
#######################################################
#                                                     #
#                        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   68 (  529),  selected   67 , name one
# Molecule2: number of CA atoms   67 (  519),  selected   67 , 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:    67       2_A - 68_A        1.00     1.00
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    67       2_A - 68_A        1.00     1.00
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    66       2_A - 67_A        0.98     1.00
  LONGEST_CONTINUOUS_SEGMENT:    66       3_A - 68_A        0.89     1.01
  LCS_AVERAGE:     98.51

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   67
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     S     2_A     S     2_A     66   67   67      9   17   31   54   64   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     P     3_A     P     3_A     66   67   67     12   36   54   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E     4_A     E     4_A     66   67   67      9   22   44   59   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E     5_A     E     5_A     66   67   67      9   28   48   63   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     Q     6_A     Q     6_A     66   67   67     13   50   62   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     K     7_A     K     7_A     66   67   67     15   58   62   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     Q     8_A     Q     8_A     66   67   67     12   50   62   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     M     9_A     M     9_A     66   67   67     15   56   62   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    10_A     L    10_A     66   67   67     31   58   62   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     G    11_A     G    11_A     66   67   67     41   58   62   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    12_A     E    12_A     66   67   67     41   58   62   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     A    13_A     A    13_A     66   67   67     41   58   62   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     I    14_A     I    14_A     66   67   67     42   58   62   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     Y    15_A     Y    15_A     66   67   67     42   58   62   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     P    16_A     P    16_A     66   67   67     42   58   62   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     K    17_A     K    17_A     66   67   67     42   58   62   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     V    18_A     V    18_A     66   67   67     42   58   62   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     A    19_A     A    19_A     66   67   67     42   58   62   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     A    20_A     A    20_A     66   67   67     31   58   62   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     S    21_A     S    21_A     66   67   67     13   53   62   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     Q    22_A     Q    22_A     66   67   67     31   58   62   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     P    23_A     P    23_A     66   67   67     17   58   62   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    24_A     E    24_A     66   67   67     40   58   62   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    25_A     L    25_A     66   67   67     42   58   62   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     A    26_A     A    26_A     66   67   67     42   58   62   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     G    27_A     G    27_A     66   67   67     42   58   62   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     K    28_A     K    28_A     66   67   67     42   58   62   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    29_A     L    29_A     66   67   67     41   58   62   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     T    30_A     T    30_A     66   67   67     42   58   62   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     G    31_A     G    31_A     66   67   67     42   58   62   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     M    32_A     M    32_A     66   67   67     41   58   62   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     I    33_A     I    33_A     66   67   67     31   58   62   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    34_A     L    34_A     66   67   67     31   58   62   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    35_A     E    35_A     66   67   67     21   58   62   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    36_A     L    36_A     66   67   67     41   58   62   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     P    37_A     P    37_A     66   67   67     42   58   62   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     V    38_A     V    38_A     66   67   67     42   58   62   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     T    39_A     T    39_A     66   67   67     42   58   62   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    40_A     E    40_A     66   67   67     42   58   62   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    41_A     L    41_A     66   67   67     42   58   62   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    42_A     L    42_A     66   67   67     42   58   62   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     H    43_A     H    43_A     66   67   67     42   58   62   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    44_A     L    44_A     66   67   67     42   58   62   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    45_A     L    45_A     66   67   67     42   58   62   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    46_A     E    46_A     66   67   67     42   58   62   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    47_A     E    47_A     66   67   67     42   58   62   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     S    48_A     S    48_A     66   67   67     42   58   62   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    49_A     E    49_A     66   67   67     42   58   62   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     A    50_A     A    50_A     66   67   67     42   58   62   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    51_A     L    51_A     66   67   67     42   58   62   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     D    52_A     D    52_A     66   67   67     42   58   62   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     A    53_A     A    53_A     66   67   67     42   58   62   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     K    54_A     K    54_A     66   67   67     42   58   62   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     V    55_A     V    55_A     66   67   67     42   58   62   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     N    56_A     N    56_A     66   67   67     42   58   62   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    57_A     E    57_A     66   67   67     42   58   62   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     A    58_A     A    58_A     66   67   67     42   58   62   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    59_A     L    59_A     66   67   67     42   58   62   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    60_A     E    60_A     66   67   67     42   58   62   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     V    61_A     V    61_A     66   67   67     42   58   62   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    62_A     L    62_A     66   67   67     42   58   62   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     K    63_A     K    63_A     66   67   67     42   58   62   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    64_A     E    64_A     66   67   67     42   58   62   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     Y    65_A     Y    65_A     66   67   67     42   58   62   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     Q    66_A     Q    66_A     66   67   67     42   58   62   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     Q    67_A     Q    67_A     66   67   67     31   58   62   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     N    68_A     N    68_A     66   67   67      3    3    3   64   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_AVERAGE  LCS_A:  99.50  (  98.51  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     42     58     62     64     66     67     67     67     67     67     67     67     67     67     67     67     67     67     67     67 
GDT PERCENT_AT  62.69  86.57  92.54  95.52  98.51 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.28   0.47   0.61   0.74   0.89   1.00   1.00   1.00   1.00   1.00   1.00   1.00   1.00   1.00   1.00   1.00   1.00   1.00   1.00   1.00
GDT RMS_ALL_AT   1.30   1.16   1.09   1.04   1.01   1.00   1.00   1.00   1.00   1.00   1.00   1.00   1.00   1.00   1.00   1.00   1.00   1.00   1.00   1.00

