
#######################################################
#                                                     #
#                        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:    52      22_A - 81_A        4.25    27.10
  LCS_AVERAGE:     61.42

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    49      33_A - 81_A        0.62    27.88
  LCS_AVERAGE:     56.52

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    49      33_A - 81_A        0.62    27.88
  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   24      0    3    3    3    3    4    6    9   14   16   23   23   23   23   23   23   23   23   23   23 
LCS_GDT     S     3_A     S     3_A     22   23   24     15   22   22   22   22   22   22   22   22   22   23   23   23   23   23   23   23   23   23   23 
LCS_GDT     L     4_A     L     4_A     22   23   24     21   22   22   22   22   22   22   22   22   22   23   23   23   23   23   23   23   23   23   23 
LCS_GDT     I     5_A     I     5_A     22   23   24     21   22   22   22   22   22   22   22   22   22   23   23   23   23   23   23   23   23   23   23 
LCS_GDT     E     6_A     E     6_A     22   23   24     21   22   22   22   22   22   22   22   22   22   23   23   23   23   23   23   23   23   23   23 
LCS_GDT     E     7_A     E     7_A     22   23   24     21   22   22   22   22   22   22   22   22   22   23   23   23   23   23   23   23   23   23   23 
LCS_GDT     L     8_A     L     8_A     22   23   24     21   22   22   22   22   22   22   22   22   22   23   23   23   23   23   23   23   23   23   23 
LCS_GDT     I     9_A     I     9_A     22   23   24     21   22   22   22   22   22   22   22   22   22   23   23   23   23   23   23   23   23   23   23 
LCS_GDT     R    10_A     R    10_A     22   23   24     21   22   22   22   22   22   22   22   22   22   23   23   23   23   23   23   23   23   23   23 
LCS_GDT     R    11_A     R    11_A     22   23   24     21   22   22   22   22   22   22   22   22   22   23   23   23   23   23   23   23   23   23   23 
LCS_GDT     S    12_A     S    12_A     22   23   24     21   22   22   22   22   22   22   22   22   22   23   23   23   23   23   23   23   23   23   23 
LCS_GDT     E    13_A     E    13_A     22   23   24     21   22   22   22   22   22   22   22   22   22   23   23   23   23   23   23   23   23   23   23 
LCS_GDT     E    14_A     E    14_A     22   23   24     21   22   22   22   22   22   22   22   22   22   23   23   23   23   23   23   23   23   23   23 
LCS_GDT     Q    15_A     Q    15_A     22   23   24     21   22   22   22   22   22   22   22   22   22   23   23   23   23   23   23   23   23   23   23 
LCS_GDT     Q    16_A     Q    16_A     22   23   24     21   22   22   22   22   22   22   22   22   22   23   23   23   23   23   23   23   23   23   23 
LCS_GDT     R    17_A     R    17_A     22   23   24     21   22   22   22   22   22   22   22   22   22   23   23   23   23   23   23   23   23   23   23 
LCS_GDT     R    18_A     R    18_A     22   23   24     21   22   22   22   22   22   22   22   22   22   23   23   23   23   23   23   23   23   23   23 
LCS_GDT     N    19_A     N    19_A     22   23   24     21   22   22   22   22   22   22   22   22   22   23   23   23   23   23   23   23   23   23   23 
LCS_GDT     E    20_A     E    20_A     22   23   24     21   22   22   22   22   22   22   22   22   22   23   23   23   23   23   23   23   23   23   23 
LCS_GDT     E    21_A     E    21_A     22   23   24     21   22   22   22   22   22   22   22   22   22   23   23   23   23   23   23   23   23   23   23 
LCS_GDT     A    22_A     A    22_A     22   23   52     21   22   22   22   22   22   22   22   22   22   23   23   23   23   23   23   23   25   35   48 
LCS_GDT     L    23_A     L    23_A     22   23   52     21   22   22   22   22   22   22   22   22   22   23   23   23   23   23   23   23   30   41   51 
LCS_GDT     R    24_A     R    24_A     22   23   52     21   22   22   22   22   22   22   22   22   22   23   23   23   28   36   45   50   50   50   51 
