
#######################################################
#                                                     #
#                        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        1.43     1.43
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    71       1_B - 71_B        1.43     1.43
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    47       1_B - 47_B        0.93     1.67
  LONGEST_CONTINUOUS_SEGMENT:    47       2_B - 48_B        0.99     1.67
  LCS_AVERAGE:     59.81

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     47   71   71      5   20   51   65   68   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     S     2_B     S     2_B     47   71   71     13   35   58   65   68   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     V     3_B     V     3_B     47   71   71     14   35   58   65   68   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     S     4_B     S     4_B     47   71   71     14   35   58   65   68   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     K     5_B     K     5_B     47   71   71     14   35   58   65   68   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     W     6_B     W     6_B     47   71   71     14   35   58   65   68   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     S     7_B     S     7_B     47   71   71     14   35   58   65   68   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     T     8_B     T     8_B     47   71   71     14   35   58   65   68   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     D     9_B     D     9_B     47   71   71     14   35   58   65   68   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    10_B     E    10_B     47   71   71     14   35   58   65   68   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     V    11_B     V    11_B     47   71   71     14   35   58   65   68   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     S    12_B     S    12_B     47   71   71     10   32   58   65   68   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    13_B     E    13_B     47   71   71     10   34   58   65   68   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     F    14_B     F    14_B     47   71   71     12   35   58   65   68   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     I    15_B     I    15_B     47   71   71     14   35   58   65   68   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     Q    16_B     Q    16_B     47   71   71     10   35   58   65   68   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     S    17_B     S    17_B     47   71   71     10   34   58   64   68   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     L    18_B     L    18_B     47   71   71     14   35   58   65   68   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     P    19_B     P    19_B     47   71   71     14   35   58   65   68   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     G    20_B     G    20_B     47   71   71     14   35   58   65   68   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     C    21_B     C    21_B     47   71   71     14   35   58   65   68   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    22_B     E    22_B     47   71   71      7   34   58   65   68   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    23_B     E    23_B     47   71   71      8   35   58   65   68   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     H    24_B     H    24_B     47   71   71     11   35   58   65   68   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     G    25_B     G    25_B     47   71   71     14   35   58   65   68   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     K    26_B     K    26_B     47   71   71     14   35   58   65   68   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     V    27_B     V    27_B     47   71   71     14   35   58   65   68   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     F    28_B     F    28_B     47   71   71     14   35   58   65   68   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     K    29_B     K    29_B     47   71   71     14   35   58   65   68   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     D    30_B     D    30_B     47   71   71     14   35   58   65   68   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    31_B     E    31_B     47   71   71     14   35   58   65   68   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     Q    32_B     Q    32_B     47   71   71     14   35   58   65   68   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     I    33_B     I    33_B     47   71   71     14   35   58   65   68   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     D    34_B     D    34_B     47   71   71     14   35   58   65   68   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     G    35_B     G    35_B     47   71   71     14   35   58   65   68   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    36_B     E    36_B     47   71   71      4   28   58   65   68   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     A    37_B     A    37_B     47   71   71      7   35   58   65   68   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     F    38_B     F    38_B     47   71   71      8   35   58   65   68   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     L    39_B     L    39_B     47   71   71     14   35   58   65   68   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     L    40_B     L    40_B     47   71   71      7   31   58   65   68   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     M    41_B     M    41_B     47   71   71     13   35   58   65   68   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     T    42_B     T    42_B     47   71   71     14   35   58   65   68   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     Q    43_B     Q    43_B     47   71   71     14   35   58   65   68   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     T    44_B     T    44_B     47   71   71     14   35   58   65   68   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     D    45_B     D    45_B     47   71   71     14   35   58   65   68   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     I    46_B     I    46_B     47   71   71      5   31   58   65   68   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     V    47_B     V    47_B     47   71   71      5   31   58   65   68   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     K    48_B     K    48_B     47   71   71      5    9   35   56   68   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     I    49_B     I    49_B     33   71   71      5    6   14   37   66   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     M    50_B     M    50_B     33   71   71     10   35   58   65   68   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     S    51_B     S    51_B     33   71   71     14   33   58   65   68   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     I    52_B     I    52_B     33   71   71      5   20   50   65   68   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     K    53_B     K    53_B     33   71   71     10   31   58   65   68   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    54_B     E    54_B     33   71   71     14   31   58   65   68   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     G    55_B     G    55_B     33   71   71     14   31   58   65   68   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     P    56_B     P    56_B     33   71   71     14   31   58   65   68   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     A    57_B     A    57_B     33   71   71     14   35   58   65   68   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    58_B     E    58_B     33   71   71     14   35   58   65   68   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     K    59_B     K    59_B     33   71   71     14   31   58   65   68   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     I    60_B     I    60_B     33   71   71     14   35   58   65   68   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     F    61_B     F    61_B     33   71   71     14   35   58   65   68   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     N    62_B     N    62_B     33   71   71     14   35   58   65   68   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     S    63_B     S    63_B     33   71   71     14   31   58   65   68   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     I    64_B     I    64_B     33   71   71     11   31   58   65   68   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     L    65_B     L    65_B     33   71   71     13   31   58   65   68   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     M    66_B     M    66_B     33   71   71     12   31   53   65   68   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     F    67_B     F    67_B     33   71   71     11   31   44   65   68   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     K    68_B     K    68_B     33   71   71     10   31   44   65   68   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     A    69_B     A    69_B     33   71   71     10   31   44   65   68   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     A    70_B     A    70_B     33   71   71     10   15   37   52   66   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    71_B     E    71_B     33   71   71      8   15   35   46   60   71   71   71   71   71   71   71   71   71   71   71   71   71   71   71 
LCS_AVERAGE  LCS_A:  86.60  (  59.81  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     14     35     58     65     68     71     71     71     71     71     71     71     71     71     71     71     71     71     71     71 
GDT PERCENT_AT  19.72  49.30  81.69  91.55  95.77 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.28   0.65   1.00   1.17   1.25   1.43   1.43   1.43   1.43   1.43   1.43   1.43   1.43   1.43   1.43   1.43   1.43   1.43   1.43   1.43
GDT RMS_ALL_AT   1.87   1.74   1.58   1.47   1.45   1.43   1.43   1.43   1.43   1.43   1.43   1.43   1.43   1.43   1.43   1.43   1.43   1.43   1.43   1.43

