
#######################################################
#                                                     #
#                        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   83 (  684),  selected   72 , name one
# Molecule2: number of CA atoms   72 (  603),  selected   72 , 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:    72       2_A - 81_A        3.17     3.17
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    56      18_A - 81_A        1.96     4.37
  LCS_AVERAGE:     71.30

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    49      33_A - 81_A        0.57     7.48
  LCS_AVERAGE:     56.52

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   72
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     T     2_A     T     2_A     23   35   72     18   24   28   30   34   38   44   54   58   65   68   71   72   72   72   72   72   72   72   72 
LCS_GDT     S     3_A     S     3_A     23   35   72     12   24   28   30   34   39   49   56   64   67   69   71   72   72   72   72   72   72   72   72 
LCS_GDT     L     4_A     L     4_A     23   35   72     17   24   28   30   34   39   50   61   66   69   70   71   72   72   72   72   72   72   72   72 
LCS_GDT     I     5_A     I     5_A     23   35   72     19   24   28   30   34   39   51   62   66   69   70   71   72   72   72   72   72   72   72   72 
LCS_GDT     E     6_A     E     6_A     23   35   72     19   24   28   30   34   39   50   61   66   69   70   71   72   72   72   72   72   72   72   72 
LCS_GDT     E     7_A     E     7_A     23   35   72     19   24   28   30   34   39   50   61   66   69   70   71   72   72   72   72   72   72   72   72 
LCS_GDT     L     8_A     L     8_A     23   35   72     19   24   28   30   34   39   55   62   66   69   70   71   72   72   72   72   72   72   72   72 
LCS_GDT     I     9_A     I     9_A     23   35   72     19   24   28   30   34   41   55   62   66   69   70   71   72   72   72   72   72   72   72   72 
LCS_GDT     R    10_A     R    10_A     23   35   72     19   24   28   30   34   39   53   62   66   69   70   71   72   72   72   72   72   72   72   72 
LCS_GDT     R    11_A     R    11_A     23   35   72     19   24   28   30   34   40   55   62   66   69   70   71   72   72   72   72   72   72   72   72 
LCS_GDT     S    12_A     S    12_A     23   35   72     19   24   28   30   40   51   58   62   66   69   70   71   72   72   72   72   72   72   72   72 
LCS_GDT     E    13_A     E    13_A     23   35   72     19   24   28   30   34   45   56   62   66   69   70   71   72   72   72   72   72   72   72   72 
LCS_GDT     E    14_A     E    14_A     23   35   72     19   24   28   30   34   43   55   62   66   69   70   71   72   72   72   72   72   72   72   72 
LCS_GDT     Q    15_A     Q    15_A     23   35   72     19   24   28   30   37   51   58   62   66   69   70   71   72   72   72   72   72   72   72   72 
LCS_GDT     Q    16_A     Q    16_A     23   35   72     19   24   28   33   47   54   58   62   66   69   70   71   72   72   72   72   72   72   72   72 
LCS_GDT     R    17_A     R    17_A     23   35   72     19   24   28   30   41   51   58   62   66   69   70   71   72   72   72   72   72   72   72   72 
LCS_GDT     R    18_A     R    18_A     23   56   72     19   24   28   30   43   52   58   62   66   69   70   71   72   72   72   72   72   72   72   72 
LCS_GDT     N    19_A     N    19_A     23   56   72     19   24   28   44   52   54   58   62   66   69   70   71   72   72   72   72   72   72   72   72 
LCS_GDT     E    20_A     E    20_A     23   56   72     19   24   28   33   48   54   58   62   66   69   70   71   72   72   72   72   72   72   72   72 
LCS_GDT     E    21_A     E    21_A     23   56   72     19   24   28   35   48   54   58   62   66   69   70   71   72   72   72   72   72   72   72   72 
LCS_GDT     A    22_A     A    22_A     23   56   72     19   24   33   44   52   54   58   62   66   69   70   71   72   72   72   72   72   72   72   72 
LCS_GDT     L    23_A     L    23_A     23   56   72     19   24   28   42   52   54   58   61   66   69   70   71   72   72   72   72   72   72   72   72 