LCS_GDT     Q    33_A     Q    33_A     49   49   52     24   47   49   49   49   49   49   49   49   49   49   49   49   49   49   49   50   50   50   51 
LCS_GDT     L    34_A     L    34_A     49   49   52     24   47   49   49   49   49   49   49   49   49   49   49   49   49   49   49   50   50   50   51 
LCS_GDT     L    35_A     L    35_A     49   49   52     24   47   49   49   49   49   49   49   49   49   49   49   49   49   49   49   50   50   50   51 
LCS_GDT     S    36_A     S    36_A     49   49   52     24   47   49   49   49   49   49   49   49   49   49   49   49   49   49   49   50   50   50   51 
LCS_GDT     G    37_A     G    37_A     49   49   52     26   47   49   49   49   49   49   49   49   49   49   49   49   49   49   49   50   50   50   51 
LCS_GDT     I    38_A     I    38_A     49   49   52     24   47   49   49   49   49   49   49   49   49   49   49   49   49   49   49   50   50   50   51 
LCS_GDT     V    39_A     V    39_A     49   49   52     24   47   49   49   49   49   49   49   49   49   49   49   49   49   49   49   50   50   50   51 
LCS_GDT     Q    40_A     Q    40_A     49   49   52     24   47   49   49   49   49   49   49   49   49   49   49   49   49   49   49   50   50   50   51 
LCS_GDT     Q    41_A     Q    41_A     49   49   52     26   47   49   49   49   49   49   49   49   49   49   49   49   49   49   49   50   50   50   51 
LCS_GDT     Q    42_A     Q    42_A     49   49   52     26   47   49   49   49   49   49   49   49   49   49   49   49   49   49   49   50   50   50   51 
LCS_GDT     N    43_A     N    43_A     49   49   52     26   47   49   49   49   49   49   49   49   49   49   49   49   49   49   49   50   50   50   51 
LCS_GDT     N    44_A     N    44_A     49   49   52     26   47   49   49   49   49   49   49   49   49   49   49   49   49   49   49   50   50   50   51 
LCS_GDT     L    45_A     L    45_A     49   49   52     26   47   49   49   49   49   49   49   49   49   49   49   49   49   49   49   50   50   50   51 
LCS_GDT     L    46_A     L    46_A     49   49   52     26   47   49   49   49   49   49   49   49   49   49   49   49   49   49   49   50   50   50   51 
LCS_GDT     R    47_A     R    47_A     49   49   52     26   47   49   49   49   49   49   49   49   49   49   49   49   49   49   49   50   50   50   51 
LCS_GDT     A    48_A     A    48_A     49   49   52     26   47   49   49   49   49   49   49   49   49   49   49   49   49   49   49   50   50   50   51 
LCS_GDT     I    49_A     I    49_A     49   49   52     26   47   49   49   49   49   49   49   49   49   49   49   49   49   49   49   50   50   50   51 
LCS_GDT     E    50_A     E    50_A     49   49   52     26   47   49   49   49   49   49   49   49   49   49   49   49   49   49   49   50   50   50   51 
LCS_GDT     A    51_A     A    51_A     49   49   52     26   47   49   49   49   49   49   49   49   49   49   49   49   49   49   49   50   50   50   51 
LCS_GDT     Q    52_A     Q    52_A     49   49   52     26   47   49   49   49   49   49   49   49   49   49   49   49   49   49   49   50   50   50   51 
LCS_GDT     Q    53_A     Q    53_A     49   49   52     26   47   49   49   49   49   49   49   49   49   49   49   49   49   49   49   50   50   50   51 
LCS_GDT     H    54_A     H    54_A     49   49   52     24   47   49   49   49   49   49   49   49   49   49   49   49   49   49   49   50   50   50   51 
LCS_GDT     L    55_A     L    55_A     49   49   52     24   39   49   49   49   49   49   49   49   49   49   49   49   49   49   49   50   50   50   51 
LCS_GDT     L    56_A     L    56_A     49   49   52     22   47   49   49   49   49   49   49   49   49   49   49   49   49   49   49   50   50   50   51 
LCS_GDT     Q    57_A     Q    57_A     49   49   52      5   47   49   49   49   49   49   49   49   49   49   49   49   49   49   49   50   50   50   51 
LCS_GDT     L    58_A     L    58_A     49   49   52     24   47   49   49   49   49   49   49   49   49   49   49   49   49   49   49   50   50   50   51 
