.461   1.431    12.773   66.905   32.341
LGA    V    64_A      V    64_A     1.590     0    0.096   1.096     4.254   72.857   65.510
LGA    E    65_A      E    65_A     2.053     0    0.011   1.560     8.007   68.810   45.185
LGA    R    66_A      R    66_A     1.572     0    0.072   1.256     5.534   72.857   65.758
LGA    G    67_A      G    67_A     1.168     0    0.047   0.047     1.740   77.143   77.143
LGA    L    68_A      L    68_A     2.365     0    0.090   0.966     2.765   62.976   67.024
LGA    R    69_A      R    69_A     3.552     0    0.093   1.431    12.865   45.000   21.991
LGA    V    70_A      V    70_A     3.347     0    0.039   1.091     3.637   48.333   51.361
LGA    I    71_A      I    71_A     2.821     0    0.024   0.643     3.848   51.905   59.464
LGA    E    72_A      E    72_A     4.430     0    0.015   0.090     6.294   32.024   27.302
LGA    M    73_A      M    73_A     5.601     0    0.019   0.862     8.455   21.548   15.893
LGA    E    74_A      E    74_A     5.246     0    0.054   0.846     5.561   25.000   32.487
LGA    R    75_A      R    75_A     4.163     0    0.013   1.081     7.081   34.286   30.996
LGA    E    76_A      E    76_A     6.067     0    0.144   0.210     7.688   15.952   16.772
LGA    G    77_A      G    77_A     7.874     0    0.247   0.247    10.295    5.476    5.476
LGA    K    78_A      K    78_A     9.934     0    0.478   1.096    13.822    0.833    0.476

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       70     280    280  100.00     578    578  100.00               141
SUMMARY(RMSD_GDC):    10.342         10.234                 10.901           14.502   11.670

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   70  141    4.0     28    2.65    19.149    18.247     1.017

LGA_LOCAL      RMSD:   2.653  Number of atoms:   28  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  14.366  Number of assigned atoms:   70 
Std_ASGN_ATOMS RMSD:  10.342  Standard rmsd on all 70 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.221975 * X  +  -0.526586 * Y  +   0.820630 * Z  +  23.224247
  Y_new =   0.316582 * X  +   0.834953 * Y  +   0.450143 * Z  +   1.082446
  Z_new =  -0.922227 * X  +   0.159876 * Y  +   0.352046 * Z  + -22.944742 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  0.959292  1.173802  0.426287   [DEG:   54.9634   67.2539   24.4244 ]
ZXZ:  2.072513  1.211040 -1.399143   [DEG:  118.7463   69.3875  -80.1650 ]
 
# END of job