LCS_GDT     R    24_A     R    24_A     23   56   72     17   24   28   31   48   54   58   62   66   69   70   71   72   72   72   72   72   72   72   72 
LCS_GDT     Q    33_A     Q    33_A     49   56   72     28   48   49   49   52   54   58   62   66   69   70   71   72   72   72   72   72   72   72   72 
LCS_GDT     L    34_A     L    34_A     49   56   72     26   48   49   49   52   54   57   62   66   69   70   71   72   72   72   72   72   72   72   72 
LCS_GDT     L    35_A     L    35_A     49   56   72     28   48   49   49   52   54   58   62   66   69   70   71   72   72   72   72   72   72   72   72 
LCS_GDT     S    36_A     S    36_A     49   56   72     28   48   49   49   52   54   58   62   66   69   70   71   72   72   72   72   72   72   72   72 
LCS_GDT     G    37_A     G    37_A     49   56   72     28   48   49   49   52   54   58   62   66   69   70   71   72   72   72   72   72   72   72   72 
LCS_GDT     I    38_A     I    38_A     49   56   72     28   48   49   49   52   54   58   62   66   69   70   71   72   72   72   72   72   72   72   72 
LCS_GDT     V    39_A     V    39_A     49   56   72     28   48   49   49   52   54   58   62   66   69   70   71   72   72   72   72   72   72   72   72 
LCS_GDT     Q    40_A     Q    40_A     49   56   72     28   48   49   49   52   54   58   62   66   69   70   71   72   72   72   72   72   72   72   72 
LCS_GDT     Q    41_A     Q    41_A     49   56   72     28   48   49   49   52   54   58   62   66   69   70   71   72   72   72   72   72   72   72   72 
LCS_GDT     Q    42_A     Q    42_A     49   56   72     28   48   49   49   52   54   58   62   66   69   70   71   72   72   72   72   72   72   72   72 
LCS_GDT     N    43_A     N    43_A     49   56   72     28   48   49   49   52   54   58   62   66   69   70   71   72   72   72   72   72   72   72   72 
LCS_GDT     N    44_A     N    44_A     49   56   72     28   48   49   49   52   54   58   62   66   69   70   71   72   72   72   72   72   72   72   72 
LCS_GDT     L    45_A     L    45_A     49   56   72     28   48   49   49   52   54   58   62   66   69   70   71   72   72   72   72   72   72   72   72 
LCS_GDT     L    46_A     L    46_A     49   56   72     28   48   49   49   52   54   58   62   66   69   70   71   72   72   72   72   72   72   72   72 
LCS_GDT     R    47_A     R    47_A     49   56   72     28   48   49   49   52   54   58   62   66   69   70   71   72   72   72   72   72   72   72   72 
LCS_GDT     A    48_A     A    48_A     49   56   72     32   48   49   49   52   54   58   62   66   69   70   71   72   72   72   72   72   72   72   72 
LCS_GDT     I    49_A     I    49_A     49   56   72     32   48   49   49   52   54   58   62   66   69   70   71   72   72   72   72   72   72   72   72 
LCS_GDT     E    50_A     E    50_A     49   56   72     32   48   49   49   52   54   58   62   66   69   70   71   72   72   72   72   72   72   72   72 
LCS_GDT     A    51_A     A    51_A     49   56   72     32   48   49   49   52   54   58   62   66   69   70   71   72   72   72   72   72   72   72   72 
LCS_GDT     Q    52_A     Q    52_A     49   56   72     32   48   49   49   52   54   58   62   66   69   70   71   72   72   72   72   72   72   72   72 
LCS_GDT     Q    53_A     Q    53_A     49   56   72     32   48   49   49   52   54   58   62   66   69   70   71   72   72   72   72   72   72   72   72 
LCS_GDT     H    54_A     H    54_A     49   56   72     32   48   49   49   52   54   58   62   66   69   70   71   72   72   72   72   72   72   72   72 
LCS_GDT     L    55_A     L    55_A     49   56   72     31   48   49   49   52   54   58   62   66   69   70   71   72   72   72   72   72   72   72   72 
LCS_GDT     L    56_A     L    56_A     49   56   72     32   48   49   49   52   54   58   62   66   69   70   71   72   72   72   72   72   72   72   72 
LCS_GDT     Q    57_A     Q    57_A     49   56   72     32   48   49   49   52   54   58   62   66   69   70   71   72   72   72   72   72   72   72   72 
LCS_GDT     L    58_A     L    58_A     49   56   72     32   48   49   49   52   54   58   62   66   69   70   71   72   72   72   72   72   72   72   72 