LCS_GDT     T    59_A     T    59_A     49   49   52     25   47   49   49   49   49   49   49   49   49   49   49   49   49   49   49   50   50   50   51 
LCS_GDT     V    60_A     V    60_A     49   49   52     26   47   49   49   49   49   49   49   49   49   49   49   49   49   49   49   50   50   50   51 
LCS_GDT     W    61_A     W    61_A     49   49   52     26   47   49   49   49   49   49   49   49   49   49   49   49   49   49   49   50   50   50   51 
LCS_GDT     G    62_A     G    62_A     49   49   52     26   47   49   49   49   49   49   49   49   49   49   49   49   49   49   49   50   50   50   51 
LCS_GDT     I    63_A     I    63_A     49   49   52     26   47   49   49   49   49   49   49   49   49   49   49   49   49   49   49   50   50   50   51 
LCS_GDT     K    64_A     K    64_A     49   49   52     26   47   49   49   49   49   49   49   49   49   49   49   49   49   49   49   50   50   50   51 
LCS_GDT     Q    65_A     Q    65_A     49   49   52     26   47   49   49   49   49   49   49   49   49   49   49   49   49   49   49   50   50   50   51 
LCS_GDT     L    66_A     L    66_A     49   49   52     26   47   49   49   49   49   49   49   49   49   49   49   49   49   49   49   50   50   50   51 
LCS_GDT     Q    67_A     Q    67_A     49   49   52     26   47   49   49   49   49   49   49   49   49   49   49   49   49   49   49   50   50   50   51 
LCS_GDT     A    68_A     A    68_A     49   49   52     26   47   49   49   49   49   49   49   49   49   49   49   49   49   49   49   50   50   50   51 
LCS_GDT     R    69_A     R    69_A     49   49   52     26   47   49   49   49   49   49   49   49   49   49   49   49   49   49   49   50   50   50   51 
LCS_GDT     I    70_A     I    70_A     49   49   52     26   47   49   49   49   49   49   49   49   49   49   49   49   49   49   49   50   50   50   51 
LCS_GDT     L    71_A     L    71_A     49   49   52     26   47   49   49   49   49   49   49   49   49   49   49   49   49   49   49   50   50   50   51 
LCS_GDT     A    72_A     A    72_A     49   49   52     26   47   49   49   49   49   49   49   49   49   49   49   49   49   49   49   50   50   50   51 
LCS_GDT     V    73_A     V    73_A     49   49   52     26   47   49   49   49   49   49   49   49   49   49   49   49   49   49   49   50   50   50   51 
LCS_GDT     E    74_A     E    74_A     49   49   52     26   47   49   49   49   49   49   49   49   49   49   49   49   49   49   49   50   50   50   51 
LCS_GDT     R    75_A     R    75_A     49   49   52     26   47   49   49   49   49   49   49   49   49   49   49   49   49   49   49   50   50   50   51 
LCS_GDT     Y    76_A     Y    76_A     49   49   52     26   47   49   49   49   49   49   49   49   49   49   49   49   49   49   49   50   50   50   51 
LCS_GDT     L    77_A     L    77_A     49   49   52     26   47   49   49   49   49   49   49   49   49   49   49   49   49   49   49   50   50   50   51 
LCS_GDT     R    78_A     R    78_A     49   49   52     26   47   49   49   49   49   49   49   49   49   49   49   49   49   49   49   50   50   50   51 
LCS_GDT     D    79_A     D    79_A     49   49   52     22   47   49   49   49   49   49   49   49   49   49   49   49   49   49   49   50   50   50   51 
LCS_GDT     Q    80_A     Q    80_A     49   49   52     26   47   49   49   49   49   49   49   49   49   49   49   49   49   49   49   50   50   50   51 
LCS_GDT     Q    81_A     Q    81_A     49   49   52      3   11   49   49   49   49   49   49   49   49   49   49   49   49   49   49   50   50   50   51 
LCS_AVERAGE  LCS_A:  57.88  (  55.71   56.52   61.42 )

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     26     47     49     49     49     49     49     49     49     49     49     49     49     49     49     49     50     50     50     51 
GDT PERCENT_AT  36.11  65.28  68.06  68.06  68.06  68.06  68.06  68.06  68.06  68.06  68.06  68.06  68.06  68.06  68.06  68.06  69.44  69.44  69.44  70.83
