
#######################################################
#                                                     #
#                        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 (  545),  selected   70 , name one
# Molecule2: number of CA atoms   92 (  680),  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:    70       8_A - 77_A        4.31     4.31
  LCS_AVERAGE:     76.09

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    20      58_A - 77_A        1.83     6.15
  LCS_AVERAGE:     17.07

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    16      61_A - 76_A        0.95     7.39
  LCS_AVERAGE:     11.15

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     G     8_A     G     8_A      3    9   70      3   11   15   20   25   30   40   46   51   55   57   60   64   66   68   69   69   70   70   70 
LCS_GDT     G     9_A     G     9_A      5    9   70      3    5    7    8   12   18   24   27   29   52   55   58   63   66   68   69   69   70   70   70 
LCS_GDT     G    10_A     G    10_A      5    9   70      3    5    7    8   12   18   24   29   47   52   57   60   64   66   68   69   69   70   70   70 
LCS_GDT     E    11_A     E    11_A      6    9   70      3    5   15   20   31   37   43   47   51   55   57   60   64   66   68   69   69   70   70   70 
LCS_GDT     R    12_A     R    12_A      6    9   70      4    7   15   23   32   38   43   47   51   55   57   60   64   66   68   69   69   70   70   70 
LCS_GDT     R    13_A     R    13_A      6    9   70      4    5   12   24   32   38   43   47   51   55   57   60   64   66   68   69   69   70   70   70 
LCS_GDT     K    14_A     K    14_A      6    9   70      4    5   11   23   32   38   43   47   51   55   57   60   64   66   68   69   69   70   70   70 
LCS_GDT     G    15_A     G    15_A      6    9   70      4    7   14   17   25   36   43   47   51   55   57   60   64   66   68   69   69   70   70   70 
LCS_GDT     S    16_A     S    16_A      6   17   70      3    8   14   22   32   38   43   47   51   55   57   60   64   66   68   69   69   70   70   70 
LCS_GDT     V    17_A     V    17_A      6   17   70      3    8   14   17   31   38   43   47   51   55   57   60   64   66   68   69   69   70   70   70 
LCS_GDT     K    18_A     K    18_A      4   17   70      3    8   14   17   25   38   43   46   51   55   57   60   64   66   68   69   69   70   70   70 
LCS_GDT     W    19_A     W    19_A     14   17   70      4   13   17   26   32   38   43   47   51   55   57   60   64   66   68   69   69   70   70   70 
LCS_GDT     F    20_A     F    20_A     14   17   70      5   13   17   26   32   38   43   47   51   55   57   60   64   66   68   69   69   70   70   70 
LCS_GDT     D    21_A     D    21_A     14   17   70      6   13   17   26   32   38   43   47   51   55   57   60   64   66   68   69   69   70   70   70 
LCS_GDT     T    22_A     T    22_A     14   17   70      6   13   16   26   32   38   43   47   51   55   57   60   64   66   68   69   69   70   70   70 
LCS_GDT     Q    23_A     Q    23_A     14   17   70      6   13   16   26   32   38   43   47   51   55   57   60   64   66   68   69   69   70   70   70 
LCS_GDT     K    24_A     K    24_A     14   17   70      7   13   16   26   32   38   43   47   51   55   57   60   64   66   68   69   69   70   70   70 
LCS_GDT     G    25_A     G    25_A     14   17   70      6   13   16   26   32   38   43   47   51   55   57   60   64   66   68   69   69   70   70   70 
LCS_GDT     F    26_A     F    26_A     14   17   70      6   13   17   26   32   38   43   47   51   55   57   60   64   66   68   69   69   70   70   70 
LCS_GDT     G    27_A     G    27_A     14   17   70      5   13   17   26   32   38   43   47   51   55   57   60   64   66   68   69   69   70   70   70 
