
#######################################################
#                                                     #
#                        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        4.80     4.80
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    49      33_A - 81_A        0.66    11.70
  LCS_AVERAGE:     56.52

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    49      33_A - 81_A        0.66    11.70
  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   23   72     21   24   25   27   31   33   36   38   42   48   56   60   65   68   69   71   72   72   72   72 
LCS_GDT     S     3_A     S     3_A     23   23   72     17   24   25   27   31   33   36   38   42   48   56   60   65   68   69   71   72   72   72   72 
LCS_GDT     L     4_A     L     4_A     23   23   72     21   24   25   27   31   33   36   38   42   48   56   60   65   68   69   71   72   72   72   72 
LCS_GDT     I     5_A     I     5_A     23   23   72     21   24   25   27   31   33   36   38   42   48   56   60   65   68   69   71   72   72   72   72 
LCS_GDT     E     6_A     E     6_A     23   23   72     21   24   25   27   31   33   36   38   42   48   56   60   65   68   69   71   72   72   72   72 
LCS_GDT     E     7_A     E     7_A     23   23   72     21   24   25   27   31   33   36   38   42   48   56   60   65   68   69   71   72   72   72   72 
LCS_GDT     L     8_A     L     8_A     23   23   72     21   24   25   27   31   33   36   38   42   48   56   60   65   68   69   71   72   72   72   72 
LCS_GDT     I     9_A     I     9_A     23   23   72     21   24   25   27   31   33   36   38   42   48   56   60   65   68   69   71   72   72   72   72 
LCS_GDT     R    10_A     R    10_A     23   23   72     21   24   25   27   31   33   36   38   42   48   56   60   65   68   69   71   72   72   72   72 
LCS_GDT     R    11_A     R    11_A     23   23   72     21   24   25   27   31   33   36   38   42   48   56   60   65   68   69   71   72   72   72   72 
LCS_GDT     S    12_A     S    12_A     23   23   72     21   24   25   27   31   33   36   38   42   48   56   60   65   68   69   71   72   72   72   72 
LCS_GDT     E    13_A     E    13_A     23   23   72     21   24   25   27   31   33   36   38   42   48   56   60   65   68   69   71   72   72   72   72 
LCS_GDT     E    14_A     E    14_A     23   23   72     21   24   25   27   31   33   36   38   42   48   56   60   65   68   69   71   72   72   72   72 
LCS_GDT     Q    15_A     Q    15_A     23   23   72     21   24   25   27   31   33   36   38   42   48   56   60   65   68   69   71   72   72   72   72 
LCS_GDT     Q    16_A     Q    16_A     23   23   72     21   24   25   27   31   33   36   38   42   48   56   60   65   68   69   71   72   72   72   72 
LCS_GDT     R    17_A     R    17_A     23   23   72     21   24   25   27   31   33   36   38   42   48   56   60   65   68   69   71   72   72   72   72 
LCS_GDT     R    18_A     R    18_A     23   23   72     21   24   25   27   31   33   36   38   42   48   56   60   65   68   69   71   72   72   72   72 
LCS_GDT     N    19_A     N    19_A     23   23   72     21   24   25   27   31   33   36   38   42   48   56   60   65   68   69   71   72   72   72   72 
LCS_GDT     E    20_A     E    20_A     23   23   72     21   24   25   27   31   33   36   38   42   48   56   60   65   68   69   71   72   72   72   72 
LCS_GDT     E    21_A     E    21_A     23   23   72     20   24   25   27   31   33   36   38   42   48   56   60   65   68   69   71   72   72   72   72 
LCS_GDT     A    22_A     A    22_A     23   23   72     21   24   25   27   31   33   36   38   42   48   56   60   65   68   69   71   72   72   72   72 
LCS_GDT     L    23_A     L    23_A     23   23   72     21   24   25   27   31   33   36   38   42   48   56   60   65   68   69   71   72   72   72   72 
LCS_GDT     R    24_A     R    24_A     23   23   72     21   24   25   27   31   33   36   38   42   48   56   60   65   68   69   71   72   72   72   72 