LCS_GDT     T    59_A     T    59_A     49   56   72     32   48   49   49   52   54   58   62   66   69   70   71   72   72   72   72   72   72   72   72 
LCS_GDT     V    60_A     V    60_A     49   56   72     32   48   49   49   52   54   58   62   66   69   70   71   72   72   72   72   72   72   72   72 
LCS_GDT     W    61_A     W    61_A     49   56   72     32   48   49   49   52   54   58   62   66   69   70   71   72   72   72   72   72   72   72   72 
LCS_GDT     G    62_A     G    62_A     49   56   72     32   48   49   49   52   54   58   62   66   69   70   71   72   72   72   72   72   72   72   72 
LCS_GDT     I    63_A     I    63_A     49   56   72     32   48   49   49   52   54   58   62   66   69   70   71   72   72   72   72   72   72   72   72 
LCS_GDT     K    64_A     K    64_A     49   56   72     32   48   49   49   52   54   58   62   66   69   70   71   72   72   72   72   72   72   72   72 
LCS_GDT     Q    65_A     Q    65_A     49   56   72     32   48   49   49   52   54   58   62   66   69   70   71   72   72   72   72   72   72   72   72 
LCS_GDT     L    66_A     L    66_A     49   56   72     32   48   49   49   52   54   58   62   66   69   70   71   72   72   72   72   72   72   72   72 
LCS_GDT     Q    67_A     Q    67_A     49   56   72     32   48   49   49   52   54   58   62   66   69   70   71   72   72   72   72   72   72   72   72 
LCS_GDT     A    68_A     A    68_A     49   56   72     32   48   49   49   52   54   58   62   66   69   70   71   72   72   72   72   72   72   72   72 
LCS_GDT     R    69_A     R    69_A     49   56   72     32   48   49   49   52   54   58   62   66   69   70   71   72   72   72   72   72   72   72   72 
LCS_GDT     I    70_A     I    70_A     49   56   72     32   48   49   49   52   54   58   62   66   69   70   71   72   72   72   72   72   72   72   72 
LCS_GDT     L    71_A     L    71_A     49   56   72     32   48   49   49   52   54   58   62   66   69   70   71   72   72   72   72   72   72   72   72 
LCS_GDT     A    72_A     A    72_A     49   56   72     32   48   49   49   52   54   58   62   66   69   70   71   72   72   72   72   72   72   72   72 
LCS_GDT     V    73_A     V    73_A     49   56   72     32   48   49   49   52   54   58   62   66   69   70   71   72   72   72   72   72   72   72   72 
LCS_GDT     E    74_A     E    74_A     49   56   72     32   48   49   49   52   54   58   62   65   69   70   71   72   72   72   72   72   72   72   72 
LCS_GDT     R    75_A     R    75_A     49   56   72     32   48   49   49   52   54   58   62   66   69   70   71   72   72   72   72   72   72   72   72 
LCS_GDT     Y    76_A     Y    76_A     49   56   72     32   48   49   49   52   54   58   62   66   69   70   71   72   72   72   72   72   72   72   72 
LCS_GDT     L    77_A     L    77_A     49   56   72     32   48   49   49   52   54   58   60   65   69   70   71   72   72   72   72   72   72   72   72 
LCS_GDT     R    78_A     R    78_A     49   56   72     32   48   49   49   52   54   58   61   65   69   70   71   72   72   72   72   72   72   72   72 
LCS_GDT     D    79_A     D    79_A     49   56   72     32   48   49   49   52   54   58   62   66   69   70   71   72   72   72   72   72   72   72   72 
LCS_GDT     Q    80_A     Q    80_A     49   56   72     32   48   49   49   52   54   58   62   66   69   70   71   72   72   72   72   72   72   72   72 
LCS_GDT     Q    81_A     Q    81_A     49   56   72     16   26   49   49   52   54   57   60   64   67   70   71   72   72   72   72   72   72   72   72 
LCS_AVERAGE  LCS_A:  75.94  (  56.52   71.30  100.00 )

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     32     48     49     49     52     54     58     62     66     69     70     71     72     72     72     72     72     72     72     72 
GDT PERCENT_AT  44.44  66.67  68.06  68.06  72.22  75.00  80.56  86.11  91.67  95.83  97.22  98.61 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.32   0.56   0.57   0.57   1.41   1.82   2.17   2.64   2.88   2.98   3.02   3.10   3.17   3.17   3.17   3.17   3.17   3.17   3.17   3.17
