
#######################################################
#                                                     #
#                        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        4.89     4.89
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    49      33_A - 81_A        0.59    11.99
  LCS_AVERAGE:     56.52

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    49      33_A - 81_A        0.59    11.99
  LCS_AVERAGE:     55.71

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      3   23   72      0    3    3    3    3    4    7   10   16   36   39   47   55   58   64   68   72   72   72   72 
LCS_GDT     S     3_A     S     3_A     22   23   72     12   23   24   26   28   32   35   37   41   48   55   60   65   67   69   71   72   72   72   72 
LCS_GDT     L     4_A     L     4_A     22   23   72     20   23   24   26   28   32   35   37   41   47   55   60   65   67   69   71   72   72   72   72 
LCS_GDT     I     5_A     I     5_A     22   23   72     20   23   24   26   28   32   35   37   41   48   55   60   65   67   69   71   72   72   72   72 
LCS_GDT     E     6_A     E     6_A     22   23   72     20   23   24   26   28   32   35   37   41   48   55   60   65   67   69   71   72   72   72   72 
LCS_GDT     E     7_A     E     7_A     22   23   72     20   23   24   26   28   32   35   37   41   47   55   60   65   67   69   71   72   72   72   72 
LCS_GDT     L     8_A     L     8_A     22   23   72     20   23   24   26   28   32   35   37   41   48   55   60   65   67   69   71   72   72   72   72 
LCS_GDT     I     9_A     I     9_A     22   23   72     20   23   24   26   28   32   35   37   41   48   55   60   65   67   69   71   72   72   72   72 
LCS_GDT     R    10_A     R    10_A     22   23   72     20   23   24   26   28   32   35   37   41   48   55   60   65   67   69   71   72   72   72   72 
LCS_GDT     R    11_A     R    11_A     22   23   72     20   23   24   26   28   32   35   37   41   48   55   60   65   67   69   71   72   72   72   72 
LCS_GDT     S    12_A     S    12_A     22   23   72     20   23   24   26   28   32   35   37   41   48   55   60   65   67   69   71   72   72   72   72 
LCS_GDT     E    13_A     E    13_A     22   23   72     20   23   24   26   28   32   35   37   41   48   55   60   65   67   69   71   72   72   72   72 
LCS_GDT     E    14_A     E    14_A     22   23   72     20   23   24   26   28   32   35   37   41   48   55   60   65   67   69   71   72   72   72   72 
LCS_GDT     Q    15_A     Q    15_A     22   23   72     20   23   24   26   28   32   35   37   41   48   55   60   65   67   69   71   72   72   72   72 
LCS_GDT     Q    16_A     Q    16_A     22   23   72     20   23   24   26   28   32   35   37   41   48   55   60   65   67   69   71   72   72   72   72 
LCS_GDT     R    17_A     R    17_A     22   23   72     20   23   24   26   28   32   35   37   41   48   55   60   65   67   69   71   72   72   72   72 
LCS_GDT     R    18_A     R    18_A     22   23   72     20   23   24   26   28   32   35   37   41   48   55   60   65   67   69   71   72   72   72   72 
LCS_GDT     N    19_A     N    19_A     22   23   72     20   23   24   26   28   32   35   37   41   48   55   60   65   67   69   71   72   72   72   72 
LCS_GDT     E    20_A     E    20_A     22   23   72     20   23   24   26   28   32   35   37   41   48   55   60   65   67   69   71   72   72   72   72 
LCS_GDT     E    21_A     E    21_A     22   23   72     20   23   24   26   28   32   35   37   41   48   55   60   65   67   69   71   72   72   72   72 
LCS_GDT     A    22_A     A    22_A     22   23   72     20   23   24   26   28   32   35   37   41   48   55   60   65   67   69   71   72   72   72   72 
LCS_GDT     L    23_A     L    23_A     22   23   72     20   23   24   26   28   32   35   37   41   48   55   60   65   67   69   71   72   72   72   72 
LCS_GDT     R    24_A     R    24_A     22   23   72     20   23   24   26   28   32   35   37   41   48   55   60   65   67   69   71   72   72   72   72 
