
#######################################################
#                                                     #
#                        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        1.61     1.61
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    72       2_A - 81_A        1.61     1.61
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    46       2_A - 55_A        1.00     3.64
  LCS_AVERAGE:     58.89

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     46   72   72     25   38   48   59   66   71   72   72   72   72   72   72   72   72   72   72   72   72   72   72 
LCS_GDT     S     3_A     S     3_A     46   72   72     16   38   48   59   66   71   72   72   72   72   72   72   72   72   72   72   72   72   72   72 
LCS_GDT     L     4_A     L     4_A     46   72   72     20   38   48   59   66   71   72   72   72   72   72   72   72   72   72   72   72   72   72   72 
LCS_GDT     I     5_A     I     5_A     46   72   72     25   38   48   59   66   71   72   72   72   72   72   72   72   72   72   72   72   72   72   72 
LCS_GDT     E     6_A     E     6_A     46   72   72     25   38   48   59   66   71   72   72   72   72   72   72   72   72   72   72   72   72   72   72 
LCS_GDT     E     7_A     E     7_A     46   72   72     25   38   48   59   66   71   72   72   72   72   72   72   72   72   72   72   72   72   72   72 
LCS_GDT     L     8_A     L     8_A     46   72   72     25   38   48   59   66   71   72   72   72   72   72   72   72   72   72   72   72   72   72   72 
LCS_GDT     I     9_A     I     9_A     46   72   72     25   38   48   59   66   71   72   72   72   72   72   72   72   72   72   72   72   72   72   72 
LCS_GDT     R    10_A     R    10_A     46   72   72     25   38   48   59   66   71   72   72   72   72   72   72   72   72   72   72   72   72   72   72 
LCS_GDT     R    11_A     R    11_A     46   72   72     25   38   48   59   66   71   72   72   72   72   72   72   72   72   72   72   72   72   72   72 
LCS_GDT     S    12_A     S    12_A     46   72   72     25   38   48   59   66   71   72   72   72   72   72   72   72   72   72   72   72   72   72   72 
LCS_GDT     E    13_A     E    13_A     46   72   72     25   38   48   59   66   71   72   72   72   72   72   72   72   72   72   72   72   72   72   72 
LCS_GDT     E    14_A     E    14_A     46   72   72     25   38   48   59   66   71   72   72   72   72   72   72   72   72   72   72   72   72   72   72 
LCS_GDT     Q    15_A     Q    15_A     46   72   72     25   38   48   59   66   71   72   72   72   72   72   72   72   72   72   72   72   72   72   72 
LCS_GDT     Q    16_A     Q    16_A     46   72   72     20   34   48   59   66   71   72   72   72   72   72   72   72   72   72   72   72   72   72   72 
LCS_GDT     R    17_A     R    17_A     46   72   72     20   33   48   59   66   71   72   72   72   72   72   72   72   72   72   72   72   72   72   72 
LCS_GDT     R    18_A     R    18_A     46   72   72     16   33   48   59   66   71   72   72   72   72   72   72   72   72   72   72   72   72   72   72 
LCS_GDT     N    19_A     N    19_A     46   72   72     16   33   45   59   66   71   72   72   72   72   72   72   72   72   72   72   72   72   72   72 
LCS_GDT     E    20_A     E    20_A     46   72   72     16   33   43   58   66   71   72   72   72   72   72   72   72   72   72   72   72   72   72   72 
LCS_GDT     E    21_A     E    21_A     46   72   72     16   33   43   58   66   71   72   72   72   72   72   72   72   72   72   72   72   72   72   72 
LCS_GDT     A    22_A     A    22_A     46   72   72     16   33   43   58   66   71   72   72   72   72   72   72   72   72   72   72   72   72   72   72 
LCS_GDT     L    23_A     L    23_A     46   72   72      7   28   39   47   56   71   72   72   72   72   72   72   72   72   72   72   72   72   72   72 
LCS_GDT     R    24_A     R    24_A     46   72   72      6   22   43   53   65   71   72   72   72   72   72   72   72   72   72   72   72   72   72   72 