LCS_GDT     F    28_A     F    28_A     14   17   70      7   13   17   26   32   38   43   47   51   55   57   60   64   66   68   69   69   70   70   70 
LCS_GDT     I    29_A     I    29_A     14   17   70      7   13   17   26   32   38   43   47   51   55   57   60   64   66   68   69   69   70   70   70 
LCS_GDT     T    30_A     T    30_A     14   17   70      4   12   17   26   32   38   43   47   51   55   57   60   64   66   68   69   69   70   70   70 
LCS_GDT     P    31_A     P    31_A     14   17   70      5   13   16   26   32   38   43   47   51   55   57   60   64   66   68   69   69   70   70   70 
LCS_GDT     D    32_A     D    32_A     14   17   70      5   13   16   23   31   37   43   47   51   55   57   60   64   66   68   69   69   70   70   70 
LCS_GDT     D    33_A     D    33_A      4   15   70      3    7   10   10   17   25   33   42   48   55   57   60   64   66   68   69   69   70   70   70 
LCS_GDT     G    34_A     G    34_A      4   11   70      3    4    7    9   11   12   22   28   40   44   50   58   60   62   64   67   69   70   70   70 
LCS_GDT     G    35_A     G    35_A      8   11   70      4    8   13   21   30   38   43   46   50   55   57   60   64   65   68   69   69   70   70   70 
LCS_GDT     D    36_A     D    36_A      8   11   70      3   10   15   23   32   38   43   46   51   55   57   60   64   66   68   69   69   70   70   70 
LCS_GDT     D    37_A     D    37_A      8   11   70      7   12   16   24   32   38   43   47   51   55   57   60   64   66   68   69   69   70   70   70 
LCS_GDT     L    38_A     L    38_A      8   11   70      7   12   16   23   32   38   43   47   51   55   57   60   64   66   68   69   69   70   70   70 
LCS_GDT     F    39_A     F    39_A      8   11   70      7   12   16   24   32   38   43   47   51   55   57   60   64   66   68   69   69   70   70   70 
LCS_GDT     V    40_A     V    40_A      8   11   70      7   12   16   23   32   38   43   47   51   55   57   60   64   66   68   69   69   70   70   70 
LCS_GDT     H    41_A     H    41_A      8   11   70      3   12   14   19   26   34   43   46   51   55   57   60   64   66   68   69   69   70   70   70 
LCS_GDT     Q    42_A     Q    42_A      8   11   70      3    8   16   23   32   38   43   46   51   55   57   60   64   66   68   69   69   70   70   70 
LCS_GDT     S    43_A     S    43_A      7   11   70      4   12   16   24   32   38   43   47   51   55   57   60   64   66   68   69   69   70   70   70 
LCS_GDT     S    44_A     S    44_A      5    6   70      4    5    5   20   25   32   39   47   51   55   57   60   64   66   68   69   69   70   70   70 
LCS_GDT     I    45_A     I    45_A      5   15   70      4    5   14   26   32   38   43   47   51   55   57   60   64   66   68   69   69   70   70   70 
LCS_GDT     R    46_A     R    46_A      5   16   70      4    5    5   16   18   20   23   28   45   53   57   59   63   65   68   69   69   70   70   70 
LCS_GDT     S    47_A     S    47_A      5   16   70      4    4   14   18   26   33   42   47   51   55   57   60   64   66   68   69   69   70   70   70 
LCS_GDT     E    48_A     E    48_A      5   16   70      4    4    6   17   19   29   37   45   51   55   57   60   64   66   68   69   69   70   70   70 
LCS_GDT     G    49_A     G    49_A      5   16   70      4    8   14   17   24   33   40   47   51   55   57   60   64   66   68   69   69   70   70   70 
LCS_GDT     F    50_A     F    50_A      5   16   70      4    4    9   18   26   34   42   47   51   55   57   60   64   66   68   69   69   70   70   70 
LCS_GDT     R    51_A     R    51_A      8   16   70      3    5   14   17   19   26   35   43   51   55   57   60   64   66   68   69   69   70   70   70 
LCS_GDT     S    52_A     S    52_A      8   16   70      3    7   12   15   18   20   24   31   41   48   52   58   63   64   68   69   69   70   70   70 