LCS_GDT     Q    33_A     Q    33_A     49   49   72     29   47   49   49   49   49   49   49   49   49   55   60   65   67   69   71   72   72   72   72 
LCS_GDT     L    34_A     L    34_A     49   49   72     29   47   49   49   49   49   49   49   49   49   54   59   65   67   69   71   72   72   72   72 
LCS_GDT     L    35_A     L    35_A     49   49   72     29   47   49   49   49   49   49   49   49   49   55   60   65   67   69   71   72   72   72   72 
LCS_GDT     S    36_A     S    36_A     49   49   72     27   47   49   49   49   49   49   49   49   49   55   60   65   67   69   71   72   72   72   72 
LCS_GDT     G    37_A     G    37_A     49   49   72     26   47   49   49   49   49   49   49   49   49   55   60   65   67   69   71   72   72   72   72 
LCS_GDT     I    38_A     I    38_A     49   49   72     29   47   49   49   49   49   49   49   49   49   55   60   65   67   69   71   72   72   72   72 
LCS_GDT     V    39_A     V    39_A     49   49   72     27   47   49   49   49   49   49   49   49   49   55   60   65   67   69   71   72   72   72   72 
LCS_GDT     Q    40_A     Q    40_A     49   49   72     25   47   49   49   49   49   49   49   49   49   55   60   65   67   69   71   72   72   72   72 
LCS_GDT     Q    41_A     Q    41_A     49   49   72     29   47   49   49   49   49   49   49   49   49   55   60   65   67   69   71   72   72   72   72 
LCS_GDT     Q    42_A     Q    42_A     49   49   72     29   47   49   49   49   49   49   49   49   49   55   60   65   67   69   71   72   72   72   72 
LCS_GDT     N    43_A     N    43_A     49   49   72     29   47   49   49   49   49   49   49   49   49   55   60   65   67   69   71   72   72   72   72 
LCS_GDT     N    44_A     N    44_A     49   49   72     29   47   49   49   49   49   49   49   49   49   55   60   65   67   69   71   72   72   72   72 
LCS_GDT     L    45_A     L    45_A     49   49   72     29   47   49   49   49   49   49   49   49   49   55   60   65   67   69   71   72   72   72   72 
LCS_GDT     L    46_A     L    46_A     49   49   72     29   47   49   49   49   49   49   49   49   49   55   60   65   67   69   71   72   72   72   72 
LCS_GDT     R    47_A     R    47_A     49   49   72     29   47   49   49   49   49   49   49   49   49   54   59   65   67   69   71   72   72   72   72 
LCS_GDT     A    48_A     A    48_A     49   49   72     31   47   49   49   49   49   49   49   49   49   55   60   65   67   69   71   72   72   72   72 
LCS_GDT     I    49_A     I    49_A     49   49   72     31   47   49   49   49   49   49   49   49   49   55   60   65   67   69   71   72   72   72   72 
LCS_GDT     E    50_A     E    50_A     49   49   72     31   47   49   49   49   49   49   49   49   49   54   59   65   67   69   71   72   72   72   72 
LCS_GDT     A    51_A     A    51_A     49   49   72     31   47   49   49   49   49   49   49   49   49   54   59   65   67   69   71   72   72   72   72 
LCS_GDT     Q    52_A     Q    52_A     49   49   72     31   47   49   49   49   49   49   49   49   49   55   60   65   67   69   71   72   72   72   72 
LCS_GDT     Q    53_A     Q    53_A     49   49   72     31   47   49   49   49   49   49   49   49   49   55   60   65   67   69   71   72   72   72   72 
LCS_GDT     H    54_A     H    54_A     49   49   72     31   47   49   49   49   49   49   49   49   49   54   59   61   67   69   71   72   72   72   72 
LCS_GDT     L    55_A     L    55_A     49   49   72     26   47   49   49   49   49   49   49   49   49   55   60   65   67   69   71   72   72   72   72 
LCS_GDT     L    56_A     L    56_A     49   49   72     26   47   49   49   49   49   49   49   49   49   55   60   65   67   69   71   72   72   72   72 
LCS_GDT     Q    57_A     Q    57_A     49   49   72     31   47   49   49   49   49   49   49   49   49   54   60   65   67   69   71   72   72   72   72 