LCS_GDT     Q    33_A     Q    33_A     46   72   72      4   15   28   36   50   71   72   72   72   72   72   72   72   72   72   72   72   72   72   72 
LCS_GDT     L    34_A     L    34_A     46   72   72     16   32   43   58   66   71   72   72   72   72   72   72   72   72   72   72   72   72   72   72 
LCS_GDT     L    35_A     L    35_A     46   72   72     16   32   43   58   66   71   72   72   72   72   72   72   72   72   72   72   72   72   72   72 
LCS_GDT     S    36_A     S    36_A     46   72   72     16   32   45   59   66   71   72   72   72   72   72   72   72   72   72   72   72   72   72   72 
LCS_GDT     G    37_A     G    37_A     46   72   72     16   33   48   59   66   71   72   72   72   72   72   72   72   72   72   72   72   72   72   72 
LCS_GDT     I    38_A     I    38_A     46   72   72     16   33   48   59   66   71   72   72   72   72   72   72   72   72   72   72   72   72   72   72 
LCS_GDT     V    39_A     V    39_A     46   72   72     14   36   48   59   66   71   72   72   72   72   72   72   72   72   72   72   72   72   72   72 
LCS_GDT     Q    40_A     Q    40_A     46   72   72     20   38   48   59   66   71   72   72   72   72   72   72   72   72   72   72   72   72   72   72 
LCS_GDT     Q    41_A     Q    41_A     46   72   72     25   38   48   59   66   71   72   72   72   72   72   72   72   72   72   72   72   72   72   72 
LCS_GDT     Q    42_A     Q    42_A     46   72   72     20   38   48   59   66   71   72   72   72   72   72   72   72   72   72   72   72   72   72   72 
LCS_GDT     N    43_A     N    43_A     46   72   72     25   38   48   59   66   71   72   72   72   72   72   72   72   72   72   72   72   72   72   72 
LCS_GDT     N    44_A     N    44_A     46   72   72     25   38   48   59   66   71   72   72   72   72   72   72   72   72   72   72   72   72   72   72 
LCS_GDT     L    45_A     L    45_A     46   72   72     25   38   48   59   66   71   72   72   72   72   72   72   72   72   72   72   72   72   72   72 
LCS_GDT     L    46_A     L    46_A     46   72   72     25   38   48   59   66   71   72   72   72   72   72   72   72   72   72   72   72   72   72   72 
LCS_GDT     R    47_A     R    47_A     46   72   72     25   38   48   59   66   71   72   72   72   72   72   72   72   72   72   72   72   72   72   72 
LCS_GDT     A    48_A     A    48_A     46   72   72     25   38   48   59   66   71   72   72   72   72   72   72   72   72   72   72   72   72   72   72 
LCS_GDT     I    49_A     I    49_A     46   72   72     25   38   48   59   66   71   72   72   72   72   72   72   72   72   72   72   72   72   72   72 
LCS_GDT     E    50_A     E    50_A     46   72   72     25   38   48   59   66   71   72   72   72   72   72   72   72   72   72   72   72   72   72   72 
LCS_GDT     A    51_A     A    51_A     46   72   72     25   38   48   59   66   71   72   72   72   72   72   72   72   72   72   72   72   72   72   72 
LCS_GDT     Q    52_A     Q    52_A     46   72   72     25   38   48   59   66   71   72   72   72   72   72   72   72   72   72   72   72   72   72   72 
LCS_GDT     Q    53_A     Q    53_A     46   72   72     23   38   48   59   66   71   72   72   72   72   72   72   72   72   72   72   72   72   72   72 
LCS_GDT     H    54_A     H    54_A     46   72   72     25   38   48   59   66   71   72   72   72   72   72   72   72   72   72   72   72   72   72   72 
LCS_GDT     L    55_A     L    55_A     46   72   72     25   38   48   59   66   71   72   72   72   72   72   72   72   72   72   72   72   72   72   72 
LCS_GDT     L    56_A     L    56_A     44   72   72     14   38   48   59   66   71   72   72   72   72   72   72   72   72   72   72   72   72   72   72 
LCS_GDT     Q    57_A     Q    57_A     37   72   72     14   38   48   59   66   71   72   72   72   72   72   72   72   72   72   72   72   72   72   72 
LCS_GDT     L    58_A     L    58_A     37   72   72     14   38   48   59   66   71   72   72   72   72   72   72   72   72   72   72   72   72   72   72 