LCS_GDT     L    53_A     L    53_A      8   16   70      3    7   12   17   18   24   32   43   48   53   57   60   64   66   68   69   69   70   70   70 
LCS_GDT     A    54_A     A    54_A      8   16   70      3    5   14   17   21   34   41   47   51   55   57   60   64   66   68   69   69   70   70   70 
LCS_GDT     A    55_A     A    55_A      8   16   70      3    8   14   17   23   34   43   47   51   55   57   60   64   66   68   69   69   70   70   70 
LCS_GDT     E    56_A     E    56_A      8   16   70      4   10   17   26   32   38   43   47   51   55   57   60   64   66   68   69   69   70   70   70 
LCS_GDT     E    57_A     E    57_A      8   16   70      4   10   17   26   32   38   43   47   51   55   57   60   64   66   68   69   69   70   70   70 
LCS_GDT     A    58_A     A    58_A      8   20   70      6   12   17   26   32   38   43   47   51   55   57   60   64   66   68   69   69   70   70   70 
LCS_GDT     V    59_A     V    59_A      8   20   70      6   12   17   26   32   38   43   47   51   55   57   60   64   66   68   69   69   70   70   70 
LCS_GDT     E    60_A     E    60_A     12   20   70      6   12   17   26   32   38   43   47   51   55   57   60   64   66   68   69   69   70   70   70 
LCS_GDT     F    61_A     F    61_A     16   20   70      6   12   17   26   32   38   43   47   51   55   57   60   64   66   68   69   69   70   70   70 
LCS_GDT     E    62_A     E    62_A     16   20   70      7   12   17   26   32   38   43   47   51   55   57   60   64   66   68   69   69   70   70   70 
LCS_GDT     V    63_A     V    63_A     16   20   70      7   11   17   26   30   37   43   47   51   55   57   60   64   66   68   69   69   70   70   70 
LCS_GDT     E    64_A     E    64_A     16   20   70      5   11   17   20   26   34   42   47   51   55   57   60   64   66   68   69   69   70   70   70 
LCS_GDT     I    65_A     I    65_A     16   20   70      5   11   17   20   25   30   38   45   51   55   57   60   64   66   68   69   69   70   70   70 
LCS_GDT     D    66_A     D    66_A     16   20   70      5   11   17   20   25   26   30   35   43   49   56   59   64   66   68   69   69   70   70   70 
LCS_GDT     N    67_A     N    67_A     16   20   70      7   11   17   20   25   26   28   35   40   49   53   57   63   66   68   69   69   70   70   70 
LCS_GDT     N    68_A     N    68_A     16   20   70      7   11   17   20   25   25   28   35   40   49   53   57   63   66   68   69   69   70   70   70 
LCS_GDT     N    69_A     N    69_A     16   20   70      7   11   17   20   25   26   30   39   46   51   57   59   64   66   68   69   69   70   70   70 
LCS_GDT     R    70_A     R    70_A     16   20   70      7   11   17   20   25   26   30   39   45   50   57   59   64   66   68   69   69   70   70   70 
LCS_GDT     P    71_A     P    71_A     16   20   70      7   11   17   20   25   27   36   43   50   55   57   60   64   66   68   69   69   70   70   70 
LCS_GDT     K    72_A     K    72_A     16   20   70      4   10   17   20   25   32   39   46   51   55   57   60   64   66   68   69   69   70   70   70 
LCS_GDT     A    73_A     A    73_A     16   20   70      4   11   17   20   25   36   43   47   51   55   57   60   64   66   68   69   69   70   70   70 
LCS_GDT     I    74_A     I    74_A     16   20   70      4   11   17   26   32   37   43   47   51   55   57   60   64   66   68   69   69   70   70   70 
LCS_GDT     D    75_A     D    75_A     16   20   70      4   12   17   26   32   38   43   47   51   55   57   60   64   66   68   69   69   70   70   70 
LCS_GDT     V    76_A     V    76_A     16   20   70      6   12   17   26   32   38   43   47   51   55   57   60   64   66   68   69   69   70   70   70 
LCS_GDT     S    77_A     S    77_A      9   20   70      3   12   17   26   32   38   43   47   51   55   57   60   64   66   68   69   69   70   70   70 
LCS_AVERAGE  LCS_A:  34.77  (  11.15   17.07   76.09 )

