
#######################################################
#                                                     #
#                        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:    55      19_A - 81_A        4.63    20.39
  LCS_AVERAGE:     66.55

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    50      24_A - 81_A        1.58    21.68
  LCS_AVERAGE:     57.99

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    49      33_A - 81_A        0.57    22.30
  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   25      0    3    3    3    3    4    6   21   23   23   23   23   23   23   23   23   23   23   24   24 
LCS_GDT     S     3_A     S     3_A     22   23   25     15   22   22   22   22   22   22   22   23   23   23   23   23   23   23   23   23   25   25   25 
LCS_GDT     L     4_A     L     4_A     22   23   25     19   22   22   22   22   22   22   22   23   23   23   23   23   23   23   23   23   25   25   25 
LCS_GDT     I     5_A     I     5_A     22   23   25     19   22   22   22   22   22   22   22   23   23   23   23   23   23   23   23   23   25   25   25 
LCS_GDT     E     6_A     E     6_A     22   23   25     19   22   22   22   22   22   22   22   23   23   23   23   23   23   23   23   23   25   25   25 
LCS_GDT     E     7_A     E     7_A     22   23   25     19   22   22   22   22   22   22   22   23   23   23   23   23   23   23   23   23   25   25   25 
LCS_GDT     L     8_A     L     8_A     22   23   25     19   22   22   22   22   22   22   22   23   23   23   23   23   23   23   23   23   25   25   25 
LCS_GDT     I     9_A     I     9_A     22   23   25     19   22   22   22   22   22   22   22   23   23   23   23   23   23   23   23   23   25   25   25 
LCS_GDT     R    10_A     R    10_A     22   23   25     19   22   22   22   22   22   22   22   23   23   23   23   23   23   23   23   23   25   25   25 
LCS_GDT     R    11_A     R    11_A     22   23   25     19   22   22   22   22   22   22   22   23   23   23   23   23   23   23   23   23   25   25   25 
LCS_GDT     S    12_A     S    12_A     22   23   25     19   22   22   22   22   22   22   22   23   23   23   23   23   23   23   23   23   25   25   25 
LCS_GDT     E    13_A     E    13_A     22   23   25     19   22   22   22   22   22   22   22   23   23   23   23   23   23   23   23   23   25   25   25 
LCS_GDT     E    14_A     E    14_A     22   23   25     19   22   22   22   22   22   22   22   23   23   23   23   23   23   23   23   23   25   25   25 
LCS_GDT     Q    15_A     Q    15_A     22   23   25     19   22   22   22   22   22   22   22   23   23   23   23   23   23   23   23   23   25   25   25 
LCS_GDT     Q    16_A     Q    16_A     22   23   25     19   22   22   22   22   22   22   22   23   23   23   23   23   23   23   23   23   25   25   25 
LCS_GDT     R    17_A     R    17_A     22   23   25     19   22   22   22   22   22   22   22   23   23   23   23   23   23   23   23   23   25   25   25 
LCS_GDT     R    18_A     R    18_A     22   23   25     19   22   22   22   22   22   22   22   23   23   23   23   23   23   23   23   23   25   25   25 
LCS_GDT     N    19_A     N    19_A     22   23   55     19   22   22   22   22   22   22   22   23   23   23   23   23   23   23   23   23   25   25   25 
LCS_GDT     E    20_A     E    20_A     22   23   55     19   22   22   22   22   22   22   22   23   23   23   23   23   23   23   23   23   25   34   51 
LCS_GDT     E    21_A     E    21_A     22   23   55     19   22   22   22   22   22   22   22   23   23   23   23   23   23   23   23   23   33   49   53 
LCS_GDT     A    22_A     A    22_A     22   23   55     19   22   22   22   22   22   22   22   23   23   23   23   23   23   27   50   52   52   52   53 
LCS_GDT     L    23_A     L    23_A     22   23   55     17   22   22   22   22   22   22   22   23   23   23   23   46   51   51   51   52   52   52   53 
LCS_GDT     R    24_A     R    24_A     22   50   55     12   22   22   22   22   22   22   22   23   23   23   39   50   51   51   51   52   52   52   53 