LCS_GDT     L    58_A     L    58_A     49   49   72     31   47   49   49   49   49   49   49   49   49   54   60   65   67   69   71   72   72   72   72 
LCS_GDT     T    59_A     T    59_A     49   49   72     31   47   49   49   49   49   49   49   49   49   55   60   65   67   69   71   72   72   72   72 
LCS_GDT     V    60_A     V    60_A     49   49   72     31   47   49   49   49   49   49   49   49   49   55   60   65   67   69   71   72   72   72   72 
LCS_GDT     W    61_A     W    61_A     49   49   72     31   47   49   49   49   49   49   49   49   49   54   60   65   67   69   71   72   72   72   72 
LCS_GDT     G    62_A     G    62_A     49   49   72     31   47   49   49   49   49   49   49   49   49   55   60   65   67   69   71   72   72   72   72 
LCS_GDT     I    63_A     I    63_A     49   49   72     31   47   49   49   49   49   49   49   49   49   55   60   65   67   69   71   72   72   72   72 
LCS_GDT     K    64_A     K    64_A     49   49   72     31   47   49   49   49   49   49   49   49   49   55   60   65   67   69   71   72   72   72   72 
LCS_GDT     Q    65_A     Q    65_A     49   49   72     31   47   49   49   49   49   49   49   49   49   55   60   65   67   69   71   72   72   72   72 
LCS_GDT     L    66_A     L    66_A     49   49   72     31   47   49   49   49   49   49   49   49   49   55   60   65   67   69   71   72   72   72   72 
LCS_GDT     Q    67_A     Q    67_A     49   49   72     31   47   49   49   49   49   49   49   49   49   55   60   65   67   69   71   72   72   72   72 
LCS_GDT     A    68_A     A    68_A     49   49   72     31   47   49   49   49   49   49   49   49   49   55   60   65   67   69   71   72   72   72   72 
LCS_GDT     R    69_A     R    69_A     49   49   72     31   47   49   49   49   49   49   49   49   49   55   60   65   67   69   71   72   72   72   72 
LCS_GDT     I    70_A     I    70_A     49   49   72     31   47   49   49   49   49   49   49   49   49   55   59   64   67   69   71   72   72   72   72 
LCS_GDT     L    71_A     L    71_A     49   49   72     31   47   49   49   49   49   49   49   49   49   55   60   65   67   69   71   72   72   72   72 
LCS_GDT     A    72_A     A    72_A     49   49   72     31   47   49   49   49   49   49   49   49   49   55   60   65   67   69   71   72   72   72   72 
LCS_GDT     V    73_A     V    73_A     49   49   72     31   47   49   49   49   49   49   49   49   49   55   60   65   67   69   71   72   72   72   72 
LCS_GDT     E    74_A     E    74_A     49   49   72     31   47   49   49   49   49   49   49   49   49   49   54   63   67   69   71   72   72   72   72 
LCS_GDT     R    75_A     R    75_A     49   49   72     31   47   49   49   49   49   49   49   49   49   55   60   65   67   69   71   72   72   72   72 
LCS_GDT     Y    76_A     Y    76_A     49   49   72     31   47   49   49   49   49   49   49   49   49   55   60   65   67   69   71   72   72   72   72 
LCS_GDT     L    77_A     L    77_A     49   49   72     31   47   49   49   49   49   49   49   49   49   49   51   62   67   69   71   72   72   72   72 
LCS_GDT     R    78_A     R    78_A     49   49   72     31   47   49   49   49   49   49   49   49   49   49   52   58   65   69   71   72   72   72   72 
LCS_GDT     D    79_A     D    79_A     49   49   72     31   47   49   49   49   49   49   49   49   49   55   60   65   67   69   71   72   72   72   72 
LCS_GDT     Q    80_A     Q    80_A     49   49   72     31   46   49   49   49   49   49   49   49   49   55   60   65   67   69   71   72   72   72   72 
LCS_GDT     Q    81_A     Q    81_A     49   49   72      3   17   49   49   49   49   49   49   49   49   49   50   53   61   67   71   72   72   72   72 
LCS_AVERAGE  LCS_A:  70.74  (  55.71   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     31     47     49     49     49     49     49     49     49     49     55     60     65     67     69     71     72     72     72     72 