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     13     17     26     32     38     43     47     51     55     57     60     64     66     68     69     69     70     70     70 
GDT PERCENT_AT   7.61  14.13  18.48  28.26  34.78  41.30  46.74  51.09  55.43  59.78  61.96  65.22  69.57  71.74  73.91  75.00  75.00  76.09  76.09  76.09
GDT RMS_LOCAL    0.28   0.69   0.91   1.39   1.71   2.03   2.18   2.54   2.71   2.98   3.12   3.37   3.75   3.99   4.11   4.19   4.19   4.31   4.31   4.31
GDT RMS_ALL_AT   8.69   4.90   4.97   4.85   4.98   5.49   5.07   4.66   4.71   4.56   4.49   4.49   4.34   4.32   4.31   4.31   4.31   4.31   4.31   4.31

# Checking swapping
#   possible swapping detected:  E    11_A      E    11_A
#   possible swapping detected:  F    20_A      F    20_A
#   possible swapping detected:  F    26_A      F    26_A
#   possible swapping detected:  F    28_A      F    28_A
#   possible swapping detected:  D    32_A      D    32_A
#   possible swapping detected:  D    33_A      D    33_A
#   possible swapping detected:  D    36_A      D    36_A
#   possible swapping detected:  D    37_A      D    37_A
#   possible swapping detected:  F    50_A      F    50_A
#   possible swapping detected:  E    56_A      E    56_A
#   possible swapping detected:  E    60_A      E    60_A
#   possible swapping detected:  E    62_A      E    62_A
#   possible swapping detected:  D    66_A      D    66_A
#   possible swapping detected:  D    75_A      D    75_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    G     8_A      G     8_A     5.702     0    0.610   0.610     8.756   16.548   16.548
LGA    G     9_A      G     9_A     9.847     0    0.237   0.237     9.847    3.333    3.333
LGA    G    10_A      G    10_A     7.576     0    0.133   0.133     8.486    9.762    9.762
LGA    E    11_A      E    11_A     3.784     0    0.228   1.016     4.829   37.381   58.254
LGA    R    12_A      R    12_A     2.862     0    0.112   1.250     6.909   53.571   37.186
LGA    R    13_A      R    13_A     1.999     0    0.026   1.006     3.640   72.857   67.965
LGA    K    14_A      K    14_A     2.382     0    0.129   0.776     5.335   60.952   46.243
LGA    G    15_A      G    15_A     3.266     0    0.154   0.154     3.266   55.357   55.357
LGA    S    16_A      S    16_A     2.578     0    0.072   0.090     3.689   51.905   54.921
LGA    V    17_A      V    17_A     3.451     0    0.650   0.660     4.754   45.476   46.599
LGA    K    18_A      K    18_A     4.711     0    0.087   0.976    10.277   47.619   24.868
LGA    W    19_A      W    19_A     1.769     0    0.527   1.405    12.600   72.857   30.510
LGA    F    20_A      F    20_A     1.799     0    0.154   1.152     7.808   70.833   44.329
LGA    D    21_A      D    21_A     1.510     0    0.186   0.616     3.247   75.000   71.071
LGA    T    22_A      T    22_A     2.347     0    0.157   0.999     4.936   62.857   54.762
LGA    Q    23_A      Q    23_A     2.298     0    0.049   1.556     4.731   64.762   63.810
LGA    K    24_A      K    24_A     1.664     0    0.054   1.066     5.184   72.857   60.529
LGA    G    25_A      G    25_A     1.708     0    0.035   0.035     1.708   77.143   77.143
LGA    F    26_A      F    26_A     0.762     0    0.192   1.180     6.945   85.952   58.874
LGA    G    27_A      G    27_A     0.532     0    0.123   0.123     1.345   88.214   88.214
LGA    F    28_A      F    28_A     0.697     0    0.036   0.293     3.232   88.214   75.152
LGA    I    29_A      I    29_A     1.464     0    0.042   0.670     2.841   79.286   72.083
LGA    T    30_A      T    30_A     0.736     0    0.181   1.017     2.832   85.952   78.367
LGA    P    31_A      P    31_A     1.572     0    0.015   0.014     1.952   75.000   79.048
LGA    D    32_A      D    32_A     2.800     0    0.039   1.360     8.227   57.262   35.714
LGA    D    33_A      D    33_A     7.385     0    0.041   1.107    11.045    9.762    7.143
LGA    G    34_A      G    34_A     9.468     0    0.415   0.415     9.468    6.667    6.667
LGA    G    35_A      G    35_A     6.107     0    0.203   0.203     7.661   19.167   19.167
LGA    D    36_A      D    36_A     4.387     0    0.006   0.645     5.959   35.952   31.786
LGA    D    37_A      D    37_A     2.662     0    0.050   0.812     3.528   50.119   58.452
LGA    L    38_A      L    38_A     3.514     0    0.072   1.227     6.291   50.119   44.583
LGA    F    39_A      F    39_A     2.893     0    0.041   1.255     9.899   50.119   27.619