# Checking swapping
#   possible swapping detected:  E     5_A      E     5_A
#   possible swapping detected:  E    24_A      E    24_A
#   possible swapping detected:  E    35_A      E    35_A
#   possible swapping detected:  E    40_A      E    40_A
#   possible swapping detected:  E    46_A      E    46_A
#   possible swapping detected:  E    47_A      E    47_A
#   possible swapping detected:  E    64_A      E    64_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    S     2_A      S     2_A     3.766     0    0.081   0.089     4.198   50.238   46.905
LGA    P     3_A      P     3_A     2.107     0    0.040   0.248     3.054   64.881   62.721
LGA    E     4_A      E     4_A     2.682     0    0.042   0.928     6.206   60.952   44.656
LGA    E     5_A      E     5_A     2.447     0    0.074   1.073     5.463   69.048   47.884
LGA    Q     6_A      Q     6_A     1.163     0    0.033   1.023     2.367   86.190   80.847
LGA    K     7_A      K     7_A     0.804     0    0.022   0.791     2.998   90.476   80.106
LGA    Q     8_A      Q     8_A     1.110     0    0.030   0.777     5.383   85.952   64.127
LGA    M     9_A      M     9_A     0.818     0    0.028   0.894     2.098   95.238   86.250
LGA    L    10_A      L    10_A     0.298     0    0.033   0.886     2.169  100.000   91.012
LGA    G    11_A      G    11_A     0.389     0    0.030   0.030     0.578   97.619   97.619
LGA    E    12_A      E    12_A     0.503     0    0.046   0.804     3.152   92.857   83.122
LGA    A    13_A      A    13_A     0.547     0    0.066   0.065     0.847   90.476   90.476
LGA    I    14_A      I    14_A     0.509     0    0.016   1.303     3.456   92.857   78.333
LGA    Y    15_A      Y    15_A     0.475     0    0.032   0.243     1.093   97.619   91.349
LGA    P    16_A      P    16_A     0.503     0    0.033   0.062     0.652   90.476   90.476
LGA    K    17_A      K    17_A     0.488     0    0.033   1.256     4.133   97.619   79.471
LGA    V    18_A      V    18_A     0.300     0    0.036   0.100     0.523  100.000   98.639
LGA    A    19_A      A    19_A     0.301     0    0.069   0.068     0.622   97.619   98.095
LGA    A    20_A      A    20_A     0.539     0    0.108   0.110     1.113   90.595   90.571
LGA    S    21_A      S    21_A     1.073     0    0.158   0.652     1.619   88.214   84.524
LGA    Q    22_A      Q    22_A     0.624     0    0.093   0.584     2.191   90.476   82.698
LGA    P    23_A      P    23_A     0.812     0    0.071   0.084     1.018   90.476   89.184
LGA    E    24_A      E    24_A     0.770     0    0.054   1.316     4.079   92.857   76.243
LGA    L    25_A      L    25_A     0.630     0    0.064   0.949     3.270   95.238   86.667
LGA    A    26_A      A    26_A     0.421     0    0.021   0.040     0.455  100.000  100.000
LGA    G    27_A      G    27_A     0.504     0    0.030   0.030     0.524   92.857   92.857
LGA    K    28_A      K    28_A     0.542     0    0.041   0.722     1.621   97.619   89.683
LGA    L    29_A      L    29_A     0.305     0    0.027   0.973     2.287   97.619   89.821
LGA    T    30_A      T    30_A     0.547     0    0.042   0.089     0.894   92.857   91.837
LGA    G    31_A      G    31_A     0.558     0    0.030   0.030     0.558   95.238   95.238
LGA    M    32_A      M    32_A     0.139     0    0.024   0.090     0.273  100.000  100.000
LGA    I    33_A      I    33_A     0.466     0    0.012   0.585     1.815   95.238   90.655
LGA    L    34_A      L    34_A     0.649     0    0.085   0.084     1.028   92.857   90.536
LGA    E    35_A      E    35_A     0.816     0    0.023   1.085     4.259   90.476   70.317
LGA    L    36_A      L    36_A     0.909     0    0.030   0.161     1.364   90.476   89.345
LGA    P    37_A      P    37_A     1.047     0    0.034   0.373     2.034   85.952   81.633
