
#######################################################
#                                                     #
#                        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   73 (  570),  selected   71 , name one
# Molecule2: number of CA atoms   71 (  553),  selected   71 , name two
# PARAMETERS: input.pdb  -ie  -3  -d:4  -sda  -swap  -ch1:B  -ch2:B  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    71       1_B - 71_B        1.17     1.17
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    71       1_B - 71_B        1.17     1.17
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    68       2_B - 69_B        1.00     1.18
  LCS_AVERAGE:     95.02

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   71
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     G     1_B     G     1_B     67   71   71      5    6   51   61   68   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     S     2_B     S     2_B     68   71   71      8   40   65   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     V     3_B     V     3_B     68   71   71     29   51   65   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     S     4_B     S     4_B     68   71   71     25   51   65   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     K     5_B     K     5_B     68   71   71     29   51   65   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     W     6_B     W     6_B     68   71   71     29   51   65   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     S     7_B     S     7_B     68   71   71     29   51   65   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     T     8_B     T     8_B     68   71   71     29   51   65   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     D     9_B     D     9_B     68   71   71     29   51   65   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    10_B     E    10_B     68   71   71     29   51   65   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     V    11_B     V    11_B     68   71   71     29   51   65   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     S    12_B     S    12_B     68   71   71     29   51   65   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    13_B     E    13_B     68   71   71     21   51   65   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     F    14_B     F    14_B     68   71   71     28   51   65   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     I    15_B     I    15_B     68   71   71     29   51   65   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     Q    16_B     Q    16_B     68   71   71     29   51   65   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     S    17_B     S    17_B     68   71   71     29   51   65   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     L    18_B     L    18_B     68   71   71     29   51   65   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     P    19_B     P    19_B     68   71   71     29   51   65   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     G    20_B     G    20_B     68   71   71     29   49   65   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     C    21_B     C    21_B     68   71   71     29   51   65   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    22_B     E    22_B     68   71   71      6   51   65   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    23_B     E    23_B     68   71   71     18   51   65   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     H    24_B     H    24_B     68   71   71     26   51   65   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     G    25_B     G    25_B     68   71   71     29   51   65   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     K    26_B     K    26_B     68   71   71     29   51   65   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     V    27_B     V    27_B     68   71   71     29   51   65   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     F    28_B     F    28_B     68   71   71     29   51   65   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     K    29_B     K    29_B     68   71   71     29   51   65   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     D    30_B     D    30_B     68   71   71     23   49   65   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    31_B     E    31_B     68   71   71     29   51   65   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     Q    32_B     Q    32_B     68   71   71     29   51   65   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     I    33_B     I    33_B     68   71   71     29   51   65   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     D    34_B     D    34_B     68   71   71     29   51   65   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     G    35_B     G    35_B     68   71   71     29   51   65   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    36_B     E    36_B     68   71   71     17   51   65   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     A    37_B     A    37_B     68   71   71     29   51   65   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     F    38_B     F    38_B     68   71   71     29   51   65   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     L    39_B     L    39_B     68   71   71     28   51   65   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     L    40_B     L    40_B     68   71   71     28   51   65   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     M    41_B     M    41_B     68   71   71     28   51   65   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     T    42_B     T    42_B     68   71   71     25   51   65   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     Q    43_B     Q    43_B     68   71   71     25   51   65   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     T    44_B     T    44_B     68   71   71     19   51   65   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     D    45_B     D    45_B     68   71   71     19   51   65   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     I    46_B     I    46_B     68   71   71     19   51   65   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     V    47_B     V    47_B     68   71   71     19   51   65   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     K    48_B     K    48_B     68   71   71     19   33   65   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     I    49_B     I    49_B     68   71   71     19   33   65   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     M    50_B     M    50_B     68   71   71     19   50   65   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     S    51_B     S    51_B     68   71   71     19   51   65   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     I    52_B     I    52_B     68   71   71     19   51   65   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     K    53_B     K    53_B     68   71   71     19   45   65   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    54_B     E    54_B     68   71   71     19   39   65   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     G    55_B     G    55_B     68   71   71     19   39   65   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     P    56_B     P    56_B     68   71   71     19   51   65   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     A    57_B     A    57_B     68   71   71     19   51   65   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    58_B     E    58_B     68   71   71     19   51   65   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     K    59_B     K    59_B     68   71   71     19   45   65   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     I    60_B     I    60_B     68   71   71     18   51   65   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     F    61_B     F    61_B     68   71   71     29   51   65   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     N    62_B     N    62_B     68   71   71     17   51   65   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     S    63_B     S    63_B     68   71   71     18   39   65   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     I    64_B     I    64_B     68   71   71     17   42   65   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     L    65_B     L    65_B     68   71   71     17   47   65   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     M    66_B     M    66_B     68   71   71     18   39   65   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     F    67_B     F    67_B     68   71   71     12   33   54   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     K    68_B     K    68_B     68   71   71     12   33   54   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     A    69_B     A    69_B     68   71   71     12   33   52   68   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     A    70_B     A    70_B     50   71   71     12   20   37   62   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    71_B     E    71_B     49   71   71     12   20   37   55   70   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_AVERAGE  LCS_A:  98.34  (  95.02  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     29     51     65     68     70     71     71     71     71     71     71     71     71     71     71     71     71     71     71     71 
GDT PERCENT_AT  40.85  71.83  91.55  95.77  98.59 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.30   0.64   0.86   1.00   1.12   1.17   1.17   1.17   1.17   1.17   1.17   1.17   1.17   1.17   1.17   1.17   1.17   1.17   1.17   1.17
GDT RMS_ALL_AT   1.56   1.36   1.25   1.18   1.17   1.17   1.17   1.17   1.17   1.17   1.17   1.17   1.17   1.17   1.17   1.17   1.17   1.17   1.17   1.17