LCS_GDT     Q    33_A     Q    33_A     49   50   55     32   47   48   49   49   49   49   49   49   49   49   49   50   51   51   51   52   52   52   53 
LCS_GDT     L    34_A     L    34_A     49   50   55     13   47   48   49   49   49   49   49   49   49   49   49   50   51   51   51   52   52   52   53 
LCS_GDT     L    35_A     L    35_A     49   50   55     40   47   48   49   49   49   49   49   49   49   49   49   50   51   51   51   52   52   52   53 
LCS_GDT     S    36_A     S    36_A     49   50   55     40   47   48   49   49   49   49   49   49   49   49   49   50   51   51   51   52   52   52   53 
LCS_GDT     G    37_A     G    37_A     49   50   55     39   47   48   49   49   49   49   49   49   49   49   49   50   51   51   51   52   52   52   53 
LCS_GDT     I    38_A     I    38_A     49   50   55     40   47   48   49   49   49   49   49   49   49   49   49   50   51   51   51   52   52   52   53 
LCS_GDT     V    39_A     V    39_A     49   50   55     40   47   48   49   49   49   49   49   49   49   49   49   50   51   51   51   52   52   52   53 
LCS_GDT     Q    40_A     Q    40_A     49   50   55     19   47   48   49   49   49   49   49   49   49   49   49   50   51   51   51   52   52   52   53 
LCS_GDT     Q    41_A     Q    41_A     49   50   55     40   47   48   49   49   49   49   49   49   49   49   49   50   51   51   51   52   52   52   53 
LCS_GDT     Q    42_A     Q    42_A     49   50   55     40   47   48   49   49   49   49   49   49   49   49   49   50   51   51   51   52   52   52   53 
LCS_GDT     N    43_A     N    43_A     49   50   55     40   47   48   49   49   49   49   49   49   49   49   49   50   51   51   51   52   52   52   53 
LCS_GDT     N    44_A     N    44_A     49   50   55     40   47   48   49   49   49   49   49   49   49   49   49   50   51   51   51   52   52   52   53 
LCS_GDT     L    45_A     L    45_A     49   50   55     40   47   48   49   49   49   49   49   49   49   49   49   50   51   51   51   52   52   52   53 
LCS_GDT     L    46_A     L    46_A     49   50   55     40   47   48   49   49   49   49   49   49   49   49   49   50   51   51   51   52   52   52   53 
LCS_GDT     R    47_A     R    47_A     49   50   55     40   47   48   49   49   49   49   49   49   49   49   49   50   51   51   51   52   52   52   53 
LCS_GDT     A    48_A     A    48_A     49   50   55     40   47   48   49   49   49   49   49   49   49   49   49   50   51   51   51   52   52   52   53 
LCS_GDT     I    49_A     I    49_A     49   50   55     40   47   48   49   49   49   49   49   49   49   49   49   50   51   51   51   52   52   52   53 
LCS_GDT     E    50_A     E    50_A     49   50   55     40   47   48   49   49   49   49   49   49   49   49   49   50   51   51   51   52   52   52   53 
LCS_GDT     A    51_A     A    51_A     49   50   55     40   47   48   49   49   49   49   49   49   49   49   49   50   51   51   51   52   52   52   53 
LCS_GDT     Q    52_A     Q    52_A     49   50   55     40   47   48   49   49   49   49   49   49   49   49   49   50   51   51   51   52   52   52   53 
LCS_GDT     Q    53_A     Q    53_A     49   50   55     40   47   48   49   49   49   49   49   49   49   49   49   50   51   51   51   52   52   52   53 
LCS_GDT     H    54_A     H    54_A     49   50   55     40   47   48   49   49   49   49   49   49   49   49   49   50   51   51   51   52   52   52   53 
LCS_GDT     L    55_A     L    55_A     49   50   55     40   47   48   49   49   49   49   49   49   49   49   49   50   51   51   51   52   52   52   53 
LCS_GDT     L    56_A     L    56_A     49   50   55     40   47   48   49   49   49   49   49   49   49   49   49   50   51   51   51   52   52   52   53 
LCS_GDT     Q    57_A     Q    57_A     49   50   55     40   47   48   49   49   49   49   49   49   49   49   49   50   51   51   51   52   52   52   53 
LCS_GDT     L    58_A     L    58_A     49   50   55     40   47   48   49   49   49   49   49   49   49   49   49   50   51   51   51   52   52   52   53 