GDT RMS_ALL_AT   7.34   7.42   7.48   7.48   5.66   4.54   3.83   3.27   3.22   3.19   3.19   3.18   3.17   3.17   3.17   3.17   3.17   3.17   3.17   3.17

# Checking swapping
#   possible swapping detected:  E     6_A      E     6_A
#   possible swapping detected:  E     7_A      E     7_A
#   possible swapping detected:  E    20_A      E    20_A
#   possible swapping detected:  E    50_A      E    50_A
#   possible swapping detected:  E    74_A      E    74_A
#   possible swapping detected:  Y    76_A      Y    76_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    T     2_A      T     2_A     7.671     0    0.556   1.213    11.491   14.167    8.095
LGA    S     3_A      S     3_A     7.361     0    0.038   0.654     7.773   11.905   10.794
LGA    L     4_A      L     4_A     6.245     0    0.031   0.150     6.785   19.524   19.940
LGA    I     5_A      I     5_A     5.059     0    0.038   0.172     5.527   26.310   28.869
LGA    E     6_A      E     6_A     6.230     0    0.081   0.157     7.941   18.214   13.069
LGA    E     7_A      E     7_A     6.245     0    0.012   0.231     7.451   20.476   16.138
LGA    L     8_A      L     8_A     4.508     0    0.050   0.164     5.138   34.524   36.607
LGA    I     9_A      I     9_A     4.283     0    0.065   0.137     4.951   38.690   35.774
LGA    R    10_A      R    10_A     5.396     0    0.064   1.282     6.322   28.810   28.788
LGA    R    11_A      R    11_A     4.573     0    0.012   1.364    11.015   37.381   22.165
LGA    S    12_A      S    12_A     2.355     0    0.067   0.679     3.540   63.095   60.079
LGA    E    13_A      E    13_A     3.435     0    0.031   0.776     4.495   50.000   44.921
LGA    E    14_A      E    14_A     4.052     0    0.024   0.370     7.392   45.119   30.000
LGA    Q    15_A      Q    15_A     2.599     0    0.043   1.159     7.422   63.214   46.772
LGA    Q    16_A      Q    16_A     1.039     0    0.032   0.794     2.174   81.429   77.672
LGA    R    17_A      R    17_A     1.884     0    0.028   1.125     7.713   77.143   49.654
LGA    R    18_A      R    18_A     2.045     0    0.015   1.061     8.636   68.810   42.078
LGA    N    19_A      N    19_A     1.930     0    0.031   0.074     2.934   68.929   63.988
LGA    E    20_A      E    20_A     1.882     0    0.000   0.230     3.400   70.833   65.026
LGA    E    21_A      E    21_A     1.277     0    0.021   0.802     3.460   75.119   69.577
LGA    A    22_A      A    22_A     2.938     0    0.093   0.106     3.859   53.810   53.048
LGA    L    23_A      L    23_A     4.045     0    0.047   0.083     5.719   40.476   34.107
LGA    R    24_A      R    24_A     2.978     0    0.324   1.071     4.346   59.048   54.719
LGA    Q    33_A      Q    33_A     3.319     0    0.086   0.395     5.790   51.786   38.254
LGA    L    34_A      L    34_A     3.772     0    0.060   0.150     6.095   50.119   36.548
LGA    L    35_A      L    35_A     1.647     0    0.007   0.453     4.514   79.643   68.095
LGA    S    36_A      S    36_A     1.473     0    0.039   0.675     2.801   79.405   71.984
LGA    G    37_A      G    37_A     3.430     0    0.069   0.069     3.430   51.786   51.786
LGA    I    38_A      I    38_A     2.904     0    0.035   0.077     4.844   62.976   50.952
LGA    V    39_A      V    39_A     0.710     0    0.017   0.044     2.568   92.857   82.109
LGA    Q    40_A      Q    40_A     2.296     0    0.012   0.922     8.121   68.929   42.487
LGA    Q    41_A      Q    41_A     3.134     0    0.065   1.010     5.109   57.262   43.016
LGA    Q    42_A      Q    42_A     1.816     0    0.056   1.133     7.390   79.405   51.429
LGA    N    43_A      N    43_A     1.783     0    0.019   0.133     4.568   75.238   58.750
LGA    N    44_A      N    44_A     3.370     0    0.016   0.038     6.280   55.476   39.762
LGA    L    45_A      L    45_A     2.504     0    0.034   0.236     5.379   69.048   52.619
LGA    L    46_A      L    46_A     1.270     0    0.045   0.128     4.260   83.690   64.643
LGA    R    47_A      R    47_A     2.735     0    0.026   0.380     8.810   62.976   34.416