GDT PERCENT_AT  43.06  65.28  68.06  68.06  68.06  68.06  68.06  68.06  68.06  68.06  76.39  83.33  90.28  93.06  95.83  98.61 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.32   0.54   0.59   0.59   0.59   0.59   0.59   0.59   0.59   0.59   3.92   4.17   4.42   4.52   4.68   4.81   4.89   4.89   4.89   4.89
GDT RMS_ALL_AT  11.60  11.99  11.99  11.99  11.99  11.99  11.99  11.99  11.99  11.99   4.95   4.97   5.01   4.99   4.90   4.89   4.89   4.89   4.89   4.89

# 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    26.418     0    0.095   1.036    27.121    0.000    0.000
LGA    S     3_A      S     3_A    26.791     0    0.656   0.768    26.883    0.000    0.000
LGA    L     4_A      L     4_A    24.572     0    0.053   0.082    25.586    0.000    0.000
LGA    I     5_A      I     5_A    18.086     0    0.041   0.115    20.301    0.000    0.000
LGA    E     6_A      E     6_A    22.558     0    0.048   1.047    27.488    0.000    0.000
LGA    E     7_A      E     7_A    25.490     0    0.015   0.114    31.342    0.000    0.000
LGA    L     8_A      L     8_A    19.395     0    0.049   0.084    21.419    0.000    0.000
LGA    I     9_A      I     9_A    17.564     0    0.063   0.118    19.564    0.000    0.000
LGA    R    10_A      R    10_A    23.906     0    0.050   1.379    35.534    0.000    0.000
LGA    R    11_A      R    11_A    22.388     0    0.010   1.482    28.829    0.000    0.000
LGA    S    12_A      S    12_A    16.018     0    0.044   0.654    18.140    0.000    0.000
LGA    E    13_A      E    13_A    20.270     0    0.022   1.281    23.974    0.000    0.000
LGA    E    14_A      E    14_A    23.966     0    0.016   0.379    29.700    0.000    0.000
LGA    Q    15_A      Q    15_A    18.447     0    0.041   0.132    20.204    0.000    0.000
LGA    Q    16_A      Q    16_A    16.344     0    0.037   0.154    18.408    0.000    0.000
LGA    R    17_A      R    17_A    22.819     0    0.024   1.128    30.978    0.000    0.000
LGA    R    18_A      R    18_A    21.459     0    0.017   1.065    27.467    0.000    0.000
LGA    N    19_A      N    19_A    14.955     0    0.015   0.069    17.125    0.000    0.000
LGA    E    20_A      E    20_A    19.188     0    0.006   1.031    22.393    0.000    0.000
LGA    E    21_A      E    21_A    23.444     0    0.019   0.928    30.430    0.000    0.000
LGA    A    22_A      A    22_A    17.953     0    0.068   0.077    19.692    0.000    0.000
LGA    L    23_A      L    23_A    16.056     0    0.051   0.251    18.323    0.000    0.000
LGA    R    24_A      R    24_A    22.669     0    0.315   1.081    28.961    0.000    0.000
LGA    Q    33_A      Q    33_A     0.403     0    0.104   1.143     4.689   97.619   74.709
LGA    L    34_A      L    34_A     0.503     0    0.053   0.104     1.676   97.619   89.583
LGA    L    35_A      L    35_A     0.616     0    0.020   0.523     2.582   92.857   85.238
LGA    S    36_A      S    36_A     0.984     0    0.015   0.666     3.047   88.214   80.714
LGA    G    37_A      G    37_A     0.759     0    0.059   0.059     0.759   92.857   92.857
LGA    I    38_A      I    38_A     0.224     0    0.042   0.065     0.653   97.619   96.429
LGA    V    39_A      V    39_A     0.907     0    0.017   0.070     1.600   90.476   85.374
LGA    Q    40_A      Q    40_A     1.053     0    0.015   0.931     2.538   85.952   77.937
LGA    Q    41_A      Q    41_A     0.498     0    0.031   0.399     1.260   97.619   95.820
LGA    Q    42_A      Q    42_A     0.394     0    0.074   0.540     1.833   97.619   91.693
LGA    N    43_A      N    43_A     0.683     0    0.045   1.251     3.633   90.476   77.321
LGA    N    44_A      N    44_A     0.334     0    0.021   0.033     0.710  100.000   96.429
LGA    L    45_A      L    45_A     0.193     0    0.023   0.204     0.889  100.000   98.810
LGA    L    46_A      L    46_A     0.486     0    0.063   1.376     3.959  100.000   84.940
LGA    R    47_A      R    47_A     0.236     0    0.039   1.140     4.466  100.000   83.810
LGA    A    48_A      A    48_A     0.261     0    0.045   0.047     0.440  100.000  100.000