LCS_GDT     Q    33_A     Q    33_A     49   49   72     28   45   49   49   49   49   49   49   49   49   56   60   65   68   69   71   72   72   72   72 
LCS_GDT     L    34_A     L    34_A     49   49   72     28   45   49   49   49   49   49   49   49   49   55   59   62   68   68   71   72   72   72   72 
LCS_GDT     L    35_A     L    35_A     49   49   72     28   45   49   49   49   49   49   49   49   49   56   60   65   68   69   71   72   72   72   72 
LCS_GDT     S    36_A     S    36_A     49   49   72     25   45   49   49   49   49   49   49   49   49   56   60   65   68   69   71   72   72   72   72 
LCS_GDT     G    37_A     G    37_A     49   49   72     25   45   49   49   49   49   49   49   49   49   56   60   65   68   69   71   72   72   72   72 
LCS_GDT     I    38_A     I    38_A     49   49   72     28   45   49   49   49   49   49   49   49   49   56   60   65   68   69   71   72   72   72   72 
LCS_GDT     V    39_A     V    39_A     49   49   72     25   45   49   49   49   49   49   49   49   49   56   60   65   68   69   71   72   72   72   72 
LCS_GDT     Q    40_A     Q    40_A     49   49   72     25   45   49   49   49   49   49   49   49   49   56   60   65   68   69   71   72   72   72   72 
LCS_GDT     Q    41_A     Q    41_A     49   49   72     28   45   49   49   49   49   49   49   49   49   56   60   65   68   69   71   72   72   72   72 
LCS_GDT     Q    42_A     Q    42_A     49   49   72     28   45   49   49   49   49   49   49   49   49   56   60   65   68   69   71   72   72   72   72 
LCS_GDT     N    43_A     N    43_A     49   49   72     28   45   49   49   49   49   49   49   49   49   56   60   65   68   69   71   72   72   72   72 
LCS_GDT     N    44_A     N    44_A     49   49   72     28   45   49   49   49   49   49   49   49   49   55   60   65   68   69   71   72   72   72   72 
LCS_GDT     L    45_A     L    45_A     49   49   72     28   45   49   49   49   49   49   49   49   49   56   60   65   68   69   71   72   72   72   72 
LCS_GDT     L    46_A     L    46_A     49   49   72     28   45   49   49   49   49   49   49   49   49   56   60   65   68   69   71   72   72   72   72 
LCS_GDT     R    47_A     R    47_A     49   49   72     28   45   49   49   49   49   49   49   49   49   55   59   65   68   69   71   72   72   72   72 
LCS_GDT     A    48_A     A    48_A     49   49   72     28   45   49   49   49   49   49   49   49   49   56   60   65   68   69   71   72   72   72   72 
LCS_GDT     I    49_A     I    49_A     49   49   72     28   45   49   49   49   49   49   49   49   49   56   60   65   68   69   71   72   72   72   72 
LCS_GDT     E    50_A     E    50_A     49   49   72     28   45   49   49   49   49   49   49   49   49   55   59   65   68   69   71   72   72   72   72 
LCS_GDT     A    51_A     A    51_A     49   49   72     28   45   49   49   49   49   49   49   49   49   55   59   64   68   69   71   72   72   72   72 
LCS_GDT     Q    52_A     Q    52_A     49   49   72     28   45   49   49   49   49   49   49   49   49   56   60   65   68   69   71   72   72   72   72 
LCS_GDT     Q    53_A     Q    53_A     49   49   72     28   45   49   49   49   49   49   49   49   49   56   60   65   68   69   71   72   72   72   72 
LCS_GDT     H    54_A     H    54_A     49   49   72     28   45   49   49   49   49   49   49   49   49   55   59   62   68   68   71   72   72   72   72 
LCS_GDT     L    55_A     L    55_A     49   49   72     28   45   49   49   49   49   49   49   49   49   56   60   65   68   69   71   72   72   72   72 
LCS_GDT     L    56_A     L    56_A     49   49   72     28   43   49   49   49   49   49   49   49   49   56   60   65   68   69   71   72   72   72   72 
LCS_GDT     Q    57_A     Q    57_A     49   49   72     28   45   49   49   49   49   49   49   49   49   55   60   65   68   69   71   72   72   72   72 
LCS_GDT     L    58_A     L    58_A     49   49   72     28   45   49   49   49   49   49   49   49   49   55   60   65   68   69   71   72   72   72   72 