LGA    V    40_A      V    40_A     3.318     0    0.042   0.072     3.705   50.119   50.136
LGA    H    41_A      H    41_A     4.600     0    0.153   1.175     8.307   35.714   23.286
LGA    Q    42_A      Q    42_A     4.240     0    0.589   0.845     5.256   34.405   44.127
LGA    S    43_A      S    43_A     3.319     0    0.234   0.229     5.919   55.714   46.905
LGA    S    44_A      S    44_A     3.896     0    0.101   0.647     5.891   45.119   37.222
LGA    I    45_A      I    45_A     2.100     0    0.318   0.712     4.370   55.714   54.940
LGA    R    46_A      R    46_A     6.198     0    0.670   0.819    17.654   29.286   11.039
LGA    S    47_A      S    47_A     3.586     0    0.189   0.617     4.931   35.833   38.651
LGA    E    48_A      E    48_A     5.367     0    0.136   1.266    10.502   27.500   16.878
LGA    G    49_A      G    49_A     4.727     0    0.053   0.053     4.787   35.833   35.833
LGA    F    50_A      F    50_A     3.617     0    0.244   1.205     6.872   41.786   32.208
LGA    R    51_A      R    51_A     5.394     0    0.014   1.317     8.899   22.024   17.662
LGA    S    52_A      S    52_A     7.517     0    0.282   0.661     8.231   11.786   10.317
LGA    L    53_A      L    53_A     5.716     0    0.010   0.169     6.390   22.738   21.548
LGA    A    54_A      A    54_A     4.041     0    0.105   0.143     4.530   38.810   38.476
LGA    A    55_A      A    55_A     3.725     0    0.614   0.593     5.914   37.857   40.286
LGA    E    56_A      E    56_A     2.246     0    0.129   0.655     4.804   66.786   56.984
LGA    E    57_A      E    57_A     1.748     0    0.079   0.999     3.898   72.976   65.238
LGA    A    58_A      A    58_A     0.951     0    0.039   0.047     1.235   85.952   85.048
LGA    V    59_A      V    59_A     1.190     0    0.019   0.184     1.584   81.429   81.497
LGA    E    60_A      E    60_A     1.122     0    0.032   0.581     2.334   81.429   77.672
LGA    F    61_A      F    61_A     1.102     0    0.021   0.067     2.430   88.214   77.013
LGA    E    62_A      E    62_A     1.246     0    0.059   0.993     4.790   73.214   55.608
LGA    V    63_A      V    63_A     2.453     0    0.020   1.203     4.595   62.976   59.252
LGA    E    64_A      E    64_A     3.802     0    0.023   1.004     7.041   39.048   32.169
LGA    I    65_A      I    65_A     6.109     0    0.007   0.094     7.312   15.833   19.702
LGA    D    66_A      D    66_A     9.066     0    0.064   0.774     9.904    2.619    2.202
LGA    N    67_A      N    67_A    10.771     0    0.047   1.017    15.686    0.000    0.000
LGA    N    68_A      N    68_A    11.461     0    0.132   1.414    16.065    0.000    0.000
LGA    N    69_A      N    69_A     8.972     0    0.145   0.188     9.685    2.738    2.143
LGA    R    70_A      R    70_A     8.667     0    0.120   0.825    15.736    4.405    1.732
LGA    P    71_A      P    71_A     6.226     0    0.063   0.076     7.429   16.429   15.170
LGA    K    72_A      K    72_A     4.377     0    0.041   0.098     4.907   38.810   42.857
LGA    A    73_A      A    73_A     3.205     0    0.046   0.061     3.638   50.119   50.095
LGA    I    74_A      I    74_A     2.047     0    0.014   0.553     4.108   68.810   63.393
LGA    D    75_A      D    75_A     1.004     0    0.080   0.505     1.845   85.952   83.750
LGA    V    76_A      V    76_A     1.153     0    0.091   0.156     1.742   79.286   77.755
LGA    S    77_A      S    77_A     1.514     0    0.628   0.791     4.102   77.143   69.762

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       70     280    280  100.00     545    545  100.00                92
SUMMARY(RMSD_GDC):     4.306          4.284                  5.231           37.035   33.094

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   70   92    4.0     47    2.54    42.120    37.900     1.782

LGA_LOCAL      RMSD:   2.538  Number of atoms:   47  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   4.656  Number of assigned atoms:   70 
Std_ASGN_ATOMS RMSD:   4.306  Standard rmsd on all 70 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.268005 * X  +  -0.790692 * Y  +  -0.550435 * Z  + -16.935503
  Y_new =   0.337124 * X  +   0.612183 * Y  +  -0.715248 * Z  +  10.363348
  Z_new =   0.902508 * X  +   0.006125 * Y  +   0.430629 * Z  +   0.290856 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  0.899126 -1.125558  0.014224   [DEG:   51.5162  -64.4897    0.8150 ]
ZXZ: -0.655910  1.125606  1.564009   [DEG:  -37.5809   64.4925   89.6111 ]
 
# END of job