LCS_GDT     T    59_A     T    59_A     49   50   55     40   47   48   49   49   49   49   49   49   49   49   49   50   51   51   51   52   52   52   53 
LCS_GDT     V    60_A     V    60_A     49   50   55     40   47   48   49   49   49   49   49   49   49   49   49   50   51   51   51   52   52   52   53 
LCS_GDT     W    61_A     W    61_A     49   50   55     40   47   48   49   49   49   49   49   49   49   49   49   50   51   51   51   52   52   52   53 
LCS_GDT     G    62_A     G    62_A     49   50   55     40   47   48   49   49   49   49   49   49   49   49   49   50   51   51   51   52   52   52   53 
LCS_GDT     I    63_A     I    63_A     49   50   55     40   47   48   49   49   49   49   49   49   49   49   49   50   51   51   51   52   52   52   53 
LCS_GDT     K    64_A     K    64_A     49   50   55     40   47   48   49   49   49   49   49   49   49   49   49   50   51   51   51   52   52   52   53 
LCS_GDT     Q    65_A     Q    65_A     49   50   55     40   47   48   49   49   49   49   49   49   49   49   49   50   51   51   51   52   52   52   53 
LCS_GDT     L    66_A     L    66_A     49   50   55     40   47   48   49   49   49   49   49   49   49   49   49   50   51   51   51   52   52   52   53 
LCS_GDT     Q    67_A     Q    67_A     49   50   55     40   47   48   49   49   49   49   49   49   49   49   49   50   51   51   51   52   52   52   53 
LCS_GDT     A    68_A     A    68_A     49   50   55     40   47   48   49   49   49   49   49   49   49   49   49   50   51   51   51   52   52   52   53 
LCS_GDT     R    69_A     R    69_A     49   50   55     40   47   48   49   49   49   49   49   49   49   49   49   50   51   51   51   52   52   52   53 
LCS_GDT     I    70_A     I    70_A     49   50   55     40   47   48   49   49   49   49   49   49   49   49   49   50   51   51   51   52   52   52   53 
LCS_GDT     L    71_A     L    71_A     49   50   55     40   47   48   49   49   49   49   49   49   49   49   49   50   51   51   51   52   52   52   53 
LCS_GDT     A    72_A     A    72_A     49   50   55     40   47   48   49   49   49   49   49   49   49   49   49   50   51   51   51   52   52   52   53 
LCS_GDT     V    73_A     V    73_A     49   50   55     40   47   48   49   49   49   49   49   49   49   49   49   50   51   51   51   52   52   52   53 
LCS_GDT     E    74_A     E    74_A     49   50   55     40   47   48   49   49   49   49   49   49   49   49   49   50   51   51   51   52   52   52   53 
LCS_GDT     R    75_A     R    75_A     49   50   55     40   47   48   49   49   49   49   49   49   49   49   49   50   51   51   51   52   52   52   53 
LCS_GDT     Y    76_A     Y    76_A     49   50   55     40   47   48   49   49   49   49   49   49   49   49   49   50   51   51   51   52   52   52   53 
LCS_GDT     L    77_A     L    77_A     49   50   55     35   47   48   49   49   49   49   49   49   49   49   49   50   51   51   51   52   52   52   53 
LCS_GDT     R    78_A     R    78_A     49   50   55     35   47   48   49   49   49   49   49   49   49   49   49   50   51   51   51   52   52   52   53 
LCS_GDT     D    79_A     D    79_A     49   50   55     27   47   48   49   49   49   49   49   49   49   49   49   50   51   51   51   52   52   52   53 
LCS_GDT     Q    80_A     Q    80_A     49   50   55     12   45   48   49   49   49   49   49   49   49   49   49   50   51   51   51   52   52   52   53 
LCS_GDT     Q    81_A     Q    81_A     49   50   55      3   11   40   49   49   49   49   49   49   49   49   49   50   51   51   51   52   52   52   53 
LCS_AVERAGE  LCS_A:  60.08  (  55.71   57.99   66.55 )

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     40     47     48     49     49     49     49     49     49     49     49     49     50     51     51     51     52     52     52     53 
GDT PERCENT_AT  55.56  65.28  66.67  68.06  68.06  68.06  68.06  68.06  68.06  68.06  68.06  68.06  69.44  70.83  70.83  70.83  72.22  72.22  72.22  73.61