# Checking swapping
#   possible swapping detected:  D     9_B      D     9_B
#   possible swapping detected:  E    13_B      E    13_B
#   possible swapping detected:  E    54_B      E    54_B
#   possible swapping detected:  E    58_B      E    58_B

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    G     1_B      G     1_B     2.794     0    0.447   0.447     5.440   57.262   57.262
LGA    S     2_B      S     2_B     1.349     0    0.020   0.711     2.671   79.286   75.952
LGA    V     3_B      V     3_B     0.727     0    0.030   1.050     2.957   90.476   80.952
LGA    S     4_B      S     4_B     0.723     0    0.032   0.136     1.166   85.952   87.460
LGA    K     5_B      K     5_B     1.285     0    0.060   0.821     5.715   81.429   60.370
LGA    W     6_B      W     6_B     1.201     0    0.041   0.134     1.471   81.429   81.429
LGA    S     7_B      S     7_B     0.950     0    0.037   0.042     1.046   88.214   88.968
LGA    T     8_B      T     8_B     0.574     0    0.069   1.139     2.567   95.238   85.918
LGA    D     9_B      D     9_B     0.171     0    0.028   0.784     3.222  100.000   84.940
LGA    E    10_B      E    10_B     0.743     0    0.016   0.372     2.421   90.476   82.698
LGA    V    11_B      V    11_B     0.489     0    0.012   0.058     0.670   95.238   95.918
LGA    S    12_B      S    12_B     0.616     0    0.027   0.106     1.047   90.595   90.556
LGA    E    13_B      E    13_B     1.238     0    0.008   0.781     4.574   83.690   67.090
LGA    F    14_B      F    14_B     1.198     0    0.054   0.144     2.231   81.429   76.840
LGA    I    15_B      I    15_B     0.706     0    0.018   0.684     2.411   90.476   88.452
LGA    Q    16_B      Q    16_B     1.224     0    0.023   0.144     2.066   79.286   77.672
LGA    S    17_B      S    17_B     1.505     0    0.037   0.659     2.182   77.143   74.365
LGA    L    18_B      L    18_B     1.208     0    0.042   0.102     1.268   81.429   84.821
LGA    P    19_B      P    19_B     1.410     0    0.013   0.388     2.267   81.429   77.823
LGA    G    20_B      G    20_B     1.451     0    0.033   0.033     1.467   81.429   81.429
LGA    C    21_B      C    21_B     0.938     0    0.044   0.051     1.159   88.214   88.968
LGA    E    22_B      E    22_B     1.070     0    0.061   0.773     4.451   83.690   68.836
LGA    E    23_B      E    23_B     0.758     0    0.084   0.824     3.504   90.476   80.423
LGA    H    24_B      H    24_B     0.699     0    0.072   0.098     1.423   90.476   85.952
LGA    G    25_B      G    25_B     0.757     0    0.038   0.038     0.865   90.476   90.476
LGA    K    26_B      K    26_B     0.889     0    0.010   0.765     1.598   90.476   83.545
LGA    V    27_B      V    27_B     1.159     0    0.046   1.067     3.702   85.952   78.571
LGA    F    28_B      F    28_B     0.552     0    0.009   0.208     1.612   90.476   88.095
LGA    K    29_B      K    29_B     0.683     0    0.009   1.056     3.396   88.214   77.302
LGA    D    30_B      D    30_B     1.383     0    0.052   0.075     1.716   81.429   77.143
LGA    E    31_B      E    31_B     1.217     0    0.014   0.135     1.770   81.429   78.571
LGA    Q    32_B      Q    32_B     1.202     0    0.019   0.834     4.284   81.429   68.624
LGA    I    33_B      I    33_B     0.686     0    0.057   0.064     0.798   92.857   91.667
LGA    D    34_B      D    34_B     0.811     0    0.015   0.128     1.533   90.476   86.012
LGA    G    35_B      G    35_B     0.857     0    0.077   0.077     0.874   90.476   90.476
LGA    E    36_B      E    36_B     1.052     0    0.014   0.047     2.238   85.952   77.831
LGA    A    37_B      A    37_B     0.837     0    0.024   0.023     0.881   90.476   90.476
LGA    F    38_B      F    38_B     0.516     0    0.054   0.208     0.864   95.238   93.074
LGA    L    39_B      L    39_B     0.344     0    0.104   0.170     0.779   97.619   95.238