LCS_GDT     T    59_A     T    59_A     49   49   72     28   45   49   49   49   49   49   49   49   49   56   60   65   68   69   71   72   72   72   72 
LCS_GDT     V    60_A     V    60_A     49   49   72     28   45   49   49   49   49   49   49   49   49   56   60   65   68   69   71   72   72   72   72 
LCS_GDT     W    61_A     W    61_A     49   49   72     28   45   49   49   49   49   49   49   49   49   55   60   65   68   69   71   72   72   72   72 
LCS_GDT     G    62_A     G    62_A     49   49   72     28   45   49   49   49   49   49   49   49   49   56   60   65   68   69   71   72   72   72   72 
LCS_GDT     I    63_A     I    63_A     49   49   72     28   45   49   49   49   49   49   49   49   49   56   60   65   68   69   71   72   72   72   72 
LCS_GDT     K    64_A     K    64_A     49   49   72     28   45   49   49   49   49   49   49   49   49   56   60   65   68   69   71   72   72   72   72 
LCS_GDT     Q    65_A     Q    65_A     49   49   72     28   45   49   49   49   49   49   49   49   49   56   60   65   68   69   71   72   72   72   72 
LCS_GDT     L    66_A     L    66_A     49   49   72     28   45   49   49   49   49   49   49   49   49   56   60   65   68   69   71   72   72   72   72 
LCS_GDT     Q    67_A     Q    67_A     49   49   72     28   45   49   49   49   49   49   49   49   49   56   60   65   68   69   71   72   72   72   72 
LCS_GDT     A    68_A     A    68_A     49   49   72     28   45   49   49   49   49   49   49   49   49   56   60   65   68   69   71   72   72   72   72 
LCS_GDT     R    69_A     R    69_A     49   49   72     28   45   49   49   49   49   49   49   49   49   56   60   65   68   69   71   72   72   72   72 
LCS_GDT     I    70_A     I    70_A     49   49   72     28   45   49   49   49   49   49   49   49   49   55   60   65   68   69   71   72   72   72   72 
LCS_GDT     L    71_A     L    71_A     49   49   72     28   45   49   49   49   49   49   49   49   49   56   60   65   68   69   71   72   72   72   72 
LCS_GDT     A    72_A     A    72_A     49   49   72     28   45   49   49   49   49   49   49   49   49   56   60   65   68   69   71   72   72   72   72 
LCS_GDT     V    73_A     V    73_A     49   49   72     28   45   49   49   49   49   49   49   49   49   55   60   65   68   69   71   72   72   72   72 
LCS_GDT     E    74_A     E    74_A     49   49   72     28   45   49   49   49   49   49   49   49   49   49   53   63   68   69   71   72   72   72   72 
LCS_GDT     R    75_A     R    75_A     49   49   72     28   45   49   49   49   49   49   49   49   49   56   60   65   68   69   71   72   72   72   72 
LCS_GDT     Y    76_A     Y    76_A     49   49   72     28   45   49   49   49   49   49   49   49   49   56   60   65   68   69   71   72   72   72   72 
LCS_GDT     L    77_A     L    77_A     49   49   72     28   45   49   49   49   49   49   49   49   49   49   50   57   68   69   71   72   72   72   72 
LCS_GDT     R    78_A     R    78_A     49   49   72     28   45   49   49   49   49   49   49   49   49   49   53   57   66   69   71   72   72   72   72 
LCS_GDT     D    79_A     D    79_A     49   49   72     28   42   49   49   49   49   49   49   49   49   56   60   65   68   69   71   72   72   72   72 
LCS_GDT     Q    80_A     Q    80_A     49   49   72     14   37   49   49   49   49   49   49   49   49   55   60   65   68   69   71   72   72   72   72 
LCS_GDT     Q    81_A     Q    81_A     49   49   72      3   25   49   49   49   49   49   49   49   49   49   49   50   61   62   71   72   72   72   72 
LCS_AVERAGE  LCS_A:  71.01  (  56.52   56.52  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     28     45     49     49     49     49     49     49     49     49     56     60     65     68     69     71     72     72     72     72 
GDT PERCENT_AT  38.89  62.50  68.06  68.06  68.06  68.06  68.06  68.06  68.06  68.06  77.78  83.33  90.28  94.44  95.83  98.61 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.24   0.55   0.66   0.66   0.66   0.66   0.66   0.66   0.66   0.66   3.86   4.04   4.31   4.48   4.60   4.72   4.80   4.80   4.80   4.80