# Checking swapping
#   possible swapping detected:  D     9_B      D     9_B
#   possible swapping detected:  E    13_B      E    13_B
#   possible swapping detected:  E    22_B      E    22_B
#   possible swapping detected:  E    54_B      E    54_B
#   possible swapping detected:  E    58_B      E    58_B
#   possible swapping detected:  E    71_B      E    71_B

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    G     1_B      G     1_B     1.896     0    0.214   0.214     2.565   73.214   73.214
LGA    S     2_B      S     2_B     1.399     0    0.025   0.711     3.390   81.429   74.762
LGA    V     3_B      V     3_B     1.579     0    0.018   0.986     4.026   75.000   65.714
LGA    S     4_B      S     4_B     1.476     0    0.032   0.146     1.797   81.429   80.000
LGA    K     5_B      K     5_B     1.261     0    0.046   0.826     5.226   83.690   64.550
LGA    W     6_B      W     6_B     1.151     0    0.083   0.160     2.284   81.429   75.408
LGA    S     7_B      S     7_B     0.858     0    0.043   0.041     0.966   90.476   90.476
LGA    T     8_B      T     8_B     0.714     0    0.012   0.094     1.024   90.476   89.184
LGA    D     9_B      D     9_B     0.692     0    0.017   0.737     3.139   90.476   80.000
LGA    E    10_B      E    10_B     0.997     0    0.013   0.350     2.634   88.214   79.841
LGA    V    11_B      V    11_B     0.891     0    0.023   0.086     1.090   90.476   87.891
LGA    S    12_B      S    12_B     1.225     0    0.025   0.082     1.485   81.429   81.429
LGA    E    13_B      E    13_B     1.666     0    0.020   0.780     5.508   75.000   58.042
LGA    F    14_B      F    14_B     1.389     0    0.053   0.245     3.333   81.429   69.697
LGA    I    15_B      I    15_B     0.914     0    0.009   0.668     1.670   85.952   83.750
LGA    Q    16_B      Q    16_B     1.846     0    0.058   0.178     3.528   72.976   65.185
LGA    S    17_B      S    17_B     2.109     0    0.018   0.023     2.333   66.786   66.111
LGA    L    18_B      L    18_B     1.688     0    0.092   0.181     1.900   72.857   73.929
LGA    P    19_B      P    19_B     1.846     0    0.013   0.386     2.691   72.857   69.456
LGA    G    20_B      G    20_B     1.587     0    0.042   0.042     1.721   77.143   77.143
LGA    C    21_B      C    21_B     1.084     0    0.044   0.056     1.300   83.690   82.937
LGA    E    22_B      E    22_B     1.574     0    0.052   1.353     6.160   77.143   59.577
LGA    E    23_B      E    23_B     0.970     0    0.088   0.832     4.136   88.214   74.127
LGA    H    24_B      H    24_B     0.531     0    0.057   0.086     1.662   95.238   86.143
LGA    G    25_B      G    25_B     0.397     0    0.037   0.037     0.562   95.238   95.238
LGA    K    26_B      K    26_B     0.769     0    0.024   0.767     1.738   90.476   85.503
LGA    V    27_B      V    27_B     1.095     0    0.045   1.047     3.761   85.952   77.347
LGA    F    28_B      F    28_B     0.698     0    0.012   0.420     1.381   90.476   88.052
LGA    K    29_B      K    29_B     0.660     0    0.011   0.809     2.339   88.214   83.915
LGA    D    30_B      D    30_B     1.310     0    0.053   0.080     1.484   81.429   81.429
LGA    E    31_B      E    31_B     1.524     0    0.016   0.107     1.916   75.000   73.810
LGA    Q    32_B      Q    32_B     1.436     0    0.024   0.815     4.200   81.429   68.413
LGA    I    33_B      I    33_B     1.269     0    0.065   0.629     1.801   81.429   79.286
LGA    D    34_B      D    34_B     1.322     0    0.016   0.143     2.046   83.690   78.333
LGA    G    35_B      G    35_B     0.812     0    0.085   0.085     1.056   88.214   88.214
LGA    E    36_B      E    36_B     1.170     0    0.018   0.089     2.905   83.690   73.280
LGA    A    37_B      A    37_B     1.130     0    0.055   0.053     1.211   81.429   81.429
LGA    F    38_B      F    38_B     0.840     0    0.030   0.965     3.300   90.476   73.247