GDT RMS_LOCAL    0.32   0.56   0.62   0.62   0.62   0.62   0.62   0.62   0.62   0.62   0.62   0.62   0.62   0.62   0.62   0.62   2.59   2.59   2.59   3.46
GDT RMS_ALL_AT  27.96  27.89  27.88  27.88  27.88  27.88  27.88  27.88  27.88  27.88  27.88  27.88  27.88  27.88  27.88  27.88  27.51  27.51  27.51  27.32

# 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:  E    21_A      E    21_A
#   possible swapping detected:  E    50_A      E    50_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    76.069     0    0.115   1.098    77.375    0.000    0.000
LGA    S     3_A      S     3_A    74.428     0    0.662   0.794    75.350    0.000    0.000
LGA    L     4_A      L     4_A    69.890     0    0.019   0.051    72.189    0.000    0.000
LGA    I     5_A      I     5_A    68.061     0    0.038   0.109    73.697    0.000    0.000
LGA    E     6_A      E     6_A    66.408     0    0.056   0.884    72.606    0.000    0.000
LGA    E     7_A      E     7_A    62.266     0    0.041   1.303    64.397    0.000    0.000
LGA    L     8_A      L     8_A    58.481     0    0.023   0.039    62.996    0.000    0.000
LGA    I     9_A      I     9_A    57.074     0    0.023   0.125    62.885    0.000    0.000
LGA    R    10_A      R    10_A    54.949     0    0.027   0.685    66.165    0.000    0.000
LGA    R    11_A      R    11_A    50.118     0    0.022   1.242    53.025    0.000    0.000
LGA    S    12_A      S    12_A    47.514     0    0.057   0.060    50.595    0.000    0.000
LGA    E    13_A      E    13_A    46.546     0    0.030   1.165    50.794    0.000    0.000
LGA    E    14_A      E    14_A    43.080     0    0.008   1.185    46.148    0.000    0.000
LGA    Q    15_A      Q    15_A    38.348     0    0.057   1.417    40.609    0.000    0.000
LGA    Q    16_A      Q    16_A    37.038     0    0.010   1.394    40.357    0.000    0.000
LGA    R    17_A      R    17_A    35.822     0    0.000   1.021    46.896    0.000    0.000
LGA    R    18_A      R    18_A    31.020     0    0.009   1.135    36.834    0.000    0.000
LGA    N    19_A      N    19_A    27.548     0    0.041   0.065    31.937    0.000    0.000
LGA    E    20_A      E    20_A    27.082     0    0.023   0.950    33.618    0.000    0.000
LGA    E    21_A      E    21_A    25.682     0    0.030   1.012    29.499    0.000    0.000
LGA    A    22_A      A    22_A    19.960     0    0.057   0.057    22.406    0.000    0.000
LGA    L    23_A      L    23_A    17.866     0    0.083   1.360    20.486    0.000    0.000
LGA    R    24_A      R    24_A    18.764     0    0.222   1.136    26.899    0.000    0.000
LGA    Q    33_A      Q    33_A     0.642     0    0.076   1.134     4.520   90.595   72.434
LGA    L    34_A      L    34_A     0.955     0    0.053   0.085     2.157   90.476   81.726
LGA    L    35_A      L    35_A     0.937     0    0.018   0.483     2.589   90.476   82.917
LGA    S    36_A      S    36_A     0.729     0    0.045   0.057     0.783   90.476   90.476
LGA    G    37_A      G    37_A     0.496     0    0.090   0.090     0.565   92.857   92.857
LGA    I    38_A      I    38_A     0.589     0    0.020   0.058     1.123   90.476   89.345
LGA    V    39_A      V    39_A     0.723     0    0.023   0.051     1.000   90.476   90.476
LGA    Q    40_A      Q    40_A     0.669     0    0.012   0.965     3.799   90.476   78.519
LGA    Q    41_A      Q    41_A     0.303     0    0.027   1.399     4.933  100.000   75.185
LGA    Q    42_A      Q    42_A     0.394     0    0.061   0.249     1.859  100.000   90.741
LGA    N    43_A      N    43_A     0.332     0    0.006   1.335     3.854  100.000   82.262
LGA    N    44_A      N    44_A     0.061     0    0.018   0.086     0.488  100.000  100.000
LGA    L    45_A      L    45_A     0.300     0    0.036   1.402     4.027  100.000   82.381
LGA    L    46_A      L    46_A     0.207     0    0.000   1.402     3.754  100.000   83.155
LGA    R    47_A      R    47_A     0.182     0    0.000   0.247     0.943  100.000   96.537
LGA    A    48_A      A    48_A     0.396     0    0.041   0.049     0.651   97.619   98.095