GDT RMS_ALL_AT  10.98  11.74  11.70  11.70  11.70  11.70  11.70  11.70  11.70  11.70   4.96   4.86   4.88   4.91   4.80   4.81   4.80   4.80   4.80   4.80

# Checking swapping
#   possible swapping detected:  E     7_A      E     7_A
#   possible swapping detected:  E    13_A      E    13_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    20.632     0    0.564   1.293    22.270    0.000    0.000
LGA    S     3_A      S     3_A    26.397     0    0.053   0.682    30.641    0.000    0.000
LGA    L     4_A      L     4_A    23.727     0    0.032   0.090    24.854    0.000    0.000
LGA    I     5_A      I     5_A    17.329     0    0.041   0.085    19.499    0.000    0.000
LGA    E     6_A      E     6_A    21.970     0    0.079   1.046    26.972    0.000    0.000
LGA    E     7_A      E     7_A    24.861     0    0.012   0.238    30.287    0.000    0.000
LGA    L     8_A      L     8_A    18.795     0    0.047   0.091    20.802    0.000    0.000
LGA    I     9_A      I     9_A    17.170     0    0.075   0.120    19.229    0.000    0.000
LGA    R    10_A      R    10_A    23.614     0    0.057   1.503    34.714    0.000    0.000
LGA    R    11_A      R    11_A    22.040     0    0.013   1.419    28.372    0.000    0.000
LGA    S    12_A      S    12_A    15.796     0    0.029   0.687    17.845    0.000    0.000
LGA    E    13_A      E    13_A    20.271     0    0.026   1.209    24.141    0.000    0.000
LGA    E    14_A      E    14_A    23.827     0    0.018   0.500    29.614    0.000    0.000
LGA    Q    15_A      Q    15_A    18.222     0    0.039   0.122    20.012    0.000    0.000
LGA    Q    16_A      Q    16_A    16.414     0    0.047   0.221    18.504    0.000    0.000
LGA    R    17_A      R    17_A    22.919     0    0.027   1.248    31.889    0.000    0.000
LGA    R    18_A      R    18_A    21.425     0    0.016   1.093    27.249    0.000    0.000
LGA    N    19_A      N    19_A    15.001     0    0.014   0.065    17.134    0.000    0.000
LGA    E    20_A      E    20_A    19.362     0    0.000   1.020    22.854    0.000    0.000
LGA    E    21_A      E    21_A    23.508     0    0.021   0.877    30.539    0.000    0.000
LGA    A    22_A      A    22_A    17.949     0    0.062   0.070    19.726    0.000    0.000
LGA    L    23_A      L    23_A    16.158     0    0.054   0.186    18.376    0.000    0.000
LGA    R    24_A      R    24_A    22.684     0    0.306   1.048    29.233    0.000    0.000
LGA    Q    33_A      Q    33_A     0.669     0    0.102   0.617     5.366   92.857   68.942
LGA    L    34_A      L    34_A     0.519     0    0.049   1.433     4.324   97.619   80.952
LGA    L    35_A      L    35_A     0.336     0    0.008   1.364     4.700   95.238   76.250
LGA    S    36_A      S    36_A     1.049     0    0.019   0.658     3.060   83.690   77.698
LGA    G    37_A      G    37_A     0.932     0    0.054   0.054     0.932   90.476   90.476
LGA    I    38_A      I    38_A     0.218     0    0.043   0.070     0.711   97.619   96.429
LGA    V    39_A      V    39_A     0.956     0    0.016   0.041     1.541   88.214   84.082
LGA    Q    40_A      Q    40_A     1.103     0    0.011   0.910     2.435   85.952   78.783
LGA    Q    41_A      Q    41_A     0.574     0    0.031   0.411     1.532   95.238   90.635
LGA    Q    42_A      Q    42_A     0.474     0    0.064   0.359     1.303   92.857   90.529
LGA    N    43_A      N    43_A     0.681     0    0.013   0.130     1.594   90.476   86.012
LGA    N    44_A      N    44_A     0.420     0    0.016   0.031     0.773  100.000   95.238
LGA    L    45_A      L    45_A     0.222     0    0.018   0.181     0.712  100.000   98.810
LGA    L    46_A      L    46_A     0.482     0    0.061   0.093     1.171  100.000   94.107
LGA    R    47_A      R    47_A     0.300     0    0.032   1.174     4.580  100.000   82.641
LGA    A    48_A      A    48_A     0.255     0    0.040   0.043     0.330  100.000  100.000