LCS_GDT     T    59_A     T    59_A     37   72   72     14   38   48   59   66   71   72   72   72   72   72   72   72   72   72   72   72   72   72   72 
LCS_GDT     V    60_A     V    60_A     37   72   72     14   34   48   59   66   71   72   72   72   72   72   72   72   72   72   72   72   72   72   72 
LCS_GDT     W    61_A     W    61_A     37   72   72     14   32   48   59   66   71   72   72   72   72   72   72   72   72   72   72   72   72   72   72 
LCS_GDT     G    62_A     G    62_A     37   72   72     10   38   48   59   66   71   72   72   72   72   72   72   72   72   72   72   72   72   72   72 
LCS_GDT     I    63_A     I    63_A     37   72   72      7   29   48   59   66   71   72   72   72   72   72   72   72   72   72   72   72   72   72   72 
LCS_GDT     K    64_A     K    64_A     37   72   72      8   28   47   59   66   71   72   72   72   72   72   72   72   72   72   72   72   72   72   72 
LCS_GDT     Q    65_A     Q    65_A     37   72   72     10   38   48   59   66   71   72   72   72   72   72   72   72   72   72   72   72   72   72   72 
LCS_GDT     L    66_A     L    66_A     37   72   72      8   28   48   59   66   71   72   72   72   72   72   72   72   72   72   72   72   72   72   72 
LCS_GDT     Q    67_A     Q    67_A     37   72   72      8   28   41   59   66   71   72   72   72   72   72   72   72   72   72   72   72   72   72   72 
LCS_GDT     A    68_A     A    68_A     37   72   72      9   33   48   59   66   71   72   72   72   72   72   72   72   72   72   72   72   72   72   72 
LCS_GDT     R    69_A     R    69_A     37   72   72      8   32   48   59   66   71   72   72   72   72   72   72   72   72   72   72   72   72   72   72 
LCS_GDT     I    70_A     I    70_A     37   72   72      8   28   44   59   66   71   72   72   72   72   72   72   72   72   72   72   72   72   72   72 
LCS_GDT     L    71_A     L    71_A     37   72   72      9   28   47   59   66   71   72   72   72   72   72   72   72   72   72   72   72   72   72   72 
LCS_GDT     A    72_A     A    72_A     37   72   72     12   38   48   59   66   71   72   72   72   72   72   72   72   72   72   72   72   72   72   72 
LCS_GDT     V    73_A     V    73_A     37   72   72      8   24   48   59   66   71   72   72   72   72   72   72   72   72   72   72   72   72   72   72 
LCS_GDT     E    74_A     E    74_A     37   72   72      8   28   41   56   66   71   72   72   72   72   72   72   72   72   72   72   72   72   72   72 
LCS_GDT     R    75_A     R    75_A     37   72   72      8   18   43   56   65   71   72   72   72   72   72   72   72   72   72   72   72   72   72   72 
LCS_GDT     Y    76_A     Y    76_A     37   72   72     13   38   48   59   66   71   72   72   72   72   72   72   72   72   72   72   72   72   72   72 
LCS_GDT     L    77_A     L    77_A     37   72   72      8   28   47   59   66   71   72   72   72   72   72   72   72   72   72   72   72   72   72   72 
LCS_GDT     R    78_A     R    78_A     37   72   72      8   24   41   56   65   71   72   72   72   72   72   72   72   72   72   72   72   72   72   72 
LCS_GDT     D    79_A     D    79_A     27   72   72      8   13   43   52   65   71   72   72   72   72   72   72   72   72   72   72   72   72   72   72 
LCS_GDT     Q    80_A     Q    80_A     27   72   72      8   36   48   59   66   71   72   72   72   72   72   72   72   72   72   72   72   72   72   72 
LCS_GDT     Q    81_A     Q    81_A     25   72   72      3   24   47   59   66   71   72   72   72   72   72   72   72   72   72   72   72   72   72   72 
LCS_AVERAGE  LCS_A:  86.30  (  58.89  100.00  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     25     38     48     59     66     71     72     72     72     72     72     72     72     72     72     72     72     72     72     72 
GDT PERCENT_AT  34.72  52.78  66.67  81.94  91.67  98.61 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.32   0.63   0.89   1.20   1.40   1.57   1.61   1.61   1.61   1.61   1.61   1.61   1.61   1.61   1.61   1.61   1.61   1.61   1.61   1.61