LGA    I    49_A      I    49_A     0.297     0    0.059   0.097     0.687  100.000   97.619
LGA    E    50_A      E    50_A     0.232     0    0.031   0.951     3.896   97.619   76.772
LGA    A    51_A      A    51_A     0.674     0    0.031   0.030     0.846   92.857   92.381
LGA    Q    52_A      Q    52_A     0.664     0    0.026   1.231     4.064   90.476   72.646
LGA    Q    53_A      Q    53_A     0.351     0    0.018   1.550     5.260   97.619   74.286
LGA    H    54_A      H    54_A     0.840     0    0.257   1.341     4.976   83.810   65.476
LGA    L    55_A      L    55_A     1.394     0    0.174   1.350     4.646   79.286   69.881
LGA    L    56_A      L    56_A     0.768     0    0.151   1.357     2.986   88.214   78.810
LGA    Q    57_A      Q    57_A     0.557     0    0.088   1.371     5.251   85.952   66.984
LGA    L    58_A      L    58_A     0.957     0    0.516   0.462     4.116   66.310   63.869
LGA    T    59_A      T    59_A     0.619     0    0.114   1.183     2.983   90.595   82.109
LGA    V    60_A      V    60_A     0.639     0    0.060   0.064     1.376   90.476   86.599
LGA    W    61_A      W    61_A     0.694     0    0.011   0.155     1.397   90.476   87.891
LGA    G    62_A      G    62_A     0.389     0    0.037   0.037     0.500  100.000  100.000
LGA    I    63_A      I    63_A     0.171     0    0.009   0.124     0.609  100.000   98.810
LGA    K    64_A      K    64_A     0.442     0    0.042   1.157     7.603  100.000   68.307
LGA    Q    65_A      Q    65_A     0.404     0    0.026   1.075     4.924  100.000   79.841
LGA    L    66_A      L    66_A     0.192     0    0.009   0.068     0.664  100.000   98.810
LGA    Q    67_A      Q    67_A     0.367     0    0.028   0.041     1.218  100.000   91.693
LGA    A    68_A      A    68_A     0.400     0    0.019   0.021     0.494  100.000  100.000
LGA    R    69_A      R    69_A     0.420     0    0.018   0.999     4.778  100.000   84.978
LGA    I    70_A      I    70_A     0.414     0    0.022   1.377     3.716  100.000   82.917
LGA    L    71_A      L    71_A     0.427     0    0.010   1.416     3.292  100.000   85.000
LGA    A    72_A      A    72_A     0.445     0    0.022   0.027     0.581   95.238   96.190
LGA    V    73_A      V    73_A     0.551     0    0.013   0.059     0.679   90.476   90.476
LGA    E    74_A      E    74_A     0.658     0    0.000   0.961     4.029   90.476   71.852
LGA    R    75_A      R    75_A     0.651     0    0.041   1.218     4.784   90.476   77.403
LGA    Y    76_A      Y    76_A     0.592     0    0.030   0.091     0.607   90.476   92.857
LGA    L    77_A      L    77_A     0.715     0    0.020   0.046     0.855   90.476   90.476
LGA    R    78_A      R    78_A     0.687     0    0.010   1.237     5.087   90.476   73.896
LGA    D    79_A      D    79_A     0.735     0    0.029   0.071     1.240   90.476   87.083
LGA    Q    80_A      Q    80_A     0.605     0    0.104   0.199     0.931   90.476   90.476
LGA    Q    81_A      Q    81_A     1.304     0    0.337   0.371     2.637   75.476   77.831

# 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):    23.121         22.694                 23.250           63.502   57.518

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   83   72    4.0     49    0.62    67.361    64.989     6.846

LGA_LOCAL      RMSD:   0.616  Number of atoms:   49  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  27.875  Number of assigned atoms:   72 
Std_ASGN_ATOMS RMSD:  23.121  Standard rmsd on all 72 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.146017 * X  +   0.905470 * Y  +  -0.398500 * Z  +   8.891604
  Y_new =  -0.241928 * X  +  -0.423270 * Y  +  -0.873106 * Z  +   7.069584
  Z_new =  -0.959244 * X  +  -0.031080 * Y  +   0.280863 * Z  + 142.449539 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -2.113826  1.284316 -0.110210   [DEG: -121.1133   73.5859   -6.3146 ]
ZXZ: -0.428177  1.286103 -1.603185   [DEG:  -24.5327   73.6883  -91.8558 ]
 
# END of job