LGA    V    38_A      V    38_A     1.136     0    0.029   0.189     1.789   81.429   80.204
LGA    T    39_A      T    39_A     1.086     0    0.039   1.106     3.445   85.952   76.054
LGA    E    40_A      E    40_A     0.742     0    0.028   0.589     1.864   90.476   86.614
LGA    L    41_A      L    41_A     0.766     0    0.028   0.086     0.817   90.476   90.476
LGA    L    42_A      L    42_A     0.892     0    0.041   0.825     2.831   90.476   84.048
LGA    H    43_A      H    43_A     0.549     0    0.033   1.130     2.357   90.476   86.286
LGA    L    44_A      L    44_A     0.585     0    0.062   0.116     0.627   90.476   91.667
LGA    L    45_A      L    45_A     0.823     0    0.057   0.187     1.310   90.476   89.345
LGA    E    46_A      E    46_A     0.937     0    0.100   0.872     3.655   88.214   73.175
LGA    E    47_A      E    47_A     0.777     0    0.092   1.053     4.289   90.476   72.698
LGA    S    48_A      S    48_A     0.461     0    0.040   0.644     2.535   97.619   91.270
LGA    E    49_A      E    49_A     0.699     0    0.118   1.496     5.792   92.857   69.524
LGA    A    50_A      A    50_A     0.197     0    0.030   0.044     0.361  100.000  100.000
LGA    L    51_A      L    51_A     0.101     0    0.040   0.954     2.514  100.000   91.250
LGA    D    52_A      D    52_A     0.236     0    0.037   0.933     3.270  100.000   85.952
LGA    A    53_A      A    53_A     0.388     0    0.047   0.048     0.562   97.619   98.095
LGA    K    54_A      K    54_A     0.331     0    0.026   0.755     3.715  100.000   83.862
LGA    V    55_A      V    55_A     0.123     0    0.026   0.114     0.254  100.000  100.000
LGA    N    56_A      N    56_A     0.498     0    0.029   0.052     0.623   95.238   94.048
LGA    E    57_A      E    57_A     0.598     0    0.040   0.761     3.382   92.857   79.577
LGA    A    58_A      A    58_A     0.576     0    0.041   0.044     0.628   90.476   90.476
LGA    L    59_A      L    59_A     0.462     0    0.028   0.445     1.890   95.238   90.655
LGA    E    60_A      E    60_A     0.975     0    0.053   1.049     4.561   85.952   70.476
LGA    V    61_A      V    61_A     1.068     0    0.022   0.160     1.321   83.690   84.014
LGA    L    62_A      L    62_A     0.862     0    0.030   0.062     0.988   90.476   90.476
LGA    K    63_A      K    63_A     0.976     0    0.041   1.150     3.825   85.952   77.513
LGA    E    64_A      E    64_A     1.283     0    0.053   0.896     3.740   79.286   64.286
LGA    Y    65_A      Y    65_A     1.326     0    0.064   0.316     3.096   79.286   69.841
LGA    Q    66_A      Q    66_A     0.921     0    0.174   0.233     3.197   88.214   74.603
LGA    Q    67_A      Q    67_A     0.749     0    0.489   1.177     6.639   84.048   61.693
LGA    N    68_A      N    68_A     1.817     0    0.626   0.812     3.702   61.548   55.833

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       67     268    268  100.00     519    519  100.00                67
SUMMARY(RMSD_GDC):     1.001          0.986                  1.752           89.977   82.954

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   68   67    4.0     67    1.00    95.522    97.971     6.085

LGA_LOCAL      RMSD:   1.001  Number of atoms:   67  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   1.001  Number of assigned atoms:   67 
Std_ASGN_ATOMS RMSD:   1.001  Standard rmsd on all 67 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.542284 * X  +   0.694706 * Y  +  -0.472558 * Z  +   9.074186
  Y_new =   0.717812 * X  +   0.675378 * Y  +   0.169147 * Z  +  18.033474
  Z_new =   0.436663 * X  +  -0.247482 * Y  +  -0.864915 * Z  +   0.617514 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  2.217788 -0.451886 -2.862905   [DEG:  127.0699  -25.8911 -164.0324 ]
ZXZ: -1.914526  2.615778  2.086414   [DEG: -109.6943  149.8730  119.5427 ]
 
# END of job