LGA    I    49_A      I    49_A     0.495     0    0.052   0.093     0.799  100.000   95.238
LGA    E    50_A      E    50_A     0.357     0    0.053   0.103     0.901  100.000   95.767
LGA    A    51_A      A    51_A     0.402     0    0.016   0.021     0.595   95.238   96.190
LGA    Q    52_A      Q    52_A     0.818     0    0.019   0.250     1.156   90.476   88.466
LGA    Q    53_A      Q    53_A     0.746     0    0.035   1.094     4.518   90.476   74.974
LGA    H    54_A      H    54_A     0.596     0    0.011   1.117     5.426   90.476   66.810
LGA    L    55_A      L    55_A     0.948     0    0.020   1.389     3.948   90.476   78.036
LGA    L    56_A      L    56_A     1.048     0    0.021   1.364     3.329   85.952   78.690
LGA    Q    57_A      Q    57_A     0.637     0    0.048   1.460     5.210   92.857   73.069
LGA    L    58_A      L    58_A     0.425     0    0.025   0.165     0.762   97.619   96.429
LGA    T    59_A      T    59_A     0.773     0    0.066   1.084     2.946   90.476   83.129
LGA    V    60_A      V    60_A     0.581     0    0.012   0.037     0.832   95.238   93.197
LGA    W    61_A      W    61_A     0.221     0    0.072   1.289     8.848  100.000   52.789
LGA    G    62_A      G    62_A     0.368     0    0.053   0.053     0.422  100.000  100.000
LGA    I    63_A      I    63_A     0.440     0    0.025   0.063     0.638  100.000   96.429
LGA    K    64_A      K    64_A     0.289     0    0.045   1.139     6.617  100.000   73.492
LGA    Q    65_A      Q    65_A     0.181     0    0.034   1.368     5.348  100.000   78.360
LGA    L    66_A      L    66_A     0.319     0    0.028   0.055     0.574  100.000   97.619
LGA    Q    67_A      Q    67_A     0.284     0    0.010   0.052     0.647  100.000   96.825
LGA    A    68_A      A    68_A     0.304     0    0.015   0.024     0.370  100.000  100.000
LGA    R    69_A      R    69_A     0.244     0    0.014   0.111     0.742  100.000   95.671
LGA    I    70_A      I    70_A     0.349     0    0.067   1.364     3.995  100.000   83.929
LGA    L    71_A      L    71_A     0.280     0    0.029   0.050     0.387  100.000  100.000
LGA    A    72_A      A    72_A     0.122     0    0.024   0.038     0.248  100.000  100.000
LGA    V    73_A      V    73_A     0.168     0    0.020   0.052     0.331  100.000  100.000
LGA    E    74_A      E    74_A     0.258     0    0.020   0.094     0.602  100.000   98.942
LGA    R    75_A      R    75_A     0.445     0    0.078   0.245     1.431  100.000   93.117
LGA    Y    76_A      Y    76_A     0.435     0    0.015   0.146     0.904   95.238   94.444
LGA    L    77_A      L    77_A     0.545     0    0.042   0.093     0.693   90.476   94.048
LGA    R    78_A      R    78_A     0.697     0    0.046   1.162     4.211   90.476   72.641
LGA    D    79_A      D    79_A     0.799     0    0.034   0.103     0.957   90.476   90.476
LGA    Q    80_A      Q    80_A     0.880     0    0.036   0.096     1.378   85.952   86.455
LGA    Q    81_A      Q    81_A     1.495     0    0.443   0.501     2.912   73.214   76.825

# 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):     4.887          4.405                  7.232           64.917   59.913

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   83   72    4.0     49    0.59    75.000    69.143     7.061

LGA_LOCAL      RMSD:   0.594  Number of atoms:   49  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  11.987  Number of assigned atoms:   72 
Std_ASGN_ATOMS RMSD:   4.887  Standard rmsd on all 72 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.295371 * X  +  -0.891915 * Y  +  -0.342409 * Z  +  -1.653867
  Y_new =   0.656138 * X  +  -0.449887 * Y  +   0.605875 * Z  +   5.008883
  Z_new =  -0.694434 * X  +  -0.045710 * Y  +   0.718103 * Z  +  65.970268 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  1.993788  0.767633 -0.063568   [DEG:  114.2356   43.9821   -3.6422 ]
ZXZ: -2.627194  0.769724 -1.636525   [DEG: -150.5271   44.1019  -93.7660 ]
 
# END of job