GDT RMS_LOCAL    0.31   0.44   0.48   0.57   0.57   0.57   0.57   0.57   0.57   0.57   0.57   0.57   1.58   2.02   2.02   2.02   2.68   2.68   2.68   3.43
GDT RMS_ALL_AT  22.37  22.28  22.27  22.30  22.30  22.30  22.30  22.30  22.30  22.30  22.30  22.30  21.68  21.55  21.55  21.55  21.25  21.25  21.25  20.86

# 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    21_A      E    21_A
#   possible swapping detected:  E    74_A      E    74_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    T     2_A      T     2_A    63.772     0    0.105   1.111    64.312    0.000    0.000
LGA    S     3_A      S     3_A    61.213     0    0.662   0.788    62.523    0.000    0.000
LGA    L     4_A      L     4_A    57.355     0    0.017   0.050    59.246    0.000    0.000
LGA    I     5_A      I     5_A    53.105     0    0.036   0.110    55.405    0.000    0.000
LGA    E     6_A      E     6_A    53.147     0    0.053   0.915    59.404    0.000    0.000
LGA    E     7_A      E     7_A    51.888     0    0.042   1.294    53.537    0.000    0.000
LGA    L     8_A      L     8_A    46.953     0    0.024   0.036    49.526    0.000    0.000
LGA    I     9_A      I     9_A    44.229     0    0.023   0.124    47.245    0.000    0.000
LGA    R    10_A      R    10_A    44.802     0    0.029   0.679    55.985    0.000    0.000
LGA    R    11_A      R    11_A    41.702     0    0.024   1.246    47.839    0.000    0.000
LGA    S    12_A      S    12_A    36.578     0    0.061   0.065    38.975    0.000    0.000
LGA    E    13_A      E    13_A    36.114     0    0.032   0.939    39.713    0.000    0.000
LGA    E    14_A      E    14_A    35.481     0    0.008   0.659    41.681    0.000    0.000
LGA    Q    15_A      Q    15_A    30.814     0    0.057   1.417    32.927    0.000    0.000
LGA    Q    16_A      Q    16_A    27.102     0    0.009   1.387    28.983    0.000    0.000
LGA    R    17_A      R    17_A    27.458     0    0.000   1.018    39.663    0.000    0.000
LGA    R    18_A      R    18_A    24.856     0    0.003   1.120    35.874    0.000    0.000
LGA    N    19_A      N    19_A    19.968     0    0.035   0.062    23.154    0.000    0.000
LGA    E    20_A      E    20_A    18.451     0    0.034   0.952    25.153    0.000    0.000
LGA    E    21_A      E    21_A    18.257     0    0.031   1.022    22.540    0.000    0.000
LGA    A    22_A      A    22_A    14.127     0    0.065   0.065    15.945    0.000    0.000
LGA    L    23_A      L    23_A     9.727     0    0.086   1.357    11.845    2.976    2.202
LGA    R    24_A      R    24_A    11.229     0    0.232   1.139    20.002    0.357    0.130
LGA    Q    33_A      Q    33_A     0.875     0    0.048   1.093     5.093   90.476   66.825
LGA    L    34_A      L    34_A     0.983     0    0.051   0.090     1.593   90.476   84.881
LGA    L    35_A      L    35_A     0.461     0    0.013   0.478     2.325   97.619   89.821
LGA    S    36_A      S    36_A     0.605     0    0.054   0.657     2.385   90.476   86.190
LGA    G    37_A      G    37_A     0.748     0    0.067   0.067     0.748   92.857   92.857
LGA    I    38_A      I    38_A     0.342     0    0.029   0.062     0.701   97.619   97.619
LGA    V    39_A      V    39_A     0.566     0    0.021   0.052     0.735   92.857   91.837
LGA    Q    40_A      Q    40_A     0.817     0    0.017   1.215     4.554   90.476   77.196
LGA    Q    41_A      Q    41_A     0.514     0    0.030   1.400     4.404   95.238   74.868
LGA    Q    42_A      Q    42_A     0.363     0    0.058   0.233     1.209  100.000   95.820
LGA    N    43_A      N    43_A     0.278     0    0.012   1.335     4.049  100.000   80.655
LGA    N    44_A      N    44_A     0.280     0    0.008   0.088     0.789  100.000   96.429
LGA    L    45_A      L    45_A     0.288     0    0.000   0.200     0.706  100.000   98.810
LGA    L    46_A      L    46_A     0.293     0    0.008   1.399     3.735  100.000   83.155
LGA    R    47_A      R    47_A     0.271     0    0.000   0.238     0.998  100.000   98.268