LGA    L    40_B      L    40_B     0.188     0    0.017   0.082     0.549  100.000   98.810
LGA    M    41_B      M    41_B     0.413     0    0.065   0.140     0.948  100.000   95.238
LGA    T    42_B      T    42_B     0.608     0    0.015   0.041     0.671   90.476   90.476
LGA    Q    43_B      Q    43_B     0.590     0    0.011   0.074     1.068   90.476   89.471
LGA    T    44_B      T    44_B     0.563     0    0.040   0.105     0.816   95.238   93.197
LGA    D    45_B      D    45_B     0.551     0    0.014   0.117     1.006   90.476   89.345
LGA    I    46_B      I    46_B     0.632     0    0.033   0.071     0.810   90.476   90.476
LGA    V    47_B      V    47_B     0.903     0    0.042   0.048     1.208   85.952   85.306
LGA    K    48_B      K    48_B     1.419     0    0.060   0.816     5.272   79.286   66.243
LGA    I    49_B      I    49_B     1.404     0    0.034   0.087     1.864   81.429   77.143
LGA    M    50_B      M    50_B     0.993     0    0.031   0.279     1.630   88.214   84.881
LGA    S    51_B      S    51_B     0.916     0    0.021   0.045     1.409   88.214   85.952
LGA    I    52_B      I    52_B     0.517     0    0.040   0.040     0.718   90.476   92.857
LGA    K    53_B      K    53_B     0.946     0    0.019   0.655     2.640   88.214   80.053
LGA    E    54_B      E    54_B     1.204     0    0.014   0.576     2.774   81.429   74.180
LGA    G    55_B      G    55_B     1.330     0    0.068   0.068     1.417   81.429   81.429
LGA    P    56_B      P    56_B     0.926     0    0.044   0.053     0.989   90.476   90.476
LGA    A    57_B      A    57_B     0.742     0    0.034   0.033     0.861   90.476   90.476
LGA    E    58_B      E    58_B     0.922     0    0.028   0.155     1.241   90.476   87.460
LGA    K    59_B      K    59_B     1.059     0    0.014   0.098     1.622   85.952   81.534
LGA    I    60_B      I    60_B     0.610     0    0.015   0.072     0.722   92.857   92.857
LGA    F    61_B      F    61_B     0.304     0    0.066   0.118     0.701  100.000   96.537
LGA    N    62_B      N    62_B     0.646     0    0.012   0.020     1.571   90.476   84.881
LGA    S    63_B      S    63_B     1.180     0    0.012   0.043     1.580   83.690   81.508
LGA    I    64_B      I    64_B     1.014     0    0.011   0.076     1.323   85.952   87.083
LGA    L    65_B      L    65_B     0.518     0    0.028   0.136     0.959   90.476   92.857
LGA    M    66_B      M    66_B     1.342     0    0.031   0.802     4.593   79.405   63.571
LGA    F    67_B      F    67_B     2.005     0    0.041   1.176     4.882   66.786   61.602
LGA    K    68_B      K    68_B     1.933     0    0.008   0.971     2.510   68.810   68.413
LGA    A    69_B      A    69_B     2.042     0    0.085   0.090     2.336   66.786   68.000
LGA    A    70_B      A    70_B     2.937     0    0.148   0.162     3.198   53.571   54.286
LGA    E    71_B      E    71_B     3.154     0    0.022   0.127     3.771   50.000   48.519

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       71     284    284  100.00     553    553  100.00                71
SUMMARY(RMSD_GDC):     1.167          1.190                  1.536           85.714   81.934

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   73   71    4.0     71    1.17    91.901    96.757     5.605

LGA_LOCAL      RMSD:   1.167  Number of atoms:   71  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   1.167  Number of assigned atoms:   71 
Std_ASGN_ATOMS RMSD:   1.167  Standard rmsd on all 71 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.149635 * X  +  -0.988015 * Y  +  -0.037882 * Z  +  26.323645
  Y_new =  -0.626645 * X  +   0.065130 * Y  +   0.776579 * Z  +  40.582294
  Z_new =  -0.764804 * X  +   0.139942 * Y  +  -0.628880 * Z  +  -9.044175 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -1.805194  0.870738  2.922635   [DEG: -103.4300   49.8896  167.4547 ]
ZXZ: -3.092851  2.250909 -1.389821   [DEG: -177.2073  128.9676  -79.6309 ]
 
# END of job