GDT RMS_ALL_AT   2.81   2.18   1.92   1.69   1.63   1.61   1.61   1.61   1.61   1.61   1.61   1.61   1.61   1.61   1.61   1.61   1.61   1.61   1.61   1.61

# Checking swapping
#   possible swapping detected:  E     7_A      E     7_A
#   possible swapping detected:  E    13_A      E    13_A
#   possible swapping detected:  E    14_A      E    14_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     0.583     0    0.560   1.347     4.841   86.429   67.347
LGA    S     3_A      S     3_A     1.031     0    0.055   0.125     2.446   88.214   81.746
LGA    L     4_A      L     4_A     1.024     0    0.026   1.132     3.424   88.214   76.964
LGA    I     5_A      I     5_A     0.796     0    0.034   1.261     3.971   90.476   77.262
LGA    E     6_A      E     6_A     0.528     0    0.048   0.950     3.894   95.238   80.635
LGA    E     7_A      E     7_A     0.624     0    0.024   1.221     4.740   90.476   72.963
LGA    L     8_A      L     8_A     1.036     0    0.034   0.197     1.802   85.952   82.619
LGA    I     9_A      I     9_A     1.017     0    0.030   0.203     1.938   88.214   82.679
LGA    R    10_A      R    10_A     0.618     0    0.051   1.342     8.827   90.476   56.364
LGA    R    11_A      R    11_A     0.479     0    0.033   0.797     3.575   95.238   84.675
LGA    S    12_A      S    12_A     0.835     0    0.038   0.724     3.473   90.476   82.222
LGA    E    13_A      E    13_A     0.936     0    0.042   0.927     4.318   90.476   72.116
LGA    E    14_A      E    14_A     0.624     0    0.037   0.475     1.635   90.476   88.571
LGA    Q    15_A      Q    15_A     0.360     0    0.042   0.214     1.079   95.238   92.646
LGA    Q    16_A      Q    16_A     0.968     0    0.026   0.130     1.735   85.952   80.582
LGA    R    17_A      R    17_A     1.307     0    0.023   1.003     5.948   81.429   64.675
LGA    R    18_A      R    18_A     1.081     0    0.063   1.186     5.999   81.429   64.502
LGA    N    19_A      N    19_A     1.449     0    0.036   0.108     2.074   75.119   78.274
LGA    E    20_A      E    20_A     2.071     0    0.035   0.580     3.299   66.786   62.328
LGA    E    21_A      E    21_A     2.287     0    0.026   0.269     2.565   62.857   67.566
LGA    A    22_A      A    22_A     2.470     0    0.054   0.054     3.072   59.167   60.286
LGA    L    23_A      L    23_A     3.362     0    0.123   0.986     5.658   48.571   47.738
LGA    R    24_A      R    24_A     2.848     0    0.219   1.666    10.659   55.357   34.502
LGA    Q    33_A      Q    33_A     3.101     0    0.111   1.262     3.999   57.738   59.947
LGA    L    34_A      L    34_A     2.008     0    0.040   0.998     3.648   70.952   62.500
LGA    L    35_A      L    35_A     1.871     0    0.030   0.634     3.222   77.381   68.274
LGA    S    36_A      S    36_A     1.517     0    0.043   0.653     3.270   77.143   70.556
LGA    G    37_A      G    37_A     0.651     0    0.020   0.020     1.048   92.976   92.976
LGA    I    38_A      I    38_A     0.394     0    0.026   0.117     1.430   97.619   91.786
LGA    V    39_A      V    39_A     0.797     0    0.045   0.168     1.673   88.333   88.095
LGA    Q    40_A      Q    40_A     1.268     0    0.029   1.172     4.860   81.429   67.460
LGA    Q    41_A      Q    41_A     1.227     0    0.040   0.155     1.502   79.286   80.476
LGA    Q    42_A      Q    42_A     1.655     0    0.065   1.004     4.280   72.976   65.820
LGA    N    43_A      N    43_A     1.982     0    0.028   0.390     3.122   68.810   66.964
LGA    N    44_A      N    44_A     1.822     0    0.053   0.082     1.931   72.857   72.857
LGA    L    45_A      L    45_A     1.981     0    0.028   0.964     3.002   68.810   64.940
LGA    L    46_A      L    46_A     2.444     0    0.025   0.205     3.465   64.762   58.274
LGA    R    47_A      R    47_A     2.147     0    0.043   1.247     6.459   66.786   56.104
LGA    A    48_A      A    48_A     1.769     0    0.035   0.055     1.971   72.857   72.857