LGA    A    48_A      A    48_A     2.845     0    0.048   0.049     3.867   64.881   60.571
LGA    I    49_A      I    49_A     1.577     0    0.047   0.102     4.176   81.548   63.393
LGA    E    50_A      E    50_A     2.271     0    0.068   0.101     5.539   67.024   49.524
LGA    A    51_A      A    51_A     3.047     0    0.020   0.026     4.023   59.167   54.762
LGA    Q    52_A      Q    52_A     1.878     0    0.020   0.576     6.124   79.405   53.651
LGA    Q    53_A      Q    53_A     1.818     0    0.021   0.152     5.687   75.238   52.487
LGA    H    54_A      H    54_A     3.145     0    0.013   1.271    10.772   57.262   29.286
LGA    L    55_A      L    55_A     2.347     0    0.036   1.399     7.571   70.952   47.976
LGA    L    56_A      L    56_A     1.174     0    0.047   1.354     6.264   83.690   61.369
LGA    Q    57_A      Q    57_A     2.474     0    0.036   1.175     7.469   66.786   43.280
LGA    L    58_A      L    58_A     2.570     0    0.042   0.208     5.532   64.881   48.393
LGA    T    59_A      T    59_A     1.676     0    0.048   0.066     3.462   77.143   67.551
LGA    V    60_A      V    60_A     2.289     0    0.000   0.048     4.622   70.952   57.483
LGA    W    61_A      W    61_A     2.550     0    0.081   1.306     7.027   66.905   42.313
LGA    G    62_A      G    62_A     2.190     0    0.044   0.044     2.190   68.810   68.810
LGA    I    63_A      I    63_A     2.001     0    0.028   0.078     4.642   75.119   57.798
LGA    K    64_A      K    64_A     2.204     0    0.043   1.153    11.160   68.810   39.683
LGA    Q    65_A      Q    65_A     2.301     0    0.038   1.426    10.298   68.810   39.841
LGA    L    66_A      L    66_A     2.371     0    0.026   0.063     5.368   68.810   51.845
LGA    Q    67_A      Q    67_A     2.307     0    0.012   0.737     5.886   70.833   50.053
LGA    A    68_A      A    68_A     2.110     0    0.017   0.026     3.294   72.976   68.381
LGA    R    69_A      R    69_A     2.446     0    0.012   0.136     8.145   66.786   36.840
LGA    I    70_A      I    70_A     2.750     0    0.075   1.364     6.249   60.952   44.107
LGA    L    71_A      L    71_A     2.148     0    0.018   0.042     5.112   72.976   55.476
LGA    A    72_A      A    72_A     1.426     0    0.025   0.042     2.749   83.690   78.381
LGA    V    73_A      V    73_A     2.972     0    0.017   0.061     5.530   59.286   46.735
LGA    E    74_A      E    74_A     3.637     0    0.020   0.092     6.616   48.452   35.344
LGA    R    75_A      R    75_A     2.017     0    0.083   0.284     7.256   70.952   45.411
LGA    Y    76_A      Y    76_A     1.481     0    0.019   0.132     7.031   77.381   45.238
LGA    L    77_A      L    77_A     4.159     0    0.045   0.090     6.871   38.929   28.750
LGA    R    78_A      R    78_A     4.326     0    0.052   1.138     9.101   41.905   25.325
LGA    D    79_A      D    79_A     1.654     0    0.024   0.113     3.374   75.119   67.202
LGA    Q    80_A      Q    80_A     2.550     0    0.030   0.110     5.131   55.833   45.608
LGA    Q    81_A      Q    81_A     5.390     0    0.460   0.560     9.006   26.667   15.450

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       72     288    288  100.00     603    603  100.00                72
SUMMARY(RMSD_GDC):     3.173          2.945                  4.356           60.369   46.903

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   83   72    4.0     62    2.64    80.208    79.624     2.264

LGA_LOCAL      RMSD:   2.638  Number of atoms:   62  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   3.267  Number of assigned atoms:   72 
Std_ASGN_ATOMS RMSD:   3.173  Standard rmsd on all 72 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.116031 * X  +  -0.969152 * Y  +  -0.217441 * Z  +   0.192199
  Y_new =  -0.844647 * X  +   0.018906 * Y  +  -0.534989 * Z  +   3.899628
  Z_new =   0.522597 * X  +   0.245737 * Y  +  -0.816398 * Z  +  66.667938 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -1.434278 -0.549894  2.849218   [DEG:  -82.1781  -31.5066  163.2481 ]
ZXZ: -0.386046  2.525942  1.131253   [DEG:  -22.1188  144.7258   64.8160 ]
 
# END of job