LGA    L    39_B      L    39_B     0.515     0    0.123   1.410     3.788   88.214   77.262
LGA    L    40_B      L    40_B     1.015     0    0.041   0.049     1.844   88.214   81.607
LGA    M    41_B      M    41_B     0.431     0    0.060   0.168     1.179   95.238   92.917
LGA    T    42_B      T    42_B     0.659     0    0.012   0.027     0.735   90.476   90.476
LGA    Q    43_B      Q    43_B     1.008     0    0.016   1.008     3.921   88.214   72.963
LGA    T    44_B      T    44_B     1.078     0    0.023   0.097     1.507   85.952   82.789
LGA    D    45_B      D    45_B     0.794     0    0.016   0.208     1.139   88.214   88.214
LGA    I    46_B      I    46_B     1.070     0    0.070   0.081     1.466   83.690   83.690
LGA    V    47_B      V    47_B     1.377     0    0.025   0.085     2.116   77.143   75.374
LGA    K    48_B      K    48_B     2.604     0    0.017   0.958     8.281   59.286   42.540
LGA    I    49_B      I    49_B     2.964     0    0.016   0.112     4.667   59.048   48.155
LGA    M    50_B      M    50_B     1.586     0    0.020   0.886     4.491   79.405   65.000
LGA    S    51_B      S    51_B     0.856     0    0.087   0.084     1.342   85.952   85.952
LGA    I    52_B      I    52_B     1.778     0    0.114   1.205     3.403   75.000   67.143
LGA    K    53_B      K    53_B     1.495     0    0.035   0.643     1.815   79.286   77.619
LGA    E    54_B      E    54_B     1.359     0    0.020   0.742     3.229   81.429   71.481
LGA    G    55_B      G    55_B     1.434     0    0.062   0.062     1.481   81.429   81.429
LGA    P    56_B      P    56_B     1.195     0    0.043   0.050     1.323   81.429   81.429
LGA    A    57_B      A    57_B     1.008     0    0.018   0.018     1.154   85.952   85.048
LGA    E    58_B      E    58_B     0.890     0    0.012   0.815     3.684   90.476   75.820
LGA    K    59_B      K    59_B     0.986     0    0.011   0.105     1.412   90.476   85.450
LGA    I    60_B      I    60_B     0.690     0    0.023   0.641     1.287   92.857   89.405
LGA    F    61_B      F    61_B     0.429     0    0.068   0.155     1.330  100.000   91.515
LGA    N    62_B      N    62_B     0.512     0    0.030   0.053     1.004   95.238   91.726
LGA    S    63_B      S    63_B     0.994     0    0.012   0.047     1.309   88.214   85.952
LGA    I    64_B      I    64_B     0.828     0    0.013   0.069     1.194   88.214   89.405
LGA    L    65_B      L    65_B     0.637     0    0.029   0.116     1.122   88.214   89.405
LGA    M    66_B      M    66_B     1.395     0    0.018   0.800     4.403   75.119   62.976
LGA    F    67_B      F    67_B     1.993     0    0.045   1.271     5.492   66.905   56.104
LGA    K    68_B      K    68_B     2.050     0    0.041   0.911     3.372   64.881   61.534
LGA    A    69_B      A    69_B     2.164     0    0.081   0.086     2.612   62.976   64.952
LGA    A    70_B      A    70_B     3.368     0    0.138   0.148     3.832   48.452   48.762
LGA    E    71_B      E    71_B     3.827     0    0.040   1.006     4.055   41.786   51.640

# 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):     1.431          1.429                  1.927           81.712   76.504

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   73   71    4.0     71    1.43    85.211    93.761     4.637

LGA_LOCAL      RMSD:   1.431  Number of atoms:   71  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   1.431  Number of assigned atoms:   71 
Std_ASGN_ATOMS RMSD:   1.431  Standard rmsd on all 71 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.084343 * X  +  -0.957928 * Y  +   0.274338 * Z  +  25.923964
  Y_new =  -0.394065 * X  +  -0.220807 * Y  +  -0.892164 * Z  +  38.972782
  Z_new =   0.915204 * X  +  -0.183355 * Y  +  -0.358862 * Z  + -10.992040 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -1.781649 -1.156014 -2.669236   [DEG: -102.0810  -66.2347 -152.9359 ]
ZXZ:  0.298320  1.937845  1.768522   [DEG:   17.0925  111.0303  101.3288 ]
 
# END of job