LGA    I    49_A      I    49_A     2.269     0    0.032   0.960     4.191   64.762   59.524
LGA    E    50_A      E    50_A     2.292     0    0.028   0.076     2.722   64.762   61.376
LGA    A    51_A      A    51_A     1.523     0    0.035   0.048     1.841   77.143   76.286
LGA    Q    52_A      Q    52_A     1.529     0    0.033   0.259     1.716   72.857   76.667
LGA    Q    53_A      Q    53_A     1.805     0    0.033   0.253     2.635   72.857   69.312
LGA    H    54_A      H    54_A     1.431     0    0.038   1.282     6.059   79.286   56.905
LGA    L    55_A      L    55_A     1.298     0    0.052   1.409     4.233   81.429   72.679
LGA    L    56_A      L    56_A     1.166     0    0.041   1.358     3.426   81.429   74.345
LGA    Q    57_A      Q    57_A     1.080     0    0.023   1.015     2.506   81.429   75.926
LGA    L    58_A      L    58_A     0.896     0    0.044   1.047     3.441   90.476   80.952
LGA    T    59_A      T    59_A     0.957     0    0.032   1.048     2.991   88.214   79.660
LGA    V    60_A      V    60_A     0.942     0    0.049   0.152     1.065   90.476   89.184
LGA    W    61_A      W    61_A     1.085     0    0.065   1.286    10.182   85.952   39.558
LGA    G    62_A      G    62_A     0.788     0    0.047   0.047     0.812   90.476   90.476
LGA    I    63_A      I    63_A     0.969     0    0.033   0.185     1.902   85.952   81.548
LGA    K    64_A      K    64_A     1.525     0    0.075   1.126     4.149   79.286   70.899
LGA    Q    65_A      Q    65_A     0.694     0    0.060   1.326     2.939   95.238   83.968
LGA    L    66_A      L    66_A     1.291     0    0.032   0.147     2.659   81.548   73.214
LGA    Q    67_A      Q    67_A     1.931     0    0.061   0.427     5.576   75.000   55.873
LGA    A    68_A      A    68_A     1.108     0    0.055   0.054     1.274   85.952   85.048
LGA    R    69_A      R    69_A     0.835     0    0.040   0.817     3.124   85.952   69.351
LGA    I    70_A      I    70_A     1.850     0    0.042   1.279     6.636   72.857   61.667
LGA    L    71_A      L    71_A     1.681     0    0.054   0.996     2.879   77.143   73.095
LGA    A    72_A      A    72_A     0.577     0    0.038   0.043     1.311   97.619   94.381
LGA    V    73_A      V    73_A     1.390     0    0.059   1.328     5.381   83.690   70.068
LGA    E    74_A      E    74_A     2.563     0    0.040   0.129     5.792   62.976   45.132
LGA    R    75_A      R    75_A     2.588     0    0.059   1.586    13.721   64.881   30.649
LGA    Y    76_A      Y    76_A     1.409     0    0.043   0.153     7.444   85.952   50.675
LGA    L    77_A      L    77_A     1.586     0    0.047   0.133     4.917   77.262   60.536
LGA    R    78_A      R    78_A     2.935     0    0.038   1.032     9.067   57.262   32.597
LGA    D    79_A      D    79_A     2.760     0    0.071   0.936     6.846   64.881   46.310
LGA    Q    80_A      Q    80_A     0.698     0    0.154   1.363     5.853   90.595   68.519
LGA    Q    81_A      Q    81_A     1.455     0    0.311   1.183     8.040   85.952   50.582

# 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):     1.608          1.558                  2.928           79.507   69.529

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   83   72    4.0     72    1.61    83.681    91.886     4.216

LGA_LOCAL      RMSD:   1.608  Number of atoms:   72  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   1.608  Number of assigned atoms:   72 
Std_ASGN_ATOMS RMSD:   1.608  Standard rmsd on all 72 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.861511 * X  +   0.228637 * Y  +  -0.453348 * Z  +  19.563154
  Y_new =   0.507488 * X  +   0.415862 * Y  +  -0.754662 * Z  +  25.233587
  Z_new =   0.015986 * X  +  -0.880218 * Y  +  -0.474300 * Z  +  81.262581 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  2.609251 -0.015987 -2.065033   [DEG:  149.4991   -0.9160 -118.3177 ]
ZXZ: -0.540956  2.064965  3.123433   [DEG:  -30.9945  118.3138  178.9595 ]
 
# END of job