LGA    A    48_A      A    48_A     0.267     0    0.024   0.031     0.272  100.000  100.000
LGA    I    49_A      I    49_A     0.509     0    0.044   0.090     0.765   97.619   94.048
LGA    E    50_A      E    50_A     0.469     0    0.022   0.126     1.240   97.619   92.646
LGA    A    51_A      A    51_A     0.222     0    0.016   0.016     0.313  100.000  100.000
LGA    Q    52_A      Q    52_A     0.463     0    0.018   0.205     1.321  100.000   93.704
LGA    Q    53_A      Q    53_A     0.472     0    0.022   1.555     5.321  100.000   73.968
LGA    H    54_A      H    54_A     0.348     0    0.020   1.141     2.323  100.000   88.381
LGA    L    55_A      L    55_A     0.351     0    0.012   1.411     3.884  100.000   81.964
LGA    L    56_A      L    56_A     0.595     0    0.012   1.376     3.087   90.476   81.071
LGA    Q    57_A      Q    57_A     0.552     0    0.026   1.458     5.215   95.238   72.434
LGA    L    58_A      L    58_A     0.325     0    0.024   0.120     0.561  100.000   98.810
LGA    T    59_A      T    59_A     0.330     0    0.064   1.115     2.351  100.000   89.728
LGA    V    60_A      V    60_A     0.391     0    0.000   0.048     0.557   97.619   98.639
LGA    W    61_A      W    61_A     0.488     0    0.078   1.272     9.106  100.000   50.850
LGA    G    62_A      G    62_A     0.327     0    0.083   0.083     0.623   97.619   97.619
LGA    I    63_A      I    63_A     0.347     0    0.017   0.094     0.580  100.000   98.810
LGA    K    64_A      K    64_A     0.342     0    0.038   1.142     6.604  100.000   74.921
LGA    Q    65_A      Q    65_A     0.379     0    0.023   1.376     5.802  100.000   77.037
LGA    L    66_A      L    66_A     0.383     0    0.015   0.065     0.659  100.000   96.429
LGA    Q    67_A      Q    67_A     0.180     0    0.022   0.036     0.433  100.000  100.000
LGA    A    68_A      A    68_A     0.314     0    0.020   0.020     0.425  100.000  100.000
LGA    R    69_A      R    69_A     0.400     0    0.000   1.015     4.840  100.000   84.978
LGA    I    70_A      I    70_A     0.501     0    0.029   1.377     4.329   97.619   81.964
LGA    L    71_A      L    71_A     0.361     0    0.011   1.416     3.179  100.000   83.095
LGA    A    72_A      A    72_A     0.274     0    0.027   0.031     0.288  100.000  100.000
LGA    V    73_A      V    73_A     0.293     0    0.011   0.060     0.489  100.000  100.000
LGA    E    74_A      E    74_A     0.264     0    0.020   0.955     3.677  100.000   79.418
LGA    R    75_A      R    75_A     0.219     0    0.036   1.219     4.801  100.000   82.424
LGA    Y    76_A      Y    76_A     0.129     0    0.034   0.108     0.944  100.000   96.825
LGA    L    77_A      L    77_A     0.378     0    0.012   0.024     0.511   97.619   96.429
LGA    R    78_A      R    78_A     0.510     0    0.012   1.235     5.165   92.857   75.758
LGA    D    79_A      D    79_A     0.847     0    0.029   0.079     1.342   85.952   85.952
LGA    Q    80_A      Q    80_A     1.161     0    0.111   0.974     4.780   83.690   67.831
LGA    Q    81_A      Q    81_A     2.090     0    0.331   0.360     3.658   61.429   64.233

# 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):    16.814         16.487                 17.264           65.789   59.410

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   83   72    4.0     49    0.57    68.056    65.550     7.346

LGA_LOCAL      RMSD:   0.567  Number of atoms:   49  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  22.303  Number of assigned atoms:   72 
Std_ASGN_ATOMS RMSD:  16.814  Standard rmsd on all 72 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.058822 * X  +  -0.963106 * Y  +   0.262615 * Z  +  17.726406
  Y_new =   0.697037 * X  +   0.227946 * Y  +   0.679838 * Z  + -39.454334
  Z_new =  -0.714618 * X  +   0.143063 * Y  +   0.684729 * Z  + 113.117096 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  1.486607  0.796078  0.205971   [DEG:   85.1763   45.6119   11.8012 ]
ZXZ:  2.772961  0.816565 -1.373214   [DEG:  158.8790   46.7857  -78.6793 ]
 
# END of job