LGA    I    49_A      I    49_A     0.526     0    0.040   0.091     0.697   95.238   92.857
LGA    E    50_A      E    50_A     0.467     0    0.068   0.106     0.971   97.619   94.709
LGA    A    51_A      A    51_A     0.414     0    0.016   0.022     0.619   95.238   96.190
LGA    Q    52_A      Q    52_A     0.838     0    0.024   0.286     1.335   90.476   89.471
LGA    Q    53_A      Q    53_A     0.876     0    0.029   0.224     1.724   90.476   86.508
LGA    H    54_A      H    54_A     0.694     0    0.011   1.303     5.705   90.476   64.524
LGA    L    55_A      L    55_A     0.969     0    0.032   0.112     1.670   90.476   84.881
LGA    L    56_A      L    56_A     1.153     0    0.016   1.361     3.547   81.429   75.595
LGA    Q    57_A      Q    57_A     0.726     0    0.025   1.193     3.832   92.857   82.381
LGA    L    58_A      L    58_A     0.425     0    0.031   0.167     0.797   97.619   96.429
LGA    T    59_A      T    59_A     0.704     0    0.048   0.076     0.844   90.476   90.476
LGA    V    60_A      V    60_A     0.595     0    0.012   0.039     0.800   95.238   93.197
LGA    W    61_A      W    61_A     0.334     0    0.087   1.299     8.911   97.619   52.109
LGA    G    62_A      G    62_A     0.402     0    0.053   0.053     0.557   97.619   97.619
LGA    I    63_A      I    63_A     0.560     0    0.021   0.070     0.835   92.857   91.667
LGA    K    64_A      K    64_A     0.479     0    0.039   1.142     6.479  100.000   74.497
LGA    Q    65_A      Q    65_A     0.197     0    0.037   1.441     5.760  100.000   77.037
LGA    L    66_A      L    66_A     0.381     0    0.021   0.067     0.741  100.000   96.429
LGA    Q    67_A      Q    67_A     0.382     0    0.013   0.704     3.857  100.000   81.164
LGA    A    68_A      A    68_A     0.312     0    0.010   0.020     0.358  100.000  100.000
LGA    R    69_A      R    69_A     0.245     0    0.014   0.127     1.037  100.000   94.848
LGA    I    70_A      I    70_A     0.491     0    0.066   1.364     4.225  100.000   83.155
LGA    L    71_A      L    71_A     0.373     0    0.019   0.032     0.635  100.000   97.619
LGA    A    72_A      A    72_A     0.132     0    0.018   0.033     0.233  100.000  100.000
LGA    V    73_A      V    73_A     0.217     0    0.018   0.056     0.485  100.000  100.000
LGA    E    74_A      E    74_A     0.168     0    0.017   0.081     0.696  100.000   96.825
LGA    R    75_A      R    75_A     0.537     0    0.083   0.278     1.954   92.857   87.273
LGA    Y    76_A      Y    76_A     0.578     0    0.019   0.072     1.245   92.857   89.008
LGA    L    77_A      L    77_A     0.566     0    0.055   0.092     0.793   90.476   91.667
LGA    R    78_A      R    78_A     0.650     0    0.045   1.195     4.451   88.214   71.126
LGA    D    79_A      D    79_A     1.031     0    0.056   0.133     1.300   83.690   82.560
LGA    Q    80_A      Q    80_A     1.221     0    0.044   0.111     1.836   79.286   78.571
LGA    Q    81_A      Q    81_A     1.612     0    0.439   0.508     2.988   71.071   75.873

# 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):     4.798          4.318                  7.163           63.950   59.137

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   83   72    4.0     49    0.66    74.306    69.015     6.447

LGA_LOCAL      RMSD:   0.660  Number of atoms:   49  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  11.704  Number of assigned atoms:   72 
Std_ASGN_ATOMS RMSD:   4.798  Standard rmsd on all 72 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.748718 * X  +  -0.140049 * Y  +   0.647925 * Z  +  -1.950127
  Y_new =  -0.137598 * X  +  -0.988973 * Y  +  -0.054764 * Z  +   3.998353
  Z_new =   0.648450 * X  +  -0.048150 * Y  +  -0.759733 * Z  +  67.598824 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -0.181750 -0.705547 -3.078299   [DEG:  -10.4135  -40.4249 -176.3736 ]
ZXZ:  1.486475  2.433698  1.644915   [DEG:   85.1687  139.4406   94.2467 ]
 
# END of job
